anno_start	anno_end	anno_text	entity_type	sentence	section
50	54	NadR	protein	Molecular Basis of Ligand-Dependent Regulation of NadR, the Transcriptional Repressor of Meningococcal Virulence Factor NadA	TITLE
60	85	Transcriptional Repressor	protein_type	Molecular Basis of Ligand-Dependent Regulation of NadR, the Transcriptional Repressor of Meningococcal Virulence Factor NadA	TITLE
89	102	Meningococcal	taxonomy_domain	Molecular Basis of Ligand-Dependent Regulation of NadR, the Transcriptional Repressor of Meningococcal Virulence Factor NadA	TITLE
120	124	NadA	protein	Molecular Basis of Ligand-Dependent Regulation of NadR, the Transcriptional Repressor of Meningococcal Virulence Factor NadA	TITLE
1	20	Neisseria adhesin A	protein	 Neisseria adhesin A (NadA) is present on the meningococcal surface and contributes to adhesion to and invasion of human cells.	ABSTRACT
22	26	NadA	protein	 Neisseria adhesin A (NadA) is present on the meningococcal surface and contributes to adhesion to and invasion of human cells.	ABSTRACT
46	59	meningococcal	taxonomy_domain	 Neisseria adhesin A (NadA) is present on the meningococcal surface and contributes to adhesion to and invasion of human cells.	ABSTRACT
115	120	human	species	 Neisseria adhesin A (NadA) is present on the meningococcal surface and contributes to adhesion to and invasion of human cells.	ABSTRACT
0	4	NadA	protein	NadA is also one of three recombinant antigens in the recently-approved Bexsero vaccine, which protects against serogroup B meningococcus.	ABSTRACT
112	137	serogroup B meningococcus	taxonomy_domain	NadA is also one of three recombinant antigens in the recently-approved Bexsero vaccine, which protects against serogroup B meningococcus.	ABSTRACT
14	18	NadA	protein	The amount of NadA on the bacterial surface is of direct relevance in the constant battle of host-pathogen interactions: it influences the ability of the pathogen to engage human cell surface-exposed receptors and, conversely, the bacterial susceptibility to the antibody-mediated immune response.	ABSTRACT
26	35	bacterial	taxonomy_domain	The amount of NadA on the bacterial surface is of direct relevance in the constant battle of host-pathogen interactions: it influences the ability of the pathogen to engage human cell surface-exposed receptors and, conversely, the bacterial susceptibility to the antibody-mediated immune response.	ABSTRACT
173	178	human	species	The amount of NadA on the bacterial surface is of direct relevance in the constant battle of host-pathogen interactions: it influences the ability of the pathogen to engage human cell surface-exposed receptors and, conversely, the bacterial susceptibility to the antibody-mediated immune response.	ABSTRACT
231	240	bacterial	taxonomy_domain	The amount of NadA on the bacterial surface is of direct relevance in the constant battle of host-pathogen interactions: it influences the ability of the pathogen to engage human cell surface-exposed receptors and, conversely, the bacterial susceptibility to the antibody-mediated immune response.	ABSTRACT
70	74	nadA	gene	It is therefore important to understand the mechanisms which regulate nadA expression levels, which are predominantly controlled by the transcriptional regulator NadR (Neisseria adhesin A Regulator) both in vitro and in vivo.	ABSTRACT
136	161	transcriptional regulator	protein_type	It is therefore important to understand the mechanisms which regulate nadA expression levels, which are predominantly controlled by the transcriptional regulator NadR (Neisseria adhesin A Regulator) both in vitro and in vivo.	ABSTRACT
162	166	NadR	protein	It is therefore important to understand the mechanisms which regulate nadA expression levels, which are predominantly controlled by the transcriptional regulator NadR (Neisseria adhesin A Regulator) both in vitro and in vivo.	ABSTRACT
168	197	Neisseria adhesin A Regulator	protein	It is therefore important to understand the mechanisms which regulate nadA expression levels, which are predominantly controlled by the transcriptional regulator NadR (Neisseria adhesin A Regulator) both in vitro and in vivo.	ABSTRACT
0	4	NadR	protein	NadR binds the nadA promoter and represses gene transcription.	ABSTRACT
15	19	nadA	gene	NadR binds the nadA promoter and represses gene transcription.	ABSTRACT
0	4	NadR	protein	NadR binds the nadA promoter and represses gene transcription.	ABSTRACT
15	19	nadA	gene	NadR binds the nadA promoter and represses gene transcription.	ABSTRACT
7	18	presence of	protein_state	In the presence of 4-hydroxyphenylacetate (4-HPA), a catabolite present in human saliva both under physiological conditions and during bacterial infection, the binding of NadR to the nadA promoter is attenuated and nadA expression is induced.	ABSTRACT
19	41	4-hydroxyphenylacetate	chemical	In the presence of 4-hydroxyphenylacetate (4-HPA), a catabolite present in human saliva both under physiological conditions and during bacterial infection, the binding of NadR to the nadA promoter is attenuated and nadA expression is induced.	ABSTRACT
43	48	4-HPA	chemical	In the presence of 4-hydroxyphenylacetate (4-HPA), a catabolite present in human saliva both under physiological conditions and during bacterial infection, the binding of NadR to the nadA promoter is attenuated and nadA expression is induced.	ABSTRACT
75	80	human	species	In the presence of 4-hydroxyphenylacetate (4-HPA), a catabolite present in human saliva both under physiological conditions and during bacterial infection, the binding of NadR to the nadA promoter is attenuated and nadA expression is induced.	ABSTRACT
135	144	bacterial	taxonomy_domain	In the presence of 4-hydroxyphenylacetate (4-HPA), a catabolite present in human saliva both under physiological conditions and during bacterial infection, the binding of NadR to the nadA promoter is attenuated and nadA expression is induced.	ABSTRACT
171	175	NadR	protein	In the presence of 4-hydroxyphenylacetate (4-HPA), a catabolite present in human saliva both under physiological conditions and during bacterial infection, the binding of NadR to the nadA promoter is attenuated and nadA expression is induced.	ABSTRACT
183	187	nadA	gene	In the presence of 4-hydroxyphenylacetate (4-HPA), a catabolite present in human saliva both under physiological conditions and during bacterial infection, the binding of NadR to the nadA promoter is attenuated and nadA expression is induced.	ABSTRACT
215	219	nadA	gene	In the presence of 4-hydroxyphenylacetate (4-HPA), a catabolite present in human saliva both under physiological conditions and during bacterial infection, the binding of NadR to the nadA promoter is attenuated and nadA expression is induced.	ABSTRACT
0	4	NadR	protein	NadR also mediates ligand-dependent regulation of many other meningococcal genes, for example the highly-conserved multiple adhesin family (maf) genes, which encode proteins emerging with important roles in host-pathogen interactions, immune evasion and niche adaptation.	ABSTRACT
61	74	meningococcal	taxonomy_domain	NadR also mediates ligand-dependent regulation of many other meningococcal genes, for example the highly-conserved multiple adhesin family (maf) genes, which encode proteins emerging with important roles in host-pathogen interactions, immune evasion and niche adaptation.	ABSTRACT
40	44	NadR	protein	To gain insights into the regulation of NadR mediated by 4-HPA, we combined structural, biochemical, and mutagenesis studies.	ABSTRACT
57	62	4-HPA	chemical	To gain insights into the regulation of NadR mediated by 4-HPA, we combined structural, biochemical, and mutagenesis studies.	ABSTRACT
76	124	structural, biochemical, and mutagenesis studies	experimental_method	To gain insights into the regulation of NadR mediated by 4-HPA, we combined structural, biochemical, and mutagenesis studies.	ABSTRACT
23	41	crystal structures	evidence	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
45	56	ligand-free	protein_state	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
61	73	ligand-bound	protein_state	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
74	78	NadR	protein	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
172	177	4-HPA	chemical	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
199	206	dimeric	oligomeric_state	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
207	211	NadR	protein	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
329	349	hydroxyphenylacetate	chemical	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
369	378	3Cl,4-HPA	chemical	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
442	449	leucine	residue_name	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
489	498	conserved	protein_state	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
507	511	MarR	protein_type	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
553	557	His7	residue_name_number	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
559	563	Ser9	residue_name_number	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
565	570	Asn11	residue_name_number	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
575	580	Phe25	residue_name_number	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
613	618	4-HPA	chemical	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
697	705	bacteria	taxonomy_domain	In particular, two new crystal structures of ligand-free and ligand-bound NadR revealed (i) the molecular basis of ‘conformational selection’ by which a single molecule of 4-HPA binds and stabilizes dimeric NadR in a conformation unsuitable for DNA-binding, (ii) molecular explanations for the binding specificities of different hydroxyphenylacetate ligands, including 3Cl,4-HPA which is produced during inflammation, (iii) the presence of a leucine residue essential for dimerization and conserved in many MarR family proteins, and (iv) four residues (His7, Ser9, Asn11 and Phe25), which are involved in binding 4-HPA, and were confirmed in vitro to have key roles in the regulatory mechanism in bacteria.	ABSTRACT
120	124	nadA	gene	Overall, this study deepens our molecular understanding of the sophisticated regulatory mechanisms of the expression of nadA and other genes governed by NadR, dependent on interactions with niche-specific signal molecules that may play important roles during meningococcal pathogenesis.	ABSTRACT
153	157	NadR	protein	Overall, this study deepens our molecular understanding of the sophisticated regulatory mechanisms of the expression of nadA and other genes governed by NadR, dependent on interactions with niche-specific signal molecules that may play important roles during meningococcal pathogenesis.	ABSTRACT
259	272	meningococcal	taxonomy_domain	Overall, this study deepens our molecular understanding of the sophisticated regulatory mechanisms of the expression of nadA and other genes governed by NadR, dependent on interactions with niche-specific signal molecules that may play important roles during meningococcal pathogenesis.	ABSTRACT
0	25	Serogroup B meningococcus	taxonomy_domain	Serogroup B meningococcus (MenB) causes fatal sepsis and invasive meningococcal disease, particularly in young children and adolescents, as highlighted by recent MenB outbreaks in universities of the United States and Canada.	ABSTRACT
27	31	MenB	species	Serogroup B meningococcus (MenB) causes fatal sepsis and invasive meningococcal disease, particularly in young children and adolescents, as highlighted by recent MenB outbreaks in universities of the United States and Canada.	ABSTRACT
66	79	meningococcal	taxonomy_domain	Serogroup B meningococcus (MenB) causes fatal sepsis and invasive meningococcal disease, particularly in young children and adolescents, as highlighted by recent MenB outbreaks in universities of the United States and Canada.	ABSTRACT
162	166	MenB	species	Serogroup B meningococcus (MenB) causes fatal sepsis and invasive meningococcal disease, particularly in young children and adolescents, as highlighted by recent MenB outbreaks in universities of the United States and Canada.	ABSTRACT
37	41	MenB	species	The Bexsero vaccine protects against MenB and has recently been approved in > 35 countries worldwide.	ABSTRACT
0	19	Neisseria adhesin A	protein	Neisseria adhesin A (NadA) present on the meningococcal surface can mediate binding to human cells and is one of the three MenB vaccine protein antigens.	ABSTRACT
21	25	NadA	protein	Neisseria adhesin A (NadA) present on the meningococcal surface can mediate binding to human cells and is one of the three MenB vaccine protein antigens.	ABSTRACT
42	55	meningococcal	taxonomy_domain	Neisseria adhesin A (NadA) present on the meningococcal surface can mediate binding to human cells and is one of the three MenB vaccine protein antigens.	ABSTRACT
87	92	human	species	Neisseria adhesin A (NadA) present on the meningococcal surface can mediate binding to human cells and is one of the three MenB vaccine protein antigens.	ABSTRACT
123	127	MenB	species	Neisseria adhesin A (NadA) present on the meningococcal surface can mediate binding to human cells and is one of the three MenB vaccine protein antigens.	ABSTRACT
14	18	NadA	protein	The amount of NadA exposed on the meningococcal surface also influences the antibody-mediated serum bactericidal response measured in vitro.	ABSTRACT
34	47	meningococcal	taxonomy_domain	The amount of NadA exposed on the meningococcal surface also influences the antibody-mediated serum bactericidal response measured in vitro.	ABSTRACT
24	28	nadA	gene	A deep understanding of nadA expression is therefore important, otherwise the contribution of NadA to vaccine-induced protection against meningococcal meningitis may be underestimated.	ABSTRACT
94	98	NadA	protein	A deep understanding of nadA expression is therefore important, otherwise the contribution of NadA to vaccine-induced protection against meningococcal meningitis may be underestimated.	ABSTRACT
137	150	meningococcal	taxonomy_domain	A deep understanding of nadA expression is therefore important, otherwise the contribution of NadA to vaccine-induced protection against meningococcal meningitis may be underestimated.	ABSTRACT
33	37	NadA	protein	The abundance of surface-exposed NadA is regulated by the ligand-responsive transcriptional repressor NadR. Here, we present functional, biochemical and high-resolution structural data on NadR. Our studies provide detailed insights into how small molecule ligands, such as hydroxyphenylacetate derivatives, found in relevant host niches, modulate the structure and activity of NadR, by ‘conformational selection’ of inactive forms.	ABSTRACT
58	101	ligand-responsive transcriptional repressor	protein_type	The abundance of surface-exposed NadA is regulated by the ligand-responsive transcriptional repressor NadR. Here, we present functional, biochemical and high-resolution structural data on NadR. Our studies provide detailed insights into how small molecule ligands, such as hydroxyphenylacetate derivatives, found in relevant host niches, modulate the structure and activity of NadR, by ‘conformational selection’ of inactive forms.	ABSTRACT
102	106	NadR	protein	The abundance of surface-exposed NadA is regulated by the ligand-responsive transcriptional repressor NadR. Here, we present functional, biochemical and high-resolution structural data on NadR. Our studies provide detailed insights into how small molecule ligands, such as hydroxyphenylacetate derivatives, found in relevant host niches, modulate the structure and activity of NadR, by ‘conformational selection’ of inactive forms.	ABSTRACT
125	184	functional, biochemical and high-resolution structural data	evidence	The abundance of surface-exposed NadA is regulated by the ligand-responsive transcriptional repressor NadR. Here, we present functional, biochemical and high-resolution structural data on NadR. Our studies provide detailed insights into how small molecule ligands, such as hydroxyphenylacetate derivatives, found in relevant host niches, modulate the structure and activity of NadR, by ‘conformational selection’ of inactive forms.	ABSTRACT
188	192	NadR	protein	The abundance of surface-exposed NadA is regulated by the ligand-responsive transcriptional repressor NadR. Here, we present functional, biochemical and high-resolution structural data on NadR. Our studies provide detailed insights into how small molecule ligands, such as hydroxyphenylacetate derivatives, found in relevant host niches, modulate the structure and activity of NadR, by ‘conformational selection’ of inactive forms.	ABSTRACT
273	293	hydroxyphenylacetate	chemical	The abundance of surface-exposed NadA is regulated by the ligand-responsive transcriptional repressor NadR. Here, we present functional, biochemical and high-resolution structural data on NadR. Our studies provide detailed insights into how small molecule ligands, such as hydroxyphenylacetate derivatives, found in relevant host niches, modulate the structure and activity of NadR, by ‘conformational selection’ of inactive forms.	ABSTRACT
377	381	NadR	protein	The abundance of surface-exposed NadA is regulated by the ligand-responsive transcriptional repressor NadR. Here, we present functional, biochemical and high-resolution structural data on NadR. Our studies provide detailed insights into how small molecule ligands, such as hydroxyphenylacetate derivatives, found in relevant host niches, modulate the structure and activity of NadR, by ‘conformational selection’ of inactive forms.	ABSTRACT
416	424	inactive	protein_state	The abundance of surface-exposed NadA is regulated by the ligand-responsive transcriptional repressor NadR. Here, we present functional, biochemical and high-resolution structural data on NadR. Our studies provide detailed insights into how small molecule ligands, such as hydroxyphenylacetate derivatives, found in relevant host niches, modulate the structure and activity of NadR, by ‘conformational selection’ of inactive forms.	ABSTRACT
47	51	NadR	protein	These findings shed light on the regulation of NadR, a key MarR-family virulence factor of this important human pathogen.	ABSTRACT
59	63	MarR	protein_type	These findings shed light on the regulation of NadR, a key MarR-family virulence factor of this important human pathogen.	ABSTRACT
106	111	human	species	These findings shed light on the regulation of NadR, a key MarR-family virulence factor of this important human pathogen.	ABSTRACT
5	24	Reverse Vaccinology	experimental_method	The ‘Reverse Vaccinology’ approach was pioneered to identify antigens for a protein-based vaccine against serogroup B Neisseria meningitidis (MenB), a human pathogen causing potentially-fatal sepsis and invasive meningococcal disease.	INTRO
106	140	serogroup B Neisseria meningitidis	species	The ‘Reverse Vaccinology’ approach was pioneered to identify antigens for a protein-based vaccine against serogroup B Neisseria meningitidis (MenB), a human pathogen causing potentially-fatal sepsis and invasive meningococcal disease.	INTRO
142	146	MenB	species	The ‘Reverse Vaccinology’ approach was pioneered to identify antigens for a protein-based vaccine against serogroup B Neisseria meningitidis (MenB), a human pathogen causing potentially-fatal sepsis and invasive meningococcal disease.	INTRO
151	156	human	species	The ‘Reverse Vaccinology’ approach was pioneered to identify antigens for a protein-based vaccine against serogroup B Neisseria meningitidis (MenB), a human pathogen causing potentially-fatal sepsis and invasive meningococcal disease.	INTRO
212	225	meningococcal	taxonomy_domain	The ‘Reverse Vaccinology’ approach was pioneered to identify antigens for a protein-based vaccine against serogroup B Neisseria meningitidis (MenB), a human pathogen causing potentially-fatal sepsis and invasive meningococcal disease.	INTRO
8	27	Reverse Vaccinology	experimental_method	Indeed, Reverse Vaccinology identified Neisseria adhesin A (NadA), a surface-exposed protein involved in epithelial cell invasion and found in ~30% of clinical isolates.	INTRO
39	58	Neisseria adhesin A	protein	Indeed, Reverse Vaccinology identified Neisseria adhesin A (NadA), a surface-exposed protein involved in epithelial cell invasion and found in ~30% of clinical isolates.	INTRO
60	64	NadA	protein	Indeed, Reverse Vaccinology identified Neisseria adhesin A (NadA), a surface-exposed protein involved in epithelial cell invasion and found in ~30% of clinical isolates.	INTRO
26	43	crystal structure	evidence	Recently, we reported the crystal structure of NadA, providing insights into its biological and immunological functions.	INTRO
47	51	NadA	protein	Recently, we reported the crystal structure of NadA, providing insights into its biological and immunological functions.	INTRO
12	16	NadA	protein	Recombinant NadA elicits a strong bactericidal immune response and is therefore included in the Bexsero vaccine that protects against MenB and which was recently approved in over 35 countries worldwide.	INTRO
134	138	MenB	species	Recombinant NadA elicits a strong bactericidal immune response and is therefore included in the Bexsero vaccine that protects against MenB and which was recently approved in over 35 countries worldwide.	INTRO
31	35	nadA	gene	Previous studies revealed that nadA expression levels are mainly regulated by the Neisseria adhesin A Regulator (NadR).	INTRO
82	111	Neisseria adhesin A Regulator	protein	Previous studies revealed that nadA expression levels are mainly regulated by the Neisseria adhesin A Regulator (NadR).	INTRO
113	117	NadR	protein	Previous studies revealed that nadA expression levels are mainly regulated by the Neisseria adhesin A Regulator (NadR).	INTRO
38	42	nadA	gene	Although additional factors influence nadA expression, we focused on its regulation by NadR, the major mediator of NadA phase variable expression.	INTRO
87	91	NadR	protein	Although additional factors influence nadA expression, we focused on its regulation by NadR, the major mediator of NadA phase variable expression.	INTRO
115	119	NadA	protein	Although additional factors influence nadA expression, we focused on its regulation by NadR, the major mediator of NadA phase variable expression.	INTRO
11	15	NadR	protein	Studies of NadR also have broader implications, since a genome-wide analysis of MenB wild-type and nadR knock-out strains revealed that NadR influences the regulation of > 30 genes, including maf genes, from the multiple adhesin family.	INTRO
80	84	MenB	species	Studies of NadR also have broader implications, since a genome-wide analysis of MenB wild-type and nadR knock-out strains revealed that NadR influences the regulation of > 30 genes, including maf genes, from the multiple adhesin family.	INTRO
85	94	wild-type	protein_state	Studies of NadR also have broader implications, since a genome-wide analysis of MenB wild-type and nadR knock-out strains revealed that NadR influences the regulation of > 30 genes, including maf genes, from the multiple adhesin family.	INTRO
99	103	nadR	gene	Studies of NadR also have broader implications, since a genome-wide analysis of MenB wild-type and nadR knock-out strains revealed that NadR influences the regulation of > 30 genes, including maf genes, from the multiple adhesin family.	INTRO
104	113	knock-out	protein_state	Studies of NadR also have broader implications, since a genome-wide analysis of MenB wild-type and nadR knock-out strains revealed that NadR influences the regulation of > 30 genes, including maf genes, from the multiple adhesin family.	INTRO
136	140	NadR	protein	Studies of NadR also have broader implications, since a genome-wide analysis of MenB wild-type and nadR knock-out strains revealed that NadR influences the regulation of > 30 genes, including maf genes, from the multiple adhesin family.	INTRO
221	228	adhesin	protein_type	Studies of NadR also have broader implications, since a genome-wide analysis of MenB wild-type and nadR knock-out strains revealed that NadR influences the regulation of > 30 genes, including maf genes, from the multiple adhesin family.	INTRO
101	110	bacterial	taxonomy_domain	These genes encode a wide variety of proteins connected to many biological processes contributing to bacterial survival, adaptation in the host niche, colonization and invasion.	INTRO
0	4	NadR	protein	NadR belongs to the MarR (Multiple Antibiotic Resistance Regulator) family, a group of ligand-responsive transcriptional regulators ubiquitous in bacteria and archaea.	INTRO
20	24	MarR	protein_type	NadR belongs to the MarR (Multiple Antibiotic Resistance Regulator) family, a group of ligand-responsive transcriptional regulators ubiquitous in bacteria and archaea.	INTRO
26	66	Multiple Antibiotic Resistance Regulator	protein_type	NadR belongs to the MarR (Multiple Antibiotic Resistance Regulator) family, a group of ligand-responsive transcriptional regulators ubiquitous in bacteria and archaea.	INTRO
87	131	ligand-responsive transcriptional regulators	protein_type	NadR belongs to the MarR (Multiple Antibiotic Resistance Regulator) family, a group of ligand-responsive transcriptional regulators ubiquitous in bacteria and archaea.	INTRO
146	154	bacteria	taxonomy_domain	NadR belongs to the MarR (Multiple Antibiotic Resistance Regulator) family, a group of ligand-responsive transcriptional regulators ubiquitous in bacteria and archaea.	INTRO
159	166	archaea	taxonomy_domain	NadR belongs to the MarR (Multiple Antibiotic Resistance Regulator) family, a group of ligand-responsive transcriptional regulators ubiquitous in bacteria and archaea.	INTRO
0	4	MarR	protein_type	MarR family proteins can promote bacterial survival in the presence of antibiotics, toxic chemicals, organic solvents or reactive oxygen species and can regulate virulence factor expression.	INTRO
33	42	bacterial	taxonomy_domain	MarR family proteins can promote bacterial survival in the presence of antibiotics, toxic chemicals, organic solvents or reactive oxygen species and can regulate virulence factor expression.	INTRO
0	4	MarR	protein_type	MarR homologues can act either as transcriptional repressors or as activators.	INTRO
14	18	MarR	protein_type	Although > 50 MarR family structures are known, a molecular understanding of their ligand-dependent regulatory mechanisms is still limited, often hampered by lack of identification of their ligands and/or DNA targets.	INTRO
26	36	structures	evidence	Although > 50 MarR family structures are known, a molecular understanding of their ligand-dependent regulatory mechanisms is still limited, often hampered by lack of identification of their ligands and/or DNA targets.	INTRO
51	62	ligand-free	protein_state	A potentially interesting exception comes from the ligand-free and salicylate-bound forms of the Methanobacterium thermoautotrophicum protein MTH313 which revealed that two salicylate molecules bind to one MTH313 dimer and induce large conformational changes, apparently sufficient to prevent DNA binding.	INTRO
67	83	salicylate-bound	protein_state	A potentially interesting exception comes from the ligand-free and salicylate-bound forms of the Methanobacterium thermoautotrophicum protein MTH313 which revealed that two salicylate molecules bind to one MTH313 dimer and induce large conformational changes, apparently sufficient to prevent DNA binding.	INTRO
97	133	Methanobacterium thermoautotrophicum	species	A potentially interesting exception comes from the ligand-free and salicylate-bound forms of the Methanobacterium thermoautotrophicum protein MTH313 which revealed that two salicylate molecules bind to one MTH313 dimer and induce large conformational changes, apparently sufficient to prevent DNA binding.	INTRO
142	148	MTH313	protein	A potentially interesting exception comes from the ligand-free and salicylate-bound forms of the Methanobacterium thermoautotrophicum protein MTH313 which revealed that two salicylate molecules bind to one MTH313 dimer and induce large conformational changes, apparently sufficient to prevent DNA binding.	INTRO
173	183	salicylate	chemical	A potentially interesting exception comes from the ligand-free and salicylate-bound forms of the Methanobacterium thermoautotrophicum protein MTH313 which revealed that two salicylate molecules bind to one MTH313 dimer and induce large conformational changes, apparently sufficient to prevent DNA binding.	INTRO
206	212	MTH313	protein	A potentially interesting exception comes from the ligand-free and salicylate-bound forms of the Methanobacterium thermoautotrophicum protein MTH313 which revealed that two salicylate molecules bind to one MTH313 dimer and induce large conformational changes, apparently sufficient to prevent DNA binding.	INTRO
213	218	dimer	oligomeric_state	A potentially interesting exception comes from the ligand-free and salicylate-bound forms of the Methanobacterium thermoautotrophicum protein MTH313 which revealed that two salicylate molecules bind to one MTH313 dimer and induce large conformational changes, apparently sufficient to prevent DNA binding.	INTRO
24	31	archeal	taxonomy_domain	However, the homologous archeal Sulfolobus tokodaii protein ST1710 presented essentially the same structure in ligand-free and salicylate-bound forms, apparently contrasting the mechanism proposed for MTH313.	INTRO
32	51	Sulfolobus tokodaii	species	However, the homologous archeal Sulfolobus tokodaii protein ST1710 presented essentially the same structure in ligand-free and salicylate-bound forms, apparently contrasting the mechanism proposed for MTH313.	INTRO
60	66	ST1710	protein	However, the homologous archeal Sulfolobus tokodaii protein ST1710 presented essentially the same structure in ligand-free and salicylate-bound forms, apparently contrasting the mechanism proposed for MTH313.	INTRO
98	107	structure	evidence	However, the homologous archeal Sulfolobus tokodaii protein ST1710 presented essentially the same structure in ligand-free and salicylate-bound forms, apparently contrasting the mechanism proposed for MTH313.	INTRO
111	122	ligand-free	protein_state	However, the homologous archeal Sulfolobus tokodaii protein ST1710 presented essentially the same structure in ligand-free and salicylate-bound forms, apparently contrasting the mechanism proposed for MTH313.	INTRO
127	143	salicylate-bound	protein_state	However, the homologous archeal Sulfolobus tokodaii protein ST1710 presented essentially the same structure in ligand-free and salicylate-bound forms, apparently contrasting the mechanism proposed for MTH313.	INTRO
201	207	MTH313	protein	However, the homologous archeal Sulfolobus tokodaii protein ST1710 presented essentially the same structure in ligand-free and salicylate-bound forms, apparently contrasting the mechanism proposed for MTH313.	INTRO
36	42	MTH313	protein	Despite these apparent differences, MTH313 and ST1710 bind salicylate in approximately the same site, between their dimerization and DNA-binding domains.	INTRO
47	53	ST1710	protein	Despite these apparent differences, MTH313 and ST1710 bind salicylate in approximately the same site, between their dimerization and DNA-binding domains.	INTRO
59	69	salicylate	chemical	Despite these apparent differences, MTH313 and ST1710 bind salicylate in approximately the same site, between their dimerization and DNA-binding domains.	INTRO
116	152	dimerization and DNA-binding domains	structure_element	Despite these apparent differences, MTH313 and ST1710 bind salicylate in approximately the same site, between their dimerization and DNA-binding domains.	INTRO
31	41	salicylate	chemical	However, it is unknown whether salicylate is a relevant in vivo ligand of either of these two proteins, which share ~20% sequence identity with NadR, rendering unclear the interpretation of these findings in relation to the regulatory mechanisms of NadR or other MarR family proteins.	INTRO
144	148	NadR	protein	However, it is unknown whether salicylate is a relevant in vivo ligand of either of these two proteins, which share ~20% sequence identity with NadR, rendering unclear the interpretation of these findings in relation to the regulatory mechanisms of NadR or other MarR family proteins.	INTRO
249	253	NadR	protein	However, it is unknown whether salicylate is a relevant in vivo ligand of either of these two proteins, which share ~20% sequence identity with NadR, rendering unclear the interpretation of these findings in relation to the regulatory mechanisms of NadR or other MarR family proteins.	INTRO
263	267	MarR	protein_type	However, it is unknown whether salicylate is a relevant in vivo ligand of either of these two proteins, which share ~20% sequence identity with NadR, rendering unclear the interpretation of these findings in relation to the regulatory mechanisms of NadR or other MarR family proteins.	INTRO
0	4	NadR	protein	NadR binds nadA on three different operators (OpI, OpII and OpIII).	INTRO
11	15	nadA	gene	NadR binds nadA on three different operators (OpI, OpII and OpIII).	INTRO
28	32	NadR	protein	The DNA-binding activity of NadR is attenuated in vitro upon addition of various hydroxyphenylacetate (HPA) derivatives, including 4-HPA.	INTRO
81	101	hydroxyphenylacetate	chemical	The DNA-binding activity of NadR is attenuated in vitro upon addition of various hydroxyphenylacetate (HPA) derivatives, including 4-HPA.	INTRO
103	106	HPA	chemical	The DNA-binding activity of NadR is attenuated in vitro upon addition of various hydroxyphenylacetate (HPA) derivatives, including 4-HPA.	INTRO
131	136	4-HPA	chemical	The DNA-binding activity of NadR is attenuated in vitro upon addition of various hydroxyphenylacetate (HPA) derivatives, including 4-HPA.	INTRO
0	5	4-HPA	chemical	4-HPA is a small molecule derived from mammalian aromatic amino acid catabolism and is released in human saliva, where it has been detected at micromolar concentration.	INTRO
39	48	mammalian	taxonomy_domain	4-HPA is a small molecule derived from mammalian aromatic amino acid catabolism and is released in human saliva, where it has been detected at micromolar concentration.	INTRO
99	104	human	species	4-HPA is a small molecule derived from mammalian aromatic amino acid catabolism and is released in human saliva, where it has been detected at micromolar concentration.	INTRO
19	24	4-HPA	chemical	In the presence of 4-HPA, NadR is unable to bind the nadA promoter and nadA gene expression is induced.	INTRO
26	30	NadR	protein	In the presence of 4-HPA, NadR is unable to bind the nadA promoter and nadA gene expression is induced.	INTRO
53	57	nadA	gene	In the presence of 4-HPA, NadR is unable to bind the nadA promoter and nadA gene expression is induced.	INTRO
71	75	nadA	gene	In the presence of 4-HPA, NadR is unable to bind the nadA promoter and nadA gene expression is induced.	INTRO
25	30	4-HPA	chemical	In vivo, the presence of 4-HPA in the host niche of N. meningitidis serves as an inducer of NadA production, thereby promoting bacterial adhesion to host cells.	INTRO
52	67	N. meningitidis	species	In vivo, the presence of 4-HPA in the host niche of N. meningitidis serves as an inducer of NadA production, thereby promoting bacterial adhesion to host cells.	INTRO
92	96	NadA	protein	In vivo, the presence of 4-HPA in the host niche of N. meningitidis serves as an inducer of NadA production, thereby promoting bacterial adhesion to host cells.	INTRO
127	136	bacterial	taxonomy_domain	In vivo, the presence of 4-HPA in the host niche of N. meningitidis serves as an inducer of NadA production, thereby promoting bacterial adhesion to host cells.	INTRO
35	44	3Cl,4-HPA	chemical	Further, we recently reported that 3Cl,4-HPA, produced during inflammation, is another inducer of nadA expression.	INTRO
98	102	nadA	gene	Further, we recently reported that 3Cl,4-HPA, produced during inflammation, is another inducer of nadA expression.	INTRO
40	85	hydrogen-deuterium exchange mass spectrometry	experimental_method	Extending our previous studies based on hydrogen-deuterium exchange mass spectrometry (HDX-MS), here we sought to reveal the molecular mechanisms and effects of NadR/HPA interactions via X-ray crystallography, NMR spectroscopy and complementary biochemical and in vivo mutagenesis studies.	INTRO
87	93	HDX-MS	experimental_method	Extending our previous studies based on hydrogen-deuterium exchange mass spectrometry (HDX-MS), here we sought to reveal the molecular mechanisms and effects of NadR/HPA interactions via X-ray crystallography, NMR spectroscopy and complementary biochemical and in vivo mutagenesis studies.	INTRO
161	165	NadR	protein	Extending our previous studies based on hydrogen-deuterium exchange mass spectrometry (HDX-MS), here we sought to reveal the molecular mechanisms and effects of NadR/HPA interactions via X-ray crystallography, NMR spectroscopy and complementary biochemical and in vivo mutagenesis studies.	INTRO
166	169	HPA	chemical	Extending our previous studies based on hydrogen-deuterium exchange mass spectrometry (HDX-MS), here we sought to reveal the molecular mechanisms and effects of NadR/HPA interactions via X-ray crystallography, NMR spectroscopy and complementary biochemical and in vivo mutagenesis studies.	INTRO
187	208	X-ray crystallography	experimental_method	Extending our previous studies based on hydrogen-deuterium exchange mass spectrometry (HDX-MS), here we sought to reveal the molecular mechanisms and effects of NadR/HPA interactions via X-ray crystallography, NMR spectroscopy and complementary biochemical and in vivo mutagenesis studies.	INTRO
210	226	NMR spectroscopy	experimental_method	Extending our previous studies based on hydrogen-deuterium exchange mass spectrometry (HDX-MS), here we sought to reveal the molecular mechanisms and effects of NadR/HPA interactions via X-ray crystallography, NMR spectroscopy and complementary biochemical and in vivo mutagenesis studies.	INTRO
245	288	biochemical and in vivo mutagenesis studies	experimental_method	Extending our previous studies based on hydrogen-deuterium exchange mass spectrometry (HDX-MS), here we sought to reveal the molecular mechanisms and effects of NadR/HPA interactions via X-ray crystallography, NMR spectroscopy and complementary biochemical and in vivo mutagenesis studies.	INTRO
127	131	NadR	protein	We obtained detailed new insights into ligand specificity, how the ligand allosterically influences the DNA-binding ability of NadR, and the regulation of nadA expression, thus also providing a deeper structural understanding of the ligand-responsive MarR super-family.	INTRO
155	159	nadA	gene	We obtained detailed new insights into ligand specificity, how the ligand allosterically influences the DNA-binding ability of NadR, and the regulation of nadA expression, thus also providing a deeper structural understanding of the ligand-responsive MarR super-family.	INTRO
251	255	MarR	protein_type	We obtained detailed new insights into ligand specificity, how the ligand allosterically influences the DNA-binding ability of NadR, and the regulation of nadA expression, thus also providing a deeper structural understanding of the ligand-responsive MarR super-family.	INTRO
63	67	NadR	protein	Moreover, these findings are important because the activity of NadR impacts the potential coverage provided by anti-NadA antibodies elicited by the Bexsero vaccine and influences host-bacteria interactions that contribute to meningococcal pathogenesis.	INTRO
116	120	NadA	protein	Moreover, these findings are important because the activity of NadR impacts the potential coverage provided by anti-NadA antibodies elicited by the Bexsero vaccine and influences host-bacteria interactions that contribute to meningococcal pathogenesis.	INTRO
184	192	bacteria	taxonomy_domain	Moreover, these findings are important because the activity of NadR impacts the potential coverage provided by anti-NadA antibodies elicited by the Bexsero vaccine and influences host-bacteria interactions that contribute to meningococcal pathogenesis.	INTRO
225	238	meningococcal	taxonomy_domain	Moreover, these findings are important because the activity of NadR impacts the potential coverage provided by anti-NadA antibodies elicited by the Bexsero vaccine and influences host-bacteria interactions that contribute to meningococcal pathogenesis.	INTRO
0	4	NadR	protein	NadR is dimeric and is stabilized by specific hydroxyphenylacetate ligands	RESULTS
8	15	dimeric	oligomeric_state	NadR is dimeric and is stabilized by specific hydroxyphenylacetate ligands	RESULTS
46	66	hydroxyphenylacetate	chemical	NadR is dimeric and is stabilized by specific hydroxyphenylacetate ligands	RESULTS
12	16	NadR	protein	Recombinant NadR was produced in E. coli using an expression construct prepared from N. meningitidis serogroup B strain MC58.	RESULTS
33	40	E. coli	species	Recombinant NadR was produced in E. coli using an expression construct prepared from N. meningitidis serogroup B strain MC58.	RESULTS
50	70	expression construct	experimental_method	Recombinant NadR was produced in E. coli using an expression construct prepared from N. meningitidis serogroup B strain MC58.	RESULTS
85	124	N. meningitidis serogroup B strain MC58	species	Recombinant NadR was produced in E. coli using an expression construct prepared from N. meningitidis serogroup B strain MC58.	RESULTS
84	88	NadR	protein	Standard chromatographic techniques were used to obtain a highly purified sample of NadR (see Materials and Methods).	RESULTS
3	67	analytical size-exclusion high-performance liquid chromatography	experimental_method	In analytical size-exclusion high-performance liquid chromatography (SE-HPLC) experiments coupled with multi-angle laser light scattering (MALLS), NadR presented a single species with an absolute molecular mass of 35 kDa (S1 Fig).	RESULTS
69	76	SE-HPLC	experimental_method	In analytical size-exclusion high-performance liquid chromatography (SE-HPLC) experiments coupled with multi-angle laser light scattering (MALLS), NadR presented a single species with an absolute molecular mass of 35 kDa (S1 Fig).	RESULTS
103	137	multi-angle laser light scattering	experimental_method	In analytical size-exclusion high-performance liquid chromatography (SE-HPLC) experiments coupled with multi-angle laser light scattering (MALLS), NadR presented a single species with an absolute molecular mass of 35 kDa (S1 Fig).	RESULTS
139	144	MALLS	experimental_method	In analytical size-exclusion high-performance liquid chromatography (SE-HPLC) experiments coupled with multi-angle laser light scattering (MALLS), NadR presented a single species with an absolute molecular mass of 35 kDa (S1 Fig).	RESULTS
147	151	NadR	protein	In analytical size-exclusion high-performance liquid chromatography (SE-HPLC) experiments coupled with multi-angle laser light scattering (MALLS), NadR presented a single species with an absolute molecular mass of 35 kDa (S1 Fig).	RESULTS
23	27	NadR	protein	These data showed that NadR was dimeric in solution, since the theoretical molecular mass of the NadR dimer is 33.73 kDa; and, there was no change in oligomeric state on addition of 4-HPA.	RESULTS
32	39	dimeric	oligomeric_state	These data showed that NadR was dimeric in solution, since the theoretical molecular mass of the NadR dimer is 33.73 kDa; and, there was no change in oligomeric state on addition of 4-HPA.	RESULTS
97	101	NadR	protein	These data showed that NadR was dimeric in solution, since the theoretical molecular mass of the NadR dimer is 33.73 kDa; and, there was no change in oligomeric state on addition of 4-HPA.	RESULTS
102	107	dimer	oligomeric_state	These data showed that NadR was dimeric in solution, since the theoretical molecular mass of the NadR dimer is 33.73 kDa; and, there was no change in oligomeric state on addition of 4-HPA.	RESULTS
182	187	4-HPA	chemical	These data showed that NadR was dimeric in solution, since the theoretical molecular mass of the NadR dimer is 33.73 kDa; and, there was no change in oligomeric state on addition of 4-HPA.	RESULTS
25	29	NadR	protein	The thermal stability of NadR was examined using differential scanning calorimetry (DSC).	RESULTS
49	82	differential scanning calorimetry	experimental_method	The thermal stability of NadR was examined using differential scanning calorimetry (DSC).	RESULTS
84	87	DSC	experimental_method	The thermal stability of NadR was examined using differential scanning calorimetry (DSC).	RESULTS
99	103	HPAs	chemical	Since ligand-binding often increases protein stability, we also investigated the effect of various HPAs (Fig 1A) on the melting temperature (Tm) of NadR. As a control of specificity, we also tested salicylate, a known ligand of some MarR proteins previously reported to increase the Tm of ST1710 and MTH313.	RESULTS
120	139	melting temperature	evidence	Since ligand-binding often increases protein stability, we also investigated the effect of various HPAs (Fig 1A) on the melting temperature (Tm) of NadR. As a control of specificity, we also tested salicylate, a known ligand of some MarR proteins previously reported to increase the Tm of ST1710 and MTH313.	RESULTS
141	143	Tm	evidence	Since ligand-binding often increases protein stability, we also investigated the effect of various HPAs (Fig 1A) on the melting temperature (Tm) of NadR. As a control of specificity, we also tested salicylate, a known ligand of some MarR proteins previously reported to increase the Tm of ST1710 and MTH313.	RESULTS
148	152	NadR	protein	Since ligand-binding often increases protein stability, we also investigated the effect of various HPAs (Fig 1A) on the melting temperature (Tm) of NadR. As a control of specificity, we also tested salicylate, a known ligand of some MarR proteins previously reported to increase the Tm of ST1710 and MTH313.	RESULTS
198	208	salicylate	chemical	Since ligand-binding often increases protein stability, we also investigated the effect of various HPAs (Fig 1A) on the melting temperature (Tm) of NadR. As a control of specificity, we also tested salicylate, a known ligand of some MarR proteins previously reported to increase the Tm of ST1710 and MTH313.	RESULTS
233	237	MarR	protein_type	Since ligand-binding often increases protein stability, we also investigated the effect of various HPAs (Fig 1A) on the melting temperature (Tm) of NadR. As a control of specificity, we also tested salicylate, a known ligand of some MarR proteins previously reported to increase the Tm of ST1710 and MTH313.	RESULTS
283	285	Tm	evidence	Since ligand-binding often increases protein stability, we also investigated the effect of various HPAs (Fig 1A) on the melting temperature (Tm) of NadR. As a control of specificity, we also tested salicylate, a known ligand of some MarR proteins previously reported to increase the Tm of ST1710 and MTH313.	RESULTS
289	295	ST1710	protein	Since ligand-binding often increases protein stability, we also investigated the effect of various HPAs (Fig 1A) on the melting temperature (Tm) of NadR. As a control of specificity, we also tested salicylate, a known ligand of some MarR proteins previously reported to increase the Tm of ST1710 and MTH313.	RESULTS
300	306	MTH313	protein	Since ligand-binding often increases protein stability, we also investigated the effect of various HPAs (Fig 1A) on the melting temperature (Tm) of NadR. As a control of specificity, we also tested salicylate, a known ligand of some MarR proteins previously reported to increase the Tm of ST1710 and MTH313.	RESULTS
4	6	Tm	evidence	The Tm of NadR was 67.4 ± 0.1°C in the absence of ligand, and was unaffected by salicylate.	RESULTS
10	14	NadR	protein	The Tm of NadR was 67.4 ± 0.1°C in the absence of ligand, and was unaffected by salicylate.	RESULTS
39	56	absence of ligand	protein_state	The Tm of NadR was 67.4 ± 0.1°C in the absence of ligand, and was unaffected by salicylate.	RESULTS
80	90	salicylate	chemical	The Tm of NadR was 67.4 ± 0.1°C in the absence of ligand, and was unaffected by salicylate.	RESULTS
55	60	4-HPA	chemical	However, an increased thermal stability was induced by 4-HPA and, to a lesser extent, by 3-HPA.	RESULTS
89	94	3-HPA	chemical	However, an increased thermal stability was induced by 4-HPA and, to a lesser extent, by 3-HPA.	RESULTS
15	19	NadR	protein	Interestingly, NadR displayed the greatest Tm increase upon addition of 3Cl,4-HPA (Table 1 and Fig 1B).	RESULTS
43	45	Tm	evidence	Interestingly, NadR displayed the greatest Tm increase upon addition of 3Cl,4-HPA (Table 1 and Fig 1B).	RESULTS
72	81	3Cl,4-HPA	chemical	Interestingly, NadR displayed the greatest Tm increase upon addition of 3Cl,4-HPA (Table 1 and Fig 1B).	RESULTS
13	17	NadR	protein	Stability of NadR is increased by small molecule ligands.	FIG
29	34	3-HPA	chemical	 (A) Molecular structures of 3-HPA (MW 152.2), 4-HPA (MW 152.2), 3Cl,4-HPA (MW 186.6) and salicylic acid (MW 160.1). (B) DSC profiles, colored as follows: apo-NadR (violet), NadR+salicylate (red), NadR+3-HPA (green), NadR+4-HPA (blue), NadR+3Cl,4-HPA (pink).	FIG
47	52	4-HPA	chemical	 (A) Molecular structures of 3-HPA (MW 152.2), 4-HPA (MW 152.2), 3Cl,4-HPA (MW 186.6) and salicylic acid (MW 160.1). (B) DSC profiles, colored as follows: apo-NadR (violet), NadR+salicylate (red), NadR+3-HPA (green), NadR+4-HPA (blue), NadR+3Cl,4-HPA (pink).	FIG
65	74	3Cl,4-HPA	chemical	 (A) Molecular structures of 3-HPA (MW 152.2), 4-HPA (MW 152.2), 3Cl,4-HPA (MW 186.6) and salicylic acid (MW 160.1). (B) DSC profiles, colored as follows: apo-NadR (violet), NadR+salicylate (red), NadR+3-HPA (green), NadR+4-HPA (blue), NadR+3Cl,4-HPA (pink).	FIG
90	104	salicylic acid	chemical	 (A) Molecular structures of 3-HPA (MW 152.2), 4-HPA (MW 152.2), 3Cl,4-HPA (MW 186.6) and salicylic acid (MW 160.1). (B) DSC profiles, colored as follows: apo-NadR (violet), NadR+salicylate (red), NadR+3-HPA (green), NadR+4-HPA (blue), NadR+3Cl,4-HPA (pink).	FIG
121	124	DSC	experimental_method	 (A) Molecular structures of 3-HPA (MW 152.2), 4-HPA (MW 152.2), 3Cl,4-HPA (MW 186.6) and salicylic acid (MW 160.1). (B) DSC profiles, colored as follows: apo-NadR (violet), NadR+salicylate (red), NadR+3-HPA (green), NadR+4-HPA (blue), NadR+3Cl,4-HPA (pink).	FIG
125	133	profiles	evidence	 (A) Molecular structures of 3-HPA (MW 152.2), 4-HPA (MW 152.2), 3Cl,4-HPA (MW 186.6) and salicylic acid (MW 160.1). (B) DSC profiles, colored as follows: apo-NadR (violet), NadR+salicylate (red), NadR+3-HPA (green), NadR+4-HPA (blue), NadR+3Cl,4-HPA (pink).	FIG
155	158	apo	protein_state	 (A) Molecular structures of 3-HPA (MW 152.2), 4-HPA (MW 152.2), 3Cl,4-HPA (MW 186.6) and salicylic acid (MW 160.1). (B) DSC profiles, colored as follows: apo-NadR (violet), NadR+salicylate (red), NadR+3-HPA (green), NadR+4-HPA (blue), NadR+3Cl,4-HPA (pink).	FIG
159	163	NadR	protein	 (A) Molecular structures of 3-HPA (MW 152.2), 4-HPA (MW 152.2), 3Cl,4-HPA (MW 186.6) and salicylic acid (MW 160.1). (B) DSC profiles, colored as follows: apo-NadR (violet), NadR+salicylate (red), NadR+3-HPA (green), NadR+4-HPA (blue), NadR+3Cl,4-HPA (pink).	FIG
174	189	NadR+salicylate	complex_assembly	 (A) Molecular structures of 3-HPA (MW 152.2), 4-HPA (MW 152.2), 3Cl,4-HPA (MW 186.6) and salicylic acid (MW 160.1). (B) DSC profiles, colored as follows: apo-NadR (violet), NadR+salicylate (red), NadR+3-HPA (green), NadR+4-HPA (blue), NadR+3Cl,4-HPA (pink).	FIG
197	207	NadR+3-HPA	complex_assembly	 (A) Molecular structures of 3-HPA (MW 152.2), 4-HPA (MW 152.2), 3Cl,4-HPA (MW 186.6) and salicylic acid (MW 160.1). (B) DSC profiles, colored as follows: apo-NadR (violet), NadR+salicylate (red), NadR+3-HPA (green), NadR+4-HPA (blue), NadR+3Cl,4-HPA (pink).	FIG
217	227	NadR+4-HPA	complex_assembly	 (A) Molecular structures of 3-HPA (MW 152.2), 4-HPA (MW 152.2), 3Cl,4-HPA (MW 186.6) and salicylic acid (MW 160.1). (B) DSC profiles, colored as follows: apo-NadR (violet), NadR+salicylate (red), NadR+3-HPA (green), NadR+4-HPA (blue), NadR+3Cl,4-HPA (pink).	FIG
236	250	NadR+3Cl,4-HPA	complex_assembly	 (A) Molecular structures of 3-HPA (MW 152.2), 4-HPA (MW 152.2), 3Cl,4-HPA (MW 186.6) and salicylic acid (MW 160.1). (B) DSC profiles, colored as follows: apo-NadR (violet), NadR+salicylate (red), NadR+3-HPA (green), NadR+4-HPA (blue), NadR+3Cl,4-HPA (pink).	FIG
4	7	DSC	experimental_method	All DSC profiles are representative of triplicate experiments.	FIG
8	16	profiles	evidence	All DSC profiles are representative of triplicate experiments.	FIG
0	13	Melting-point	evidence	Melting-point (Tm) and its ligand-induced increase (ΔTm) derived from DSC thermostability experiments.	TABLE
15	17	Tm	evidence	Melting-point (Tm) and its ligand-induced increase (ΔTm) derived from DSC thermostability experiments.	TABLE
52	55	ΔTm	evidence	Melting-point (Tm) and its ligand-induced increase (ΔTm) derived from DSC thermostability experiments.	TABLE
70	73	DSC	experimental_method	Melting-point (Tm) and its ligand-induced increase (ΔTm) derived from DSC thermostability experiments.	TABLE
74	101	thermostability experiments	experimental_method	Melting-point (Tm) and its ligand-induced increase (ΔTm) derived from DSC thermostability experiments.	TABLE
0	22	Dissociation constants	evidence	Dissociation constants (KD) of the NadR/ligand interactions from SPR steady-state binding experiments.	TABLE
24	26	KD	evidence	Dissociation constants (KD) of the NadR/ligand interactions from SPR steady-state binding experiments.	TABLE
35	39	NadR	protein	Dissociation constants (KD) of the NadR/ligand interactions from SPR steady-state binding experiments.	TABLE
65	101	SPR steady-state binding experiments	experimental_method	Dissociation constants (KD) of the NadR/ligand interactions from SPR steady-state binding experiments.	TABLE
7	9	Tm	evidence	"Ligand	Tm (°C)	ΔTm (°C)	KD (mM)	 	No ligand	67.4 ± 0.1	n.a.	n.a."	TABLE
15	18	ΔTm	evidence	"Ligand	Tm (°C)	ΔTm (°C)	KD (mM)	 	No ligand	67.4 ± 0.1	n.a.	n.a."	TABLE
24	26	KD	evidence	"Ligand	Tm (°C)	ΔTm (°C)	KD (mM)	 	No ligand	67.4 ± 0.1	n.a.	n.a."	TABLE
2	7	3-HPA	chemical	"	 	3-HPA	70.0 ± 0.1	2.7	2.7 ± 0.1	 	4-HPA	70.7 ± 0.1	3.3	1.5 ± 0.1	 	3Cl,4-HPA	71.3 ± 0.2	3.9	1.1 ± 0.1	 	"	TABLE
35	40	4-HPA	chemical	"	 	3-HPA	70.0 ± 0.1	2.7	2.7 ± 0.1	 	4-HPA	70.7 ± 0.1	3.3	1.5 ± 0.1	 	3Cl,4-HPA	71.3 ± 0.2	3.9	1.1 ± 0.1	 	"	TABLE
68	77	3Cl,4-HPA	chemical	"	 	3-HPA	70.0 ± 0.1	2.7	2.7 ± 0.1	 	4-HPA	70.7 ± 0.1	3.3	1.5 ± 0.1	 	3Cl,4-HPA	71.3 ± 0.2	3.9	1.1 ± 0.1	 	"	TABLE
0	4	NadR	protein	NadR displays distinct binding affinities for hydroxyphenylacetate ligands	RESULTS
23	41	binding affinities	evidence	NadR displays distinct binding affinities for hydroxyphenylacetate ligands	RESULTS
46	66	hydroxyphenylacetate	chemical	NadR displays distinct binding affinities for hydroxyphenylacetate ligands	RESULTS
38	42	HPAs	chemical	To further investigate the binding of HPAs to NadR, we used surface plasmon resonance (SPR).	RESULTS
46	50	NadR	protein	To further investigate the binding of HPAs to NadR, we used surface plasmon resonance (SPR).	RESULTS
60	85	surface plasmon resonance	experimental_method	To further investigate the binding of HPAs to NadR, we used surface plasmon resonance (SPR).	RESULTS
87	90	SPR	experimental_method	To further investigate the binding of HPAs to NadR, we used surface plasmon resonance (SPR).	RESULTS
4	7	SPR	experimental_method	The SPR sensorgrams revealed very fast association and dissociation events, typical of small molecule ligands, thus prohibiting a detailed study of binding kinetics.	RESULTS
8	19	sensorgrams	evidence	The SPR sensorgrams revealed very fast association and dissociation events, typical of small molecule ligands, thus prohibiting a detailed study of binding kinetics.	RESULTS
9	25	steady-state SPR	experimental_method	However, steady-state SPR analyses of the NadR-HPA interactions allowed determination of the equilibrium dissociation constants (KD) (Table 1 and S2 Fig).	RESULTS
42	50	NadR-HPA	complex_assembly	However, steady-state SPR analyses of the NadR-HPA interactions allowed determination of the equilibrium dissociation constants (KD) (Table 1 and S2 Fig).	RESULTS
93	127	equilibrium dissociation constants	evidence	However, steady-state SPR analyses of the NadR-HPA interactions allowed determination of the equilibrium dissociation constants (KD) (Table 1 and S2 Fig).	RESULTS
129	131	KD	evidence	However, steady-state SPR analyses of the NadR-HPA interactions allowed determination of the equilibrium dissociation constants (KD) (Table 1 and S2 Fig).	RESULTS
20	25	4-HPA	chemical	The interactions of 4-HPA and 3Cl,4-HPA with NadR exhibited KD values of 1.5 mM and 1.1 mM, respectively.	RESULTS
30	39	3Cl,4-HPA	chemical	The interactions of 4-HPA and 3Cl,4-HPA with NadR exhibited KD values of 1.5 mM and 1.1 mM, respectively.	RESULTS
45	49	NadR	protein	The interactions of 4-HPA and 3Cl,4-HPA with NadR exhibited KD values of 1.5 mM and 1.1 mM, respectively.	RESULTS
60	62	KD	evidence	The interactions of 4-HPA and 3Cl,4-HPA with NadR exhibited KD values of 1.5 mM and 1.1 mM, respectively.	RESULTS
0	5	3-HPA	chemical	3-HPA showed a weaker interaction, with a KD of 2.7 mM, while salicylate showed only a very weak response that did not reach saturation, indicating a non-specific interaction with NadR. A ranking of these KD values showed that 3Cl,4-HPA was the tightest binder, and thus matched the ranking of ligand-induced Tm increases observed in the DSC experiments.	RESULTS
42	44	KD	evidence	3-HPA showed a weaker interaction, with a KD of 2.7 mM, while salicylate showed only a very weak response that did not reach saturation, indicating a non-specific interaction with NadR. A ranking of these KD values showed that 3Cl,4-HPA was the tightest binder, and thus matched the ranking of ligand-induced Tm increases observed in the DSC experiments.	RESULTS
62	72	salicylate	chemical	3-HPA showed a weaker interaction, with a KD of 2.7 mM, while salicylate showed only a very weak response that did not reach saturation, indicating a non-specific interaction with NadR. A ranking of these KD values showed that 3Cl,4-HPA was the tightest binder, and thus matched the ranking of ligand-induced Tm increases observed in the DSC experiments.	RESULTS
180	184	NadR	protein	3-HPA showed a weaker interaction, with a KD of 2.7 mM, while salicylate showed only a very weak response that did not reach saturation, indicating a non-specific interaction with NadR. A ranking of these KD values showed that 3Cl,4-HPA was the tightest binder, and thus matched the ranking of ligand-induced Tm increases observed in the DSC experiments.	RESULTS
205	207	KD	evidence	3-HPA showed a weaker interaction, with a KD of 2.7 mM, while salicylate showed only a very weak response that did not reach saturation, indicating a non-specific interaction with NadR. A ranking of these KD values showed that 3Cl,4-HPA was the tightest binder, and thus matched the ranking of ligand-induced Tm increases observed in the DSC experiments.	RESULTS
227	236	3Cl,4-HPA	chemical	3-HPA showed a weaker interaction, with a KD of 2.7 mM, while salicylate showed only a very weak response that did not reach saturation, indicating a non-specific interaction with NadR. A ranking of these KD values showed that 3Cl,4-HPA was the tightest binder, and thus matched the ranking of ligand-induced Tm increases observed in the DSC experiments.	RESULTS
309	311	Tm	evidence	3-HPA showed a weaker interaction, with a KD of 2.7 mM, while salicylate showed only a very weak response that did not reach saturation, indicating a non-specific interaction with NadR. A ranking of these KD values showed that 3Cl,4-HPA was the tightest binder, and thus matched the ranking of ligand-induced Tm increases observed in the DSC experiments.	RESULTS
338	341	DSC	experimental_method	3-HPA showed a weaker interaction, with a KD of 2.7 mM, while salicylate showed only a very weak response that did not reach saturation, indicating a non-specific interaction with NadR. A ranking of these KD values showed that 3Cl,4-HPA was the tightest binder, and thus matched the ranking of ligand-induced Tm increases observed in the DSC experiments.	RESULTS
15	17	KD	evidence	Although these KD values indicate rather weak interactions, they are similar to the values reported previously for the MarR/salicylate interaction (KD ~1 mM) and the MTH313/salicylate interaction (KD 2–3 mM), and approximately 20-fold tighter than the ST1710/salicylate interaction (KD ~20 mM).	RESULTS
119	123	MarR	protein_type	Although these KD values indicate rather weak interactions, they are similar to the values reported previously for the MarR/salicylate interaction (KD ~1 mM) and the MTH313/salicylate interaction (KD 2–3 mM), and approximately 20-fold tighter than the ST1710/salicylate interaction (KD ~20 mM).	RESULTS
124	134	salicylate	chemical	Although these KD values indicate rather weak interactions, they are similar to the values reported previously for the MarR/salicylate interaction (KD ~1 mM) and the MTH313/salicylate interaction (KD 2–3 mM), and approximately 20-fold tighter than the ST1710/salicylate interaction (KD ~20 mM).	RESULTS
166	172	MTH313	protein	Although these KD values indicate rather weak interactions, they are similar to the values reported previously for the MarR/salicylate interaction (KD ~1 mM) and the MTH313/salicylate interaction (KD 2–3 mM), and approximately 20-fold tighter than the ST1710/salicylate interaction (KD ~20 mM).	RESULTS
173	183	salicylate	chemical	Although these KD values indicate rather weak interactions, they are similar to the values reported previously for the MarR/salicylate interaction (KD ~1 mM) and the MTH313/salicylate interaction (KD 2–3 mM), and approximately 20-fold tighter than the ST1710/salicylate interaction (KD ~20 mM).	RESULTS
252	258	ST1710	protein	Although these KD values indicate rather weak interactions, they are similar to the values reported previously for the MarR/salicylate interaction (KD ~1 mM) and the MTH313/salicylate interaction (KD 2–3 mM), and approximately 20-fold tighter than the ST1710/salicylate interaction (KD ~20 mM).	RESULTS
259	269	salicylate	chemical	Although these KD values indicate rather weak interactions, they are similar to the values reported previously for the MarR/salicylate interaction (KD ~1 mM) and the MTH313/salicylate interaction (KD 2–3 mM), and approximately 20-fold tighter than the ST1710/salicylate interaction (KD ~20 mM).	RESULTS
0	18	Crystal structures	evidence	Crystal structures of holo-NadR and apo-NadR	RESULTS
22	26	holo	protein_state	Crystal structures of holo-NadR and apo-NadR	RESULTS
27	31	NadR	protein	Crystal structures of holo-NadR and apo-NadR	RESULTS
36	39	apo	protein_state	Crystal structures of holo-NadR and apo-NadR	RESULTS
40	44	NadR	protein	Crystal structures of holo-NadR and apo-NadR	RESULTS
26	30	NadR	protein	To fully characterize the NadR/HPA interactions, we sought to determine crystal structures of NadR in ligand-bound (holo) and ligand-free (apo) forms.	RESULTS
31	34	HPA	chemical	To fully characterize the NadR/HPA interactions, we sought to determine crystal structures of NadR in ligand-bound (holo) and ligand-free (apo) forms.	RESULTS
72	90	crystal structures	evidence	To fully characterize the NadR/HPA interactions, we sought to determine crystal structures of NadR in ligand-bound (holo) and ligand-free (apo) forms.	RESULTS
94	98	NadR	protein	To fully characterize the NadR/HPA interactions, we sought to determine crystal structures of NadR in ligand-bound (holo) and ligand-free (apo) forms.	RESULTS
102	114	ligand-bound	protein_state	To fully characterize the NadR/HPA interactions, we sought to determine crystal structures of NadR in ligand-bound (holo) and ligand-free (apo) forms.	RESULTS
116	120	holo	protein_state	To fully characterize the NadR/HPA interactions, we sought to determine crystal structures of NadR in ligand-bound (holo) and ligand-free (apo) forms.	RESULTS
126	137	ligand-free	protein_state	To fully characterize the NadR/HPA interactions, we sought to determine crystal structures of NadR in ligand-bound (holo) and ligand-free (apo) forms.	RESULTS
139	142	apo	protein_state	To fully characterize the NadR/HPA interactions, we sought to determine crystal structures of NadR in ligand-bound (holo) and ligand-free (apo) forms.	RESULTS
10	22	crystallized	experimental_method	First, we crystallized NadR (a selenomethionine-labelled derivative) in the presence of a 200-fold molar excess of 4-HPA.	RESULTS
23	27	NadR	protein	First, we crystallized NadR (a selenomethionine-labelled derivative) in the presence of a 200-fold molar excess of 4-HPA.	RESULTS
31	67	selenomethionine-labelled derivative	experimental_method	First, we crystallized NadR (a selenomethionine-labelled derivative) in the presence of a 200-fold molar excess of 4-HPA.	RESULTS
115	120	4-HPA	chemical	First, we crystallized NadR (a selenomethionine-labelled derivative) in the presence of a 200-fold molar excess of 4-HPA.	RESULTS
4	13	structure	evidence	The structure of the NadR/4-HPA complex was determined at 2.3 Å resolution using a combination of the single-wavelength anomalous dispersion (SAD) and molecular replacement (MR) methods, and was refined to R work/R free values of 20.9/26.0% (Table 2).	RESULTS
21	31	NadR/4-HPA	complex_assembly	The structure of the NadR/4-HPA complex was determined at 2.3 Å resolution using a combination of the single-wavelength anomalous dispersion (SAD) and molecular replacement (MR) methods, and was refined to R work/R free values of 20.9/26.0% (Table 2).	RESULTS
102	140	single-wavelength anomalous dispersion	experimental_method	The structure of the NadR/4-HPA complex was determined at 2.3 Å resolution using a combination of the single-wavelength anomalous dispersion (SAD) and molecular replacement (MR) methods, and was refined to R work/R free values of 20.9/26.0% (Table 2).	RESULTS
142	145	SAD	experimental_method	The structure of the NadR/4-HPA complex was determined at 2.3 Å resolution using a combination of the single-wavelength anomalous dispersion (SAD) and molecular replacement (MR) methods, and was refined to R work/R free values of 20.9/26.0% (Table 2).	RESULTS
151	172	molecular replacement	experimental_method	The structure of the NadR/4-HPA complex was determined at 2.3 Å resolution using a combination of the single-wavelength anomalous dispersion (SAD) and molecular replacement (MR) methods, and was refined to R work/R free values of 20.9/26.0% (Table 2).	RESULTS
174	176	MR	experimental_method	The structure of the NadR/4-HPA complex was determined at 2.3 Å resolution using a combination of the single-wavelength anomalous dispersion (SAD) and molecular replacement (MR) methods, and was refined to R work/R free values of 20.9/26.0% (Table 2).	RESULTS
206	219	R work/R free	evidence	The structure of the NadR/4-HPA complex was determined at 2.3 Å resolution using a combination of the single-wavelength anomalous dispersion (SAD) and molecular replacement (MR) methods, and was refined to R work/R free values of 20.9/26.0% (Table 2).	RESULTS
65	73	crystals	evidence	Despite numerous attempts, we were unable to obtain high-quality crystals of NadR complexed with 3Cl,4-HPA, 3,4-HPA, 3-HPA or DNA targets.	RESULTS
77	81	NadR	protein	Despite numerous attempts, we were unable to obtain high-quality crystals of NadR complexed with 3Cl,4-HPA, 3,4-HPA, 3-HPA or DNA targets.	RESULTS
82	96	complexed with	protein_state	Despite numerous attempts, we were unable to obtain high-quality crystals of NadR complexed with 3Cl,4-HPA, 3,4-HPA, 3-HPA or DNA targets.	RESULTS
97	106	3Cl,4-HPA	chemical	Despite numerous attempts, we were unable to obtain high-quality crystals of NadR complexed with 3Cl,4-HPA, 3,4-HPA, 3-HPA or DNA targets.	RESULTS
108	115	3,4-HPA	chemical	Despite numerous attempts, we were unable to obtain high-quality crystals of NadR complexed with 3Cl,4-HPA, 3,4-HPA, 3-HPA or DNA targets.	RESULTS
117	122	3-HPA	chemical	Despite numerous attempts, we were unable to obtain high-quality crystals of NadR complexed with 3Cl,4-HPA, 3,4-HPA, 3-HPA or DNA targets.	RESULTS
39	50	crystallize	experimental_method	However, it was eventually possible to crystallize apo-NadR, and the structure was determined at 2.7 Å resolution by MR methods using the NadR/4-HPA complex as the search model.	RESULTS
51	54	apo	protein_state	However, it was eventually possible to crystallize apo-NadR, and the structure was determined at 2.7 Å resolution by MR methods using the NadR/4-HPA complex as the search model.	RESULTS
55	59	NadR	protein	However, it was eventually possible to crystallize apo-NadR, and the structure was determined at 2.7 Å resolution by MR methods using the NadR/4-HPA complex as the search model.	RESULTS
69	78	structure	evidence	However, it was eventually possible to crystallize apo-NadR, and the structure was determined at 2.7 Å resolution by MR methods using the NadR/4-HPA complex as the search model.	RESULTS
117	119	MR	experimental_method	However, it was eventually possible to crystallize apo-NadR, and the structure was determined at 2.7 Å resolution by MR methods using the NadR/4-HPA complex as the search model.	RESULTS
138	148	NadR/4-HPA	complex_assembly	However, it was eventually possible to crystallize apo-NadR, and the structure was determined at 2.7 Å resolution by MR methods using the NadR/4-HPA complex as the search model.	RESULTS
4	7	apo	protein_state	The apo-NadR structure was refined to R work/R free values of 19.1/26.8% (Table 2).	RESULTS
8	12	NadR	protein	The apo-NadR structure was refined to R work/R free values of 19.1/26.8% (Table 2).	RESULTS
13	22	structure	evidence	The apo-NadR structure was refined to R work/R free values of 19.1/26.8% (Table 2).	RESULTS
38	51	R work/R free	evidence	The apo-NadR structure was refined to R work/R free values of 19.1/26.8% (Table 2).	RESULTS
46	50	NadR	protein	Data collection and refinement statistics for NadR structures.	TABLE
51	61	structures	evidence	Data collection and refinement statistics for NadR structures.	TABLE
27	37	NadR/4-HPA	complex_assembly	The asymmetric unit of the NadR/4-HPA crystals (holo-NadR) contained one NadR homodimer, while the apo-NadR crystals contained two homodimers.	RESULTS
38	46	crystals	evidence	The asymmetric unit of the NadR/4-HPA crystals (holo-NadR) contained one NadR homodimer, while the apo-NadR crystals contained two homodimers.	RESULTS
48	52	holo	protein_state	The asymmetric unit of the NadR/4-HPA crystals (holo-NadR) contained one NadR homodimer, while the apo-NadR crystals contained two homodimers.	RESULTS
53	57	NadR	protein	The asymmetric unit of the NadR/4-HPA crystals (holo-NadR) contained one NadR homodimer, while the apo-NadR crystals contained two homodimers.	RESULTS
73	77	NadR	protein	The asymmetric unit of the NadR/4-HPA crystals (holo-NadR) contained one NadR homodimer, while the apo-NadR crystals contained two homodimers.	RESULTS
78	87	homodimer	oligomeric_state	The asymmetric unit of the NadR/4-HPA crystals (holo-NadR) contained one NadR homodimer, while the apo-NadR crystals contained two homodimers.	RESULTS
99	102	apo	protein_state	The asymmetric unit of the NadR/4-HPA crystals (holo-NadR) contained one NadR homodimer, while the apo-NadR crystals contained two homodimers.	RESULTS
103	107	NadR	protein	The asymmetric unit of the NadR/4-HPA crystals (holo-NadR) contained one NadR homodimer, while the apo-NadR crystals contained two homodimers.	RESULTS
108	116	crystals	evidence	The asymmetric unit of the NadR/4-HPA crystals (holo-NadR) contained one NadR homodimer, while the apo-NadR crystals contained two homodimers.	RESULTS
131	141	homodimers	oligomeric_state	The asymmetric unit of the NadR/4-HPA crystals (holo-NadR) contained one NadR homodimer, while the apo-NadR crystals contained two homodimers.	RESULTS
7	10	apo	protein_state	In the apo-NadR crystals, the two homodimers were related by a rotation of ~90°; the observed association of the two dimers was presumably merely an effect of crystal packing, since the interface between the two homodimers is small (< 550 Å2 of buried surface area), and is not predicted to be physiologically relevant by the PISA software.	RESULTS
11	15	NadR	protein	In the apo-NadR crystals, the two homodimers were related by a rotation of ~90°; the observed association of the two dimers was presumably merely an effect of crystal packing, since the interface between the two homodimers is small (< 550 Å2 of buried surface area), and is not predicted to be physiologically relevant by the PISA software.	RESULTS
16	24	crystals	evidence	In the apo-NadR crystals, the two homodimers were related by a rotation of ~90°; the observed association of the two dimers was presumably merely an effect of crystal packing, since the interface between the two homodimers is small (< 550 Å2 of buried surface area), and is not predicted to be physiologically relevant by the PISA software.	RESULTS
34	44	homodimers	oligomeric_state	In the apo-NadR crystals, the two homodimers were related by a rotation of ~90°; the observed association of the two dimers was presumably merely an effect of crystal packing, since the interface between the two homodimers is small (< 550 Å2 of buried surface area), and is not predicted to be physiologically relevant by the PISA software.	RESULTS
117	123	dimers	oligomeric_state	In the apo-NadR crystals, the two homodimers were related by a rotation of ~90°; the observed association of the two dimers was presumably merely an effect of crystal packing, since the interface between the two homodimers is small (< 550 Å2 of buried surface area), and is not predicted to be physiologically relevant by the PISA software.	RESULTS
186	195	interface	site	In the apo-NadR crystals, the two homodimers were related by a rotation of ~90°; the observed association of the two dimers was presumably merely an effect of crystal packing, since the interface between the two homodimers is small (< 550 Å2 of buried surface area), and is not predicted to be physiologically relevant by the PISA software.	RESULTS
212	222	homodimers	oligomeric_state	In the apo-NadR crystals, the two homodimers were related by a rotation of ~90°; the observed association of the two dimers was presumably merely an effect of crystal packing, since the interface between the two homodimers is small (< 550 Å2 of buried surface area), and is not predicted to be physiologically relevant by the PISA software.	RESULTS
14	27	SE-HPLC/MALLS	experimental_method	Moreover, our SE-HPLC/MALLS analyses (see above) revealed that in solution NadR is dimeric, and previous studies using native mass spectrometry (MS) revealed dimers, not tetramers.	RESULTS
75	79	NadR	protein	Moreover, our SE-HPLC/MALLS analyses (see above) revealed that in solution NadR is dimeric, and previous studies using native mass spectrometry (MS) revealed dimers, not tetramers.	RESULTS
83	90	dimeric	oligomeric_state	Moreover, our SE-HPLC/MALLS analyses (see above) revealed that in solution NadR is dimeric, and previous studies using native mass spectrometry (MS) revealed dimers, not tetramers.	RESULTS
119	143	native mass spectrometry	experimental_method	Moreover, our SE-HPLC/MALLS analyses (see above) revealed that in solution NadR is dimeric, and previous studies using native mass spectrometry (MS) revealed dimers, not tetramers.	RESULTS
145	147	MS	experimental_method	Moreover, our SE-HPLC/MALLS analyses (see above) revealed that in solution NadR is dimeric, and previous studies using native mass spectrometry (MS) revealed dimers, not tetramers.	RESULTS
158	164	dimers	oligomeric_state	Moreover, our SE-HPLC/MALLS analyses (see above) revealed that in solution NadR is dimeric, and previous studies using native mass spectrometry (MS) revealed dimers, not tetramers.	RESULTS
170	179	tetramers	oligomeric_state	Moreover, our SE-HPLC/MALLS analyses (see above) revealed that in solution NadR is dimeric, and previous studies using native mass spectrometry (MS) revealed dimers, not tetramers.	RESULTS
4	8	NadR	protein	The NadR homodimer bound to 4-HPA has a dimerization interface mostly involving the top of its ‘triangular’ form, while the two DNA-binding domains are located at the base (Fig 2A).	RESULTS
9	18	homodimer	oligomeric_state	The NadR homodimer bound to 4-HPA has a dimerization interface mostly involving the top of its ‘triangular’ form, while the two DNA-binding domains are located at the base (Fig 2A).	RESULTS
19	27	bound to	protein_state	The NadR homodimer bound to 4-HPA has a dimerization interface mostly involving the top of its ‘triangular’ form, while the two DNA-binding domains are located at the base (Fig 2A).	RESULTS
28	33	4-HPA	chemical	The NadR homodimer bound to 4-HPA has a dimerization interface mostly involving the top of its ‘triangular’ form, while the two DNA-binding domains are located at the base (Fig 2A).	RESULTS
40	62	dimerization interface	site	The NadR homodimer bound to 4-HPA has a dimerization interface mostly involving the top of its ‘triangular’ form, while the two DNA-binding domains are located at the base (Fig 2A).	RESULTS
96	106	triangular	protein_state	The NadR homodimer bound to 4-HPA has a dimerization interface mostly involving the top of its ‘triangular’ form, while the two DNA-binding domains are located at the base (Fig 2A).	RESULTS
128	147	DNA-binding domains	structure_element	The NadR homodimer bound to 4-HPA has a dimerization interface mostly involving the top of its ‘triangular’ form, while the two DNA-binding domains are located at the base (Fig 2A).	RESULTS
13	34	electron density maps	evidence	High-quality electron density maps allowed clear identification of the bound ligand, 4-HPA (Fig 2B).	RESULTS
71	76	bound	protein_state	High-quality electron density maps allowed clear identification of the bound ligand, 4-HPA (Fig 2B).	RESULTS
85	90	4-HPA	chemical	High-quality electron density maps allowed clear identification of the bound ligand, 4-HPA (Fig 2B).	RESULTS
12	21	structure	evidence	The overall structure of NadR shows dimensions of ~50 × 65 × 50 Å and a large homodimer interface that buries a total surface area of ~ 4800 Å2.	RESULTS
25	29	NadR	protein	The overall structure of NadR shows dimensions of ~50 × 65 × 50 Å and a large homodimer interface that buries a total surface area of ~ 4800 Å2.	RESULTS
78	97	homodimer interface	site	The overall structure of NadR shows dimensions of ~50 × 65 × 50 Å and a large homodimer interface that buries a total surface area of ~ 4800 Å2.	RESULTS
5	9	NadR	protein	Each NadR monomer consists of six α-helices and two short β-strands, with helices α1, α5, and α6 forming the dimer interface.	RESULTS
10	17	monomer	oligomeric_state	Each NadR monomer consists of six α-helices and two short β-strands, with helices α1, α5, and α6 forming the dimer interface.	RESULTS
34	43	α-helices	structure_element	Each NadR monomer consists of six α-helices and two short β-strands, with helices α1, α5, and α6 forming the dimer interface.	RESULTS
52	67	short β-strands	structure_element	Each NadR monomer consists of six α-helices and two short β-strands, with helices α1, α5, and α6 forming the dimer interface.	RESULTS
74	81	helices	structure_element	Each NadR monomer consists of six α-helices and two short β-strands, with helices α1, α5, and α6 forming the dimer interface.	RESULTS
82	84	α1	structure_element	Each NadR monomer consists of six α-helices and two short β-strands, with helices α1, α5, and α6 forming the dimer interface.	RESULTS
86	88	α5	structure_element	Each NadR monomer consists of six α-helices and two short β-strands, with helices α1, α5, and α6 forming the dimer interface.	RESULTS
94	96	α6	structure_element	Each NadR monomer consists of six α-helices and two short β-strands, with helices α1, α5, and α6 forming the dimer interface.	RESULTS
109	124	dimer interface	site	Each NadR monomer consists of six α-helices and two short β-strands, with helices α1, α5, and α6 forming the dimer interface.	RESULTS
0	7	Helices	structure_element	Helices α3 and α4 form a helix-turn-helix motif, followed by the “wing motif” comprised of two short antiparallel β-strands (β1-β2) linked by a relatively long and flexible loop.	RESULTS
8	10	α3	structure_element	Helices α3 and α4 form a helix-turn-helix motif, followed by the “wing motif” comprised of two short antiparallel β-strands (β1-β2) linked by a relatively long and flexible loop.	RESULTS
15	17	α4	structure_element	Helices α3 and α4 form a helix-turn-helix motif, followed by the “wing motif” comprised of two short antiparallel β-strands (β1-β2) linked by a relatively long and flexible loop.	RESULTS
25	47	helix-turn-helix motif	structure_element	Helices α3 and α4 form a helix-turn-helix motif, followed by the “wing motif” comprised of two short antiparallel β-strands (β1-β2) linked by a relatively long and flexible loop.	RESULTS
66	76	wing motif	structure_element	Helices α3 and α4 form a helix-turn-helix motif, followed by the “wing motif” comprised of two short antiparallel β-strands (β1-β2) linked by a relatively long and flexible loop.	RESULTS
95	123	short antiparallel β-strands	structure_element	Helices α3 and α4 form a helix-turn-helix motif, followed by the “wing motif” comprised of two short antiparallel β-strands (β1-β2) linked by a relatively long and flexible loop.	RESULTS
125	130	β1-β2	structure_element	Helices α3 and α4 form a helix-turn-helix motif, followed by the “wing motif” comprised of two short antiparallel β-strands (β1-β2) linked by a relatively long and flexible loop.	RESULTS
173	177	loop	structure_element	Helices α3 and α4 form a helix-turn-helix motif, followed by the “wing motif” comprised of two short antiparallel β-strands (β1-β2) linked by a relatively long and flexible loop.	RESULTS
22	34	α4-β2 region	structure_element	Interestingly, in the α4-β2 region, the stretch of residues from R64-R91 presents seven positively-charged side chains, all available for potential interactions with DNA.	RESULTS
65	72	R64-R91	residue_range	Interestingly, in the α4-β2 region, the stretch of residues from R64-R91 presents seven positively-charged side chains, all available for potential interactions with DNA.	RESULTS
166	169	DNA	chemical	Interestingly, in the α4-β2 region, the stretch of residues from R64-R91 presents seven positively-charged side chains, all available for potential interactions with DNA.	RESULTS
51	74	winged helix-turn-helix	structure_element	Together, these structural elements constitute the winged helix-turn-helix (wHTH) DNA-binding domain and, together with the dimeric organization, are the hallmarks of MarR family structures.	RESULTS
76	80	wHTH	structure_element	Together, these structural elements constitute the winged helix-turn-helix (wHTH) DNA-binding domain and, together with the dimeric organization, are the hallmarks of MarR family structures.	RESULTS
82	100	DNA-binding domain	structure_element	Together, these structural elements constitute the winged helix-turn-helix (wHTH) DNA-binding domain and, together with the dimeric organization, are the hallmarks of MarR family structures.	RESULTS
124	131	dimeric	oligomeric_state	Together, these structural elements constitute the winged helix-turn-helix (wHTH) DNA-binding domain and, together with the dimeric organization, are the hallmarks of MarR family structures.	RESULTS
167	171	MarR	protein_type	Together, these structural elements constitute the winged helix-turn-helix (wHTH) DNA-binding domain and, together with the dimeric organization, are the hallmarks of MarR family structures.	RESULTS
179	189	structures	evidence	Together, these structural elements constitute the winged helix-turn-helix (wHTH) DNA-binding domain and, together with the dimeric organization, are the hallmarks of MarR family structures.	RESULTS
4	21	crystal structure	evidence	The crystal structure of NadR in complex with 4-HPA.	FIG
25	29	NadR	protein	The crystal structure of NadR in complex with 4-HPA.	FIG
30	45	in complex with	protein_state	The crystal structure of NadR in complex with 4-HPA.	FIG
46	51	4-HPA	chemical	The crystal structure of NadR in complex with 4-HPA.	FIG
9	13	holo	protein_state	 (A) The holo-NadR homodimer is depicted in green and blue for chains A and B respectively, while yellow sticks depict the 4-HPA ligand (labelled).	FIG
14	18	NadR	protein	 (A) The holo-NadR homodimer is depicted in green and blue for chains A and B respectively, while yellow sticks depict the 4-HPA ligand (labelled).	FIG
19	28	homodimer	oligomeric_state	 (A) The holo-NadR homodimer is depicted in green and blue for chains A and B respectively, while yellow sticks depict the 4-HPA ligand (labelled).	FIG
63	77	chains A and B	structure_element	 (A) The holo-NadR homodimer is depicted in green and blue for chains A and B respectively, while yellow sticks depict the 4-HPA ligand (labelled).	FIG
123	128	4-HPA	chemical	 (A) The holo-NadR homodimer is depicted in green and blue for chains A and B respectively, while yellow sticks depict the 4-HPA ligand (labelled).	FIG
62	69	chain B	structure_element	For simplicity, secondary structure elements are labelled for chain B only.	FIG
42	49	chain B	structure_element	Red dashes show hypothetical positions of chain B residues 88–90 that were not modeled due to lack of electron density.	FIG
59	64	88–90	residue_range	Red dashes show hypothetical positions of chain B residues 88–90 that were not modeled due to lack of electron density.	FIG
102	118	electron density	evidence	Red dashes show hypothetical positions of chain B residues 88–90 that were not modeled due to lack of electron density.	FIG
20	26	pocket	site	(B) A zoom into the pocket occupied by 4-HPA shows that the ligand contacts both chains A and B; blue mesh shows electron density around 4-HPA calculated from a composite omit map (omitting 4-HPA), using phenix.	FIG
39	44	4-HPA	chemical	(B) A zoom into the pocket occupied by 4-HPA shows that the ligand contacts both chains A and B; blue mesh shows electron density around 4-HPA calculated from a composite omit map (omitting 4-HPA), using phenix.	FIG
81	95	chains A and B	structure_element	(B) A zoom into the pocket occupied by 4-HPA shows that the ligand contacts both chains A and B; blue mesh shows electron density around 4-HPA calculated from a composite omit map (omitting 4-HPA), using phenix.	FIG
113	129	electron density	evidence	(B) A zoom into the pocket occupied by 4-HPA shows that the ligand contacts both chains A and B; blue mesh shows electron density around 4-HPA calculated from a composite omit map (omitting 4-HPA), using phenix.	FIG
137	142	4-HPA	chemical	(B) A zoom into the pocket occupied by 4-HPA shows that the ligand contacts both chains A and B; blue mesh shows electron density around 4-HPA calculated from a composite omit map (omitting 4-HPA), using phenix.	FIG
161	179	composite omit map	evidence	(B) A zoom into the pocket occupied by 4-HPA shows that the ligand contacts both chains A and B; blue mesh shows electron density around 4-HPA calculated from a composite omit map (omitting 4-HPA), using phenix.	FIG
190	195	4-HPA	chemical	(B) A zoom into the pocket occupied by 4-HPA shows that the ligand contacts both chains A and B; blue mesh shows electron density around 4-HPA calculated from a composite omit map (omitting 4-HPA), using phenix.	FIG
204	210	phenix	experimental_method	(B) A zoom into the pocket occupied by 4-HPA shows that the ligand contacts both chains A and B; blue mesh shows electron density around 4-HPA calculated from a composite omit map (omitting 4-HPA), using phenix.	FIG
4	7	map	evidence	The map is contoured at 1σ and the figure was prepared with a density mesh carve factor of 1.7, using Pymol (www.pymol.org).	FIG
62	74	density mesh	evidence	The map is contoured at 1σ and the figure was prepared with a density mesh carve factor of 1.7, using Pymol (www.pymol.org).	FIG
9	18	conserved	protein_state	A single conserved leucine residue (L130) is crucial for dimerization	RESULTS
19	26	leucine	residue_name	A single conserved leucine residue (L130) is crucial for dimerization	RESULTS
36	40	L130	residue_name_number	A single conserved leucine residue (L130) is crucial for dimerization	RESULTS
4	8	NadR	protein	The NadR dimer interface is formed by at least 32 residues, which establish numerous inter-chain salt bridges or hydrogen bonds, and many hydrophobic packing interactions (Fig 3A and 3B).	RESULTS
9	24	dimer interface	site	The NadR dimer interface is formed by at least 32 residues, which establish numerous inter-chain salt bridges or hydrogen bonds, and many hydrophobic packing interactions (Fig 3A and 3B).	RESULTS
97	109	salt bridges	bond_interaction	The NadR dimer interface is formed by at least 32 residues, which establish numerous inter-chain salt bridges or hydrogen bonds, and many hydrophobic packing interactions (Fig 3A and 3B).	RESULTS
113	127	hydrogen bonds	bond_interaction	The NadR dimer interface is formed by at least 32 residues, which establish numerous inter-chain salt bridges or hydrogen bonds, and many hydrophobic packing interactions (Fig 3A and 3B).	RESULTS
138	170	hydrophobic packing interactions	bond_interaction	The NadR dimer interface is formed by at least 32 residues, which establish numerous inter-chain salt bridges or hydrogen bonds, and many hydrophobic packing interactions (Fig 3A and 3B).	RESULTS
81	90	interface	site	To determine which residues were most important for dimerization, we studied the interface in silico and identified several residues as potential mediators of key stabilizing interactions.	RESULTS
6	31	site-directed mutagenesis	experimental_method	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
50	56	mutant	protein_state	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
57	61	NadR	protein	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
105	108	H7A	mutant	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
110	113	S9A	mutant	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
115	119	N11A	mutant	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
121	126	D112A	mutant	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
128	133	R114A	mutant	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
135	140	Y115A	mutant	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
142	147	K126A	mutant	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
149	154	L130K	mutant	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
159	164	L133K	mutant	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
200	215	dimer interface	site	Using site-directed mutagenesis, a panel of eight mutant NadR proteins was prepared (including mutations H7A, S9A, N11A, D112A, R114A, Y115A, K126A, L130K and L133K), sufficient to explore the entire dimer interface.	RESULTS
5	11	mutant	protein_state	Each mutant NadR protein was purified, and then its oligomeric state was examined by analytical SE-HPLC.	RESULTS
12	16	NadR	protein	Each mutant NadR protein was purified, and then its oligomeric state was examined by analytical SE-HPLC.	RESULTS
85	103	analytical SE-HPLC	experimental_method	Each mutant NadR protein was purified, and then its oligomeric state was examined by analytical SE-HPLC.	RESULTS
62	71	wild-type	protein_state	Almost all the mutants showed the same elution profile as the wild-type (WT) NadR protein.	RESULTS
73	75	WT	protein_state	Almost all the mutants showed the same elution profile as the wild-type (WT) NadR protein.	RESULTS
77	81	NadR	protein	Almost all the mutants showed the same elution profile as the wild-type (WT) NadR protein.	RESULTS
9	14	L130K	mutant	Only the L130K mutation induced a notable change in the oligomeric state of NadR (Fig 3C).	RESULTS
76	80	NadR	protein	Only the L130K mutation induced a notable change in the oligomeric state of NadR (Fig 3C).	RESULTS
12	20	SE-MALLS	experimental_method	Further, in SE-MALLS analyses, the L130K mutant displayed two distinct species in solution, approximately 80% being monomeric (a 19 kDa species), and only 20% retaining the typical native dimeric state (a 35 kDa species) (Fig 3D), demonstrating that Leu130 is crucial for stable dimerization.	RESULTS
35	40	L130K	mutant	Further, in SE-MALLS analyses, the L130K mutant displayed two distinct species in solution, approximately 80% being monomeric (a 19 kDa species), and only 20% retaining the typical native dimeric state (a 35 kDa species) (Fig 3D), demonstrating that Leu130 is crucial for stable dimerization.	RESULTS
41	47	mutant	protein_state	Further, in SE-MALLS analyses, the L130K mutant displayed two distinct species in solution, approximately 80% being monomeric (a 19 kDa species), and only 20% retaining the typical native dimeric state (a 35 kDa species) (Fig 3D), demonstrating that Leu130 is crucial for stable dimerization.	RESULTS
116	125	monomeric	oligomeric_state	Further, in SE-MALLS analyses, the L130K mutant displayed two distinct species in solution, approximately 80% being monomeric (a 19 kDa species), and only 20% retaining the typical native dimeric state (a 35 kDa species) (Fig 3D), demonstrating that Leu130 is crucial for stable dimerization.	RESULTS
188	195	dimeric	oligomeric_state	Further, in SE-MALLS analyses, the L130K mutant displayed two distinct species in solution, approximately 80% being monomeric (a 19 kDa species), and only 20% retaining the typical native dimeric state (a 35 kDa species) (Fig 3D), demonstrating that Leu130 is crucial for stable dimerization.	RESULTS
250	256	Leu130	residue_name_number	Further, in SE-MALLS analyses, the L130K mutant displayed two distinct species in solution, approximately 80% being monomeric (a 19 kDa species), and only 20% retaining the typical native dimeric state (a 35 kDa species) (Fig 3D), demonstrating that Leu130 is crucial for stable dimerization.	RESULTS
19	23	L130	residue_name_number	It is notable that L130 is usually present as Leu, or an alternative bulky hydrophobic amino acid (e.g. Phe, Val), in many MarR family proteins, suggesting a conserved role in stabilizing the dimer interface.	RESULTS
46	49	Leu	residue_name	It is notable that L130 is usually present as Leu, or an alternative bulky hydrophobic amino acid (e.g. Phe, Val), in many MarR family proteins, suggesting a conserved role in stabilizing the dimer interface.	RESULTS
104	107	Phe	residue_name	It is notable that L130 is usually present as Leu, or an alternative bulky hydrophobic amino acid (e.g. Phe, Val), in many MarR family proteins, suggesting a conserved role in stabilizing the dimer interface.	RESULTS
109	112	Val	residue_name	It is notable that L130 is usually present as Leu, or an alternative bulky hydrophobic amino acid (e.g. Phe, Val), in many MarR family proteins, suggesting a conserved role in stabilizing the dimer interface.	RESULTS
123	127	MarR	protein_type	It is notable that L130 is usually present as Leu, or an alternative bulky hydrophobic amino acid (e.g. Phe, Val), in many MarR family proteins, suggesting a conserved role in stabilizing the dimer interface.	RESULTS
158	167	conserved	protein_state	It is notable that L130 is usually present as Leu, or an alternative bulky hydrophobic amino acid (e.g. Phe, Val), in many MarR family proteins, suggesting a conserved role in stabilizing the dimer interface.	RESULTS
192	207	dimer interface	site	It is notable that L130 is usually present as Leu, or an alternative bulky hydrophobic amino acid (e.g. Phe, Val), in many MarR family proteins, suggesting a conserved role in stabilizing the dimer interface.	RESULTS
58	62	NadR	protein	In contrast, most of the other residues identified in the NadR dimer interface were poorly conserved in the MarR family.	RESULTS
63	78	dimer interface	site	In contrast, most of the other residues identified in the NadR dimer interface were poorly conserved in the MarR family.	RESULTS
84	100	poorly conserved	protein_state	In contrast, most of the other residues identified in the NadR dimer interface were poorly conserved in the MarR family.	RESULTS
108	112	MarR	protein_type	In contrast, most of the other residues identified in the NadR dimer interface were poorly conserved in the MarR family.	RESULTS
16	20	NadR	protein	Analysis of the NadR dimer interface.	FIG
21	36	dimer interface	site	Analysis of the NadR dimer interface.	FIG
28	35	chain A	structure_element	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
145	157	salt bridges	bond_interaction	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
161	175	hydrogen bonds	bond_interaction	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
186	188	Q4	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
190	192	S5	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
194	196	K6	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
198	200	H7	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
202	204	S9	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
206	209	I10	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
211	214	N11	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
216	219	I15	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
221	224	Q16	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
226	229	R18	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
231	234	D36	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
236	239	R43	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
241	244	A46	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
246	249	Q59	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
251	254	C61	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
256	260	Y104	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
262	266	D112	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
268	272	R114	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
274	278	Y115	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
280	284	D116	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
286	290	E119	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
292	296	K126	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
298	302	E136	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
304	308	E141	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
310	314	N145	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
324	356	hydrophobic packing interactions	bond_interaction	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
367	370	I10	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
372	375	I12	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
377	380	L14	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
382	385	I15	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
387	390	R18	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
392	396	Y115	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
398	402	I118	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
404	408	L130	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
410	414	L133	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
416	420	L134	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
425	429	L137	residue_name_number	 (A) Both orientations show chain A, green backbone ribbon, colored red to highlight all locations involved in dimerization; namely, inter-chain salt bridges or hydrogen bonds involving Q4, S5, K6, H7, S9, I10, N11, I15, Q16, R18, D36, R43, A46, Q59, C61, Y104, D112, R114, Y115, D116, E119, K126, E136, E141, N145, and the hydrophobic packing interactions involving I10, I12, L14, I15, R18, Y115, I118, L130, L133, L134 and L137.	FIG
0	7	Chain B	structure_element	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
70	95	site-directed mutagenesis	experimental_method	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
97	101	E136	residue_name_number	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
115	126	salt bridge	bond_interaction	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
132	136	K126	residue_name_number	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
178	183	K126A	mutant	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
226	243	ionic interaction	bond_interaction	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
249	251	H7	residue_name_number	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
277	284	monomer	oligomeric_state	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
285	286	A	structure_element	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
294	310	electron density	evidence	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
327	334	monomer	oligomeric_state	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
335	336	B	structure_element	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
374	379	helix	structure_element	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
380	382	α6	structure_element	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
403	407	L130	residue_name_number	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
408	415	chain B	structure_element	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
448	480	hydrophobic packing interactions	bond_interaction	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
486	490	L130	residue_name_number	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
492	496	L133	residue_name_number	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
498	502	L134	residue_name_number	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
507	511	L137	residue_name_number	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
515	522	chain A	structure_element	Chain B, grey surface, is marked blue to highlight residues probed by site-directed mutagenesis (E136 only makes a salt bridge with K126, therefore it was sufficient to make the K126A mutation to assess the importance of this ionic interaction; the H7 position is labelled for monomer A, since electron density was lacking for monomer B). (B) A zoom into the environment of helix α6 to show how residue L130 chain B (blue side chain) is a focus of hydrophobic packing interactions with L130, L133, L134 and L137 of chain A (red side chains).	FIG
4	11	SE-HPLC	experimental_method	(C) SE-HPLC analyses of all mutant forms of NadR are compared with the wild-type (WT) protein.	FIG
28	34	mutant	protein_state	(C) SE-HPLC analyses of all mutant forms of NadR are compared with the wild-type (WT) protein.	FIG
44	48	NadR	protein	(C) SE-HPLC analyses of all mutant forms of NadR are compared with the wild-type (WT) protein.	FIG
71	80	wild-type	protein_state	(C) SE-HPLC analyses of all mutant forms of NadR are compared with the wild-type (WT) protein.	FIG
82	84	WT	protein_state	(C) SE-HPLC analyses of all mutant forms of NadR are compared with the wild-type (WT) protein.	FIG
4	6	WT	protein_state	The WT and most of the mutants show a single elution peak with an absorbance maximum at 17.5 min.	FIG
18	23	L130K	mutant	Only the mutation L130K has a noteworthy effect on the oligomeric state, inducing a second peak with a longer retention time and a second peak maximum at 18.6 min.	FIG
29	34	L133K	mutant	To a much lesser extent, the L133K mutation also appears to induce a ‘shoulder’ to the main peak, suggesting very weak ability to disrupt the dimer. (D) SE-HPLC/MALLS analyses of the L130K mutant, shows 20% dimer and 80% monomer.	FIG
142	147	dimer	oligomeric_state	To a much lesser extent, the L133K mutation also appears to induce a ‘shoulder’ to the main peak, suggesting very weak ability to disrupt the dimer. (D) SE-HPLC/MALLS analyses of the L130K mutant, shows 20% dimer and 80% monomer.	FIG
153	166	SE-HPLC/MALLS	experimental_method	To a much lesser extent, the L133K mutation also appears to induce a ‘shoulder’ to the main peak, suggesting very weak ability to disrupt the dimer. (D) SE-HPLC/MALLS analyses of the L130K mutant, shows 20% dimer and 80% monomer.	FIG
183	188	L130K	mutant	To a much lesser extent, the L133K mutation also appears to induce a ‘shoulder’ to the main peak, suggesting very weak ability to disrupt the dimer. (D) SE-HPLC/MALLS analyses of the L130K mutant, shows 20% dimer and 80% monomer.	FIG
189	195	mutant	protein_state	To a much lesser extent, the L133K mutation also appears to induce a ‘shoulder’ to the main peak, suggesting very weak ability to disrupt the dimer. (D) SE-HPLC/MALLS analyses of the L130K mutant, shows 20% dimer and 80% monomer.	FIG
207	212	dimer	oligomeric_state	To a much lesser extent, the L133K mutation also appears to induce a ‘shoulder’ to the main peak, suggesting very weak ability to disrupt the dimer. (D) SE-HPLC/MALLS analyses of the L130K mutant, shows 20% dimer and 80% monomer.	FIG
221	228	monomer	oligomeric_state	To a much lesser extent, the L133K mutation also appears to induce a ‘shoulder’ to the main peak, suggesting very weak ability to disrupt the dimer. (D) SE-HPLC/MALLS analyses of the L130K mutant, shows 20% dimer and 80% monomer.	FIG
4	8	holo	protein_state	The holo-NadR structure presents only one occupied ligand-binding pocket	RESULTS
9	13	NadR	protein	The holo-NadR structure presents only one occupied ligand-binding pocket	RESULTS
14	23	structure	evidence	The holo-NadR structure presents only one occupied ligand-binding pocket	RESULTS
51	72	ligand-binding pocket	site	The holo-NadR structure presents only one occupied ligand-binding pocket	RESULTS
4	14	NadR/4-HPA	complex_assembly	The NadR/4-HPA structure revealed the ligand-binding site nestled between the dimerization and DNA-binding domains (Fig 2).	RESULTS
15	24	structure	evidence	The NadR/4-HPA structure revealed the ligand-binding site nestled between the dimerization and DNA-binding domains (Fig 2).	RESULTS
38	57	ligand-binding site	site	The NadR/4-HPA structure revealed the ligand-binding site nestled between the dimerization and DNA-binding domains (Fig 2).	RESULTS
78	114	dimerization and DNA-binding domains	structure_element	The NadR/4-HPA structure revealed the ligand-binding site nestled between the dimerization and DNA-binding domains (Fig 2).	RESULTS
67	77	salicylate	chemical	The ligand showed a different position and orientation compared to salicylate complexed with MTH313 and ST1710 (see Discussion).	RESULTS
78	92	complexed with	protein_state	The ligand showed a different position and orientation compared to salicylate complexed with MTH313 and ST1710 (see Discussion).	RESULTS
93	99	MTH313	protein	The ligand showed a different position and orientation compared to salicylate complexed with MTH313 and ST1710 (see Discussion).	RESULTS
104	110	ST1710	protein	The ligand showed a different position and orientation compared to salicylate complexed with MTH313 and ST1710 (see Discussion).	RESULTS
4	18	binding pocket	site	The binding pocket was almost entirely filled by 4-HPA and one water molecule, although there also remained a small tunnel 2-4Å in diameter and 5-6Å long leading from the pocket (proximal to the 4-hydroxyl position) to the protein surface.	RESULTS
49	54	4-HPA	chemical	The binding pocket was almost entirely filled by 4-HPA and one water molecule, although there also remained a small tunnel 2-4Å in diameter and 5-6Å long leading from the pocket (proximal to the 4-hydroxyl position) to the protein surface.	RESULTS
63	68	water	chemical	The binding pocket was almost entirely filled by 4-HPA and one water molecule, although there also remained a small tunnel 2-4Å in diameter and 5-6Å long leading from the pocket (proximal to the 4-hydroxyl position) to the protein surface.	RESULTS
116	122	tunnel	site	The binding pocket was almost entirely filled by 4-HPA and one water molecule, although there also remained a small tunnel 2-4Å in diameter and 5-6Å long leading from the pocket (proximal to the 4-hydroxyl position) to the protein surface.	RESULTS
171	177	pocket	site	The binding pocket was almost entirely filled by 4-HPA and one water molecule, although there also remained a small tunnel 2-4Å in diameter and 5-6Å long leading from the pocket (proximal to the 4-hydroxyl position) to the protein surface.	RESULTS
4	10	tunnel	site	The tunnel was lined with rather hydrophobic amino acids, and did not contain water molecules.	RESULTS
78	83	water	chemical	The tunnel was lined with rather hydrophobic amino acids, and did not contain water molecules.	RESULTS
23	30	monomer	oligomeric_state	Unexpectedly, only one monomer of the holo-NadR homodimer contained 4-HPA in the binding pocket, whereas the corresponding pocket of the other monomer was unoccupied by ligand, despite the large excess of 4-HPA used in the crystallization conditions.	RESULTS
38	42	holo	protein_state	Unexpectedly, only one monomer of the holo-NadR homodimer contained 4-HPA in the binding pocket, whereas the corresponding pocket of the other monomer was unoccupied by ligand, despite the large excess of 4-HPA used in the crystallization conditions.	RESULTS
43	47	NadR	protein	Unexpectedly, only one monomer of the holo-NadR homodimer contained 4-HPA in the binding pocket, whereas the corresponding pocket of the other monomer was unoccupied by ligand, despite the large excess of 4-HPA used in the crystallization conditions.	RESULTS
48	57	homodimer	oligomeric_state	Unexpectedly, only one monomer of the holo-NadR homodimer contained 4-HPA in the binding pocket, whereas the corresponding pocket of the other monomer was unoccupied by ligand, despite the large excess of 4-HPA used in the crystallization conditions.	RESULTS
68	73	4-HPA	chemical	Unexpectedly, only one monomer of the holo-NadR homodimer contained 4-HPA in the binding pocket, whereas the corresponding pocket of the other monomer was unoccupied by ligand, despite the large excess of 4-HPA used in the crystallization conditions.	RESULTS
81	95	binding pocket	site	Unexpectedly, only one monomer of the holo-NadR homodimer contained 4-HPA in the binding pocket, whereas the corresponding pocket of the other monomer was unoccupied by ligand, despite the large excess of 4-HPA used in the crystallization conditions.	RESULTS
123	129	pocket	site	Unexpectedly, only one monomer of the holo-NadR homodimer contained 4-HPA in the binding pocket, whereas the corresponding pocket of the other monomer was unoccupied by ligand, despite the large excess of 4-HPA used in the crystallization conditions.	RESULTS
143	150	monomer	oligomeric_state	Unexpectedly, only one monomer of the holo-NadR homodimer contained 4-HPA in the binding pocket, whereas the corresponding pocket of the other monomer was unoccupied by ligand, despite the large excess of 4-HPA used in the crystallization conditions.	RESULTS
205	210	4-HPA	chemical	Unexpectedly, only one monomer of the holo-NadR homodimer contained 4-HPA in the binding pocket, whereas the corresponding pocket of the other monomer was unoccupied by ligand, despite the large excess of 4-HPA used in the crystallization conditions.	RESULTS
18	52	protein-ligand interaction network	site	Inspection of the protein-ligand interaction network revealed no bonds from NadR backbone groups to the ligand, but several key side chain mediated hydrogen (H)-bonds and ionic interactions, most notably between the carboxylate group of 4-HPA and Ser9 of chain A (SerA9), and chain B residues TrpB39, ArgB43 and TyrB115 (Fig 4A).	RESULTS
76	80	NadR	protein	Inspection of the protein-ligand interaction network revealed no bonds from NadR backbone groups to the ligand, but several key side chain mediated hydrogen (H)-bonds and ionic interactions, most notably between the carboxylate group of 4-HPA and Ser9 of chain A (SerA9), and chain B residues TrpB39, ArgB43 and TyrB115 (Fig 4A).	RESULTS
148	166	hydrogen (H)-bonds	bond_interaction	Inspection of the protein-ligand interaction network revealed no bonds from NadR backbone groups to the ligand, but several key side chain mediated hydrogen (H)-bonds and ionic interactions, most notably between the carboxylate group of 4-HPA and Ser9 of chain A (SerA9), and chain B residues TrpB39, ArgB43 and TyrB115 (Fig 4A).	RESULTS
171	189	ionic interactions	bond_interaction	Inspection of the protein-ligand interaction network revealed no bonds from NadR backbone groups to the ligand, but several key side chain mediated hydrogen (H)-bonds and ionic interactions, most notably between the carboxylate group of 4-HPA and Ser9 of chain A (SerA9), and chain B residues TrpB39, ArgB43 and TyrB115 (Fig 4A).	RESULTS
237	242	4-HPA	chemical	Inspection of the protein-ligand interaction network revealed no bonds from NadR backbone groups to the ligand, but several key side chain mediated hydrogen (H)-bonds and ionic interactions, most notably between the carboxylate group of 4-HPA and Ser9 of chain A (SerA9), and chain B residues TrpB39, ArgB43 and TyrB115 (Fig 4A).	RESULTS
247	251	Ser9	residue_name_number	Inspection of the protein-ligand interaction network revealed no bonds from NadR backbone groups to the ligand, but several key side chain mediated hydrogen (H)-bonds and ionic interactions, most notably between the carboxylate group of 4-HPA and Ser9 of chain A (SerA9), and chain B residues TrpB39, ArgB43 and TyrB115 (Fig 4A).	RESULTS
255	262	chain A	structure_element	Inspection of the protein-ligand interaction network revealed no bonds from NadR backbone groups to the ligand, but several key side chain mediated hydrogen (H)-bonds and ionic interactions, most notably between the carboxylate group of 4-HPA and Ser9 of chain A (SerA9), and chain B residues TrpB39, ArgB43 and TyrB115 (Fig 4A).	RESULTS
264	269	SerA9	residue_name_number	Inspection of the protein-ligand interaction network revealed no bonds from NadR backbone groups to the ligand, but several key side chain mediated hydrogen (H)-bonds and ionic interactions, most notably between the carboxylate group of 4-HPA and Ser9 of chain A (SerA9), and chain B residues TrpB39, ArgB43 and TyrB115 (Fig 4A).	RESULTS
276	283	chain B	structure_element	Inspection of the protein-ligand interaction network revealed no bonds from NadR backbone groups to the ligand, but several key side chain mediated hydrogen (H)-bonds and ionic interactions, most notably between the carboxylate group of 4-HPA and Ser9 of chain A (SerA9), and chain B residues TrpB39, ArgB43 and TyrB115 (Fig 4A).	RESULTS
293	299	TrpB39	residue_name_number	Inspection of the protein-ligand interaction network revealed no bonds from NadR backbone groups to the ligand, but several key side chain mediated hydrogen (H)-bonds and ionic interactions, most notably between the carboxylate group of 4-HPA and Ser9 of chain A (SerA9), and chain B residues TrpB39, ArgB43 and TyrB115 (Fig 4A).	RESULTS
301	307	ArgB43	residue_name_number	Inspection of the protein-ligand interaction network revealed no bonds from NadR backbone groups to the ligand, but several key side chain mediated hydrogen (H)-bonds and ionic interactions, most notably between the carboxylate group of 4-HPA and Ser9 of chain A (SerA9), and chain B residues TrpB39, ArgB43 and TyrB115 (Fig 4A).	RESULTS
312	319	TyrB115	residue_name_number	Inspection of the protein-ligand interaction network revealed no bonds from NadR backbone groups to the ligand, but several key side chain mediated hydrogen (H)-bonds and ionic interactions, most notably between the carboxylate group of 4-HPA and Ser9 of chain A (SerA9), and chain B residues TrpB39, ArgB43 and TyrB115 (Fig 4A).	RESULTS
71	77	AspB36	residue_name_number	At the other ‘end’ of the ligand, the 4-hydroxyl group was proximal to AspB36, with which it may establish an H-bond (see bond distances in Table 3).	RESULTS
110	116	H-bond	bond_interaction	At the other ‘end’ of the ligand, the 4-hydroxyl group was proximal to AspB36, with which it may establish an H-bond (see bond distances in Table 3).	RESULTS
4	9	water	chemical	The water molecule observed in the pocket was bound by the carboxylate group and the side chains of SerA9 and AsnA11.	RESULTS
100	105	SerA9	residue_name_number	The water molecule observed in the pocket was bound by the carboxylate group and the side chains of SerA9 and AsnA11.	RESULTS
110	116	AsnA11	residue_name_number	The water molecule observed in the pocket was bound by the carboxylate group and the side chains of SerA9 and AsnA11.	RESULTS
18	22	NadR	protein	Atomic details of NadR/HPA interactions.	FIG
23	26	HPA	chemical	Atomic details of NadR/HPA interactions.	FIG
32	46	binding pocket	site	 A) A stereo-view zoom into the binding pocket showing side chain sticks for all interactions between NadR and 4-HPA.	FIG
102	106	NadR	protein	 A) A stereo-view zoom into the binding pocket showing side chain sticks for all interactions between NadR and 4-HPA.	FIG
111	116	4-HPA	chemical	 A) A stereo-view zoom into the binding pocket showing side chain sticks for all interactions between NadR and 4-HPA.	FIG
30	34	NadR	protein	Green and blue ribbons depict NadR chains A and B, respectively.	FIG
35	49	chains A and B	structure_element	Green and blue ribbons depict NadR chains A and B, respectively.	FIG
0	5	4-HPA	chemical	4-HPA is shown in yellow sticks, with oxygen atoms in red.	FIG
2	7	water	chemical	A water molecule is shown by the red sphere.	FIG
0	7	H-bonds	bond_interaction	H-bonds up to 3.6Å are shown as dashed lines.	FIG
34	41	H-bonds	bond_interaction	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
45	64	non-bonded contacts	bond_interaction	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
70	75	4-HPA	chemical	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
91	96	SerA9	residue_name_number	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
98	104	AsnA11	residue_name_number	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
106	112	LeuB21	residue_name_number	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
114	120	MetB22	residue_name_number	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
122	128	PheB25	residue_name_number	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
130	136	LeuB29	residue_name_number	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
138	144	AspB36	residue_name_number	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
146	152	TrpB39	residue_name_number	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
154	160	ArgB43	residue_name_number	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
162	169	ValB111	residue_name_number	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
174	181	TyrB115	residue_name_number	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
218	224	PDBsum	experimental_method	The entire set of residues making H-bonds or non-bonded contacts with 4-HPA is as follows: SerA9, AsnA11, LeuB21, MetB22, PheB25, LeuB29, AspB36, TrpB39, ArgB43, ValB111 and TyrB115 (automated analysis performed using PDBsum and verified manually).	FIG
9	15	AsnA11	residue_name_number	Residues AsnA11 and ArgB18 likely make indirect yet local contributions to ligand binding, mainly by stabilizing the position of AspB36.	FIG
20	26	ArgB18	residue_name_number	Residues AsnA11 and ArgB18 likely make indirect yet local contributions to ligand binding, mainly by stabilizing the position of AspB36.	FIG
129	135	AspB36	residue_name_number	Residues AsnA11 and ArgB18 likely make indirect yet local contributions to ligand binding, mainly by stabilizing the position of AspB36.	FIG
22	46	hydrophobic interactions	bond_interaction	Side chains mediating hydrophobic interactions are shown in orange. (B) A model was prepared to visualize putative interactions of 3Cl,4-HPA (pink) with NadR, revealing the potential for additional contacts (dashed lines) of the chloro moiety (green stick) with LeuB29 and AspB36.	FIG
131	140	3Cl,4-HPA	chemical	Side chains mediating hydrophobic interactions are shown in orange. (B) A model was prepared to visualize putative interactions of 3Cl,4-HPA (pink) with NadR, revealing the potential for additional contacts (dashed lines) of the chloro moiety (green stick) with LeuB29 and AspB36.	FIG
153	157	NadR	protein	Side chains mediating hydrophobic interactions are shown in orange. (B) A model was prepared to visualize putative interactions of 3Cl,4-HPA (pink) with NadR, revealing the potential for additional contacts (dashed lines) of the chloro moiety (green stick) with LeuB29 and AspB36.	FIG
262	268	LeuB29	residue_name_number	Side chains mediating hydrophobic interactions are shown in orange. (B) A model was prepared to visualize putative interactions of 3Cl,4-HPA (pink) with NadR, revealing the potential for additional contacts (dashed lines) of the chloro moiety (green stick) with LeuB29 and AspB36.	FIG
273	279	AspB36	residue_name_number	Side chains mediating hydrophobic interactions are shown in orange. (B) A model was prepared to visualize putative interactions of 3Cl,4-HPA (pink) with NadR, revealing the potential for additional contacts (dashed lines) of the chloro moiety (green stick) with LeuB29 and AspB36.	FIG
8	13	4-HPA	chemical	List of 4-HPA atoms bound to NadR via ionic interactions and/or H-bonds.	TABLE
29	33	NadR	protein	List of 4-HPA atoms bound to NadR via ionic interactions and/or H-bonds.	TABLE
38	56	ionic interactions	bond_interaction	List of 4-HPA atoms bound to NadR via ionic interactions and/or H-bonds.	TABLE
64	71	H-bonds	bond_interaction	List of 4-HPA atoms bound to NadR via ionic interactions and/or H-bonds.	TABLE
0	5	4-HPA	chemical	"4-HPA atom	NadR residue/atom	Distance (Å)	 	O2	TrpB39/NE1	2.83	 	O2	ArgB43/NH1	2.76	 	O1	ArgB43/NH1	3.84	 	O1	SerA9/OG	2.75	 	O1	TyrB115/OH	2.50	 	O2	Water (*Ser9/Asn11)	2.88	 	OH	AspB36/OD1/OD2	3.6/3.7	 	"	TABLE
11	15	NadR	protein	"4-HPA atom	NadR residue/atom	Distance (Å)	 	O2	TrpB39/NE1	2.83	 	O2	ArgB43/NH1	2.76	 	O1	ArgB43/NH1	3.84	 	O1	SerA9/OG	2.75	 	O1	TyrB115/OH	2.50	 	O2	Water (*Ser9/Asn11)	2.88	 	OH	AspB36/OD1/OD2	3.6/3.7	 	"	TABLE
47	53	TrpB39	residue_name_number	"4-HPA atom	NadR residue/atom	Distance (Å)	 	O2	TrpB39/NE1	2.83	 	O2	ArgB43/NH1	2.76	 	O1	ArgB43/NH1	3.84	 	O1	SerA9/OG	2.75	 	O1	TyrB115/OH	2.50	 	O2	Water (*Ser9/Asn11)	2.88	 	OH	AspB36/OD1/OD2	3.6/3.7	 	"	TABLE
68	74	ArgB43	residue_name_number	"4-HPA atom	NadR residue/atom	Distance (Å)	 	O2	TrpB39/NE1	2.83	 	O2	ArgB43/NH1	2.76	 	O1	ArgB43/NH1	3.84	 	O1	SerA9/OG	2.75	 	O1	TyrB115/OH	2.50	 	O2	Water (*Ser9/Asn11)	2.88	 	OH	AspB36/OD1/OD2	3.6/3.7	 	"	TABLE
89	95	ArgB43	residue_name_number	"4-HPA atom	NadR residue/atom	Distance (Å)	 	O2	TrpB39/NE1	2.83	 	O2	ArgB43/NH1	2.76	 	O1	ArgB43/NH1	3.84	 	O1	SerA9/OG	2.75	 	O1	TyrB115/OH	2.50	 	O2	Water (*Ser9/Asn11)	2.88	 	OH	AspB36/OD1/OD2	3.6/3.7	 	"	TABLE
110	115	SerA9	residue_name_number	"4-HPA atom	NadR residue/atom	Distance (Å)	 	O2	TrpB39/NE1	2.83	 	O2	ArgB43/NH1	2.76	 	O1	ArgB43/NH1	3.84	 	O1	SerA9/OG	2.75	 	O1	TyrB115/OH	2.50	 	O2	Water (*Ser9/Asn11)	2.88	 	OH	AspB36/OD1/OD2	3.6/3.7	 	"	TABLE
129	136	TyrB115	residue_name_number	"4-HPA atom	NadR residue/atom	Distance (Å)	 	O2	TrpB39/NE1	2.83	 	O2	ArgB43/NH1	2.76	 	O1	ArgB43/NH1	3.84	 	O1	SerA9/OG	2.75	 	O1	TyrB115/OH	2.50	 	O2	Water (*Ser9/Asn11)	2.88	 	OH	AspB36/OD1/OD2	3.6/3.7	 	"	TABLE
150	155	Water	chemical	"4-HPA atom	NadR residue/atom	Distance (Å)	 	O2	TrpB39/NE1	2.83	 	O2	ArgB43/NH1	2.76	 	O1	ArgB43/NH1	3.84	 	O1	SerA9/OG	2.75	 	O1	TyrB115/OH	2.50	 	O2	Water (*Ser9/Asn11)	2.88	 	OH	AspB36/OD1/OD2	3.6/3.7	 	"	TABLE
158	162	Ser9	residue_name_number	"4-HPA atom	NadR residue/atom	Distance (Å)	 	O2	TrpB39/NE1	2.83	 	O2	ArgB43/NH1	2.76	 	O1	ArgB43/NH1	3.84	 	O1	SerA9/OG	2.75	 	O1	TyrB115/OH	2.50	 	O2	Water (*Ser9/Asn11)	2.88	 	OH	AspB36/OD1/OD2	3.6/3.7	 	"	TABLE
163	168	Asn11	residue_name_number	"4-HPA atom	NadR residue/atom	Distance (Å)	 	O2	TrpB39/NE1	2.83	 	O2	ArgB43/NH1	2.76	 	O1	ArgB43/NH1	3.84	 	O1	SerA9/OG	2.75	 	O1	TyrB115/OH	2.50	 	O2	Water (*Ser9/Asn11)	2.88	 	OH	AspB36/OD1/OD2	3.6/3.7	 	"	TABLE
180	186	AspB36	residue_name_number	"4-HPA atom	NadR residue/atom	Distance (Å)	 	O2	TrpB39/NE1	2.83	 	O2	ArgB43/NH1	2.76	 	O1	ArgB43/NH1	3.84	 	O1	SerA9/OG	2.75	 	O1	TyrB115/OH	2.50	 	O2	Water (*Ser9/Asn11)	2.88	 	OH	AspB36/OD1/OD2	3.6/3.7	 	"	TABLE
61	66	water	chemical	* Bond distance between the ligand carboxylate group and the water molecule, which in turn makes H-bond to the SerA9 and AsnA11 side chains.	TABLE
97	103	H-bond	bond_interaction	* Bond distance between the ligand carboxylate group and the water molecule, which in turn makes H-bond to the SerA9 and AsnA11 side chains.	TABLE
111	116	SerA9	residue_name_number	* Bond distance between the ligand carboxylate group and the water molecule, which in turn makes H-bond to the SerA9 and AsnA11 side chains.	TABLE
121	127	AsnA11	residue_name_number	* Bond distance between the ligand carboxylate group and the water molecule, which in turn makes H-bond to the SerA9 and AsnA11 side chains.	TABLE
19	26	H-bonds	bond_interaction	In addition to the H-bonds involving the carboxylate and hydroxyl groups of 4-HPA, binding of the phenyl moiety appeared to be stabilized by several van der Waals’ contacts, particularly those involving the hydrophobic side chain atoms of LeuB21, MetB22, PheB25, LeuB29 and ValB111 (Fig 4A).	RESULTS
76	81	4-HPA	chemical	In addition to the H-bonds involving the carboxylate and hydroxyl groups of 4-HPA, binding of the phenyl moiety appeared to be stabilized by several van der Waals’ contacts, particularly those involving the hydrophobic side chain atoms of LeuB21, MetB22, PheB25, LeuB29 and ValB111 (Fig 4A).	RESULTS
149	172	van der Waals’ contacts	bond_interaction	In addition to the H-bonds involving the carboxylate and hydroxyl groups of 4-HPA, binding of the phenyl moiety appeared to be stabilized by several van der Waals’ contacts, particularly those involving the hydrophobic side chain atoms of LeuB21, MetB22, PheB25, LeuB29 and ValB111 (Fig 4A).	RESULTS
239	245	LeuB21	residue_name_number	In addition to the H-bonds involving the carboxylate and hydroxyl groups of 4-HPA, binding of the phenyl moiety appeared to be stabilized by several van der Waals’ contacts, particularly those involving the hydrophobic side chain atoms of LeuB21, MetB22, PheB25, LeuB29 and ValB111 (Fig 4A).	RESULTS
247	253	MetB22	residue_name_number	In addition to the H-bonds involving the carboxylate and hydroxyl groups of 4-HPA, binding of the phenyl moiety appeared to be stabilized by several van der Waals’ contacts, particularly those involving the hydrophobic side chain atoms of LeuB21, MetB22, PheB25, LeuB29 and ValB111 (Fig 4A).	RESULTS
255	261	PheB25	residue_name_number	In addition to the H-bonds involving the carboxylate and hydroxyl groups of 4-HPA, binding of the phenyl moiety appeared to be stabilized by several van der Waals’ contacts, particularly those involving the hydrophobic side chain atoms of LeuB21, MetB22, PheB25, LeuB29 and ValB111 (Fig 4A).	RESULTS
263	269	LeuB29	residue_name_number	In addition to the H-bonds involving the carboxylate and hydroxyl groups of 4-HPA, binding of the phenyl moiety appeared to be stabilized by several van der Waals’ contacts, particularly those involving the hydrophobic side chain atoms of LeuB21, MetB22, PheB25, LeuB29 and ValB111 (Fig 4A).	RESULTS
274	281	ValB111	residue_name_number	In addition to the H-bonds involving the carboxylate and hydroxyl groups of 4-HPA, binding of the phenyl moiety appeared to be stabilized by several van der Waals’ contacts, particularly those involving the hydrophobic side chain atoms of LeuB21, MetB22, PheB25, LeuB29 and ValB111 (Fig 4A).	RESULTS
28	34	PheB25	residue_name_number	Notably, the phenyl ring of PheB25 was positioned parallel to the phenyl ring of 4-HPA, potentially forming π-π parallel-displaced stacking interactions.	RESULTS
81	86	4-HPA	chemical	Notably, the phenyl ring of PheB25 was positioned parallel to the phenyl ring of 4-HPA, potentially forming π-π parallel-displaced stacking interactions.	RESULTS
108	152	π-π parallel-displaced stacking interactions	bond_interaction	Notably, the phenyl ring of PheB25 was positioned parallel to the phenyl ring of 4-HPA, potentially forming π-π parallel-displaced stacking interactions.	RESULTS
30	50	4-HPA binding pocket	site	Consequently, residues in the 4-HPA binding pocket are mostly contributed by NadR chain B, and effectively created a polar ‘floor’ and a hydrophobic ‘ceiling’, which house the ligand.	RESULTS
77	81	NadR	protein	Consequently, residues in the 4-HPA binding pocket are mostly contributed by NadR chain B, and effectively created a polar ‘floor’ and a hydrophobic ‘ceiling’, which house the ligand.	RESULTS
82	89	chain B	structure_element	Consequently, residues in the 4-HPA binding pocket are mostly contributed by NadR chain B, and effectively created a polar ‘floor’ and a hydrophobic ‘ceiling’, which house the ligand.	RESULTS
36	70	polar and hydrophobic interactions	bond_interaction	Collectively, this mixed network of polar and hydrophobic interactions endows NadR with a strong recognition pattern for HPAs, with additional medium-range interactions potentially established with the hydroxyl group at the 4-position.	RESULTS
78	82	NadR	protein	Collectively, this mixed network of polar and hydrophobic interactions endows NadR with a strong recognition pattern for HPAs, with additional medium-range interactions potentially established with the hydroxyl group at the 4-position.	RESULTS
121	125	HPAs	chemical	Collectively, this mixed network of polar and hydrophobic interactions endows NadR with a strong recognition pattern for HPAs, with additional medium-range interactions potentially established with the hydroxyl group at the 4-position.	RESULTS
79	88	3Cl,4-HPA	chemical	Structure-activity relationships: molecular basis of enhanced stabilization by 3Cl,4-HPA	RESULTS
3	11	modelled	experimental_method	We modelled the binding of other HPAs by in silico superposition onto 4-HPA in the holo-NadR structure, and thereby obtained molecular explanations for the binding specificities of diverse ligands.	RESULTS
33	37	HPAs	chemical	We modelled the binding of other HPAs by in silico superposition onto 4-HPA in the holo-NadR structure, and thereby obtained molecular explanations for the binding specificities of diverse ligands.	RESULTS
41	64	in silico superposition	experimental_method	We modelled the binding of other HPAs by in silico superposition onto 4-HPA in the holo-NadR structure, and thereby obtained molecular explanations for the binding specificities of diverse ligands.	RESULTS
70	75	4-HPA	chemical	We modelled the binding of other HPAs by in silico superposition onto 4-HPA in the holo-NadR structure, and thereby obtained molecular explanations for the binding specificities of diverse ligands.	RESULTS
83	87	holo	protein_state	We modelled the binding of other HPAs by in silico superposition onto 4-HPA in the holo-NadR structure, and thereby obtained molecular explanations for the binding specificities of diverse ligands.	RESULTS
88	92	NadR	protein	We modelled the binding of other HPAs by in silico superposition onto 4-HPA in the holo-NadR structure, and thereby obtained molecular explanations for the binding specificities of diverse ligands.	RESULTS
93	102	structure	evidence	We modelled the binding of other HPAs by in silico superposition onto 4-HPA in the holo-NadR structure, and thereby obtained molecular explanations for the binding specificities of diverse ligands.	RESULTS
24	29	4-HPA	chemical	For example, similar to 4-HPA, the binding of 3Cl,4-HPA could involve multiple bonds towards the carboxylate group of the ligand and some to the 4-hydroxyl group.	RESULTS
46	55	3Cl,4-HPA	chemical	For example, similar to 4-HPA, the binding of 3Cl,4-HPA could involve multiple bonds towards the carboxylate group of the ligand and some to the 4-hydroxyl group.	RESULTS
33	39	LeuB29	residue_name_number	Additionally, the side chains of LeuB29 and AspB36 would be only 2.6–3.5 Å from the chlorine atom, thus providing van der Waals’ interactions or H-bonds to generate the additional binding affinity observed for 3Cl,4-HPA (Fig 4B).	RESULTS
44	50	AspB36	residue_name_number	Additionally, the side chains of LeuB29 and AspB36 would be only 2.6–3.5 Å from the chlorine atom, thus providing van der Waals’ interactions or H-bonds to generate the additional binding affinity observed for 3Cl,4-HPA (Fig 4B).	RESULTS
114	141	van der Waals’ interactions	bond_interaction	Additionally, the side chains of LeuB29 and AspB36 would be only 2.6–3.5 Å from the chlorine atom, thus providing van der Waals’ interactions or H-bonds to generate the additional binding affinity observed for 3Cl,4-HPA (Fig 4B).	RESULTS
145	152	H-bonds	bond_interaction	Additionally, the side chains of LeuB29 and AspB36 would be only 2.6–3.5 Å from the chlorine atom, thus providing van der Waals’ interactions or H-bonds to generate the additional binding affinity observed for 3Cl,4-HPA (Fig 4B).	RESULTS
180	196	binding affinity	evidence	Additionally, the side chains of LeuB29 and AspB36 would be only 2.6–3.5 Å from the chlorine atom, thus providing van der Waals’ interactions or H-bonds to generate the additional binding affinity observed for 3Cl,4-HPA (Fig 4B).	RESULTS
210	219	3Cl,4-HPA	chemical	Additionally, the side chains of LeuB29 and AspB36 would be only 2.6–3.5 Å from the chlorine atom, thus providing van der Waals’ interactions or H-bonds to generate the additional binding affinity observed for 3Cl,4-HPA (Fig 4B).	RESULTS
61	66	2-HPA	chemical	The presence of a single hydroxyl group at position 2, as in 2-HPA, rather than at position 4, would eliminate the possibility of favorable interactions with AspB36, resulting in the lack of NadR regulation by 2-HPA described previously.	RESULTS
158	164	AspB36	residue_name_number	The presence of a single hydroxyl group at position 2, as in 2-HPA, rather than at position 4, would eliminate the possibility of favorable interactions with AspB36, resulting in the lack of NadR regulation by 2-HPA described previously.	RESULTS
191	195	NadR	protein	The presence of a single hydroxyl group at position 2, as in 2-HPA, rather than at position 4, would eliminate the possibility of favorable interactions with AspB36, resulting in the lack of NadR regulation by 2-HPA described previously.	RESULTS
210	215	2-HPA	chemical	The presence of a single hydroxyl group at position 2, as in 2-HPA, rather than at position 4, would eliminate the possibility of favorable interactions with AspB36, resulting in the lack of NadR regulation by 2-HPA described previously.	RESULTS
9	19	salicylate	chemical	Finally, salicylate is presumably unable to specifically bind NadR due to the 2-hydroxyl substitution and the shorter aliphatic chain connecting its carboxylate group (Fig 1A): the compound simply seems too small to simultaneously establish the network of beneficial bonds observed in the NadR/HPA interactions.	RESULTS
62	66	NadR	protein	Finally, salicylate is presumably unable to specifically bind NadR due to the 2-hydroxyl substitution and the shorter aliphatic chain connecting its carboxylate group (Fig 1A): the compound simply seems too small to simultaneously establish the network of beneficial bonds observed in the NadR/HPA interactions.	RESULTS
289	293	NadR	protein	Finally, salicylate is presumably unable to specifically bind NadR due to the 2-hydroxyl substitution and the shorter aliphatic chain connecting its carboxylate group (Fig 1A): the compound simply seems too small to simultaneously establish the network of beneficial bonds observed in the NadR/HPA interactions.	RESULTS
294	297	HPA	chemical	Finally, salicylate is presumably unable to specifically bind NadR due to the 2-hydroxyl substitution and the shorter aliphatic chain connecting its carboxylate group (Fig 1A): the compound simply seems too small to simultaneously establish the network of beneficial bonds observed in the NadR/HPA interactions.	RESULTS
16	23	pockets	site	Analysis of the pockets reveals the molecular basis for asymmetric binding and stoichiometry	RESULTS
26	49	tryptophan fluorescence	experimental_method	However, studies based on tryptophan fluorescence were confounded by the fluorescence of the HPA ligands, and isothermal titration calorimetry (ITC) was unfeasible due to the need for very high concentrations of NadR in the ITC chamber (due to the relatively low affinity), which exceeded the solubility limits of the protein.	RESULTS
93	96	HPA	chemical	However, studies based on tryptophan fluorescence were confounded by the fluorescence of the HPA ligands, and isothermal titration calorimetry (ITC) was unfeasible due to the need for very high concentrations of NadR in the ITC chamber (due to the relatively low affinity), which exceeded the solubility limits of the protein.	RESULTS
110	142	isothermal titration calorimetry	experimental_method	However, studies based on tryptophan fluorescence were confounded by the fluorescence of the HPA ligands, and isothermal titration calorimetry (ITC) was unfeasible due to the need for very high concentrations of NadR in the ITC chamber (due to the relatively low affinity), which exceeded the solubility limits of the protein.	RESULTS
144	147	ITC	experimental_method	However, studies based on tryptophan fluorescence were confounded by the fluorescence of the HPA ligands, and isothermal titration calorimetry (ITC) was unfeasible due to the need for very high concentrations of NadR in the ITC chamber (due to the relatively low affinity), which exceeded the solubility limits of the protein.	RESULTS
212	216	NadR	protein	However, studies based on tryptophan fluorescence were confounded by the fluorescence of the HPA ligands, and isothermal titration calorimetry (ITC) was unfeasible due to the need for very high concentrations of NadR in the ITC chamber (due to the relatively low affinity), which exceeded the solubility limits of the protein.	RESULTS
224	227	ITC	experimental_method	However, studies based on tryptophan fluorescence were confounded by the fluorescence of the HPA ligands, and isothermal titration calorimetry (ITC) was unfeasible due to the need for very high concentrations of NadR in the ITC chamber (due to the relatively low affinity), which exceeded the solubility limits of the protein.	RESULTS
42	63	binding stoichiometry	evidence	However, it was possible to calculate the binding stoichiometry of the NadR-HPA interactions using an SPR-based approach.	RESULTS
71	79	NadR-HPA	complex_assembly	However, it was possible to calculate the binding stoichiometry of the NadR-HPA interactions using an SPR-based approach.	RESULTS
102	105	SPR	experimental_method	However, it was possible to calculate the binding stoichiometry of the NadR-HPA interactions using an SPR-based approach.	RESULTS
3	6	SPR	experimental_method	In SPR, the signal measured is proportional to the total molecular mass proximal to the sensor surface; consequently, if the molecular weights of the interactors are known, then the stoichiometry of the resulting complex can be determined.	RESULTS
93	96	SPR	experimental_method	This approach relies on the assumption that the captured protein (‘the ligand’, according to SPR conventions) is 100% active and freely-accessible to potential interactors (‘the analytes’).	RESULTS
9	13	NadR	protein	Firstly, NadR is expected to be covalently immobilized on the sensor chip as a dimer in random orientations, since it is a stable dimer in solution and has sixteen lysines well-distributed around its surface, all able to act as potential sites for amine coupling to the chip, and none of which are close to the ligand-binding pocket.	RESULTS
79	84	dimer	oligomeric_state	Firstly, NadR is expected to be covalently immobilized on the sensor chip as a dimer in random orientations, since it is a stable dimer in solution and has sixteen lysines well-distributed around its surface, all able to act as potential sites for amine coupling to the chip, and none of which are close to the ligand-binding pocket.	RESULTS
123	129	stable	protein_state	Firstly, NadR is expected to be covalently immobilized on the sensor chip as a dimer in random orientations, since it is a stable dimer in solution and has sixteen lysines well-distributed around its surface, all able to act as potential sites for amine coupling to the chip, and none of which are close to the ligand-binding pocket.	RESULTS
130	135	dimer	oligomeric_state	Firstly, NadR is expected to be covalently immobilized on the sensor chip as a dimer in random orientations, since it is a stable dimer in solution and has sixteen lysines well-distributed around its surface, all able to act as potential sites for amine coupling to the chip, and none of which are close to the ligand-binding pocket.	RESULTS
164	171	lysines	residue_name	Firstly, NadR is expected to be covalently immobilized on the sensor chip as a dimer in random orientations, since it is a stable dimer in solution and has sixteen lysines well-distributed around its surface, all able to act as potential sites for amine coupling to the chip, and none of which are close to the ligand-binding pocket.	RESULTS
311	332	ligand-binding pocket	site	Firstly, NadR is expected to be covalently immobilized on the sensor chip as a dimer in random orientations, since it is a stable dimer in solution and has sixteen lysines well-distributed around its surface, all able to act as potential sites for amine coupling to the chip, and none of which are close to the ligand-binding pocket.	RESULTS
14	17	HPA	chemical	Secondly, the HPA analytes are all very small (MW 150–170, Fig 1A) and therefore are expected to be able to diffuse readily into all potential binding sites, irrespective of the random orientations of the immobilized NadR dimers on the chip.	RESULTS
143	156	binding sites	site	Secondly, the HPA analytes are all very small (MW 150–170, Fig 1A) and therefore are expected to be able to diffuse readily into all potential binding sites, irrespective of the random orientations of the immobilized NadR dimers on the chip.	RESULTS
217	221	NadR	protein	Secondly, the HPA analytes are all very small (MW 150–170, Fig 1A) and therefore are expected to be able to diffuse readily into all potential binding sites, irrespective of the random orientations of the immobilized NadR dimers on the chip.	RESULTS
222	228	dimers	oligomeric_state	Secondly, the HPA analytes are all very small (MW 150–170, Fig 1A) and therefore are expected to be able to diffuse readily into all potential binding sites, irrespective of the random orientations of the immobilized NadR dimers on the chip.	RESULTS
25	33	NadR-HPA	complex_assembly	The stoichiometry of the NadR-HPA interactions was determined using Eq 1 (see Materials and Methods), and revealed stoichiometries of 1.13 for 4-HPA, 1.02 for 3-HPA, and 1.21 for 3Cl,4-HPA, strongly suggesting that one NadR dimer bound to 1 HPA analyte molecule.	RESULTS
115	130	stoichiometries	evidence	The stoichiometry of the NadR-HPA interactions was determined using Eq 1 (see Materials and Methods), and revealed stoichiometries of 1.13 for 4-HPA, 1.02 for 3-HPA, and 1.21 for 3Cl,4-HPA, strongly suggesting that one NadR dimer bound to 1 HPA analyte molecule.	RESULTS
143	148	4-HPA	chemical	The stoichiometry of the NadR-HPA interactions was determined using Eq 1 (see Materials and Methods), and revealed stoichiometries of 1.13 for 4-HPA, 1.02 for 3-HPA, and 1.21 for 3Cl,4-HPA, strongly suggesting that one NadR dimer bound to 1 HPA analyte molecule.	RESULTS
159	164	3-HPA	chemical	The stoichiometry of the NadR-HPA interactions was determined using Eq 1 (see Materials and Methods), and revealed stoichiometries of 1.13 for 4-HPA, 1.02 for 3-HPA, and 1.21 for 3Cl,4-HPA, strongly suggesting that one NadR dimer bound to 1 HPA analyte molecule.	RESULTS
179	188	3Cl,4-HPA	chemical	The stoichiometry of the NadR-HPA interactions was determined using Eq 1 (see Materials and Methods), and revealed stoichiometries of 1.13 for 4-HPA, 1.02 for 3-HPA, and 1.21 for 3Cl,4-HPA, strongly suggesting that one NadR dimer bound to 1 HPA analyte molecule.	RESULTS
219	223	NadR	protein	The stoichiometry of the NadR-HPA interactions was determined using Eq 1 (see Materials and Methods), and revealed stoichiometries of 1.13 for 4-HPA, 1.02 for 3-HPA, and 1.21 for 3Cl,4-HPA, strongly suggesting that one NadR dimer bound to 1 HPA analyte molecule.	RESULTS
224	229	dimer	oligomeric_state	The stoichiometry of the NadR-HPA interactions was determined using Eq 1 (see Materials and Methods), and revealed stoichiometries of 1.13 for 4-HPA, 1.02 for 3-HPA, and 1.21 for 3Cl,4-HPA, strongly suggesting that one NadR dimer bound to 1 HPA analyte molecule.	RESULTS
230	238	bound to	protein_state	The stoichiometry of the NadR-HPA interactions was determined using Eq 1 (see Materials and Methods), and revealed stoichiometries of 1.13 for 4-HPA, 1.02 for 3-HPA, and 1.21 for 3Cl,4-HPA, strongly suggesting that one NadR dimer bound to 1 HPA analyte molecule.	RESULTS
241	244	HPA	chemical	The stoichiometry of the NadR-HPA interactions was determined using Eq 1 (see Materials and Methods), and revealed stoichiometries of 1.13 for 4-HPA, 1.02 for 3-HPA, and 1.21 for 3Cl,4-HPA, strongly suggesting that one NadR dimer bound to 1 HPA analyte molecule.	RESULTS
4	25	crystallographic data	evidence	The crystallographic data, supported by the SPR studies of binding stoichiometry, revealed the lack of a second 4-HPA molecule in the homodimer, suggesting negative co-operativity, a phenomenon previously described for the MTH313/salicylate interaction and for other MarR family proteins.	RESULTS
44	47	SPR	experimental_method	The crystallographic data, supported by the SPR studies of binding stoichiometry, revealed the lack of a second 4-HPA molecule in the homodimer, suggesting negative co-operativity, a phenomenon previously described for the MTH313/salicylate interaction and for other MarR family proteins.	RESULTS
59	80	binding stoichiometry	evidence	The crystallographic data, supported by the SPR studies of binding stoichiometry, revealed the lack of a second 4-HPA molecule in the homodimer, suggesting negative co-operativity, a phenomenon previously described for the MTH313/salicylate interaction and for other MarR family proteins.	RESULTS
112	117	4-HPA	chemical	The crystallographic data, supported by the SPR studies of binding stoichiometry, revealed the lack of a second 4-HPA molecule in the homodimer, suggesting negative co-operativity, a phenomenon previously described for the MTH313/salicylate interaction and for other MarR family proteins.	RESULTS
134	143	homodimer	oligomeric_state	The crystallographic data, supported by the SPR studies of binding stoichiometry, revealed the lack of a second 4-HPA molecule in the homodimer, suggesting negative co-operativity, a phenomenon previously described for the MTH313/salicylate interaction and for other MarR family proteins.	RESULTS
223	229	MTH313	protein	The crystallographic data, supported by the SPR studies of binding stoichiometry, revealed the lack of a second 4-HPA molecule in the homodimer, suggesting negative co-operativity, a phenomenon previously described for the MTH313/salicylate interaction and for other MarR family proteins.	RESULTS
230	240	salicylate	chemical	The crystallographic data, supported by the SPR studies of binding stoichiometry, revealed the lack of a second 4-HPA molecule in the homodimer, suggesting negative co-operativity, a phenomenon previously described for the MTH313/salicylate interaction and for other MarR family proteins.	RESULTS
267	271	MarR	protein_type	The crystallographic data, supported by the SPR studies of binding stoichiometry, revealed the lack of a second 4-HPA molecule in the homodimer, suggesting negative co-operativity, a phenomenon previously described for the MTH313/salicylate interaction and for other MarR family proteins.	RESULTS
47	51	holo	protein_state	To explore the molecular basis of asymmetry in holo-NadR, we superposed its ligand-free monomer (chain A) onto the ligand-occupied monomer (chain B).	RESULTS
52	56	NadR	protein	To explore the molecular basis of asymmetry in holo-NadR, we superposed its ligand-free monomer (chain A) onto the ligand-occupied monomer (chain B).	RESULTS
61	71	superposed	experimental_method	To explore the molecular basis of asymmetry in holo-NadR, we superposed its ligand-free monomer (chain A) onto the ligand-occupied monomer (chain B).	RESULTS
76	87	ligand-free	protein_state	To explore the molecular basis of asymmetry in holo-NadR, we superposed its ligand-free monomer (chain A) onto the ligand-occupied monomer (chain B).	RESULTS
88	95	monomer	oligomeric_state	To explore the molecular basis of asymmetry in holo-NadR, we superposed its ligand-free monomer (chain A) onto the ligand-occupied monomer (chain B).	RESULTS
97	104	chain A	structure_element	To explore the molecular basis of asymmetry in holo-NadR, we superposed its ligand-free monomer (chain A) onto the ligand-occupied monomer (chain B).	RESULTS
115	130	ligand-occupied	protein_state	To explore the molecular basis of asymmetry in holo-NadR, we superposed its ligand-free monomer (chain A) onto the ligand-occupied monomer (chain B).	RESULTS
131	138	monomer	oligomeric_state	To explore the molecular basis of asymmetry in holo-NadR, we superposed its ligand-free monomer (chain A) onto the ligand-occupied monomer (chain B).	RESULTS
140	147	chain B	structure_element	To explore the molecular basis of asymmetry in holo-NadR, we superposed its ligand-free monomer (chain A) onto the ligand-occupied monomer (chain B).	RESULTS
13	26	superposition	experimental_method	Overall, the superposition revealed a high degree of structural similarity (Cα root mean square deviation (rmsd) of 1.5Å), though on closer inspection a rotational difference of ~9 degrees along the long axis of helix α6 was observed, suggesting that 4-HPA induced a slight conformational change (Fig 5A).	RESULTS
79	105	root mean square deviation	evidence	Overall, the superposition revealed a high degree of structural similarity (Cα root mean square deviation (rmsd) of 1.5Å), though on closer inspection a rotational difference of ~9 degrees along the long axis of helix α6 was observed, suggesting that 4-HPA induced a slight conformational change (Fig 5A).	RESULTS
107	111	rmsd	evidence	Overall, the superposition revealed a high degree of structural similarity (Cα root mean square deviation (rmsd) of 1.5Å), though on closer inspection a rotational difference of ~9 degrees along the long axis of helix α6 was observed, suggesting that 4-HPA induced a slight conformational change (Fig 5A).	RESULTS
212	217	helix	structure_element	Overall, the superposition revealed a high degree of structural similarity (Cα root mean square deviation (rmsd) of 1.5Å), though on closer inspection a rotational difference of ~9 degrees along the long axis of helix α6 was observed, suggesting that 4-HPA induced a slight conformational change (Fig 5A).	RESULTS
218	220	α6	structure_element	Overall, the superposition revealed a high degree of structural similarity (Cα root mean square deviation (rmsd) of 1.5Å), though on closer inspection a rotational difference of ~9 degrees along the long axis of helix α6 was observed, suggesting that 4-HPA induced a slight conformational change (Fig 5A).	RESULTS
251	256	4-HPA	chemical	Overall, the superposition revealed a high degree of structural similarity (Cα root mean square deviation (rmsd) of 1.5Å), though on closer inspection a rotational difference of ~9 degrees along the long axis of helix α6 was observed, suggesting that 4-HPA induced a slight conformational change (Fig 5A).	RESULTS
27	32	helix	structure_element	However, since residues of helix α6 were not directly involved in ligand binding, an explanation for the lack of 4-HPA in monomer A did not emerge by analyzing only these backbone atom positions, suggesting that a more complex series of allosteric events may occur.	RESULTS
33	35	α6	structure_element	However, since residues of helix α6 were not directly involved in ligand binding, an explanation for the lack of 4-HPA in monomer A did not emerge by analyzing only these backbone atom positions, suggesting that a more complex series of allosteric events may occur.	RESULTS
113	118	4-HPA	chemical	However, since residues of helix α6 were not directly involved in ligand binding, an explanation for the lack of 4-HPA in monomer A did not emerge by analyzing only these backbone atom positions, suggesting that a more complex series of allosteric events may occur.	RESULTS
122	129	monomer	oligomeric_state	However, since residues of helix α6 were not directly involved in ligand binding, an explanation for the lack of 4-HPA in monomer A did not emerge by analyzing only these backbone atom positions, suggesting that a more complex series of allosteric events may occur.	RESULTS
130	131	A	structure_element	However, since residues of helix α6 were not directly involved in ligand binding, an explanation for the lack of 4-HPA in monomer A did not emerge by analyzing only these backbone atom positions, suggesting that a more complex series of allosteric events may occur.	RESULTS
63	68	Met22	residue_name_number	Indeed, we noted interesting differences in the side chains of Met22, Phe25 and Arg43, which in monomer B are used to contact the ligand while in monomer A they partially occupied the pocket and collectively reduced its volume significantly.	RESULTS
70	75	Phe25	residue_name_number	Indeed, we noted interesting differences in the side chains of Met22, Phe25 and Arg43, which in monomer B are used to contact the ligand while in monomer A they partially occupied the pocket and collectively reduced its volume significantly.	RESULTS
80	85	Arg43	residue_name_number	Indeed, we noted interesting differences in the side chains of Met22, Phe25 and Arg43, which in monomer B are used to contact the ligand while in monomer A they partially occupied the pocket and collectively reduced its volume significantly.	RESULTS
96	103	monomer	oligomeric_state	Indeed, we noted interesting differences in the side chains of Met22, Phe25 and Arg43, which in monomer B are used to contact the ligand while in monomer A they partially occupied the pocket and collectively reduced its volume significantly.	RESULTS
104	105	B	structure_element	Indeed, we noted interesting differences in the side chains of Met22, Phe25 and Arg43, which in monomer B are used to contact the ligand while in monomer A they partially occupied the pocket and collectively reduced its volume significantly.	RESULTS
146	153	monomer	oligomeric_state	Indeed, we noted interesting differences in the side chains of Met22, Phe25 and Arg43, which in monomer B are used to contact the ligand while in monomer A they partially occupied the pocket and collectively reduced its volume significantly.	RESULTS
154	155	A	structure_element	Indeed, we noted interesting differences in the side chains of Met22, Phe25 and Arg43, which in monomer B are used to contact the ligand while in monomer A they partially occupied the pocket and collectively reduced its volume significantly.	RESULTS
184	190	pocket	site	Indeed, we noted interesting differences in the side chains of Met22, Phe25 and Arg43, which in monomer B are used to contact the ligand while in monomer A they partially occupied the pocket and collectively reduced its volume significantly.	RESULTS
37	42	CASTp	experimental_method	Specifically, upon analysis with the CASTp software, the pocket in chain B containing the 4-HPA exhibited a total volume of approximately 370 Å3, while the pocket in chain A was occupied by these three side chains that adopted ‘inward’ positions and thereby divided the space into a few much smaller pockets, each with volume < 50 Å3, evidently rendering chain A unfavorable for ligand binding.	RESULTS
57	63	pocket	site	Specifically, upon analysis with the CASTp software, the pocket in chain B containing the 4-HPA exhibited a total volume of approximately 370 Å3, while the pocket in chain A was occupied by these three side chains that adopted ‘inward’ positions and thereby divided the space into a few much smaller pockets, each with volume < 50 Å3, evidently rendering chain A unfavorable for ligand binding.	RESULTS
67	74	chain B	structure_element	Specifically, upon analysis with the CASTp software, the pocket in chain B containing the 4-HPA exhibited a total volume of approximately 370 Å3, while the pocket in chain A was occupied by these three side chains that adopted ‘inward’ positions and thereby divided the space into a few much smaller pockets, each with volume < 50 Å3, evidently rendering chain A unfavorable for ligand binding.	RESULTS
90	95	4-HPA	chemical	Specifically, upon analysis with the CASTp software, the pocket in chain B containing the 4-HPA exhibited a total volume of approximately 370 Å3, while the pocket in chain A was occupied by these three side chains that adopted ‘inward’ positions and thereby divided the space into a few much smaller pockets, each with volume < 50 Å3, evidently rendering chain A unfavorable for ligand binding.	RESULTS
156	162	pocket	site	Specifically, upon analysis with the CASTp software, the pocket in chain B containing the 4-HPA exhibited a total volume of approximately 370 Å3, while the pocket in chain A was occupied by these three side chains that adopted ‘inward’ positions and thereby divided the space into a few much smaller pockets, each with volume < 50 Å3, evidently rendering chain A unfavorable for ligand binding.	RESULTS
166	173	chain A	structure_element	Specifically, upon analysis with the CASTp software, the pocket in chain B containing the 4-HPA exhibited a total volume of approximately 370 Å3, while the pocket in chain A was occupied by these three side chains that adopted ‘inward’ positions and thereby divided the space into a few much smaller pockets, each with volume < 50 Å3, evidently rendering chain A unfavorable for ligand binding.	RESULTS
228	234	inward	protein_state	Specifically, upon analysis with the CASTp software, the pocket in chain B containing the 4-HPA exhibited a total volume of approximately 370 Å3, while the pocket in chain A was occupied by these three side chains that adopted ‘inward’ positions and thereby divided the space into a few much smaller pockets, each with volume < 50 Å3, evidently rendering chain A unfavorable for ligand binding.	RESULTS
355	362	chain A	structure_element	Specifically, upon analysis with the CASTp software, the pocket in chain B containing the 4-HPA exhibited a total volume of approximately 370 Å3, while the pocket in chain A was occupied by these three side chains that adopted ‘inward’ positions and thereby divided the space into a few much smaller pockets, each with volume < 50 Å3, evidently rendering chain A unfavorable for ligand binding.	RESULTS
71	77	MetA22	residue_name_number	Most notably, atomic clashes between the ligand and the side chains of MetA22, PheA25 and ArgA43 would occur if 4-HPA were present in the monomer A pocket (Fig 5B).	RESULTS
79	85	PheA25	residue_name_number	Most notably, atomic clashes between the ligand and the side chains of MetA22, PheA25 and ArgA43 would occur if 4-HPA were present in the monomer A pocket (Fig 5B).	RESULTS
90	96	ArgA43	residue_name_number	Most notably, atomic clashes between the ligand and the side chains of MetA22, PheA25 and ArgA43 would occur if 4-HPA were present in the monomer A pocket (Fig 5B).	RESULTS
112	117	4-HPA	chemical	Most notably, atomic clashes between the ligand and the side chains of MetA22, PheA25 and ArgA43 would occur if 4-HPA were present in the monomer A pocket (Fig 5B).	RESULTS
138	145	monomer	oligomeric_state	Most notably, atomic clashes between the ligand and the side chains of MetA22, PheA25 and ArgA43 would occur if 4-HPA were present in the monomer A pocket (Fig 5B).	RESULTS
146	147	A	structure_element	Most notably, atomic clashes between the ligand and the side chains of MetA22, PheA25 and ArgA43 would occur if 4-HPA were present in the monomer A pocket (Fig 5B).	RESULTS
148	154	pocket	site	Most notably, atomic clashes between the ligand and the side chains of MetA22, PheA25 and ArgA43 would occur if 4-HPA were present in the monomer A pocket (Fig 5B).	RESULTS
30	37	pockets	site	Subsequently, analyses of the pockets in apo-NadR revealed that in the absence of ligand the long Arg43 side chain was always in the open ‘outward’ position compatible with binding to the 4-HPA carboxylate group.	RESULTS
41	44	apo	protein_state	Subsequently, analyses of the pockets in apo-NadR revealed that in the absence of ligand the long Arg43 side chain was always in the open ‘outward’ position compatible with binding to the 4-HPA carboxylate group.	RESULTS
45	49	NadR	protein	Subsequently, analyses of the pockets in apo-NadR revealed that in the absence of ligand the long Arg43 side chain was always in the open ‘outward’ position compatible with binding to the 4-HPA carboxylate group.	RESULTS
71	88	absence of ligand	protein_state	Subsequently, analyses of the pockets in apo-NadR revealed that in the absence of ligand the long Arg43 side chain was always in the open ‘outward’ position compatible with binding to the 4-HPA carboxylate group.	RESULTS
98	103	Arg43	residue_name_number	Subsequently, analyses of the pockets in apo-NadR revealed that in the absence of ligand the long Arg43 side chain was always in the open ‘outward’ position compatible with binding to the 4-HPA carboxylate group.	RESULTS
139	146	outward	protein_state	Subsequently, analyses of the pockets in apo-NadR revealed that in the absence of ligand the long Arg43 side chain was always in the open ‘outward’ position compatible with binding to the 4-HPA carboxylate group.	RESULTS
188	193	4-HPA	chemical	Subsequently, analyses of the pockets in apo-NadR revealed that in the absence of ligand the long Arg43 side chain was always in the open ‘outward’ position compatible with binding to the 4-HPA carboxylate group.	RESULTS
17	20	apo	protein_state	In contrast, the apo-form Met22 and Phe25 residues were still encroaching the spaces of the 4-hydroxyl group and the phenyl ring of the ligand, respectively (Fig 5C).	RESULTS
26	31	Met22	residue_name_number	In contrast, the apo-form Met22 and Phe25 residues were still encroaching the spaces of the 4-hydroxyl group and the phenyl ring of the ligand, respectively (Fig 5C).	RESULTS
36	41	Phe25	residue_name_number	In contrast, the apo-form Met22 and Phe25 residues were still encroaching the spaces of the 4-hydroxyl group and the phenyl ring of the ligand, respectively (Fig 5C).	RESULTS
5	12	outward	protein_state	The ‘outward’ position of Arg43 generated an open apo-form pocket with volume approximately 380Å3.	RESULTS
26	31	Arg43	residue_name_number	The ‘outward’ position of Arg43 generated an open apo-form pocket with volume approximately 380Å3.	RESULTS
45	49	open	protein_state	The ‘outward’ position of Arg43 generated an open apo-form pocket with volume approximately 380Å3.	RESULTS
50	53	apo	protein_state	The ‘outward’ position of Arg43 generated an open apo-form pocket with volume approximately 380Å3.	RESULTS
59	65	pocket	site	The ‘outward’ position of Arg43 generated an open apo-form pocket with volume approximately 380Å3.	RESULTS
48	53	Arg43	residue_name_number	Taken together, these observations suggest that Arg43 is a major determinant of ligand binding, and that its ‘inward’ position inhibits the binding of 4-HPA to the empty pocket of holo-NadR.	RESULTS
110	116	inward	protein_state	Taken together, these observations suggest that Arg43 is a major determinant of ligand binding, and that its ‘inward’ position inhibits the binding of 4-HPA to the empty pocket of holo-NadR.	RESULTS
151	156	4-HPA	chemical	Taken together, these observations suggest that Arg43 is a major determinant of ligand binding, and that its ‘inward’ position inhibits the binding of 4-HPA to the empty pocket of holo-NadR.	RESULTS
170	176	pocket	site	Taken together, these observations suggest that Arg43 is a major determinant of ligand binding, and that its ‘inward’ position inhibits the binding of 4-HPA to the empty pocket of holo-NadR.	RESULTS
180	184	holo	protein_state	Taken together, these observations suggest that Arg43 is a major determinant of ligand binding, and that its ‘inward’ position inhibits the binding of 4-HPA to the empty pocket of holo-NadR.	RESULTS
185	189	NadR	protein	Taken together, these observations suggest that Arg43 is a major determinant of ligand binding, and that its ‘inward’ position inhibits the binding of 4-HPA to the empty pocket of holo-NadR.	RESULTS
26	30	NadR	protein	Structural differences of NadR in ligand-bound or free forms.	FIG
34	46	ligand-bound	protein_state	Structural differences of NadR in ligand-bound or free forms.	FIG
50	54	free	protein_state	Structural differences of NadR in ligand-bound or free forms.	FIG
5	12	Aligned	experimental_method	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
13	21	monomers	oligomeric_state	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
25	29	holo	protein_state	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
30	34	NadR	protein	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
36	43	chain A	structure_element	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
52	59	chain B	structure_element	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
117	122	helix	structure_element	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
123	125	α6	structure_element	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
131	141	Comparison	experimental_method	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
153	168	binding pockets	site	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
172	176	holo	protein_state	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
177	181	NadR	protein	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
200	211	ligand-free	protein_state	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
212	219	monomer	oligomeric_state	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
220	221	A	structure_element	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
239	244	Met22	residue_name_number	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
246	251	Phe25	residue_name_number	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
256	261	Arg43	residue_name_number	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
269	275	inward	protein_state	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
327	342	ligand-occupied	protein_state	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
343	349	pocket	site	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
374	380	inward	protein_state	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
430	435	4-HPA	chemical	 (A) Aligned monomers of holo-NadR (chain A: green; chain B: blue), reveal major overall differences by the shift of helix α6. (B) Comparison of the two binding pockets in holo-NadR shows that in the ligand-free monomer A (green) residues Met22, Phe25 and Arg43 adopt ‘inward’ positions (highlighted by arrows) compared to the ligand-occupied pocket (blue residues); these ‘inward’ conformations appear unfavorable for binding of 4-HPA due to clashes with the 4-hydroxyl group, the phenyl ring and the carboxylate group, respectively.	FIG
9	17	crystals	evidence	In these crystals, the ArgA43 side chain showed two alternate conformations, modelled with 50% occupancy in each state, as indicated by the two ‘mirrored’ arrows.	FIG
23	29	ArgA43	residue_name_number	In these crystals, the ArgA43 side chain showed two alternate conformations, modelled with 50% occupancy in each state, as indicated by the two ‘mirrored’ arrows.	FIG
67	72	4-HPA	chemical	The inner conformer is the one that would display major clashes if 4-HPA were present. (C) Comparison of the empty pocket from holo-NadR (green residues) with the four empty pockets of apo-NadR (grey residues), shows that in the absence of 4-HPA the Arg43 side chain is always observed in the ‘outward’ conformation.	FIG
115	121	pocket	site	The inner conformer is the one that would display major clashes if 4-HPA were present. (C) Comparison of the empty pocket from holo-NadR (green residues) with the four empty pockets of apo-NadR (grey residues), shows that in the absence of 4-HPA the Arg43 side chain is always observed in the ‘outward’ conformation.	FIG
127	131	holo	protein_state	The inner conformer is the one that would display major clashes if 4-HPA were present. (C) Comparison of the empty pocket from holo-NadR (green residues) with the four empty pockets of apo-NadR (grey residues), shows that in the absence of 4-HPA the Arg43 side chain is always observed in the ‘outward’ conformation.	FIG
132	136	NadR	protein	The inner conformer is the one that would display major clashes if 4-HPA were present. (C) Comparison of the empty pocket from holo-NadR (green residues) with the four empty pockets of apo-NadR (grey residues), shows that in the absence of 4-HPA the Arg43 side chain is always observed in the ‘outward’ conformation.	FIG
174	181	pockets	site	The inner conformer is the one that would display major clashes if 4-HPA were present. (C) Comparison of the empty pocket from holo-NadR (green residues) with the four empty pockets of apo-NadR (grey residues), shows that in the absence of 4-HPA the Arg43 side chain is always observed in the ‘outward’ conformation.	FIG
185	188	apo	protein_state	The inner conformer is the one that would display major clashes if 4-HPA were present. (C) Comparison of the empty pocket from holo-NadR (green residues) with the four empty pockets of apo-NadR (grey residues), shows that in the absence of 4-HPA the Arg43 side chain is always observed in the ‘outward’ conformation.	FIG
189	193	NadR	protein	The inner conformer is the one that would display major clashes if 4-HPA were present. (C) Comparison of the empty pocket from holo-NadR (green residues) with the four empty pockets of apo-NadR (grey residues), shows that in the absence of 4-HPA the Arg43 side chain is always observed in the ‘outward’ conformation.	FIG
229	239	absence of	protein_state	The inner conformer is the one that would display major clashes if 4-HPA were present. (C) Comparison of the empty pocket from holo-NadR (green residues) with the four empty pockets of apo-NadR (grey residues), shows that in the absence of 4-HPA the Arg43 side chain is always observed in the ‘outward’ conformation.	FIG
240	245	4-HPA	chemical	The inner conformer is the one that would display major clashes if 4-HPA were present. (C) Comparison of the empty pocket from holo-NadR (green residues) with the four empty pockets of apo-NadR (grey residues), shows that in the absence of 4-HPA the Arg43 side chain is always observed in the ‘outward’ conformation.	FIG
250	255	Arg43	residue_name_number	The inner conformer is the one that would display major clashes if 4-HPA were present. (C) Comparison of the empty pocket from holo-NadR (green residues) with the four empty pockets of apo-NadR (grey residues), shows that in the absence of 4-HPA the Arg43 side chain is always observed in the ‘outward’ conformation.	FIG
294	301	outward	protein_state	The inner conformer is the one that would display major clashes if 4-HPA were present. (C) Comparison of the empty pocket from holo-NadR (green residues) with the four empty pockets of apo-NadR (grey residues), shows that in the absence of 4-HPA the Arg43 side chain is always observed in the ‘outward’ conformation.	FIG
20	63	15N heteronuclear solution NMR spectroscopy	experimental_method	Finally, we applied 15N heteronuclear solution NMR spectroscopy to examine the interaction of 4-HPA with apo NadR. We collected NMR spectra on NadR in the presence and absence of 4-HPA (see Materials and Methods).	RESULTS
94	99	4-HPA	chemical	Finally, we applied 15N heteronuclear solution NMR spectroscopy to examine the interaction of 4-HPA with apo NadR. We collected NMR spectra on NadR in the presence and absence of 4-HPA (see Materials and Methods).	RESULTS
105	108	apo	protein_state	Finally, we applied 15N heteronuclear solution NMR spectroscopy to examine the interaction of 4-HPA with apo NadR. We collected NMR spectra on NadR in the presence and absence of 4-HPA (see Materials and Methods).	RESULTS
109	113	NadR	protein	Finally, we applied 15N heteronuclear solution NMR spectroscopy to examine the interaction of 4-HPA with apo NadR. We collected NMR spectra on NadR in the presence and absence of 4-HPA (see Materials and Methods).	RESULTS
128	131	NMR	experimental_method	Finally, we applied 15N heteronuclear solution NMR spectroscopy to examine the interaction of 4-HPA with apo NadR. We collected NMR spectra on NadR in the presence and absence of 4-HPA (see Materials and Methods).	RESULTS
132	139	spectra	evidence	Finally, we applied 15N heteronuclear solution NMR spectroscopy to examine the interaction of 4-HPA with apo NadR. We collected NMR spectra on NadR in the presence and absence of 4-HPA (see Materials and Methods).	RESULTS
143	147	NadR	protein	Finally, we applied 15N heteronuclear solution NMR spectroscopy to examine the interaction of 4-HPA with apo NadR. We collected NMR spectra on NadR in the presence and absence of 4-HPA (see Materials and Methods).	RESULTS
148	163	in the presence	protein_state	Finally, we applied 15N heteronuclear solution NMR spectroscopy to examine the interaction of 4-HPA with apo NadR. We collected NMR spectra on NadR in the presence and absence of 4-HPA (see Materials and Methods).	RESULTS
168	178	absence of	protein_state	Finally, we applied 15N heteronuclear solution NMR spectroscopy to examine the interaction of 4-HPA with apo NadR. We collected NMR spectra on NadR in the presence and absence of 4-HPA (see Materials and Methods).	RESULTS
179	184	4-HPA	chemical	Finally, we applied 15N heteronuclear solution NMR spectroscopy to examine the interaction of 4-HPA with apo NadR. We collected NMR spectra on NadR in the presence and absence of 4-HPA (see Materials and Methods).	RESULTS
4	21	1H-15N TROSY-HSQC	experimental_method	The 1H-15N TROSY-HSQC spectrum of apo-NadR, acquired at 25°C, displayed approximately 140 distinct peaks (Fig 6A), most of which correspond to backbone amide N-H groups.	RESULTS
22	30	spectrum	evidence	The 1H-15N TROSY-HSQC spectrum of apo-NadR, acquired at 25°C, displayed approximately 140 distinct peaks (Fig 6A), most of which correspond to backbone amide N-H groups.	RESULTS
34	37	apo	protein_state	The 1H-15N TROSY-HSQC spectrum of apo-NadR, acquired at 25°C, displayed approximately 140 distinct peaks (Fig 6A), most of which correspond to backbone amide N-H groups.	RESULTS
38	42	NadR	protein	The 1H-15N TROSY-HSQC spectrum of apo-NadR, acquired at 25°C, displayed approximately 140 distinct peaks (Fig 6A), most of which correspond to backbone amide N-H groups.	RESULTS
168	171	apo	protein_state	The broad spectral dispersion and the number of peaks observed, which is close to the number of expected backbone amide N-H groups for this polypeptide, confirmed that apo-NadR is well-folded under these conditions and exhibits one conformation appreciable on the NMR timescale, i.e. in the NMR experiments at 25°C, two or more distinct conformations of apo-NadR monomers were not readily apparent.	RESULTS
172	176	NadR	protein	The broad spectral dispersion and the number of peaks observed, which is close to the number of expected backbone amide N-H groups for this polypeptide, confirmed that apo-NadR is well-folded under these conditions and exhibits one conformation appreciable on the NMR timescale, i.e. in the NMR experiments at 25°C, two or more distinct conformations of apo-NadR monomers were not readily apparent.	RESULTS
180	191	well-folded	protein_state	The broad spectral dispersion and the number of peaks observed, which is close to the number of expected backbone amide N-H groups for this polypeptide, confirmed that apo-NadR is well-folded under these conditions and exhibits one conformation appreciable on the NMR timescale, i.e. in the NMR experiments at 25°C, two or more distinct conformations of apo-NadR monomers were not readily apparent.	RESULTS
264	267	NMR	experimental_method	The broad spectral dispersion and the number of peaks observed, which is close to the number of expected backbone amide N-H groups for this polypeptide, confirmed that apo-NadR is well-folded under these conditions and exhibits one conformation appreciable on the NMR timescale, i.e. in the NMR experiments at 25°C, two or more distinct conformations of apo-NadR monomers were not readily apparent.	RESULTS
291	294	NMR	experimental_method	The broad spectral dispersion and the number of peaks observed, which is close to the number of expected backbone amide N-H groups for this polypeptide, confirmed that apo-NadR is well-folded under these conditions and exhibits one conformation appreciable on the NMR timescale, i.e. in the NMR experiments at 25°C, two or more distinct conformations of apo-NadR monomers were not readily apparent.	RESULTS
354	357	apo	protein_state	The broad spectral dispersion and the number of peaks observed, which is close to the number of expected backbone amide N-H groups for this polypeptide, confirmed that apo-NadR is well-folded under these conditions and exhibits one conformation appreciable on the NMR timescale, i.e. in the NMR experiments at 25°C, two or more distinct conformations of apo-NadR monomers were not readily apparent.	RESULTS
358	362	NadR	protein	The broad spectral dispersion and the number of peaks observed, which is close to the number of expected backbone amide N-H groups for this polypeptide, confirmed that apo-NadR is well-folded under these conditions and exhibits one conformation appreciable on the NMR timescale, i.e. in the NMR experiments at 25°C, two or more distinct conformations of apo-NadR monomers were not readily apparent.	RESULTS
363	371	monomers	oligomeric_state	The broad spectral dispersion and the number of peaks observed, which is close to the number of expected backbone amide N-H groups for this polypeptide, confirmed that apo-NadR is well-folded under these conditions and exhibits one conformation appreciable on the NMR timescale, i.e. in the NMR experiments at 25°C, two or more distinct conformations of apo-NadR monomers were not readily apparent.	RESULTS
21	26	4-HPA	chemical	Upon the addition of 4-HPA, over 45 peaks showed chemical shift perturbations, i.e. changed position in the spectrum or disappeared, while the remaining peaks remained unchanged.	RESULTS
29	34	4-HPA	chemical	This observation showed that 4-HPA was able to bind NadR and induce notable changes in specific regions of the protein.	RESULTS
52	56	NadR	protein	This observation showed that 4-HPA was able to bind NadR and induce notable changes in specific regions of the protein.	RESULTS
0	3	NMR	experimental_method	NMR spectra of NadR in the presence and absence of 4-HPA.	FIG
4	11	spectra	evidence	NMR spectra of NadR in the presence and absence of 4-HPA.	FIG
15	19	NadR	protein	NMR spectra of NadR in the presence and absence of 4-HPA.	FIG
20	35	in the presence	protein_state	NMR spectra of NadR in the presence and absence of 4-HPA.	FIG
40	50	absence of	protein_state	NMR spectra of NadR in the presence and absence of 4-HPA.	FIG
51	56	4-HPA	chemical	NMR spectra of NadR in the presence and absence of 4-HPA.	FIG
5	18	Superposition	experimental_method	 (A) Superposition of two 1H-15N TROSY-HSQC spectra recorded at 25°C on apo-NadR (cyan) and on NadR in the presence of 4-HPA (red).	FIG
26	43	1H-15N TROSY-HSQC	experimental_method	 (A) Superposition of two 1H-15N TROSY-HSQC spectra recorded at 25°C on apo-NadR (cyan) and on NadR in the presence of 4-HPA (red).	FIG
44	51	spectra	evidence	 (A) Superposition of two 1H-15N TROSY-HSQC spectra recorded at 25°C on apo-NadR (cyan) and on NadR in the presence of 4-HPA (red).	FIG
72	75	apo	protein_state	 (A) Superposition of two 1H-15N TROSY-HSQC spectra recorded at 25°C on apo-NadR (cyan) and on NadR in the presence of 4-HPA (red).	FIG
76	80	NadR	protein	 (A) Superposition of two 1H-15N TROSY-HSQC spectra recorded at 25°C on apo-NadR (cyan) and on NadR in the presence of 4-HPA (red).	FIG
95	99	NadR	protein	 (A) Superposition of two 1H-15N TROSY-HSQC spectra recorded at 25°C on apo-NadR (cyan) and on NadR in the presence of 4-HPA (red).	FIG
107	118	presence of	protein_state	 (A) Superposition of two 1H-15N TROSY-HSQC spectra recorded at 25°C on apo-NadR (cyan) and on NadR in the presence of 4-HPA (red).	FIG
119	124	4-HPA	chemical	 (A) Superposition of two 1H-15N TROSY-HSQC spectra recorded at 25°C on apo-NadR (cyan) and on NadR in the presence of 4-HPA (red).	FIG
6	13	Overlay	experimental_method	(B,C) Overlay of selected regions of the 1H-15N TROSY-HSQC spectra acquired at 25°C of apo-NadR (cyan) and NadR/4-HPA (red) superimposed with the spectra acquired at 10°C of apo-NadR (blue) and NadR/4-HPA (green).	FIG
41	58	1H-15N TROSY-HSQC	experimental_method	(B,C) Overlay of selected regions of the 1H-15N TROSY-HSQC spectra acquired at 25°C of apo-NadR (cyan) and NadR/4-HPA (red) superimposed with the spectra acquired at 10°C of apo-NadR (blue) and NadR/4-HPA (green).	FIG
59	66	spectra	evidence	(B,C) Overlay of selected regions of the 1H-15N TROSY-HSQC spectra acquired at 25°C of apo-NadR (cyan) and NadR/4-HPA (red) superimposed with the spectra acquired at 10°C of apo-NadR (blue) and NadR/4-HPA (green).	FIG
87	90	apo	protein_state	(B,C) Overlay of selected regions of the 1H-15N TROSY-HSQC spectra acquired at 25°C of apo-NadR (cyan) and NadR/4-HPA (red) superimposed with the spectra acquired at 10°C of apo-NadR (blue) and NadR/4-HPA (green).	FIG
91	95	NadR	protein	(B,C) Overlay of selected regions of the 1H-15N TROSY-HSQC spectra acquired at 25°C of apo-NadR (cyan) and NadR/4-HPA (red) superimposed with the spectra acquired at 10°C of apo-NadR (blue) and NadR/4-HPA (green).	FIG
107	117	NadR/4-HPA	complex_assembly	(B,C) Overlay of selected regions of the 1H-15N TROSY-HSQC spectra acquired at 25°C of apo-NadR (cyan) and NadR/4-HPA (red) superimposed with the spectra acquired at 10°C of apo-NadR (blue) and NadR/4-HPA (green).	FIG
124	136	superimposed	experimental_method	(B,C) Overlay of selected regions of the 1H-15N TROSY-HSQC spectra acquired at 25°C of apo-NadR (cyan) and NadR/4-HPA (red) superimposed with the spectra acquired at 10°C of apo-NadR (blue) and NadR/4-HPA (green).	FIG
146	153	spectra	evidence	(B,C) Overlay of selected regions of the 1H-15N TROSY-HSQC spectra acquired at 25°C of apo-NadR (cyan) and NadR/4-HPA (red) superimposed with the spectra acquired at 10°C of apo-NadR (blue) and NadR/4-HPA (green).	FIG
174	177	apo	protein_state	(B,C) Overlay of selected regions of the 1H-15N TROSY-HSQC spectra acquired at 25°C of apo-NadR (cyan) and NadR/4-HPA (red) superimposed with the spectra acquired at 10°C of apo-NadR (blue) and NadR/4-HPA (green).	FIG
178	182	NadR	protein	(B,C) Overlay of selected regions of the 1H-15N TROSY-HSQC spectra acquired at 25°C of apo-NadR (cyan) and NadR/4-HPA (red) superimposed with the spectra acquired at 10°C of apo-NadR (blue) and NadR/4-HPA (green).	FIG
194	204	NadR/4-HPA	complex_assembly	(B,C) Overlay of selected regions of the 1H-15N TROSY-HSQC spectra acquired at 25°C of apo-NadR (cyan) and NadR/4-HPA (red) superimposed with the spectra acquired at 10°C of apo-NadR (blue) and NadR/4-HPA (green).	FIG
4	11	spectra	evidence	The spectra acquired at 10°C are excluded from panel A for simplicity.	FIG
16	27	presence of	protein_state	However, in the presence of 4-HPA, the 1H-15N TROSY-HSQC spectrum of NadR displayed approximately 140 peaks, as for apo-NadR, i.e. two distinct stable conformations (that might have potentially revealed the molecular asymmetry observed crystallographically) were not notable.	RESULTS
28	33	4-HPA	chemical	However, in the presence of 4-HPA, the 1H-15N TROSY-HSQC spectrum of NadR displayed approximately 140 peaks, as for apo-NadR, i.e. two distinct stable conformations (that might have potentially revealed the molecular asymmetry observed crystallographically) were not notable.	RESULTS
39	56	1H-15N TROSY-HSQC	experimental_method	However, in the presence of 4-HPA, the 1H-15N TROSY-HSQC spectrum of NadR displayed approximately 140 peaks, as for apo-NadR, i.e. two distinct stable conformations (that might have potentially revealed the molecular asymmetry observed crystallographically) were not notable.	RESULTS
57	65	spectrum	evidence	However, in the presence of 4-HPA, the 1H-15N TROSY-HSQC spectrum of NadR displayed approximately 140 peaks, as for apo-NadR, i.e. two distinct stable conformations (that might have potentially revealed the molecular asymmetry observed crystallographically) were not notable.	RESULTS
69	73	NadR	protein	However, in the presence of 4-HPA, the 1H-15N TROSY-HSQC spectrum of NadR displayed approximately 140 peaks, as for apo-NadR, i.e. two distinct stable conformations (that might have potentially revealed the molecular asymmetry observed crystallographically) were not notable.	RESULTS
116	119	apo	protein_state	However, in the presence of 4-HPA, the 1H-15N TROSY-HSQC spectrum of NadR displayed approximately 140 peaks, as for apo-NadR, i.e. two distinct stable conformations (that might have potentially revealed the molecular asymmetry observed crystallographically) were not notable.	RESULTS
120	124	NadR	protein	However, in the presence of 4-HPA, the 1H-15N TROSY-HSQC spectrum of NadR displayed approximately 140 peaks, as for apo-NadR, i.e. two distinct stable conformations (that might have potentially revealed the molecular asymmetry observed crystallographically) were not notable.	RESULTS
236	256	crystallographically	experimental_method	However, in the presence of 4-HPA, the 1H-15N TROSY-HSQC spectrum of NadR displayed approximately 140 peaks, as for apo-NadR, i.e. two distinct stable conformations (that might have potentially revealed the molecular asymmetry observed crystallographically) were not notable.	RESULTS
62	78	binding affinity	evidence	Considering the small size, fast diffusion and relatively low binding affinity of 4-HPA, it would not be surprising if the ligand associates and dissociates rapidly on the NMR time scale, resulting in only one set of peaks whose chemical shifts represent the average environment of the bound and unbound states.	RESULTS
82	87	4-HPA	chemical	Considering the small size, fast diffusion and relatively low binding affinity of 4-HPA, it would not be surprising if the ligand associates and dissociates rapidly on the NMR time scale, resulting in only one set of peaks whose chemical shifts represent the average environment of the bound and unbound states.	RESULTS
172	175	NMR	experimental_method	Considering the small size, fast diffusion and relatively low binding affinity of 4-HPA, it would not be surprising if the ligand associates and dissociates rapidly on the NMR time scale, resulting in only one set of peaks whose chemical shifts represent the average environment of the bound and unbound states.	RESULTS
286	291	bound	protein_state	Considering the small size, fast diffusion and relatively low binding affinity of 4-HPA, it would not be surprising if the ligand associates and dissociates rapidly on the NMR time scale, resulting in only one set of peaks whose chemical shifts represent the average environment of the bound and unbound states.	RESULTS
296	303	unbound	protein_state	Considering the small size, fast diffusion and relatively low binding affinity of 4-HPA, it would not be surprising if the ligand associates and dissociates rapidly on the NMR time scale, resulting in only one set of peaks whose chemical shifts represent the average environment of the bound and unbound states.	RESULTS
109	114	4-HPA	chemical	Interestingly, by cooling the samples to 10°C, we observed that a number of those peaks strongly affected by 4-HPA (and therefore likely to be in the ligand-binding site) demonstrated evidence of peak splitting, i.e. a tendency to become two distinct peaks rather than one single peak (Fig 6B and 6C).	RESULTS
150	169	ligand-binding site	site	Interestingly, by cooling the samples to 10°C, we observed that a number of those peaks strongly affected by 4-HPA (and therefore likely to be in the ligand-binding site) demonstrated evidence of peak splitting, i.e. a tendency to become two distinct peaks rather than one single peak (Fig 6B and 6C).	RESULTS
140	148	presence	protein_state	These doubled peaks may therefore reveal that the cooler temperature partially trapped the existence in solution of two distinct states, in presence or absence of 4-HPA, with minor conformational differences occurring at least in proximity to the binding pocket.	RESULTS
152	162	absence of	protein_state	These doubled peaks may therefore reveal that the cooler temperature partially trapped the existence in solution of two distinct states, in presence or absence of 4-HPA, with minor conformational differences occurring at least in proximity to the binding pocket.	RESULTS
163	168	4-HPA	chemical	These doubled peaks may therefore reveal that the cooler temperature partially trapped the existence in solution of two distinct states, in presence or absence of 4-HPA, with minor conformational differences occurring at least in proximity to the binding pocket.	RESULTS
247	261	binding pocket	site	These doubled peaks may therefore reveal that the cooler temperature partially trapped the existence in solution of two distinct states, in presence or absence of 4-HPA, with minor conformational differences occurring at least in proximity to the binding pocket.	RESULTS
28	31	NMR	experimental_method	Although more comprehensive NMR experiments and full chemical shift assignment of the spectra would be required to precisely define this multi-state behavior, the NMR data clearly demonstrate that NadR exhibits conformational flexibility which is modulated by 4-HPA in solution.	RESULTS
86	93	spectra	evidence	Although more comprehensive NMR experiments and full chemical shift assignment of the spectra would be required to precisely define this multi-state behavior, the NMR data clearly demonstrate that NadR exhibits conformational flexibility which is modulated by 4-HPA in solution.	RESULTS
163	166	NMR	experimental_method	Although more comprehensive NMR experiments and full chemical shift assignment of the spectra would be required to precisely define this multi-state behavior, the NMR data clearly demonstrate that NadR exhibits conformational flexibility which is modulated by 4-HPA in solution.	RESULTS
197	201	NadR	protein	Although more comprehensive NMR experiments and full chemical shift assignment of the spectra would be required to precisely define this multi-state behavior, the NMR data clearly demonstrate that NadR exhibits conformational flexibility which is modulated by 4-HPA in solution.	RESULTS
260	265	4-HPA	chemical	Although more comprehensive NMR experiments and full chemical shift assignment of the spectra would be required to precisely define this multi-state behavior, the NMR data clearly demonstrate that NadR exhibits conformational flexibility which is modulated by 4-HPA in solution.	RESULTS
0	3	Apo	protein_state	Apo-NadR structures reveal intrinsic conformational flexibility	RESULTS
4	8	NadR	protein	Apo-NadR structures reveal intrinsic conformational flexibility	RESULTS
9	19	structures	evidence	Apo-NadR structures reveal intrinsic conformational flexibility	RESULTS
4	7	apo	protein_state	The apo-NadR crystal structure contained two homodimers in the asymmetric unit (chains A+B and chains C+D).	RESULTS
8	12	NadR	protein	The apo-NadR crystal structure contained two homodimers in the asymmetric unit (chains A+B and chains C+D).	RESULTS
13	30	crystal structure	evidence	The apo-NadR crystal structure contained two homodimers in the asymmetric unit (chains A+B and chains C+D).	RESULTS
45	55	homodimers	oligomeric_state	The apo-NadR crystal structure contained two homodimers in the asymmetric unit (chains A+B and chains C+D).	RESULTS
80	90	chains A+B	structure_element	The apo-NadR crystal structure contained two homodimers in the asymmetric unit (chains A+B and chains C+D).	RESULTS
95	105	chains C+D	structure_element	The apo-NadR crystal structure contained two homodimers in the asymmetric unit (chains A+B and chains C+D).	RESULTS
13	37	structural superposition	experimental_method	Upon overall structural superposition, these dimers revealed a few minor differences in the α6 helix (a major component of the dimer interface) and the helices α4-α5 (the DNA binding region), and an rmsd of 1.55Å (Fig 7A).	RESULTS
45	51	dimers	oligomeric_state	Upon overall structural superposition, these dimers revealed a few minor differences in the α6 helix (a major component of the dimer interface) and the helices α4-α5 (the DNA binding region), and an rmsd of 1.55Å (Fig 7A).	RESULTS
92	100	α6 helix	structure_element	Upon overall structural superposition, these dimers revealed a few minor differences in the α6 helix (a major component of the dimer interface) and the helices α4-α5 (the DNA binding region), and an rmsd of 1.55Å (Fig 7A).	RESULTS
127	142	dimer interface	site	Upon overall structural superposition, these dimers revealed a few minor differences in the α6 helix (a major component of the dimer interface) and the helices α4-α5 (the DNA binding region), and an rmsd of 1.55Å (Fig 7A).	RESULTS
152	159	helices	structure_element	Upon overall structural superposition, these dimers revealed a few minor differences in the α6 helix (a major component of the dimer interface) and the helices α4-α5 (the DNA binding region), and an rmsd of 1.55Å (Fig 7A).	RESULTS
160	165	α4-α5	structure_element	Upon overall structural superposition, these dimers revealed a few minor differences in the α6 helix (a major component of the dimer interface) and the helices α4-α5 (the DNA binding region), and an rmsd of 1.55Å (Fig 7A).	RESULTS
171	189	DNA binding region	site	Upon overall structural superposition, these dimers revealed a few minor differences in the α6 helix (a major component of the dimer interface) and the helices α4-α5 (the DNA binding region), and an rmsd of 1.55Å (Fig 7A).	RESULTS
199	203	rmsd	evidence	Upon overall structural superposition, these dimers revealed a few minor differences in the α6 helix (a major component of the dimer interface) and the helices α4-α5 (the DNA binding region), and an rmsd of 1.55Å (Fig 7A).	RESULTS
22	26	holo	protein_state	Similarly, the entire holo-homodimer could be closely superposed onto each of the apo-homodimers, showing rmsd values of 1.29Å and 1.31Å, and with more notable differences in the α6 helix positions (Fig 7B).	RESULTS
27	36	homodimer	oligomeric_state	Similarly, the entire holo-homodimer could be closely superposed onto each of the apo-homodimers, showing rmsd values of 1.29Å and 1.31Å, and with more notable differences in the α6 helix positions (Fig 7B).	RESULTS
46	64	closely superposed	experimental_method	Similarly, the entire holo-homodimer could be closely superposed onto each of the apo-homodimers, showing rmsd values of 1.29Å and 1.31Å, and with more notable differences in the α6 helix positions (Fig 7B).	RESULTS
82	85	apo	protein_state	Similarly, the entire holo-homodimer could be closely superposed onto each of the apo-homodimers, showing rmsd values of 1.29Å and 1.31Å, and with more notable differences in the α6 helix positions (Fig 7B).	RESULTS
86	96	homodimers	oligomeric_state	Similarly, the entire holo-homodimer could be closely superposed onto each of the apo-homodimers, showing rmsd values of 1.29Å and 1.31Å, and with more notable differences in the α6 helix positions (Fig 7B).	RESULTS
106	110	rmsd	evidence	Similarly, the entire holo-homodimer could be closely superposed onto each of the apo-homodimers, showing rmsd values of 1.29Å and 1.31Å, and with more notable differences in the α6 helix positions (Fig 7B).	RESULTS
179	187	α6 helix	structure_element	Similarly, the entire holo-homodimer could be closely superposed onto each of the apo-homodimers, showing rmsd values of 1.29Å and 1.31Å, and with more notable differences in the α6 helix positions (Fig 7B).	RESULTS
20	24	rmsd	evidence	The slightly larger rmsd between the two apo-homodimers, rather than between apo- and holo-homodimers, further indicate that apo-NadR possesses a notable degree of intrinsic conformational flexibility.	RESULTS
41	44	apo	protein_state	The slightly larger rmsd between the two apo-homodimers, rather than between apo- and holo-homodimers, further indicate that apo-NadR possesses a notable degree of intrinsic conformational flexibility.	RESULTS
45	55	homodimers	oligomeric_state	The slightly larger rmsd between the two apo-homodimers, rather than between apo- and holo-homodimers, further indicate that apo-NadR possesses a notable degree of intrinsic conformational flexibility.	RESULTS
77	80	apo	protein_state	The slightly larger rmsd between the two apo-homodimers, rather than between apo- and holo-homodimers, further indicate that apo-NadR possesses a notable degree of intrinsic conformational flexibility.	RESULTS
86	90	holo	protein_state	The slightly larger rmsd between the two apo-homodimers, rather than between apo- and holo-homodimers, further indicate that apo-NadR possesses a notable degree of intrinsic conformational flexibility.	RESULTS
91	101	homodimers	oligomeric_state	The slightly larger rmsd between the two apo-homodimers, rather than between apo- and holo-homodimers, further indicate that apo-NadR possesses a notable degree of intrinsic conformational flexibility.	RESULTS
125	128	apo	protein_state	The slightly larger rmsd between the two apo-homodimers, rather than between apo- and holo-homodimers, further indicate that apo-NadR possesses a notable degree of intrinsic conformational flexibility.	RESULTS
129	133	NadR	protein	The slightly larger rmsd between the two apo-homodimers, rather than between apo- and holo-homodimers, further indicate that apo-NadR possesses a notable degree of intrinsic conformational flexibility.	RESULTS
8	11	apo	protein_state	Overall apo- and holo-NadR structures are similar.	FIG
17	21	holo	protein_state	Overall apo- and holo-NadR structures are similar.	FIG
22	26	NadR	protein	Overall apo- and holo-NadR structures are similar.	FIG
27	37	structures	evidence	Overall apo- and holo-NadR structures are similar.	FIG
5	23	Pairwise alignment	experimental_method	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
44	47	apo	protein_state	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
48	52	NadR	protein	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
53	63	homodimers	oligomeric_state	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
65	67	AB	structure_element	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
72	74	CD	structure_element	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
91	94	apo	protein_state	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
95	99	NadR	protein	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
100	108	crystals	evidence	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
114	123	Alignment	experimental_method	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
131	135	holo	protein_state	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
136	140	NadR	protein	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
141	150	homodimer	oligomeric_state	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
184	187	apo	protein_state	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
188	192	NadR	protein	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
193	203	homodimers	oligomeric_state	 (A) Pairwise alignment of the two distinct apo-NadR homodimers (AB and CD) present in the apo-NadR crystals. (B) Alignment of the holo-NadR homodimer (green and blue chains) onto the apo-NadR homodimers.	FIG
45	55	α6 helices	structure_element	Here, larger differences are observed in the α6 helices (top).	FIG
0	5	4-HPA	chemical	4-HPA stabilizes concerted conformational changes in NadR that prevent DNA-binding	RESULTS
53	57	NadR	protein	4-HPA stabilizes concerted conformational changes in NadR that prevent DNA-binding	RESULTS
60	64	NadR	protein	To further investigate the conformational rearrangements of NadR, we performed local structural alignments using only a subset of residues in the DNA-binding helix (α4).	RESULTS
79	106	local structural alignments	experimental_method	To further investigate the conformational rearrangements of NadR, we performed local structural alignments using only a subset of residues in the DNA-binding helix (α4).	RESULTS
146	163	DNA-binding helix	structure_element	To further investigate the conformational rearrangements of NadR, we performed local structural alignments using only a subset of residues in the DNA-binding helix (α4).	RESULTS
165	167	α4	structure_element	To further investigate the conformational rearrangements of NadR, we performed local structural alignments using only a subset of residues in the DNA-binding helix (α4).	RESULTS
3	12	selecting	experimental_method	By selecting and aligning residues Arg64-Ala77 of one α4 helix per dimer, superposition of the holo-homodimer onto the two apo-homodimers revealed differences in the monomer conformations of each structure.	RESULTS
17	25	aligning	experimental_method	By selecting and aligning residues Arg64-Ala77 of one α4 helix per dimer, superposition of the holo-homodimer onto the two apo-homodimers revealed differences in the monomer conformations of each structure.	RESULTS
35	46	Arg64-Ala77	residue_range	By selecting and aligning residues Arg64-Ala77 of one α4 helix per dimer, superposition of the holo-homodimer onto the two apo-homodimers revealed differences in the monomer conformations of each structure.	RESULTS
54	62	α4 helix	structure_element	By selecting and aligning residues Arg64-Ala77 of one α4 helix per dimer, superposition of the holo-homodimer onto the two apo-homodimers revealed differences in the monomer conformations of each structure.	RESULTS
67	72	dimer	oligomeric_state	By selecting and aligning residues Arg64-Ala77 of one α4 helix per dimer, superposition of the holo-homodimer onto the two apo-homodimers revealed differences in the monomer conformations of each structure.	RESULTS
74	87	superposition	experimental_method	By selecting and aligning residues Arg64-Ala77 of one α4 helix per dimer, superposition of the holo-homodimer onto the two apo-homodimers revealed differences in the monomer conformations of each structure.	RESULTS
95	99	holo	protein_state	By selecting and aligning residues Arg64-Ala77 of one α4 helix per dimer, superposition of the holo-homodimer onto the two apo-homodimers revealed differences in the monomer conformations of each structure.	RESULTS
100	109	homodimer	oligomeric_state	By selecting and aligning residues Arg64-Ala77 of one α4 helix per dimer, superposition of the holo-homodimer onto the two apo-homodimers revealed differences in the monomer conformations of each structure.	RESULTS
123	126	apo	protein_state	By selecting and aligning residues Arg64-Ala77 of one α4 helix per dimer, superposition of the holo-homodimer onto the two apo-homodimers revealed differences in the monomer conformations of each structure.	RESULTS
127	137	homodimers	oligomeric_state	By selecting and aligning residues Arg64-Ala77 of one α4 helix per dimer, superposition of the holo-homodimer onto the two apo-homodimers revealed differences in the monomer conformations of each structure.	RESULTS
166	173	monomer	oligomeric_state	By selecting and aligning residues Arg64-Ala77 of one α4 helix per dimer, superposition of the holo-homodimer onto the two apo-homodimers revealed differences in the monomer conformations of each structure.	RESULTS
196	205	structure	evidence	By selecting and aligning residues Arg64-Ala77 of one α4 helix per dimer, superposition of the holo-homodimer onto the two apo-homodimers revealed differences in the monomer conformations of each structure.	RESULTS
10	17	monomer	oligomeric_state	While one monomer from each structure was closely superimposable (Fig 8A, left side), the second monomer displayed quite large differences (Fig 8A, right side).	RESULTS
28	37	structure	evidence	While one monomer from each structure was closely superimposable (Fig 8A, left side), the second monomer displayed quite large differences (Fig 8A, right side).	RESULTS
97	104	monomer	oligomeric_state	While one monomer from each structure was closely superimposable (Fig 8A, left side), the second monomer displayed quite large differences (Fig 8A, right side).	RESULTS
34	37	DNA	chemical	Most notably, the position of the DNA-binding helix α4 shifted by as much as 6 Å (Fig 8B).	RESULTS
46	51	helix	structure_element	Most notably, the position of the DNA-binding helix α4 shifted by as much as 6 Å (Fig 8B).	RESULTS
52	54	α4	structure_element	Most notably, the position of the DNA-binding helix α4 shifted by as much as 6 Å (Fig 8B).	RESULTS
13	18	helix	structure_element	Accordingly, helix α4 was also found to be one of the most dynamic regions in previous HDX-MS analyses of apo-NadR in solution.	RESULTS
19	21	α4	structure_element	Accordingly, helix α4 was also found to be one of the most dynamic regions in previous HDX-MS analyses of apo-NadR in solution.	RESULTS
87	93	HDX-MS	experimental_method	Accordingly, helix α4 was also found to be one of the most dynamic regions in previous HDX-MS analyses of apo-NadR in solution.	RESULTS
106	109	apo	protein_state	Accordingly, helix α4 was also found to be one of the most dynamic regions in previous HDX-MS analyses of apo-NadR in solution.	RESULTS
110	114	NadR	protein	Accordingly, helix α4 was also found to be one of the most dynamic regions in previous HDX-MS analyses of apo-NadR in solution.	RESULTS
0	22	Structural comparisons	experimental_method	Structural comparisons of NadR and modelling of interactions with DNA.	FIG
26	30	NadR	protein	Structural comparisons of NadR and modelling of interactions with DNA.	FIG
66	69	DNA	chemical	Structural comparisons of NadR and modelling of interactions with DNA.	FIG
9	13	holo	protein_state	 (A) The holo-homodimer structure is shown as green and blue cartoons, for chain A and B, respectively, while the two homodimers of apo-NadR are both cyan and pale blue for chains A/C and B/D, respectively.	FIG
14	23	homodimer	oligomeric_state	 (A) The holo-homodimer structure is shown as green and blue cartoons, for chain A and B, respectively, while the two homodimers of apo-NadR are both cyan and pale blue for chains A/C and B/D, respectively.	FIG
24	33	structure	evidence	 (A) The holo-homodimer structure is shown as green and blue cartoons, for chain A and B, respectively, while the two homodimers of apo-NadR are both cyan and pale blue for chains A/C and B/D, respectively.	FIG
75	88	chain A and B	structure_element	 (A) The holo-homodimer structure is shown as green and blue cartoons, for chain A and B, respectively, while the two homodimers of apo-NadR are both cyan and pale blue for chains A/C and B/D, respectively.	FIG
118	128	homodimers	oligomeric_state	 (A) The holo-homodimer structure is shown as green and blue cartoons, for chain A and B, respectively, while the two homodimers of apo-NadR are both cyan and pale blue for chains A/C and B/D, respectively.	FIG
132	135	apo	protein_state	 (A) The holo-homodimer structure is shown as green and blue cartoons, for chain A and B, respectively, while the two homodimers of apo-NadR are both cyan and pale blue for chains A/C and B/D, respectively.	FIG
136	140	NadR	protein	 (A) The holo-homodimer structure is shown as green and blue cartoons, for chain A and B, respectively, while the two homodimers of apo-NadR are both cyan and pale blue for chains A/C and B/D, respectively.	FIG
180	183	A/C	structure_element	 (A) The holo-homodimer structure is shown as green and blue cartoons, for chain A and B, respectively, while the two homodimers of apo-NadR are both cyan and pale blue for chains A/C and B/D, respectively.	FIG
188	191	B/D	structure_element	 (A) The holo-homodimer structure is shown as green and blue cartoons, for chain A and B, respectively, while the two homodimers of apo-NadR are both cyan and pale blue for chains A/C and B/D, respectively.	FIG
10	20	homodimers	oligomeric_state	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
29	31	AB	structure_element	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
32	36	holo	protein_state	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
38	40	AB	structure_element	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
41	44	apo	protein_state	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
50	52	CD	structure_element	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
53	56	apo	protein_state	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
63	71	overlaid	experimental_method	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
75	95	structural alignment	experimental_method	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
139	146	R64-A77	residue_range	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
196	197	A	structure_element	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
198	202	holo	protein_state	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
204	205	A	structure_element	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
206	209	apo	protein_state	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
215	216	C	structure_element	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
217	220	apo	protein_state	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
235	240	helix	structure_element	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
241	243	α4	structure_element	The three homodimers (chains AB holo, AB apo, and CD apo) were overlaid by structural alignment exclusively of all heavy atoms in residues R64-A77 (shown in red, with side chain sticks) of chains A holo, A apo, and C apo, belonging to helix α4 (left).	FIG
4	14	α4 helices	structure_element	The α4 helices aligned closely, Cα rmsd 0.2Å for 14 residues.	FIG
35	39	rmsd	evidence	The α4 helices aligned closely, Cα rmsd 0.2Å for 14 residues.	FIG
34	44	α4 helices	structure_element	(B) The relative positions of the α4 helices of the 4-HPA-bound holo homodimer chain B (blue), and of apo homodimers AB and CD (showing chains B and D) in pale blue.	FIG
52	63	4-HPA-bound	protein_state	(B) The relative positions of the α4 helices of the 4-HPA-bound holo homodimer chain B (blue), and of apo homodimers AB and CD (showing chains B and D) in pale blue.	FIG
64	68	holo	protein_state	(B) The relative positions of the α4 helices of the 4-HPA-bound holo homodimer chain B (blue), and of apo homodimers AB and CD (showing chains B and D) in pale blue.	FIG
69	78	homodimer	oligomeric_state	(B) The relative positions of the α4 helices of the 4-HPA-bound holo homodimer chain B (blue), and of apo homodimers AB and CD (showing chains B and D) in pale blue.	FIG
79	86	chain B	structure_element	(B) The relative positions of the α4 helices of the 4-HPA-bound holo homodimer chain B (blue), and of apo homodimers AB and CD (showing chains B and D) in pale blue.	FIG
102	105	apo	protein_state	(B) The relative positions of the α4 helices of the 4-HPA-bound holo homodimer chain B (blue), and of apo homodimers AB and CD (showing chains B and D) in pale blue.	FIG
106	116	homodimers	oligomeric_state	(B) The relative positions of the α4 helices of the 4-HPA-bound holo homodimer chain B (blue), and of apo homodimers AB and CD (showing chains B and D) in pale blue.	FIG
117	119	AB	structure_element	(B) The relative positions of the α4 helices of the 4-HPA-bound holo homodimer chain B (blue), and of apo homodimers AB and CD (showing chains B and D) in pale blue.	FIG
124	126	CD	structure_element	(B) The relative positions of the α4 helices of the 4-HPA-bound holo homodimer chain B (blue), and of apo homodimers AB and CD (showing chains B and D) in pale blue.	FIG
136	150	chains B and D	structure_element	(B) The relative positions of the α4 helices of the 4-HPA-bound holo homodimer chain B (blue), and of apo homodimers AB and CD (showing chains B and D) in pale blue.	FIG
20	25	Ala77	residue_name_number	Dashes indicate the Ala77 Cα atoms, in the most highly shifted region of the ‘non-fixed’ α4 helix.	FIG
89	97	α4 helix	structure_element	Dashes indicate the Ala77 Cα atoms, in the most highly shifted region of the ‘non-fixed’ α4 helix.	FIG
24	27	DNA	chemical	(C) The double-stranded DNA molecule (grey cartoon) from the OhrR-ohrA complex is shown after superposition with NadR, to highlight the expected positions of the NadR α4 helices in the DNA major grooves.	FIG
61	70	OhrR-ohrA	complex_assembly	(C) The double-stranded DNA molecule (grey cartoon) from the OhrR-ohrA complex is shown after superposition with NadR, to highlight the expected positions of the NadR α4 helices in the DNA major grooves.	FIG
94	107	superposition	experimental_method	(C) The double-stranded DNA molecule (grey cartoon) from the OhrR-ohrA complex is shown after superposition with NadR, to highlight the expected positions of the NadR α4 helices in the DNA major grooves.	FIG
113	117	NadR	protein	(C) The double-stranded DNA molecule (grey cartoon) from the OhrR-ohrA complex is shown after superposition with NadR, to highlight the expected positions of the NadR α4 helices in the DNA major grooves.	FIG
162	166	NadR	protein	(C) The double-stranded DNA molecule (grey cartoon) from the OhrR-ohrA complex is shown after superposition with NadR, to highlight the expected positions of the NadR α4 helices in the DNA major grooves.	FIG
167	177	α4 helices	structure_element	(C) The double-stranded DNA molecule (grey cartoon) from the OhrR-ohrA complex is shown after superposition with NadR, to highlight the expected positions of the NadR α4 helices in the DNA major grooves.	FIG
185	188	DNA	chemical	(C) The double-stranded DNA molecule (grey cartoon) from the OhrR-ohrA complex is shown after superposition with NadR, to highlight the expected positions of the NadR α4 helices in the DNA major grooves.	FIG
22	32	α4 helices	structure_element	For clarity, only the α4 helices are shown in panels (B) and (C). (D) Upon comparison with the experimentally-determined OhrR:ohrA structure (grey), the α4 helix of holo-NadR (blue) is shifted ~8Å out of the major groove.	FIG
121	130	OhrR:ohrA	complex_assembly	For clarity, only the α4 helices are shown in panels (B) and (C). (D) Upon comparison with the experimentally-determined OhrR:ohrA structure (grey), the α4 helix of holo-NadR (blue) is shifted ~8Å out of the major groove.	FIG
131	140	structure	evidence	For clarity, only the α4 helices are shown in panels (B) and (C). (D) Upon comparison with the experimentally-determined OhrR:ohrA structure (grey), the α4 helix of holo-NadR (blue) is shifted ~8Å out of the major groove.	FIG
153	161	α4 helix	structure_element	For clarity, only the α4 helices are shown in panels (B) and (C). (D) Upon comparison with the experimentally-determined OhrR:ohrA structure (grey), the α4 helix of holo-NadR (blue) is shifted ~8Å out of the major groove.	FIG
165	169	holo	protein_state	For clarity, only the α4 helices are shown in panels (B) and (C). (D) Upon comparison with the experimentally-determined OhrR:ohrA structure (grey), the α4 helix of holo-NadR (blue) is shifted ~8Å out of the major groove.	FIG
170	174	NadR	protein	For clarity, only the α4 helices are shown in panels (B) and (C). (D) Upon comparison with the experimentally-determined OhrR:ohrA structure (grey), the α4 helix of holo-NadR (blue) is shifted ~8Å out of the major groove.	FIG
9	31	structural comparisons	experimental_method	However, structural comparisons revealed that the shift of holo-NadR helix α4 induced by the presence of 4-HPA was also accompanied by several changes at the holo dimer interface, while such extensive structural differences were not observed in the apo dimer interfaces, particularly notable when comparing the α6 helices (S3 Fig).	RESULTS
59	63	holo	protein_state	However, structural comparisons revealed that the shift of holo-NadR helix α4 induced by the presence of 4-HPA was also accompanied by several changes at the holo dimer interface, while such extensive structural differences were not observed in the apo dimer interfaces, particularly notable when comparing the α6 helices (S3 Fig).	RESULTS
64	68	NadR	protein	However, structural comparisons revealed that the shift of holo-NadR helix α4 induced by the presence of 4-HPA was also accompanied by several changes at the holo dimer interface, while such extensive structural differences were not observed in the apo dimer interfaces, particularly notable when comparing the α6 helices (S3 Fig).	RESULTS
69	74	helix	structure_element	However, structural comparisons revealed that the shift of holo-NadR helix α4 induced by the presence of 4-HPA was also accompanied by several changes at the holo dimer interface, while such extensive structural differences were not observed in the apo dimer interfaces, particularly notable when comparing the α6 helices (S3 Fig).	RESULTS
75	77	α4	structure_element	However, structural comparisons revealed that the shift of holo-NadR helix α4 induced by the presence of 4-HPA was also accompanied by several changes at the holo dimer interface, while such extensive structural differences were not observed in the apo dimer interfaces, particularly notable when comparing the α6 helices (S3 Fig).	RESULTS
93	104	presence of	protein_state	However, structural comparisons revealed that the shift of holo-NadR helix α4 induced by the presence of 4-HPA was also accompanied by several changes at the holo dimer interface, while such extensive structural differences were not observed in the apo dimer interfaces, particularly notable when comparing the α6 helices (S3 Fig).	RESULTS
105	110	4-HPA	chemical	However, structural comparisons revealed that the shift of holo-NadR helix α4 induced by the presence of 4-HPA was also accompanied by several changes at the holo dimer interface, while such extensive structural differences were not observed in the apo dimer interfaces, particularly notable when comparing the α6 helices (S3 Fig).	RESULTS
158	162	holo	protein_state	However, structural comparisons revealed that the shift of holo-NadR helix α4 induced by the presence of 4-HPA was also accompanied by several changes at the holo dimer interface, while such extensive structural differences were not observed in the apo dimer interfaces, particularly notable when comparing the α6 helices (S3 Fig).	RESULTS
163	178	dimer interface	site	However, structural comparisons revealed that the shift of holo-NadR helix α4 induced by the presence of 4-HPA was also accompanied by several changes at the holo dimer interface, while such extensive structural differences were not observed in the apo dimer interfaces, particularly notable when comparing the α6 helices (S3 Fig).	RESULTS
249	252	apo	protein_state	However, structural comparisons revealed that the shift of holo-NadR helix α4 induced by the presence of 4-HPA was also accompanied by several changes at the holo dimer interface, while such extensive structural differences were not observed in the apo dimer interfaces, particularly notable when comparing the α6 helices (S3 Fig).	RESULTS
253	269	dimer interfaces	site	However, structural comparisons revealed that the shift of holo-NadR helix α4 induced by the presence of 4-HPA was also accompanied by several changes at the holo dimer interface, while such extensive structural differences were not observed in the apo dimer interfaces, particularly notable when comparing the α6 helices (S3 Fig).	RESULTS
311	321	α6 helices	structure_element	However, structural comparisons revealed that the shift of holo-NadR helix α4 induced by the presence of 4-HPA was also accompanied by several changes at the holo dimer interface, while such extensive structural differences were not observed in the apo dimer interfaces, particularly notable when comparing the α6 helices (S3 Fig).	RESULTS
24	41	ligand-stabilized	protein_state	In summary, compared to ligand-stabilized holo-NadR, apo-NadR displayed an intrinsic flexibility focused in the DNA-binding region.	RESULTS
42	46	holo	protein_state	In summary, compared to ligand-stabilized holo-NadR, apo-NadR displayed an intrinsic flexibility focused in the DNA-binding region.	RESULTS
47	51	NadR	protein	In summary, compared to ligand-stabilized holo-NadR, apo-NadR displayed an intrinsic flexibility focused in the DNA-binding region.	RESULTS
53	56	apo	protein_state	In summary, compared to ligand-stabilized holo-NadR, apo-NadR displayed an intrinsic flexibility focused in the DNA-binding region.	RESULTS
57	61	NadR	protein	In summary, compared to ligand-stabilized holo-NadR, apo-NadR displayed an intrinsic flexibility focused in the DNA-binding region.	RESULTS
112	130	DNA-binding region	site	In summary, compared to ligand-stabilized holo-NadR, apo-NadR displayed an intrinsic flexibility focused in the DNA-binding region.	RESULTS
70	86	electron density	evidence	This was also evident in the greater disorder (i.e. less well-defined electron density) in the β1-β2 loops of the apo dimers (density for 16 residues per dimer was missing) compared to the holo dimer (density for only 3 residues was missing).	RESULTS
95	106	β1-β2 loops	structure_element	This was also evident in the greater disorder (i.e. less well-defined electron density) in the β1-β2 loops of the apo dimers (density for 16 residues per dimer was missing) compared to the holo dimer (density for only 3 residues was missing).	RESULTS
114	117	apo	protein_state	This was also evident in the greater disorder (i.e. less well-defined electron density) in the β1-β2 loops of the apo dimers (density for 16 residues per dimer was missing) compared to the holo dimer (density for only 3 residues was missing).	RESULTS
118	124	dimers	oligomeric_state	This was also evident in the greater disorder (i.e. less well-defined electron density) in the β1-β2 loops of the apo dimers (density for 16 residues per dimer was missing) compared to the holo dimer (density for only 3 residues was missing).	RESULTS
126	133	density	evidence	This was also evident in the greater disorder (i.e. less well-defined electron density) in the β1-β2 loops of the apo dimers (density for 16 residues per dimer was missing) compared to the holo dimer (density for only 3 residues was missing).	RESULTS
154	159	dimer	oligomeric_state	This was also evident in the greater disorder (i.e. less well-defined electron density) in the β1-β2 loops of the apo dimers (density for 16 residues per dimer was missing) compared to the holo dimer (density for only 3 residues was missing).	RESULTS
189	193	holo	protein_state	This was also evident in the greater disorder (i.e. less well-defined electron density) in the β1-β2 loops of the apo dimers (density for 16 residues per dimer was missing) compared to the holo dimer (density for only 3 residues was missing).	RESULTS
194	199	dimer	oligomeric_state	This was also evident in the greater disorder (i.e. less well-defined electron density) in the β1-β2 loops of the apo dimers (density for 16 residues per dimer was missing) compared to the holo dimer (density for only 3 residues was missing).	RESULTS
201	208	density	evidence	This was also evident in the greater disorder (i.e. less well-defined electron density) in the β1-β2 loops of the apo dimers (density for 16 residues per dimer was missing) compared to the holo dimer (density for only 3 residues was missing).	RESULTS
3	7	holo	protein_state	In holo-NadR, the distance separating the two DNA-binding α4 helices was 32 Å, while in apo-NadR it was 29 Å for homodimer AB, and 34 Å for homodimer CD (Fig 8C).	RESULTS
8	12	NadR	protein	In holo-NadR, the distance separating the two DNA-binding α4 helices was 32 Å, while in apo-NadR it was 29 Å for homodimer AB, and 34 Å for homodimer CD (Fig 8C).	RESULTS
58	68	α4 helices	structure_element	In holo-NadR, the distance separating the two DNA-binding α4 helices was 32 Å, while in apo-NadR it was 29 Å for homodimer AB, and 34 Å for homodimer CD (Fig 8C).	RESULTS
88	91	apo	protein_state	In holo-NadR, the distance separating the two DNA-binding α4 helices was 32 Å, while in apo-NadR it was 29 Å for homodimer AB, and 34 Å for homodimer CD (Fig 8C).	RESULTS
92	96	NadR	protein	In holo-NadR, the distance separating the two DNA-binding α4 helices was 32 Å, while in apo-NadR it was 29 Å for homodimer AB, and 34 Å for homodimer CD (Fig 8C).	RESULTS
113	122	homodimer	oligomeric_state	In holo-NadR, the distance separating the two DNA-binding α4 helices was 32 Å, while in apo-NadR it was 29 Å for homodimer AB, and 34 Å for homodimer CD (Fig 8C).	RESULTS
123	125	AB	structure_element	In holo-NadR, the distance separating the two DNA-binding α4 helices was 32 Å, while in apo-NadR it was 29 Å for homodimer AB, and 34 Å for homodimer CD (Fig 8C).	RESULTS
140	149	homodimer	oligomeric_state	In holo-NadR, the distance separating the two DNA-binding α4 helices was 32 Å, while in apo-NadR it was 29 Å for homodimer AB, and 34 Å for homodimer CD (Fig 8C).	RESULTS
150	152	CD	structure_element	In holo-NadR, the distance separating the two DNA-binding α4 helices was 32 Å, while in apo-NadR it was 29 Å for homodimer AB, and 34 Å for homodimer CD (Fig 8C).	RESULTS
10	13	apo	protein_state	Thus, the apo-homodimer AB presented the DNA-binding helices in a conformation similar to that observed in the protein:DNA complex of OhrR:ohrA from Bacillus subtilis (Fig 8C).	RESULTS
14	23	homodimer	oligomeric_state	Thus, the apo-homodimer AB presented the DNA-binding helices in a conformation similar to that observed in the protein:DNA complex of OhrR:ohrA from Bacillus subtilis (Fig 8C).	RESULTS
24	26	AB	structure_element	Thus, the apo-homodimer AB presented the DNA-binding helices in a conformation similar to that observed in the protein:DNA complex of OhrR:ohrA from Bacillus subtilis (Fig 8C).	RESULTS
41	60	DNA-binding helices	structure_element	Thus, the apo-homodimer AB presented the DNA-binding helices in a conformation similar to that observed in the protein:DNA complex of OhrR:ohrA from Bacillus subtilis (Fig 8C).	RESULTS
134	143	OhrR:ohrA	complex_assembly	Thus, the apo-homodimer AB presented the DNA-binding helices in a conformation similar to that observed in the protein:DNA complex of OhrR:ohrA from Bacillus subtilis (Fig 8C).	RESULTS
149	166	Bacillus subtilis	species	Thus, the apo-homodimer AB presented the DNA-binding helices in a conformation similar to that observed in the protein:DNA complex of OhrR:ohrA from Bacillus subtilis (Fig 8C).	RESULTS
15	19	OhrR	protein	Interestingly, OhrR contacts ohrA across 22 base pairs (bp), and similarly the main NadR target sites identified in the nadA promoter (the operators Op I and Op II) both span 22 bp.	RESULTS
29	33	ohrA	gene	Interestingly, OhrR contacts ohrA across 22 base pairs (bp), and similarly the main NadR target sites identified in the nadA promoter (the operators Op I and Op II) both span 22 bp.	RESULTS
84	88	NadR	protein	Interestingly, OhrR contacts ohrA across 22 base pairs (bp), and similarly the main NadR target sites identified in the nadA promoter (the operators Op I and Op II) both span 22 bp.	RESULTS
89	101	target sites	site	Interestingly, OhrR contacts ohrA across 22 base pairs (bp), and similarly the main NadR target sites identified in the nadA promoter (the operators Op I and Op II) both span 22 bp.	RESULTS
120	124	nadA	gene	Interestingly, OhrR contacts ohrA across 22 base pairs (bp), and similarly the main NadR target sites identified in the nadA promoter (the operators Op I and Op II) both span 22 bp.	RESULTS
0	23	Pairwise superpositions	experimental_method	Pairwise superpositions showed that the NadR apo-homodimer AB was the most similar to OhrR (rmsd 2.6 Å), while the holo-homodimer was the most divergent (rmsd 3.3 Å) (Fig 8C).	RESULTS
40	44	NadR	protein	Pairwise superpositions showed that the NadR apo-homodimer AB was the most similar to OhrR (rmsd 2.6 Å), while the holo-homodimer was the most divergent (rmsd 3.3 Å) (Fig 8C).	RESULTS
45	48	apo	protein_state	Pairwise superpositions showed that the NadR apo-homodimer AB was the most similar to OhrR (rmsd 2.6 Å), while the holo-homodimer was the most divergent (rmsd 3.3 Å) (Fig 8C).	RESULTS
49	58	homodimer	oligomeric_state	Pairwise superpositions showed that the NadR apo-homodimer AB was the most similar to OhrR (rmsd 2.6 Å), while the holo-homodimer was the most divergent (rmsd 3.3 Å) (Fig 8C).	RESULTS
59	61	AB	structure_element	Pairwise superpositions showed that the NadR apo-homodimer AB was the most similar to OhrR (rmsd 2.6 Å), while the holo-homodimer was the most divergent (rmsd 3.3 Å) (Fig 8C).	RESULTS
86	90	OhrR	protein	Pairwise superpositions showed that the NadR apo-homodimer AB was the most similar to OhrR (rmsd 2.6 Å), while the holo-homodimer was the most divergent (rmsd 3.3 Å) (Fig 8C).	RESULTS
92	96	rmsd	evidence	Pairwise superpositions showed that the NadR apo-homodimer AB was the most similar to OhrR (rmsd 2.6 Å), while the holo-homodimer was the most divergent (rmsd 3.3 Å) (Fig 8C).	RESULTS
115	119	holo	protein_state	Pairwise superpositions showed that the NadR apo-homodimer AB was the most similar to OhrR (rmsd 2.6 Å), while the holo-homodimer was the most divergent (rmsd 3.3 Å) (Fig 8C).	RESULTS
120	129	homodimer	oligomeric_state	Pairwise superpositions showed that the NadR apo-homodimer AB was the most similar to OhrR (rmsd 2.6 Å), while the holo-homodimer was the most divergent (rmsd 3.3 Å) (Fig 8C).	RESULTS
154	158	rmsd	evidence	Pairwise superpositions showed that the NadR apo-homodimer AB was the most similar to OhrR (rmsd 2.6 Å), while the holo-homodimer was the most divergent (rmsd 3.3 Å) (Fig 8C).	RESULTS
18	21	DNA	chemical	Assuming the same DNA-binding mechanism is used by OhrR and NadR, the apo-homodimer AB seems ideally pre-configured for DNA binding, while 4-HPA appeared to stabilize holo-NadR in a conformation poorly suited for DNA binding.	RESULTS
51	55	OhrR	protein	Assuming the same DNA-binding mechanism is used by OhrR and NadR, the apo-homodimer AB seems ideally pre-configured for DNA binding, while 4-HPA appeared to stabilize holo-NadR in a conformation poorly suited for DNA binding.	RESULTS
60	64	NadR	protein	Assuming the same DNA-binding mechanism is used by OhrR and NadR, the apo-homodimer AB seems ideally pre-configured for DNA binding, while 4-HPA appeared to stabilize holo-NadR in a conformation poorly suited for DNA binding.	RESULTS
70	73	apo	protein_state	Assuming the same DNA-binding mechanism is used by OhrR and NadR, the apo-homodimer AB seems ideally pre-configured for DNA binding, while 4-HPA appeared to stabilize holo-NadR in a conformation poorly suited for DNA binding.	RESULTS
74	83	homodimer	oligomeric_state	Assuming the same DNA-binding mechanism is used by OhrR and NadR, the apo-homodimer AB seems ideally pre-configured for DNA binding, while 4-HPA appeared to stabilize holo-NadR in a conformation poorly suited for DNA binding.	RESULTS
84	86	AB	structure_element	Assuming the same DNA-binding mechanism is used by OhrR and NadR, the apo-homodimer AB seems ideally pre-configured for DNA binding, while 4-HPA appeared to stabilize holo-NadR in a conformation poorly suited for DNA binding.	RESULTS
120	123	DNA	chemical	Assuming the same DNA-binding mechanism is used by OhrR and NadR, the apo-homodimer AB seems ideally pre-configured for DNA binding, while 4-HPA appeared to stabilize holo-NadR in a conformation poorly suited for DNA binding.	RESULTS
139	144	4-HPA	chemical	Assuming the same DNA-binding mechanism is used by OhrR and NadR, the apo-homodimer AB seems ideally pre-configured for DNA binding, while 4-HPA appeared to stabilize holo-NadR in a conformation poorly suited for DNA binding.	RESULTS
167	171	holo	protein_state	Assuming the same DNA-binding mechanism is used by OhrR and NadR, the apo-homodimer AB seems ideally pre-configured for DNA binding, while 4-HPA appeared to stabilize holo-NadR in a conformation poorly suited for DNA binding.	RESULTS
172	176	NadR	protein	Assuming the same DNA-binding mechanism is used by OhrR and NadR, the apo-homodimer AB seems ideally pre-configured for DNA binding, while 4-HPA appeared to stabilize holo-NadR in a conformation poorly suited for DNA binding.	RESULTS
213	216	DNA	chemical	Assuming the same DNA-binding mechanism is used by OhrR and NadR, the apo-homodimer AB seems ideally pre-configured for DNA binding, while 4-HPA appeared to stabilize holo-NadR in a conformation poorly suited for DNA binding.	RESULTS
43	80	inter-helical translational distances	evidence	Specifically, in addition to the different inter-helical translational distances, the α4 helices in the holo-NadR homodimer were also reoriented, resulting in movement of α4 out of the major groove, by up to 8Å, and presumably preventing efficient DNA binding in the presence of 4-HPA (Fig 8D).	RESULTS
86	96	α4 helices	structure_element	Specifically, in addition to the different inter-helical translational distances, the α4 helices in the holo-NadR homodimer were also reoriented, resulting in movement of α4 out of the major groove, by up to 8Å, and presumably preventing efficient DNA binding in the presence of 4-HPA (Fig 8D).	RESULTS
104	108	holo	protein_state	Specifically, in addition to the different inter-helical translational distances, the α4 helices in the holo-NadR homodimer were also reoriented, resulting in movement of α4 out of the major groove, by up to 8Å, and presumably preventing efficient DNA binding in the presence of 4-HPA (Fig 8D).	RESULTS
109	113	NadR	protein	Specifically, in addition to the different inter-helical translational distances, the α4 helices in the holo-NadR homodimer were also reoriented, resulting in movement of α4 out of the major groove, by up to 8Å, and presumably preventing efficient DNA binding in the presence of 4-HPA (Fig 8D).	RESULTS
114	123	homodimer	oligomeric_state	Specifically, in addition to the different inter-helical translational distances, the α4 helices in the holo-NadR homodimer were also reoriented, resulting in movement of α4 out of the major groove, by up to 8Å, and presumably preventing efficient DNA binding in the presence of 4-HPA (Fig 8D).	RESULTS
171	173	α4	structure_element	Specifically, in addition to the different inter-helical translational distances, the α4 helices in the holo-NadR homodimer were also reoriented, resulting in movement of α4 out of the major groove, by up to 8Å, and presumably preventing efficient DNA binding in the presence of 4-HPA (Fig 8D).	RESULTS
248	251	DNA	chemical	Specifically, in addition to the different inter-helical translational distances, the α4 helices in the holo-NadR homodimer were also reoriented, resulting in movement of α4 out of the major groove, by up to 8Å, and presumably preventing efficient DNA binding in the presence of 4-HPA (Fig 8D).	RESULTS
279	284	4-HPA	chemical	Specifically, in addition to the different inter-helical translational distances, the α4 helices in the holo-NadR homodimer were also reoriented, resulting in movement of α4 out of the major groove, by up to 8Å, and presumably preventing efficient DNA binding in the presence of 4-HPA (Fig 8D).	RESULTS
5	12	aligned	experimental_method	When aligned with OhrR, the apo-homodimer CD presented yet another different intermediate conformation (rmsd 2.9Å), apparently not ideally pre-configured for DNA binding, but which in solution can presumably readily adopt the AB conformation due to the intrinsic flexibility described above.	RESULTS
18	22	OhrR	protein	When aligned with OhrR, the apo-homodimer CD presented yet another different intermediate conformation (rmsd 2.9Å), apparently not ideally pre-configured for DNA binding, but which in solution can presumably readily adopt the AB conformation due to the intrinsic flexibility described above.	RESULTS
28	31	apo	protein_state	When aligned with OhrR, the apo-homodimer CD presented yet another different intermediate conformation (rmsd 2.9Å), apparently not ideally pre-configured for DNA binding, but which in solution can presumably readily adopt the AB conformation due to the intrinsic flexibility described above.	RESULTS
32	41	homodimer	oligomeric_state	When aligned with OhrR, the apo-homodimer CD presented yet another different intermediate conformation (rmsd 2.9Å), apparently not ideally pre-configured for DNA binding, but which in solution can presumably readily adopt the AB conformation due to the intrinsic flexibility described above.	RESULTS
42	44	CD	structure_element	When aligned with OhrR, the apo-homodimer CD presented yet another different intermediate conformation (rmsd 2.9Å), apparently not ideally pre-configured for DNA binding, but which in solution can presumably readily adopt the AB conformation due to the intrinsic flexibility described above.	RESULTS
104	108	rmsd	evidence	When aligned with OhrR, the apo-homodimer CD presented yet another different intermediate conformation (rmsd 2.9Å), apparently not ideally pre-configured for DNA binding, but which in solution can presumably readily adopt the AB conformation due to the intrinsic flexibility described above.	RESULTS
158	161	DNA	chemical	When aligned with OhrR, the apo-homodimer CD presented yet another different intermediate conformation (rmsd 2.9Å), apparently not ideally pre-configured for DNA binding, but which in solution can presumably readily adopt the AB conformation due to the intrinsic flexibility described above.	RESULTS
226	228	AB	structure_element	When aligned with OhrR, the apo-homodimer CD presented yet another different intermediate conformation (rmsd 2.9Å), apparently not ideally pre-configured for DNA binding, but which in solution can presumably readily adopt the AB conformation due to the intrinsic flexibility described above.	RESULTS
0	4	NadR	protein	NadR residues His7, Ser9, Asn11 and Phe25 are essential for regulation of NadA expression in vivo	RESULTS
14	18	His7	residue_name_number	NadR residues His7, Ser9, Asn11 and Phe25 are essential for regulation of NadA expression in vivo	RESULTS
20	24	Ser9	residue_name_number	NadR residues His7, Ser9, Asn11 and Phe25 are essential for regulation of NadA expression in vivo	RESULTS
26	31	Asn11	residue_name_number	NadR residues His7, Ser9, Asn11 and Phe25 are essential for regulation of NadA expression in vivo	RESULTS
36	41	Phe25	residue_name_number	NadR residues His7, Ser9, Asn11 and Phe25 are essential for regulation of NadA expression in vivo	RESULTS
74	78	NadA	protein	NadR residues His7, Ser9, Asn11 and Phe25 are essential for regulation of NadA expression in vivo	RESULTS
74	78	NadR	protein	While previous studies had correctly suggested the involvement of several NadR residues in ligand binding, the crystal structures presented here revealed additional residues with previously unknown roles in dimerization and/or binding to 4-HPA.	RESULTS
111	129	crystal structures	evidence	While previous studies had correctly suggested the involvement of several NadR residues in ligand binding, the crystal structures presented here revealed additional residues with previously unknown roles in dimerization and/or binding to 4-HPA.	RESULTS
238	243	4-HPA	chemical	While previous studies had correctly suggested the involvement of several NadR residues in ligand binding, the crystal structures presented here revealed additional residues with previously unknown roles in dimerization and/or binding to 4-HPA.	RESULTS
99	103	NadR	protein	To explore the functional involvement of these residues, we characterized the behavior of four new NadR mutants (H7A, S9A, N11A and F25A) in an in vivo assay using the previously described MC58-Δ1843 nadR-null mutant strain, which was complemented either by wild-type nadR or by the nadR mutants.	RESULTS
113	116	H7A	mutant	To explore the functional involvement of these residues, we characterized the behavior of four new NadR mutants (H7A, S9A, N11A and F25A) in an in vivo assay using the previously described MC58-Δ1843 nadR-null mutant strain, which was complemented either by wild-type nadR or by the nadR mutants.	RESULTS
118	121	S9A	mutant	To explore the functional involvement of these residues, we characterized the behavior of four new NadR mutants (H7A, S9A, N11A and F25A) in an in vivo assay using the previously described MC58-Δ1843 nadR-null mutant strain, which was complemented either by wild-type nadR or by the nadR mutants.	RESULTS
123	127	N11A	mutant	To explore the functional involvement of these residues, we characterized the behavior of four new NadR mutants (H7A, S9A, N11A and F25A) in an in vivo assay using the previously described MC58-Δ1843 nadR-null mutant strain, which was complemented either by wild-type nadR or by the nadR mutants.	RESULTS
132	136	F25A	mutant	To explore the functional involvement of these residues, we characterized the behavior of four new NadR mutants (H7A, S9A, N11A and F25A) in an in vivo assay using the previously described MC58-Δ1843 nadR-null mutant strain, which was complemented either by wild-type nadR or by the nadR mutants.	RESULTS
189	199	MC58-Δ1843	mutant	To explore the functional involvement of these residues, we characterized the behavior of four new NadR mutants (H7A, S9A, N11A and F25A) in an in vivo assay using the previously described MC58-Δ1843 nadR-null mutant strain, which was complemented either by wild-type nadR or by the nadR mutants.	RESULTS
200	204	nadR	gene	To explore the functional involvement of these residues, we characterized the behavior of four new NadR mutants (H7A, S9A, N11A and F25A) in an in vivo assay using the previously described MC58-Δ1843 nadR-null mutant strain, which was complemented either by wild-type nadR or by the nadR mutants.	RESULTS
210	216	mutant	protein_state	To explore the functional involvement of these residues, we characterized the behavior of four new NadR mutants (H7A, S9A, N11A and F25A) in an in vivo assay using the previously described MC58-Δ1843 nadR-null mutant strain, which was complemented either by wild-type nadR or by the nadR mutants.	RESULTS
258	267	wild-type	protein_state	To explore the functional involvement of these residues, we characterized the behavior of four new NadR mutants (H7A, S9A, N11A and F25A) in an in vivo assay using the previously described MC58-Δ1843 nadR-null mutant strain, which was complemented either by wild-type nadR or by the nadR mutants.	RESULTS
268	272	nadR	gene	To explore the functional involvement of these residues, we characterized the behavior of four new NadR mutants (H7A, S9A, N11A and F25A) in an in vivo assay using the previously described MC58-Δ1843 nadR-null mutant strain, which was complemented either by wild-type nadR or by the nadR mutants.	RESULTS
283	287	nadR	gene	To explore the functional involvement of these residues, we characterized the behavior of four new NadR mutants (H7A, S9A, N11A and F25A) in an in vivo assay using the previously described MC58-Δ1843 nadR-null mutant strain, which was complemented either by wild-type nadR or by the nadR mutants.	RESULTS
288	295	mutants	protein_state	To explore the functional involvement of these residues, we characterized the behavior of four new NadR mutants (H7A, S9A, N11A and F25A) in an in vivo assay using the previously described MC58-Δ1843 nadR-null mutant strain, which was complemented either by wild-type nadR or by the nadR mutants.	RESULTS
0	4	NadA	protein	NadA protein abundance levels were assessed by Western blotting to evaluate the ability of the NadR mutants to repress the nadA promoter, in the presence or absence of 4-HPA.	RESULTS
47	63	Western blotting	experimental_method	NadA protein abundance levels were assessed by Western blotting to evaluate the ability of the NadR mutants to repress the nadA promoter, in the presence or absence of 4-HPA.	RESULTS
95	99	NadR	protein	NadA protein abundance levels were assessed by Western blotting to evaluate the ability of the NadR mutants to repress the nadA promoter, in the presence or absence of 4-HPA.	RESULTS
100	107	mutants	protein_state	NadA protein abundance levels were assessed by Western blotting to evaluate the ability of the NadR mutants to repress the nadA promoter, in the presence or absence of 4-HPA.	RESULTS
123	127	nadA	gene	NadA protein abundance levels were assessed by Western blotting to evaluate the ability of the NadR mutants to repress the nadA promoter, in the presence or absence of 4-HPA.	RESULTS
168	173	4-HPA	chemical	NadA protein abundance levels were assessed by Western blotting to evaluate the ability of the NadR mutants to repress the nadA promoter, in the presence or absence of 4-HPA.	RESULTS
4	8	nadR	gene	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
9	12	H7A	mutant	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
14	17	S9A	mutant	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
22	26	F25A	mutant	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
75	79	nadA	gene	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
129	133	nadA	gene	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
160	164	NadR	protein	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
165	167	WT	protein_state	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
214	219	4-HPA	chemical	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
248	257	wild-type	protein_state	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
258	262	nadR	gene	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
294	298	NadA	protein	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
323	328	4-HPA	chemical	The nadR H7A, S9A and F25A complemented strains showed hyper-repression of nadA expression in vivo, i.e. these mutants repressed nadA more efficiently than the NadR WT protein, either in the presence or absence of 4-HPA, while complementation with wild-type nadR resulted in high production of NadA only in the presence of 4-HPA (Fig 9).	RESULTS
40	44	nadR	gene	Interestingly, and on the contrary, the nadR N11A complemented strain showed hypo-repression (i.e. exhibited high expression of nadA both in absence and presence of 4-HPA).	RESULTS
45	49	N11A	mutant	Interestingly, and on the contrary, the nadR N11A complemented strain showed hypo-repression (i.e. exhibited high expression of nadA both in absence and presence of 4-HPA).	RESULTS
128	132	nadA	gene	Interestingly, and on the contrary, the nadR N11A complemented strain showed hypo-repression (i.e. exhibited high expression of nadA both in absence and presence of 4-HPA).	RESULTS
165	170	4-HPA	chemical	Interestingly, and on the contrary, the nadR N11A complemented strain showed hypo-repression (i.e. exhibited high expression of nadA both in absence and presence of 4-HPA).	RESULTS
5	16	mutagenesis	experimental_method	This mutagenesis data revealed that NadR residues His7, Ser9, Asn11 and Phe25 play key roles in the ligand-mediated regulation of NadR; they are each involved in the controlled de-repression of the nadA promoter and synthesis of NadA in response to 4-HPA in vivo.	RESULTS
36	40	NadR	protein	This mutagenesis data revealed that NadR residues His7, Ser9, Asn11 and Phe25 play key roles in the ligand-mediated regulation of NadR; they are each involved in the controlled de-repression of the nadA promoter and synthesis of NadA in response to 4-HPA in vivo.	RESULTS
50	54	His7	residue_name_number	This mutagenesis data revealed that NadR residues His7, Ser9, Asn11 and Phe25 play key roles in the ligand-mediated regulation of NadR; they are each involved in the controlled de-repression of the nadA promoter and synthesis of NadA in response to 4-HPA in vivo.	RESULTS
56	60	Ser9	residue_name_number	This mutagenesis data revealed that NadR residues His7, Ser9, Asn11 and Phe25 play key roles in the ligand-mediated regulation of NadR; they are each involved in the controlled de-repression of the nadA promoter and synthesis of NadA in response to 4-HPA in vivo.	RESULTS
62	67	Asn11	residue_name_number	This mutagenesis data revealed that NadR residues His7, Ser9, Asn11 and Phe25 play key roles in the ligand-mediated regulation of NadR; they are each involved in the controlled de-repression of the nadA promoter and synthesis of NadA in response to 4-HPA in vivo.	RESULTS
72	77	Phe25	residue_name_number	This mutagenesis data revealed that NadR residues His7, Ser9, Asn11 and Phe25 play key roles in the ligand-mediated regulation of NadR; they are each involved in the controlled de-repression of the nadA promoter and synthesis of NadA in response to 4-HPA in vivo.	RESULTS
130	134	NadR	protein	This mutagenesis data revealed that NadR residues His7, Ser9, Asn11 and Phe25 play key roles in the ligand-mediated regulation of NadR; they are each involved in the controlled de-repression of the nadA promoter and synthesis of NadA in response to 4-HPA in vivo.	RESULTS
198	202	nadA	gene	This mutagenesis data revealed that NadR residues His7, Ser9, Asn11 and Phe25 play key roles in the ligand-mediated regulation of NadR; they are each involved in the controlled de-repression of the nadA promoter and synthesis of NadA in response to 4-HPA in vivo.	RESULTS
229	233	NadA	protein	This mutagenesis data revealed that NadR residues His7, Ser9, Asn11 and Phe25 play key roles in the ligand-mediated regulation of NadR; they are each involved in the controlled de-repression of the nadA promoter and synthesis of NadA in response to 4-HPA in vivo.	RESULTS
249	254	4-HPA	chemical	This mutagenesis data revealed that NadR residues His7, Ser9, Asn11 and Phe25 play key roles in the ligand-mediated regulation of NadR; they are each involved in the controlled de-repression of the nadA promoter and synthesis of NadA in response to 4-HPA in vivo.	RESULTS
0	31	Structure-based point mutations	experimental_method	Structure-based point mutations shed light on ligand-induced regulation of NadR.	FIG
75	79	NadR	protein	Structure-based point mutations shed light on ligand-induced regulation of NadR.	FIG
0	12	Western blot	experimental_method	Western blot analyses of wild-type (WT) strain (lanes 1–2) or isogenic nadR knockout strains (ΔNadR) complemented to express the indicated NadR WT or mutant proteins (lanes 3–12) or not complemented (lanes 13–14), grown in the presence (even lanes) or absence (odd lanes) of 5mM 4-HPA, showing NadA and NadR expression.	FIG
25	34	wild-type	protein_state	Western blot analyses of wild-type (WT) strain (lanes 1–2) or isogenic nadR knockout strains (ΔNadR) complemented to express the indicated NadR WT or mutant proteins (lanes 3–12) or not complemented (lanes 13–14), grown in the presence (even lanes) or absence (odd lanes) of 5mM 4-HPA, showing NadA and NadR expression.	FIG
36	38	WT	protein_state	Western blot analyses of wild-type (WT) strain (lanes 1–2) or isogenic nadR knockout strains (ΔNadR) complemented to express the indicated NadR WT or mutant proteins (lanes 3–12) or not complemented (lanes 13–14), grown in the presence (even lanes) or absence (odd lanes) of 5mM 4-HPA, showing NadA and NadR expression.	FIG
71	75	nadR	gene	Western blot analyses of wild-type (WT) strain (lanes 1–2) or isogenic nadR knockout strains (ΔNadR) complemented to express the indicated NadR WT or mutant proteins (lanes 3–12) or not complemented (lanes 13–14), grown in the presence (even lanes) or absence (odd lanes) of 5mM 4-HPA, showing NadA and NadR expression.	FIG
94	99	ΔNadR	mutant	Western blot analyses of wild-type (WT) strain (lanes 1–2) or isogenic nadR knockout strains (ΔNadR) complemented to express the indicated NadR WT or mutant proteins (lanes 3–12) or not complemented (lanes 13–14), grown in the presence (even lanes) or absence (odd lanes) of 5mM 4-HPA, showing NadA and NadR expression.	FIG
139	143	NadR	protein	Western blot analyses of wild-type (WT) strain (lanes 1–2) or isogenic nadR knockout strains (ΔNadR) complemented to express the indicated NadR WT or mutant proteins (lanes 3–12) or not complemented (lanes 13–14), grown in the presence (even lanes) or absence (odd lanes) of 5mM 4-HPA, showing NadA and NadR expression.	FIG
144	146	WT	protein_state	Western blot analyses of wild-type (WT) strain (lanes 1–2) or isogenic nadR knockout strains (ΔNadR) complemented to express the indicated NadR WT or mutant proteins (lanes 3–12) or not complemented (lanes 13–14), grown in the presence (even lanes) or absence (odd lanes) of 5mM 4-HPA, showing NadA and NadR expression.	FIG
150	156	mutant	protein_state	Western blot analyses of wild-type (WT) strain (lanes 1–2) or isogenic nadR knockout strains (ΔNadR) complemented to express the indicated NadR WT or mutant proteins (lanes 3–12) or not complemented (lanes 13–14), grown in the presence (even lanes) or absence (odd lanes) of 5mM 4-HPA, showing NadA and NadR expression.	FIG
279	284	4-HPA	chemical	Western blot analyses of wild-type (WT) strain (lanes 1–2) or isogenic nadR knockout strains (ΔNadR) complemented to express the indicated NadR WT or mutant proteins (lanes 3–12) or not complemented (lanes 13–14), grown in the presence (even lanes) or absence (odd lanes) of 5mM 4-HPA, showing NadA and NadR expression.	FIG
294	298	NadA	protein	Western blot analyses of wild-type (WT) strain (lanes 1–2) or isogenic nadR knockout strains (ΔNadR) complemented to express the indicated NadR WT or mutant proteins (lanes 3–12) or not complemented (lanes 13–14), grown in the presence (even lanes) or absence (odd lanes) of 5mM 4-HPA, showing NadA and NadR expression.	FIG
303	307	NadR	protein	Western blot analyses of wild-type (WT) strain (lanes 1–2) or isogenic nadR knockout strains (ΔNadR) complemented to express the indicated NadR WT or mutant proteins (lanes 3–12) or not complemented (lanes 13–14), grown in the presence (even lanes) or absence (odd lanes) of 5mM 4-HPA, showing NadA and NadR expression.	FIG
19	24	ΔNadR	mutant	Complementation of ΔNadR with WT NadR enables induction of nadA expression by 4-HPA.	FIG
30	32	WT	protein_state	Complementation of ΔNadR with WT NadR enables induction of nadA expression by 4-HPA.	FIG
33	37	NadR	protein	Complementation of ΔNadR with WT NadR enables induction of nadA expression by 4-HPA.	FIG
59	63	nadA	gene	Complementation of ΔNadR with WT NadR enables induction of nadA expression by 4-HPA.	FIG
78	83	4-HPA	chemical	Complementation of ΔNadR with WT NadR enables induction of nadA expression by 4-HPA.	FIG
4	7	H7A	mutant	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
9	12	S9A	mutant	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
17	21	F25A	mutant	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
50	54	nadA	gene	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
102	104	WT	protein_state	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
105	109	NadR	protein	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
115	119	N11A	mutant	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
120	126	mutant	protein_state	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
156	160	nadA	gene	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
205	210	4-HPA	chemical	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
249	262	meningococcal	taxonomy_domain	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
263	287	factor H binding protein	protein	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
289	293	fHbp	protein	The H7A, S9A and F25A mutants efficiently repress nadA expression but are less ligand-responsive than WT NadR. The N11A mutant does not efficiently repress nadA expression either in presence or absence of 4-HPA. (The protein abundance levels of the meningococcal factor H binding protein (fHbp) were used as a gel loading control).	FIG
0	4	NadA	protein	NadA is a surface-exposed meningococcal protein contributing to pathogenesis, and is one of three main antigens present in the vaccine Bexsero.	DISCUSS
26	39	meningococcal	taxonomy_domain	NadA is a surface-exposed meningococcal protein contributing to pathogenesis, and is one of three main antigens present in the vaccine Bexsero.	DISCUSS
55	59	nadA	gene	A detailed understanding of the in vitro repression of nadA expression by the transcriptional regulator NadR is important, both because it is a relevant disease-related model of how small-molecule ligands can regulate MarR family proteins and thereby impact bacterial virulence, and because nadA expression levels are linked to the prediction of vaccine coverage.	DISCUSS
78	103	transcriptional regulator	protein_type	A detailed understanding of the in vitro repression of nadA expression by the transcriptional regulator NadR is important, both because it is a relevant disease-related model of how small-molecule ligands can regulate MarR family proteins and thereby impact bacterial virulence, and because nadA expression levels are linked to the prediction of vaccine coverage.	DISCUSS
104	108	NadR	protein	A detailed understanding of the in vitro repression of nadA expression by the transcriptional regulator NadR is important, both because it is a relevant disease-related model of how small-molecule ligands can regulate MarR family proteins and thereby impact bacterial virulence, and because nadA expression levels are linked to the prediction of vaccine coverage.	DISCUSS
218	222	MarR	protein_type	A detailed understanding of the in vitro repression of nadA expression by the transcriptional regulator NadR is important, both because it is a relevant disease-related model of how small-molecule ligands can regulate MarR family proteins and thereby impact bacterial virulence, and because nadA expression levels are linked to the prediction of vaccine coverage.	DISCUSS
258	267	bacterial	taxonomy_domain	A detailed understanding of the in vitro repression of nadA expression by the transcriptional regulator NadR is important, both because it is a relevant disease-related model of how small-molecule ligands can regulate MarR family proteins and thereby impact bacterial virulence, and because nadA expression levels are linked to the prediction of vaccine coverage.	DISCUSS
291	295	nadA	gene	A detailed understanding of the in vitro repression of nadA expression by the transcriptional regulator NadR is important, both because it is a relevant disease-related model of how small-molecule ligands can regulate MarR family proteins and thereby impact bacterial virulence, and because nadA expression levels are linked to the prediction of vaccine coverage.	DISCUSS
27	31	NadR	protein	The repressive activity of NadR can be relieved by hydroxyphenylacetate (HPA) ligands, and HDX-MS studies previously indicated that 4-HPA stabilizes dimeric NadR in a configuration incompatible with DNA binding.	DISCUSS
51	71	hydroxyphenylacetate	chemical	The repressive activity of NadR can be relieved by hydroxyphenylacetate (HPA) ligands, and HDX-MS studies previously indicated that 4-HPA stabilizes dimeric NadR in a configuration incompatible with DNA binding.	DISCUSS
73	76	HPA	chemical	The repressive activity of NadR can be relieved by hydroxyphenylacetate (HPA) ligands, and HDX-MS studies previously indicated that 4-HPA stabilizes dimeric NadR in a configuration incompatible with DNA binding.	DISCUSS
91	97	HDX-MS	experimental_method	The repressive activity of NadR can be relieved by hydroxyphenylacetate (HPA) ligands, and HDX-MS studies previously indicated that 4-HPA stabilizes dimeric NadR in a configuration incompatible with DNA binding.	DISCUSS
132	137	4-HPA	chemical	The repressive activity of NadR can be relieved by hydroxyphenylacetate (HPA) ligands, and HDX-MS studies previously indicated that 4-HPA stabilizes dimeric NadR in a configuration incompatible with DNA binding.	DISCUSS
149	156	dimeric	oligomeric_state	The repressive activity of NadR can be relieved by hydroxyphenylacetate (HPA) ligands, and HDX-MS studies previously indicated that 4-HPA stabilizes dimeric NadR in a configuration incompatible with DNA binding.	DISCUSS
157	161	NadR	protein	The repressive activity of NadR can be relieved by hydroxyphenylacetate (HPA) ligands, and HDX-MS studies previously indicated that 4-HPA stabilizes dimeric NadR in a configuration incompatible with DNA binding.	DISCUSS
84	88	MarR	protein_type	Despite these and other studies, the molecular mechanisms by which ligands regulate MarR family proteins are relatively poorly understood and likely differ depending on the specific ligand.	DISCUSS
24	28	NadR	protein	Given the importance of NadR-mediated regulation of NadA levels in the contexts of meningococcal pathogenesis, we sought to characterize NadR, and its interaction with ligands, at atomic resolution.	DISCUSS
52	56	NadA	protein	Given the importance of NadR-mediated regulation of NadA levels in the contexts of meningococcal pathogenesis, we sought to characterize NadR, and its interaction with ligands, at atomic resolution.	DISCUSS
83	96	meningococcal	taxonomy_domain	Given the importance of NadR-mediated regulation of NadA levels in the contexts of meningococcal pathogenesis, we sought to characterize NadR, and its interaction with ligands, at atomic resolution.	DISCUSS
137	141	NadR	protein	Given the importance of NadR-mediated regulation of NadA levels in the contexts of meningococcal pathogenesis, we sought to characterize NadR, and its interaction with ligands, at atomic resolution.	DISCUSS
27	31	NadR	protein	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
35	42	dimeric	oligomeric_state	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
92	99	dimeric	oligomeric_state	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
113	124	presence of	protein_state	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
125	130	4-HPA	chemical	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
163	172	monomeric	oligomeric_state	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
207	212	4-HPA	chemical	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
223	227	NadR	protein	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
295	299	NadR	protein	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
316	319	SEC	experimental_method	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
324	341	mass spectrometry	experimental_method	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
352	376	crystallographic studies	experimental_method	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
398	402	MarR	protein_type	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
418	425	dimeric	oligomeric_state	Firstly, we confirmed that NadR is dimeric in solution and demonstrated that it retains its dimeric state in the presence of 4-HPA, indicating that induction of a monomeric status is not the manner by which 4-HPA regulates NadR. These observations were in agreement with (i) a previous study of NadR performed using SEC and mass spectrometry, and (ii) crystallographic studies showing that several MarR homologues are dimeric.	DISCUSS
13	55	structure-guided site-directed mutagenesis	experimental_method	We also used structure-guided site-directed mutagenesis to identify an important conserved residue, Leu130, which stabilizes the NadR dimer interface, knowledge of which may also inform future studies to explore the regulatory mechanisms of other MarR family proteins.	DISCUSS
81	90	conserved	protein_state	We also used structure-guided site-directed mutagenesis to identify an important conserved residue, Leu130, which stabilizes the NadR dimer interface, knowledge of which may also inform future studies to explore the regulatory mechanisms of other MarR family proteins.	DISCUSS
100	106	Leu130	residue_name_number	We also used structure-guided site-directed mutagenesis to identify an important conserved residue, Leu130, which stabilizes the NadR dimer interface, knowledge of which may also inform future studies to explore the regulatory mechanisms of other MarR family proteins.	DISCUSS
129	133	NadR	protein	We also used structure-guided site-directed mutagenesis to identify an important conserved residue, Leu130, which stabilizes the NadR dimer interface, knowledge of which may also inform future studies to explore the regulatory mechanisms of other MarR family proteins.	DISCUSS
134	149	dimer interface	site	We also used structure-guided site-directed mutagenesis to identify an important conserved residue, Leu130, which stabilizes the NadR dimer interface, knowledge of which may also inform future studies to explore the regulatory mechanisms of other MarR family proteins.	DISCUSS
247	251	MarR	protein_type	We also used structure-guided site-directed mutagenesis to identify an important conserved residue, Leu130, which stabilizes the NadR dimer interface, knowledge of which may also inform future studies to explore the regulatory mechanisms of other MarR family proteins.	DISCUSS
13	43	assessed the thermal stability	experimental_method	Secondly, we assessed the thermal stability and unfolding of NadR in the presence or absence of ligands.	DISCUSS
61	65	NadR	protein	Secondly, we assessed the thermal stability and unfolding of NadR in the presence or absence of ligands.	DISCUSS
66	81	in the presence	protein_state	Secondly, we assessed the thermal stability and unfolding of NadR in the presence or absence of ligands.	DISCUSS
85	95	absence of	protein_state	Secondly, we assessed the thermal stability and unfolding of NadR in the presence or absence of ligands.	DISCUSS
4	7	DSC	experimental_method	All DSC profiles showed a single peak, suggesting that a single unfolding event simultaneously disrupted the dimer and the monomer.	DISCUSS
8	16	profiles	evidence	All DSC profiles showed a single peak, suggesting that a single unfolding event simultaneously disrupted the dimer and the monomer.	DISCUSS
109	114	dimer	oligomeric_state	All DSC profiles showed a single peak, suggesting that a single unfolding event simultaneously disrupted the dimer and the monomer.	DISCUSS
123	130	monomer	oligomeric_state	All DSC profiles showed a single peak, suggesting that a single unfolding event simultaneously disrupted the dimer and the monomer.	DISCUSS
52	56	NadR	protein	HPA ligands specifically increased the stability of NadR. The largest effects were induced by the naturally-occurring compounds 4-HPA and 3Cl,4-HPA, which, in SPR assays, were found to bind NadR with KD values of 1.5 mM and 1.1 mM, respectively.	DISCUSS
128	133	4-HPA	chemical	HPA ligands specifically increased the stability of NadR. The largest effects were induced by the naturally-occurring compounds 4-HPA and 3Cl,4-HPA, which, in SPR assays, were found to bind NadR with KD values of 1.5 mM and 1.1 mM, respectively.	DISCUSS
138	147	3Cl,4-HPA	chemical	HPA ligands specifically increased the stability of NadR. The largest effects were induced by the naturally-occurring compounds 4-HPA and 3Cl,4-HPA, which, in SPR assays, were found to bind NadR with KD values of 1.5 mM and 1.1 mM, respectively.	DISCUSS
159	169	SPR assays	experimental_method	HPA ligands specifically increased the stability of NadR. The largest effects were induced by the naturally-occurring compounds 4-HPA and 3Cl,4-HPA, which, in SPR assays, were found to bind NadR with KD values of 1.5 mM and 1.1 mM, respectively.	DISCUSS
190	194	NadR	protein	HPA ligands specifically increased the stability of NadR. The largest effects were induced by the naturally-occurring compounds 4-HPA and 3Cl,4-HPA, which, in SPR assays, were found to bind NadR with KD values of 1.5 mM and 1.1 mM, respectively.	DISCUSS
200	202	KD	evidence	HPA ligands specifically increased the stability of NadR. The largest effects were induced by the naturally-occurring compounds 4-HPA and 3Cl,4-HPA, which, in SPR assays, were found to bind NadR with KD values of 1.5 mM and 1.1 mM, respectively.	DISCUSS
15	19	NadR	protein	Although these NadR/HPA interactions appeared rather weak, their distinct affinities and specificities matched their in vitro effects and their biological relevance appears similar to previous proposals that certain small molecules, including some antibiotics, in the millimolar concentration range may be broad inhibitors of MarR family proteins.	DISCUSS
20	23	HPA	chemical	Although these NadR/HPA interactions appeared rather weak, their distinct affinities and specificities matched their in vitro effects and their biological relevance appears similar to previous proposals that certain small molecules, including some antibiotics, in the millimolar concentration range may be broad inhibitors of MarR family proteins.	DISCUSS
326	330	MarR	protein_type	Although these NadR/HPA interactions appeared rather weak, their distinct affinities and specificities matched their in vitro effects and their biological relevance appears similar to previous proposals that certain small molecules, including some antibiotics, in the millimolar concentration range may be broad inhibitors of MarR family proteins.	DISCUSS
8	13	4-HPA	chemical	Indeed, 4-HPA is found in human saliva and 3Cl,4-HPA is produced during inflammatory processes, suggesting that these natural ligands are encountered by N. meningitidis in the mucosa of the oropharynx during infections.	DISCUSS
26	31	human	species	Indeed, 4-HPA is found in human saliva and 3Cl,4-HPA is produced during inflammatory processes, suggesting that these natural ligands are encountered by N. meningitidis in the mucosa of the oropharynx during infections.	DISCUSS
43	52	3Cl,4-HPA	chemical	Indeed, 4-HPA is found in human saliva and 3Cl,4-HPA is produced during inflammatory processes, suggesting that these natural ligands are encountered by N. meningitidis in the mucosa of the oropharynx during infections.	DISCUSS
153	168	N. meningitidis	species	Indeed, 4-HPA is found in human saliva and 3Cl,4-HPA is produced during inflammatory processes, suggesting that these natural ligands are encountered by N. meningitidis in the mucosa of the oropharynx during infections.	DISCUSS
25	29	NadR	protein	It is also possible that NadR responds to currently unidentified HPA analogues.	DISCUSS
65	68	HPA	chemical	It is also possible that NadR responds to currently unidentified HPA analogues.	DISCUSS
15	25	NadR/4-HPA	complex_assembly	Indeed, in the NadR/4-HPA complex there was a water molecule close to the carboxylate group and also a small unfilled tunnel ~5Å long, both factors suggesting that alternative larger ligands could occupy the pocket.	DISCUSS
46	51	water	chemical	Indeed, in the NadR/4-HPA complex there was a water molecule close to the carboxylate group and also a small unfilled tunnel ~5Å long, both factors suggesting that alternative larger ligands could occupy the pocket.	DISCUSS
118	124	tunnel	site	Indeed, in the NadR/4-HPA complex there was a water molecule close to the carboxylate group and also a small unfilled tunnel ~5Å long, both factors suggesting that alternative larger ligands could occupy the pocket.	DISCUSS
55	59	NadR	protein	The ability to respond to various ligands might enable NadR in vivo to orchestrate multiple response mechanisms and modulate expression of genes other than nadA. Ultimately, confirmation of the relevance of each ligand will require a deeper understanding of the available concentration in vivo in the host niche during bacterial colonization and inflammation.	DISCUSS
156	160	nadA	gene	The ability to respond to various ligands might enable NadR in vivo to orchestrate multiple response mechanisms and modulate expression of genes other than nadA. Ultimately, confirmation of the relevance of each ligand will require a deeper understanding of the available concentration in vivo in the host niche during bacterial colonization and inflammation.	DISCUSS
319	328	bacterial	taxonomy_domain	The ability to respond to various ligands might enable NadR in vivo to orchestrate multiple response mechanisms and modulate expression of genes other than nadA. Ultimately, confirmation of the relevance of each ligand will require a deeper understanding of the available concentration in vivo in the host niche during bacterial colonization and inflammation.	DISCUSS
30	48	crystal structures	evidence	Here, we determined the first crystal structures of apo-NadR and holo-NadR. These experimentally-determined structures enabled a new detailed characterization of the ligand-binding pocket.	DISCUSS
52	55	apo	protein_state	Here, we determined the first crystal structures of apo-NadR and holo-NadR. These experimentally-determined structures enabled a new detailed characterization of the ligand-binding pocket.	DISCUSS
56	60	NadR	protein	Here, we determined the first crystal structures of apo-NadR and holo-NadR. These experimentally-determined structures enabled a new detailed characterization of the ligand-binding pocket.	DISCUSS
65	69	holo	protein_state	Here, we determined the first crystal structures of apo-NadR and holo-NadR. These experimentally-determined structures enabled a new detailed characterization of the ligand-binding pocket.	DISCUSS
70	74	NadR	protein	Here, we determined the first crystal structures of apo-NadR and holo-NadR. These experimentally-determined structures enabled a new detailed characterization of the ligand-binding pocket.	DISCUSS
108	118	structures	evidence	Here, we determined the first crystal structures of apo-NadR and holo-NadR. These experimentally-determined structures enabled a new detailed characterization of the ligand-binding pocket.	DISCUSS
166	187	ligand-binding pocket	site	Here, we determined the first crystal structures of apo-NadR and holo-NadR. These experimentally-determined structures enabled a new detailed characterization of the ligand-binding pocket.	DISCUSS
3	7	holo	protein_state	In holo-NadR, 4-HPA interacted directly with at least 11 polar and hydrophobic residues.	DISCUSS
8	12	NadR	protein	In holo-NadR, 4-HPA interacted directly with at least 11 polar and hydrophobic residues.	DISCUSS
14	19	4-HPA	chemical	In holo-NadR, 4-HPA interacted directly with at least 11 polar and hydrophobic residues.	DISCUSS
73	91	homology modelling	experimental_method	Several, but not all, of these interactions were predicted previously by homology modelling combined with ligand docking in silico.	DISCUSS
106	120	ligand docking	experimental_method	Several, but not all, of these interactions were predicted previously by homology modelling combined with ligand docking in silico.	DISCUSS
58	62	His7	residue_name_number	Subsequently, we established the functional importance of His7, Ser9, Asn11 and Phe25 in the in vitro response of meningococcus to 4-HPA, via site-directed mutagenesis.	DISCUSS
64	68	Ser9	residue_name_number	Subsequently, we established the functional importance of His7, Ser9, Asn11 and Phe25 in the in vitro response of meningococcus to 4-HPA, via site-directed mutagenesis.	DISCUSS
70	75	Asn11	residue_name_number	Subsequently, we established the functional importance of His7, Ser9, Asn11 and Phe25 in the in vitro response of meningococcus to 4-HPA, via site-directed mutagenesis.	DISCUSS
80	85	Phe25	residue_name_number	Subsequently, we established the functional importance of His7, Ser9, Asn11 and Phe25 in the in vitro response of meningococcus to 4-HPA, via site-directed mutagenesis.	DISCUSS
114	127	meningococcus	taxonomy_domain	Subsequently, we established the functional importance of His7, Ser9, Asn11 and Phe25 in the in vitro response of meningococcus to 4-HPA, via site-directed mutagenesis.	DISCUSS
131	136	4-HPA	chemical	Subsequently, we established the functional importance of His7, Ser9, Asn11 and Phe25 in the in vitro response of meningococcus to 4-HPA, via site-directed mutagenesis.	DISCUSS
142	167	site-directed mutagenesis	experimental_method	Subsequently, we established the functional importance of His7, Ser9, Asn11 and Phe25 in the in vitro response of meningococcus to 4-HPA, via site-directed mutagenesis.	DISCUSS
23	40	crystal structure	evidence	More unexpectedly, the crystal structure revealed that only one molecule of 4-HPA was bound per NadR dimer.	DISCUSS
76	81	4-HPA	chemical	More unexpectedly, the crystal structure revealed that only one molecule of 4-HPA was bound per NadR dimer.	DISCUSS
86	91	bound	protein_state	More unexpectedly, the crystal structure revealed that only one molecule of 4-HPA was bound per NadR dimer.	DISCUSS
96	100	NadR	protein	More unexpectedly, the crystal structure revealed that only one molecule of 4-HPA was bound per NadR dimer.	DISCUSS
101	106	dimer	oligomeric_state	More unexpectedly, the crystal structure revealed that only one molecule of 4-HPA was bound per NadR dimer.	DISCUSS
50	53	SPR	experimental_method	We confirmed this stoichiometry in solution using SPR methods.	DISCUSS
13	43	heteronuclear NMR spectroscopy	experimental_method	We also used heteronuclear NMR spectroscopy to detect substantial conformational changes of NadR occurring in solution upon addition of 4-HPA.	DISCUSS
92	96	NadR	protein	We also used heteronuclear NMR spectroscopy to detect substantial conformational changes of NadR occurring in solution upon addition of 4-HPA.	DISCUSS
136	141	4-HPA	chemical	We also used heteronuclear NMR spectroscopy to detect substantial conformational changes of NadR occurring in solution upon addition of 4-HPA.	DISCUSS
10	13	NMR	experimental_method	Moreover, NMR spectra at 10°C suggested the existence of two distinct conformations of NadR in the vicinity of the ligand-binding pocket.	DISCUSS
14	21	spectra	evidence	Moreover, NMR spectra at 10°C suggested the existence of two distinct conformations of NadR in the vicinity of the ligand-binding pocket.	DISCUSS
87	91	NadR	protein	Moreover, NMR spectra at 10°C suggested the existence of two distinct conformations of NadR in the vicinity of the ligand-binding pocket.	DISCUSS
115	136	ligand-binding pocket	site	Moreover, NMR spectra at 10°C suggested the existence of two distinct conformations of NadR in the vicinity of the ligand-binding pocket.	DISCUSS
28	56	crystallographic observation	evidence	More powerfully, our unique crystallographic observation of this ‘occupied vs unoccupied site’ asymmetry in the NadR/4-HPA interaction is, to our knowledge, the first example reported for a MarR family protein.	DISCUSS
66	74	occupied	protein_state	More powerfully, our unique crystallographic observation of this ‘occupied vs unoccupied site’ asymmetry in the NadR/4-HPA interaction is, to our knowledge, the first example reported for a MarR family protein.	DISCUSS
78	88	unoccupied	protein_state	More powerfully, our unique crystallographic observation of this ‘occupied vs unoccupied site’ asymmetry in the NadR/4-HPA interaction is, to our knowledge, the first example reported for a MarR family protein.	DISCUSS
112	122	NadR/4-HPA	complex_assembly	More powerfully, our unique crystallographic observation of this ‘occupied vs unoccupied site’ asymmetry in the NadR/4-HPA interaction is, to our knowledge, the first example reported for a MarR family protein.	DISCUSS
190	194	MarR	protein_type	More powerfully, our unique crystallographic observation of this ‘occupied vs unoccupied site’ asymmetry in the NadR/4-HPA interaction is, to our knowledge, the first example reported for a MarR family protein.	DISCUSS
0	19	Structural analyses	experimental_method	Structural analyses suggested that ‘inward’ side chain positions of Met22, Phe25 and especially Arg43 precluded binding of a second ligand molecule.	DISCUSS
36	42	inward	protein_state	Structural analyses suggested that ‘inward’ side chain positions of Met22, Phe25 and especially Arg43 precluded binding of a second ligand molecule.	DISCUSS
68	73	Met22	residue_name_number	Structural analyses suggested that ‘inward’ side chain positions of Met22, Phe25 and especially Arg43 precluded binding of a second ligand molecule.	DISCUSS
75	80	Phe25	residue_name_number	Structural analyses suggested that ‘inward’ side chain positions of Met22, Phe25 and especially Arg43 precluded binding of a second ligand molecule.	DISCUSS
96	101	Arg43	residue_name_number	Structural analyses suggested that ‘inward’ side chain positions of Met22, Phe25 and especially Arg43 precluded binding of a second ligand molecule.	DISCUSS
98	102	NadR	protein	Such a mechanism indicates negative cooperativity, which may enhance the ligand-responsiveness of NadR.	DISCUSS
19	29	NadR/4-HPA	complex_assembly	Comparisons of the NadR/4-HPA complex with available MarR family/salicylate complexes revealed that 4-HPA has a previously unobserved binding mode.	DISCUSS
53	57	MarR	protein_type	Comparisons of the NadR/4-HPA complex with available MarR family/salicylate complexes revealed that 4-HPA has a previously unobserved binding mode.	DISCUSS
65	75	salicylate	chemical	Comparisons of the NadR/4-HPA complex with available MarR family/salicylate complexes revealed that 4-HPA has a previously unobserved binding mode.	DISCUSS
100	105	4-HPA	chemical	Comparisons of the NadR/4-HPA complex with available MarR family/salicylate complexes revealed that 4-HPA has a previously unobserved binding mode.	DISCUSS
16	38	M. thermoautotrophicum	species	Briefly, in the M. thermoautotrophicum MTH313 dimer, one molecule of salicylate binds in the pocket of each monomer, though with two rather different positions and orientations, only one of which (site-1) is thought to be biologically relevant (Fig 10A).	DISCUSS
39	45	MTH313	protein	Briefly, in the M. thermoautotrophicum MTH313 dimer, one molecule of salicylate binds in the pocket of each monomer, though with two rather different positions and orientations, only one of which (site-1) is thought to be biologically relevant (Fig 10A).	DISCUSS
46	51	dimer	oligomeric_state	Briefly, in the M. thermoautotrophicum MTH313 dimer, one molecule of salicylate binds in the pocket of each monomer, though with two rather different positions and orientations, only one of which (site-1) is thought to be biologically relevant (Fig 10A).	DISCUSS
69	79	salicylate	chemical	Briefly, in the M. thermoautotrophicum MTH313 dimer, one molecule of salicylate binds in the pocket of each monomer, though with two rather different positions and orientations, only one of which (site-1) is thought to be biologically relevant (Fig 10A).	DISCUSS
93	99	pocket	site	Briefly, in the M. thermoautotrophicum MTH313 dimer, one molecule of salicylate binds in the pocket of each monomer, though with two rather different positions and orientations, only one of which (site-1) is thought to be biologically relevant (Fig 10A).	DISCUSS
108	115	monomer	oligomeric_state	Briefly, in the M. thermoautotrophicum MTH313 dimer, one molecule of salicylate binds in the pocket of each monomer, though with two rather different positions and orientations, only one of which (site-1) is thought to be biologically relevant (Fig 10A).	DISCUSS
197	203	site-1	site	Briefly, in the M. thermoautotrophicum MTH313 dimer, one molecule of salicylate binds in the pocket of each monomer, though with two rather different positions and orientations, only one of which (site-1) is thought to be biologically relevant (Fig 10A).	DISCUSS
7	18	S. tokodaii	species	In the S. tokodaii protein ST1710, salicylate binds to the same position in each monomer of the dimer, in a site equivalent to the putative biologically relevant site of MTH313 (Fig 10B).	DISCUSS
27	33	ST1710	protein	In the S. tokodaii protein ST1710, salicylate binds to the same position in each monomer of the dimer, in a site equivalent to the putative biologically relevant site of MTH313 (Fig 10B).	DISCUSS
35	45	salicylate	chemical	In the S. tokodaii protein ST1710, salicylate binds to the same position in each monomer of the dimer, in a site equivalent to the putative biologically relevant site of MTH313 (Fig 10B).	DISCUSS
81	88	monomer	oligomeric_state	In the S. tokodaii protein ST1710, salicylate binds to the same position in each monomer of the dimer, in a site equivalent to the putative biologically relevant site of MTH313 (Fig 10B).	DISCUSS
96	101	dimer	oligomeric_state	In the S. tokodaii protein ST1710, salicylate binds to the same position in each monomer of the dimer, in a site equivalent to the putative biologically relevant site of MTH313 (Fig 10B).	DISCUSS
170	176	MTH313	protein	In the S. tokodaii protein ST1710, salicylate binds to the same position in each monomer of the dimer, in a site equivalent to the putative biologically relevant site of MTH313 (Fig 10B).	DISCUSS
13	17	MarR	protein_type	Unlike other MarR family proteins which revealed multiple ligand binding interactions, we observed only 1 molecule of 4-HPA bound to NadR, suggesting a more specific and less promiscuous interaction.	DISCUSS
118	123	4-HPA	chemical	Unlike other MarR family proteins which revealed multiple ligand binding interactions, we observed only 1 molecule of 4-HPA bound to NadR, suggesting a more specific and less promiscuous interaction.	DISCUSS
124	132	bound to	protein_state	Unlike other MarR family proteins which revealed multiple ligand binding interactions, we observed only 1 molecule of 4-HPA bound to NadR, suggesting a more specific and less promiscuous interaction.	DISCUSS
133	137	NadR	protein	Unlike other MarR family proteins which revealed multiple ligand binding interactions, we observed only 1 molecule of 4-HPA bound to NadR, suggesting a more specific and less promiscuous interaction.	DISCUSS
3	7	NadR	protein	In NadR, the single molecule of 4-HPA binds in a position distinctly different from the salicylate binding site: translated by > 10 Å and with a 180° inverted orientation (Fig 10C).	DISCUSS
32	37	4-HPA	chemical	In NadR, the single molecule of 4-HPA binds in a position distinctly different from the salicylate binding site: translated by > 10 Å and with a 180° inverted orientation (Fig 10C).	DISCUSS
88	111	salicylate binding site	site	In NadR, the single molecule of 4-HPA binds in a position distinctly different from the salicylate binding site: translated by > 10 Å and with a 180° inverted orientation (Fig 10C).	DISCUSS
0	4	NadR	protein	NadR shows a ligand binding site distinct from other MarR homologues.	FIG
13	32	ligand binding site	site	NadR shows a ligand binding site distinct from other MarR homologues.	FIG
53	57	MarR	protein_type	NadR shows a ligand binding site distinct from other MarR homologues.	FIG
7	27	structural alignment	experimental_method	 (A) A structural alignment of MTH313 chains A and B shows that salicylate is bound in distinct locations in each monomer; site-1 (thought to be the biologically relevant site) and site-2 differ by ~7Å (indicated by black dotted line) and also by ligand orientation.	FIG
31	37	MTH313	protein	 (A) A structural alignment of MTH313 chains A and B shows that salicylate is bound in distinct locations in each monomer; site-1 (thought to be the biologically relevant site) and site-2 differ by ~7Å (indicated by black dotted line) and also by ligand orientation.	FIG
38	52	chains A and B	structure_element	 (A) A structural alignment of MTH313 chains A and B shows that salicylate is bound in distinct locations in each monomer; site-1 (thought to be the biologically relevant site) and site-2 differ by ~7Å (indicated by black dotted line) and also by ligand orientation.	FIG
64	74	salicylate	chemical	 (A) A structural alignment of MTH313 chains A and B shows that salicylate is bound in distinct locations in each monomer; site-1 (thought to be the biologically relevant site) and site-2 differ by ~7Å (indicated by black dotted line) and also by ligand orientation.	FIG
78	83	bound	protein_state	 (A) A structural alignment of MTH313 chains A and B shows that salicylate is bound in distinct locations in each monomer; site-1 (thought to be the biologically relevant site) and site-2 differ by ~7Å (indicated by black dotted line) and also by ligand orientation.	FIG
114	121	monomer	oligomeric_state	 (A) A structural alignment of MTH313 chains A and B shows that salicylate is bound in distinct locations in each monomer; site-1 (thought to be the biologically relevant site) and site-2 differ by ~7Å (indicated by black dotted line) and also by ligand orientation.	FIG
123	129	site-1	site	 (A) A structural alignment of MTH313 chains A and B shows that salicylate is bound in distinct locations in each monomer; site-1 (thought to be the biologically relevant site) and site-2 differ by ~7Å (indicated by black dotted line) and also by ligand orientation.	FIG
181	187	site-2	site	 (A) A structural alignment of MTH313 chains A and B shows that salicylate is bound in distinct locations in each monomer; site-1 (thought to be the biologically relevant site) and site-2 differ by ~7Å (indicated by black dotted line) and also by ligand orientation.	FIG
6	26	structural alignment	experimental_method	(B) A structural alignment of MTH313 chain A and ST1710 (pink) (Cα rmsd 2.3Å), shows that they bind salicylate in equivalent sites (differing by only ~3Å) and with the same orientation.	FIG
30	36	MTH313	protein	(B) A structural alignment of MTH313 chain A and ST1710 (pink) (Cα rmsd 2.3Å), shows that they bind salicylate in equivalent sites (differing by only ~3Å) and with the same orientation.	FIG
37	44	chain A	structure_element	(B) A structural alignment of MTH313 chain A and ST1710 (pink) (Cα rmsd 2.3Å), shows that they bind salicylate in equivalent sites (differing by only ~3Å) and with the same orientation.	FIG
49	55	ST1710	protein	(B) A structural alignment of MTH313 chain A and ST1710 (pink) (Cα rmsd 2.3Å), shows that they bind salicylate in equivalent sites (differing by only ~3Å) and with the same orientation.	FIG
67	71	rmsd	evidence	(B) A structural alignment of MTH313 chain A and ST1710 (pink) (Cα rmsd 2.3Å), shows that they bind salicylate in equivalent sites (differing by only ~3Å) and with the same orientation.	FIG
100	110	salicylate	chemical	(B) A structural alignment of MTH313 chain A and ST1710 (pink) (Cα rmsd 2.3Å), shows that they bind salicylate in equivalent sites (differing by only ~3Å) and with the same orientation.	FIG
16	20	holo	protein_state	(C) Addition of holo-NadR (chain B, blue) to the alignment reveals that bound 4-HPA differs in position by > 10 Å compared to salicylate, and adopts a novel orientation.	FIG
21	25	NadR	protein	(C) Addition of holo-NadR (chain B, blue) to the alignment reveals that bound 4-HPA differs in position by > 10 Å compared to salicylate, and adopts a novel orientation.	FIG
27	34	chain B	structure_element	(C) Addition of holo-NadR (chain B, blue) to the alignment reveals that bound 4-HPA differs in position by > 10 Å compared to salicylate, and adopts a novel orientation.	FIG
49	58	alignment	experimental_method	(C) Addition of holo-NadR (chain B, blue) to the alignment reveals that bound 4-HPA differs in position by > 10 Å compared to salicylate, and adopts a novel orientation.	FIG
72	77	bound	protein_state	(C) Addition of holo-NadR (chain B, blue) to the alignment reveals that bound 4-HPA differs in position by > 10 Å compared to salicylate, and adopts a novel orientation.	FIG
78	83	4-HPA	chemical	(C) Addition of holo-NadR (chain B, blue) to the alignment reveals that bound 4-HPA differs in position by > 10 Å compared to salicylate, and adopts a novel orientation.	FIG
126	136	salicylate	chemical	(C) Addition of holo-NadR (chain B, blue) to the alignment reveals that bound 4-HPA differs in position by > 10 Å compared to salicylate, and adopts a novel orientation.	FIG
17	34	crystal structure	evidence	Interestingly, a crystal structure was previously reported for a functionally-uncharacterized meningococcal homologue of NadR, termed NMB1585, which shares 16% sequence identity with NadR. The two structures can be closely aligned (rmsd 2.3 Å), but NMB1585 appears unsuited for binding HPAs, since its corresponding ‘pocket’ region is occupied by several bulky hydrophobic side chains.	DISCUSS
94	107	meningococcal	taxonomy_domain	Interestingly, a crystal structure was previously reported for a functionally-uncharacterized meningococcal homologue of NadR, termed NMB1585, which shares 16% sequence identity with NadR. The two structures can be closely aligned (rmsd 2.3 Å), but NMB1585 appears unsuited for binding HPAs, since its corresponding ‘pocket’ region is occupied by several bulky hydrophobic side chains.	DISCUSS
121	125	NadR	protein	Interestingly, a crystal structure was previously reported for a functionally-uncharacterized meningococcal homologue of NadR, termed NMB1585, which shares 16% sequence identity with NadR. The two structures can be closely aligned (rmsd 2.3 Å), but NMB1585 appears unsuited for binding HPAs, since its corresponding ‘pocket’ region is occupied by several bulky hydrophobic side chains.	DISCUSS
134	141	NMB1585	protein	Interestingly, a crystal structure was previously reported for a functionally-uncharacterized meningococcal homologue of NadR, termed NMB1585, which shares 16% sequence identity with NadR. The two structures can be closely aligned (rmsd 2.3 Å), but NMB1585 appears unsuited for binding HPAs, since its corresponding ‘pocket’ region is occupied by several bulky hydrophobic side chains.	DISCUSS
183	187	NadR	protein	Interestingly, a crystal structure was previously reported for a functionally-uncharacterized meningococcal homologue of NadR, termed NMB1585, which shares 16% sequence identity with NadR. The two structures can be closely aligned (rmsd 2.3 Å), but NMB1585 appears unsuited for binding HPAs, since its corresponding ‘pocket’ region is occupied by several bulky hydrophobic side chains.	DISCUSS
197	207	structures	evidence	Interestingly, a crystal structure was previously reported for a functionally-uncharacterized meningococcal homologue of NadR, termed NMB1585, which shares 16% sequence identity with NadR. The two structures can be closely aligned (rmsd 2.3 Å), but NMB1585 appears unsuited for binding HPAs, since its corresponding ‘pocket’ region is occupied by several bulky hydrophobic side chains.	DISCUSS
232	236	rmsd	evidence	Interestingly, a crystal structure was previously reported for a functionally-uncharacterized meningococcal homologue of NadR, termed NMB1585, which shares 16% sequence identity with NadR. The two structures can be closely aligned (rmsd 2.3 Å), but NMB1585 appears unsuited for binding HPAs, since its corresponding ‘pocket’ region is occupied by several bulky hydrophobic side chains.	DISCUSS
249	256	NMB1585	protein	Interestingly, a crystal structure was previously reported for a functionally-uncharacterized meningococcal homologue of NadR, termed NMB1585, which shares 16% sequence identity with NadR. The two structures can be closely aligned (rmsd 2.3 Å), but NMB1585 appears unsuited for binding HPAs, since its corresponding ‘pocket’ region is occupied by several bulky hydrophobic side chains.	DISCUSS
286	290	HPAs	chemical	Interestingly, a crystal structure was previously reported for a functionally-uncharacterized meningococcal homologue of NadR, termed NMB1585, which shares 16% sequence identity with NadR. The two structures can be closely aligned (rmsd 2.3 Å), but NMB1585 appears unsuited for binding HPAs, since its corresponding ‘pocket’ region is occupied by several bulky hydrophobic side chains.	DISCUSS
316	323	‘pocket	site	Interestingly, a crystal structure was previously reported for a functionally-uncharacterized meningococcal homologue of NadR, termed NMB1585, which shares 16% sequence identity with NadR. The two structures can be closely aligned (rmsd 2.3 Å), but NMB1585 appears unsuited for binding HPAs, since its corresponding ‘pocket’ region is occupied by several bulky hydrophobic side chains.	DISCUSS
26	30	MarR	protein_type	It can be speculated that MarR family members have evolved separately to engage distinct signaling molecules, thus enabling bacteria to use the overall conserved MarR scaffold to adapt and respond to diverse changing environmental stimuli experienced in their natural niches.	DISCUSS
124	132	bacteria	taxonomy_domain	It can be speculated that MarR family members have evolved separately to engage distinct signaling molecules, thus enabling bacteria to use the overall conserved MarR scaffold to adapt and respond to diverse changing environmental stimuli experienced in their natural niches.	DISCUSS
162	166	MarR	protein_type	It can be speculated that MarR family members have evolved separately to engage distinct signaling molecules, thus enabling bacteria to use the overall conserved MarR scaffold to adapt and respond to diverse changing environmental stimuli experienced in their natural niches.	DISCUSS
41	45	MarR	protein_type	Alternatively, it is possible that other MarR homologues (e.g. NMB1585) may have no extant functional binding pocket and thus may have lost the ability to respond to a ligand, acting instead as constitutive DNA-binding regulatory proteins.	DISCUSS
63	70	NMB1585	protein	Alternatively, it is possible that other MarR homologues (e.g. NMB1585) may have no extant functional binding pocket and thus may have lost the ability to respond to a ligand, acting instead as constitutive DNA-binding regulatory proteins.	DISCUSS
102	116	binding pocket	site	Alternatively, it is possible that other MarR homologues (e.g. NMB1585) may have no extant functional binding pocket and thus may have lost the ability to respond to a ligand, acting instead as constitutive DNA-binding regulatory proteins.	DISCUSS
207	210	DNA	chemical	Alternatively, it is possible that other MarR homologues (e.g. NMB1585) may have no extant functional binding pocket and thus may have lost the ability to respond to a ligand, acting instead as constitutive DNA-binding regulatory proteins.	DISCUSS
4	7	apo	protein_state	The apo-NadR crystal structures revealed two dimers with slightly different conformations, most divergent in the DNA-binding domain.	DISCUSS
8	12	NadR	protein	The apo-NadR crystal structures revealed two dimers with slightly different conformations, most divergent in the DNA-binding domain.	DISCUSS
13	31	crystal structures	evidence	The apo-NadR crystal structures revealed two dimers with slightly different conformations, most divergent in the DNA-binding domain.	DISCUSS
45	51	dimers	oligomeric_state	The apo-NadR crystal structures revealed two dimers with slightly different conformations, most divergent in the DNA-binding domain.	DISCUSS
113	131	DNA-binding domain	structure_element	The apo-NadR crystal structures revealed two dimers with slightly different conformations, most divergent in the DNA-binding domain.	DISCUSS
24	41	crystal structure	evidence	It is not unusual for a crystal structure to reveal multiple copies of the same protein in very slightly different conformations, which are likely representative of the lowest-energy conformations sampled by the dynamic ensemble of molecular states occurring in solution, and which likely have only small energetic differences, as described previously for MexR (a MarR protein) or more recently for the solute-binding protein FhuD2.	DISCUSS
356	360	MexR	protein	It is not unusual for a crystal structure to reveal multiple copies of the same protein in very slightly different conformations, which are likely representative of the lowest-energy conformations sampled by the dynamic ensemble of molecular states occurring in solution, and which likely have only small energetic differences, as described previously for MexR (a MarR protein) or more recently for the solute-binding protein FhuD2.	DISCUSS
364	368	MarR	protein_type	It is not unusual for a crystal structure to reveal multiple copies of the same protein in very slightly different conformations, which are likely representative of the lowest-energy conformations sampled by the dynamic ensemble of molecular states occurring in solution, and which likely have only small energetic differences, as described previously for MexR (a MarR protein) or more recently for the solute-binding protein FhuD2.	DISCUSS
403	425	solute-binding protein	protein_type	It is not unusual for a crystal structure to reveal multiple copies of the same protein in very slightly different conformations, which are likely representative of the lowest-energy conformations sampled by the dynamic ensemble of molecular states occurring in solution, and which likely have only small energetic differences, as described previously for MexR (a MarR protein) or more recently for the solute-binding protein FhuD2.	DISCUSS
426	431	FhuD2	protein	It is not unusual for a crystal structure to reveal multiple copies of the same protein in very slightly different conformations, which are likely representative of the lowest-energy conformations sampled by the dynamic ensemble of molecular states occurring in solution, and which likely have only small energetic differences, as described previously for MexR (a MarR protein) or more recently for the solute-binding protein FhuD2.	DISCUSS
13	17	holo	protein_state	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
18	22	NadR	protein	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
23	32	structure	evidence	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
73	76	apo	protein_state	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
77	81	NadR	protein	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
82	92	structures	evidence	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
94	98	rmsd	evidence	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
193	197	NadR	protein	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
231	236	4-HPA	chemical	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
357	363	active	protein_state	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
368	376	inactive	protein_state	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
430	434	NadR	protein	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
457	460	DNA	chemical	Further, the holo-NadR structure was overall more different from the two apo-NadR structures (rmsd values ~1.3Å), suggesting that the ligand selected and stabilized yet another conformation of NadR. These observations suggest that 4-HPA, and potentially other similar ligands, can shift the molecular equilibrium, changing the energy barriers that separate active and inactive states, and stabilizing the specific conformation of NadR poorly suited to bind DNA.	DISCUSS
19	22	apo	protein_state	Comparisons of the apo- and holo-NadR structures revealed that the largest differences occurred in the DNA-binding helix α4.	DISCUSS
28	32	holo	protein_state	Comparisons of the apo- and holo-NadR structures revealed that the largest differences occurred in the DNA-binding helix α4.	DISCUSS
33	37	NadR	protein	Comparisons of the apo- and holo-NadR structures revealed that the largest differences occurred in the DNA-binding helix α4.	DISCUSS
38	48	structures	evidence	Comparisons of the apo- and holo-NadR structures revealed that the largest differences occurred in the DNA-binding helix α4.	DISCUSS
103	106	DNA	chemical	Comparisons of the apo- and holo-NadR structures revealed that the largest differences occurred in the DNA-binding helix α4.	DISCUSS
115	120	helix	structure_element	Comparisons of the apo- and holo-NadR structures revealed that the largest differences occurred in the DNA-binding helix α4.	DISCUSS
121	123	α4	structure_element	Comparisons of the apo- and holo-NadR structures revealed that the largest differences occurred in the DNA-binding helix α4.	DISCUSS
13	18	helix	structure_element	The shift of helix α4 in holo-NadR was also accompanied by rearrangements at the dimer interface, involving helices α1, α5, and α6, and this holo-form appeared poorly suited for DNA-binding when compared with the known OhrR:ohrA complex.	DISCUSS
19	21	α4	structure_element	The shift of helix α4 in holo-NadR was also accompanied by rearrangements at the dimer interface, involving helices α1, α5, and α6, and this holo-form appeared poorly suited for DNA-binding when compared with the known OhrR:ohrA complex.	DISCUSS
25	29	holo	protein_state	The shift of helix α4 in holo-NadR was also accompanied by rearrangements at the dimer interface, involving helices α1, α5, and α6, and this holo-form appeared poorly suited for DNA-binding when compared with the known OhrR:ohrA complex.	DISCUSS
30	34	NadR	protein	The shift of helix α4 in holo-NadR was also accompanied by rearrangements at the dimer interface, involving helices α1, α5, and α6, and this holo-form appeared poorly suited for DNA-binding when compared with the known OhrR:ohrA complex.	DISCUSS
81	96	dimer interface	site	The shift of helix α4 in holo-NadR was also accompanied by rearrangements at the dimer interface, involving helices α1, α5, and α6, and this holo-form appeared poorly suited for DNA-binding when compared with the known OhrR:ohrA complex.	DISCUSS
108	115	helices	structure_element	The shift of helix α4 in holo-NadR was also accompanied by rearrangements at the dimer interface, involving helices α1, α5, and α6, and this holo-form appeared poorly suited for DNA-binding when compared with the known OhrR:ohrA complex.	DISCUSS
116	118	α1	structure_element	The shift of helix α4 in holo-NadR was also accompanied by rearrangements at the dimer interface, involving helices α1, α5, and α6, and this holo-form appeared poorly suited for DNA-binding when compared with the known OhrR:ohrA complex.	DISCUSS
120	122	α5	structure_element	The shift of helix α4 in holo-NadR was also accompanied by rearrangements at the dimer interface, involving helices α1, α5, and α6, and this holo-form appeared poorly suited for DNA-binding when compared with the known OhrR:ohrA complex.	DISCUSS
128	130	α6	structure_element	The shift of helix α4 in holo-NadR was also accompanied by rearrangements at the dimer interface, involving helices α1, α5, and α6, and this holo-form appeared poorly suited for DNA-binding when compared with the known OhrR:ohrA complex.	DISCUSS
141	145	holo	protein_state	The shift of helix α4 in holo-NadR was also accompanied by rearrangements at the dimer interface, involving helices α1, α5, and α6, and this holo-form appeared poorly suited for DNA-binding when compared with the known OhrR:ohrA complex.	DISCUSS
178	181	DNA	chemical	The shift of helix α4 in holo-NadR was also accompanied by rearrangements at the dimer interface, involving helices α1, α5, and α6, and this holo-form appeared poorly suited for DNA-binding when compared with the known OhrR:ohrA complex.	DISCUSS
219	228	OhrR:ohrA	complex_assembly	The shift of helix α4 in holo-NadR was also accompanied by rearrangements at the dimer interface, involving helices α1, α5, and α6, and this holo-form appeared poorly suited for DNA-binding when compared with the known OhrR:ohrA complex.	DISCUSS
26	31	helix	structure_element	While some flexibility of helix α4 was also observed in the two apo-structures, concomitant changes in the dimer interfaces were not observed, possibly due to the absence of ligand.	DISCUSS
32	34	α4	structure_element	While some flexibility of helix α4 was also observed in the two apo-structures, concomitant changes in the dimer interfaces were not observed, possibly due to the absence of ligand.	DISCUSS
64	67	apo	protein_state	While some flexibility of helix α4 was also observed in the two apo-structures, concomitant changes in the dimer interfaces were not observed, possibly due to the absence of ligand.	DISCUSS
68	78	structures	evidence	While some flexibility of helix α4 was also observed in the two apo-structures, concomitant changes in the dimer interfaces were not observed, possibly due to the absence of ligand.	DISCUSS
107	123	dimer interfaces	site	While some flexibility of helix α4 was also observed in the two apo-structures, concomitant changes in the dimer interfaces were not observed, possibly due to the absence of ligand.	DISCUSS
163	180	absence of ligand	protein_state	While some flexibility of helix α4 was also observed in the two apo-structures, concomitant changes in the dimer interfaces were not observed, possibly due to the absence of ligand.	DISCUSS
32	35	apo	protein_state	One of the two conformations of apo-NadR appeared ideally suited for DNA-binding.	DISCUSS
36	40	NadR	protein	One of the two conformations of apo-NadR appeared ideally suited for DNA-binding.	DISCUSS
69	72	DNA	chemical	One of the two conformations of apo-NadR appeared ideally suited for DNA-binding.	DISCUSS
41	44	apo	protein_state	Overall, these analyses suggest that the apo-NadR dimer has a pre-existing equilibrium that samples a variety of conformations, some of which are compatible with DNA binding.	DISCUSS
45	49	NadR	protein	Overall, these analyses suggest that the apo-NadR dimer has a pre-existing equilibrium that samples a variety of conformations, some of which are compatible with DNA binding.	DISCUSS
50	55	dimer	oligomeric_state	Overall, these analyses suggest that the apo-NadR dimer has a pre-existing equilibrium that samples a variety of conformations, some of which are compatible with DNA binding.	DISCUSS
162	165	DNA	chemical	Overall, these analyses suggest that the apo-NadR dimer has a pre-existing equilibrium that samples a variety of conformations, some of which are compatible with DNA binding.	DISCUSS
43	47	NadR	protein	The noted flexibility may also explain how NadR can adapt to bind various DNA target sequences with slightly different structural features.	DISCUSS
74	77	DNA	chemical	The noted flexibility may also explain how NadR can adapt to bind various DNA target sequences with slightly different structural features.	DISCUSS
35	39	holo	protein_state	Subsequently, upon ligand binding, holo-NadR adopts a structure less suited for DNA-binding and this conformation is selected and stabilized by a network of protein-ligand interactions and concomitant rearrangements at the NadR holo dimer interface.	DISCUSS
40	44	NadR	protein	Subsequently, upon ligand binding, holo-NadR adopts a structure less suited for DNA-binding and this conformation is selected and stabilized by a network of protein-ligand interactions and concomitant rearrangements at the NadR holo dimer interface.	DISCUSS
80	83	DNA	chemical	Subsequently, upon ligand binding, holo-NadR adopts a structure less suited for DNA-binding and this conformation is selected and stabilized by a network of protein-ligand interactions and concomitant rearrangements at the NadR holo dimer interface.	DISCUSS
223	227	NadR	protein	Subsequently, upon ligand binding, holo-NadR adopts a structure less suited for DNA-binding and this conformation is selected and stabilized by a network of protein-ligand interactions and concomitant rearrangements at the NadR holo dimer interface.	DISCUSS
228	232	holo	protein_state	Subsequently, upon ligand binding, holo-NadR adopts a structure less suited for DNA-binding and this conformation is selected and stabilized by a network of protein-ligand interactions and concomitant rearrangements at the NadR holo dimer interface.	DISCUSS
233	248	dimer interface	site	Subsequently, upon ligand binding, holo-NadR adopts a structure less suited for DNA-binding and this conformation is selected and stabilized by a network of protein-ligand interactions and concomitant rearrangements at the NadR holo dimer interface.	DISCUSS
64	74	salicylate	chemical	In an alternative and less extensive manner, the binding of two salicylate molecules to the M. thermoautotrophicum protein MTH313 appeared to induce large changes in the wHTH domain, which was associated with reduced DNA-binding activity.	DISCUSS
92	114	M. thermoautotrophicum	species	In an alternative and less extensive manner, the binding of two salicylate molecules to the M. thermoautotrophicum protein MTH313 appeared to induce large changes in the wHTH domain, which was associated with reduced DNA-binding activity.	DISCUSS
123	129	MTH313	protein	In an alternative and less extensive manner, the binding of two salicylate molecules to the M. thermoautotrophicum protein MTH313 appeared to induce large changes in the wHTH domain, which was associated with reduced DNA-binding activity.	DISCUSS
170	181	wHTH domain	structure_element	In an alternative and less extensive manner, the binding of two salicylate molecules to the M. thermoautotrophicum protein MTH313 appeared to induce large changes in the wHTH domain, which was associated with reduced DNA-binding activity.	DISCUSS
31	49	crystal structures	evidence	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
57	77	transcription factor	protein_type	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
79	83	NadR	protein	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
119	132	meningococcal	taxonomy_domain	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
187	191	NadA	protein	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
202	221	structural analyses	experimental_method	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
295	299	NadR	protein	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
336	349	meningococcal	taxonomy_domain	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
369	373	NadR	protein	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
385	389	nadA	gene	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
405	409	NadR	protein	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
493	497	mafA	gene	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
534	538	NadR	protein	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
596	601	4-HPA	chemical	Here we have presented two new crystal structures of the transcription factor, NadR, which regulates expression of the meningococcal surface protein, virulence factor and vaccine antigen NadA. Detailed structural analyses provided a molecular explanation for the ligand-responsive regulation by NadR on the majority of the promoters of meningococcal genes regulated by NadR, including nadA. Intriguingly, NadR exhibits a reversed regulatory mechanism on a second class of promoters, including mafA of the multiple adhesin family–i.e. NadR represses these genes in the presence but not absence of 4-HPA.	DISCUSS
98	114	highly conserved	protein_state	The latter may influence the surface abundance or secretion of maf proteins, an emerging class of highly conserved meningococcal putative adhesins and toxins with many important roles.	DISCUSS
115	128	meningococcal	taxonomy_domain	The latter may influence the surface abundance or secretion of maf proteins, an emerging class of highly conserved meningococcal putative adhesins and toxins with many important roles.	DISCUSS
116	120	NadR	protein	Further work is required to investigate how the two different promoter types influence the ligand-responsiveness of NadR during bacterial infection and may provide insights into the regulatory mechanisms occurring during these host-pathogen interactions.	DISCUSS
128	137	bacterial	taxonomy_domain	Further work is required to investigate how the two different promoter types influence the ligand-responsiveness of NadR during bacterial infection and may provide insights into the regulatory mechanisms occurring during these host-pathogen interactions.	DISCUSS
58	62	NadR	protein	Ultimately, knowledge of the ligand-dependent activity of NadR will continue to deepen our understanding of nadA expression levels, which influence meningococcal pathogenesis.	DISCUSS
108	112	nadA	gene	Ultimately, knowledge of the ligand-dependent activity of NadR will continue to deepen our understanding of nadA expression levels, which influence meningococcal pathogenesis.	DISCUSS
148	161	meningococcal	taxonomy_domain	Ultimately, knowledge of the ligand-dependent activity of NadR will continue to deepen our understanding of nadA expression levels, which influence meningococcal pathogenesis.	DISCUSS
21	25	ohrA	gene	Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family	REF
17	24	NMB1585	protein	The structure of NMB1585, a MarR-family regulator from Neisseria meningitidis	REF