cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4225/03/57428ceb4c932
title: The X-ray crystal structure of Escherichia coli succinic semialdehyde dehydrogenase; structural insights into NADP+ / enzyme interactions (3JZ4)

description: In mammals succinic semialdehyde dehydrogenase (SSADH) plays an essential role in the metabolism of the inhibitory neurotransmitter ≈í‚â•-aminobutyric acid (GABA) to succinic acid (SA). Deficiency of SSADH in humans results in elevated levels of GABA and ≈í‚â•-Hydroxybutyric acid (GHB) which leads to psychomotor retardation, muscular hypotonia, non-progressive ataxia and seizures. In Escherichia coli, two genetically distinct forms of SSADHs had been described which are essential for preventing accumulation of toxic levels of succinic semialdehyde (SSA) in cells. Here we structurally characterise SSADH encoded by the E coli gabD gene and compare these data with the structure of human SSADH. Interestingly, in contrast to the human enzyme in the E. coli SSADH structure, electron density for the complete NADP+ cofactor in the binding sites is clearly evident; these data in particular revealing how the nicotinamide ring of the co-facto is positioned in each active site. Furthermore, our structural data suggest that a deletion of three amino acids in E. coli SSADH permits this enzyme to use NADP+ whereas in contrast the human enzyme utilises NAD+. Finally, the structure of E. coli SSADH gives additional insight into human mutations that result in disease.<br>
DOI: 10.4225/03/57428d242d678
title: The structure of granzyme C reveals an unusual mechanism of protease auto-inhibition (3FZZ)

description: Proteases act in important homeostatic pathways and are tightly regulated. Here, we report an unusual structural mechanism of regulation observed by the 2.5-A X-ray crystal structure of the serine protease, granzyme C. Although the active-site triad residues adopt canonical conformations, the oxyanion hole is improperly formed, and access to the primary specificity (S1) pocket is blocked through a reversible rearrangement involving Phe-191. Specifically, a register shift in the 190-strand preceding the active-site serine leads to Phe-191 filling the S1 pocket. Mutation of a unique Glu-Glu motif at positions 192-193 unlocks the enzyme, which displays chymase activity, and proteomic analysis confirms that activity of the wild-type protease can be released through interactions with an appropriate substrate. The 2.5-A structure of the unlocked enzyme reveals unprecedented flexibility in the 190-strand preceding the active-site serine that results in Phe-191 vacating the S1 pocket. Overall, these observations describe a broadly applicable mechanism of protease regulation that cannot be predicted by template-based modeling or bioinformatic approaches alone.<br>
DOI: 10.25794/reference/id52ofys
title: XCC8004-XANTHOMIX-20140103

description: Structural annotation using EuGene-P (v1.0, eugene-4.1c) (doi://10.1093/dnares/dst014) with - RNAseq libraries (see rnaseq.list.tsv) - Swiss-Prot Bacteria - reference proteome as training set (xanc8,xancb,xancp)
description: proteins sequence file
description: Public genome re-annotated using Xanthomix RNAseq data
description: mRNA sequence file
description: ncRNA, rRNA and tRNA
description: List of RNAseq dataset used to annotate
description: Correspondance table between this annotation and NCBI automatic annotation
description: Correspondance table between this annotation and public annotation (NC_007086.1)
description: Genes sequence file (include UTR sequence)
description: CDS sequence file
DOI: 10.4225/03/57428cc73e914
title: The 1.6 A Crystal Structure of the Catalytic Domain of PlyB, a Bacteriophage Lysin Active Against Bacillus anthracis. (2NW0)

description: Lysins are peptidoglycan hydrolases that are produced by bacteriophage and act to lyse the bacterial host cell wall during progeny phage release. Here, we describe the structure and function of a novel bacteriophage-derived lysin, PlyB, which displays potent lytic activity against the Bacillus anthracis-like strain ATCC 4342. This molecule comprises an N-terminal catalytic domain (PlyB(cat)) and a C-terminal bacterial SH3-like domain, SH3b. It is shown that both domains are required for effective catalytic activity against ATCC 4342. Further, PlyB has specific activity comparable to the phage lysin PlyG, an amidase being developed as a therapeutic against anthrax. In contrast to PlyG, however, the 1.6 A X-ray crystal structure of PlyB(cat) reveals that the catalytic domain adopts the glycosyl hydrolase (GH)-25, rather than phage T7 lysozyme-like fold. PlyB therefore represents a new class of anthrax lysin and a new defensive tool in the armament against anthrax-mediated bioterrorism.<br>
DOI: 10.4225/03/57428caa78f2b
title: Synthesis of new (-)-Bestatin-based inhibitor libraries reveals a novel binding mode in the S1 pocket of the essential malaria M1 metalloaminopeptidase.

description: The essential malarial PfA-M1 metalloaminopeptidase is a validated drug target that functions in the terminal stages of hemoglobin digestion. The natural product dipeptide mimetic, bestatin, is a potent inhibitor of PfA-M1 and provides an excellent scaffold for the development of novel research tools as well as more effective PfA-M1 inhibitors. Here we present a new, efficient and high yielding protocol for the synthesis of bestatin-derivatives from commercially available natural and unnatural N-Boc-D-amino acids. We developed a diverse library of bestatin derivatives with variants at the sidechain of either the Œ±-hydroxy-Œ≤-amino acid or the adjacent natural Œ±-amino acid. Surprisingly we found that large aromatic rings at the P1 position resulted in potent inhibition against PfA-M1, while small hydrophobic sidechains were favored at the P1‚Äô position. These data contrast previous studies that suggested the primary substrate specificity (S1) pocket of the PfA-M1 enzyme is unable to accommodate side-chains much larger than a P1 phenylalanine. To understand these apparently contradictory data, we determined the X-ray crystal structure of the PfA-M1 / bestatin-Tyr(OBzl) complex. The structure revealed a substantial inhibitor-induced rearrangement of the primary loop that forms the S1 pocket that permits accommodation of the bestatin-Tyr(OBzl) inhibitor. These findings are in contrast to most proteases where the S1 pocket is considered to define primary enzyme specificity through substantial rigidity. Taken together, our data provide important insights for the rational design of more potent and selective inhibitors of this enzyme, which may eventually be of therapeutic value for the treatment of malaria.
DOI: 10.4225/03/57428c34851a3
title: X-ray crystal structure of MENT: evidence for functional loop-sheet polymers in chromatin condensation. (2H4R)

description: Most serpins are associated with protease inhibition, and their ability to form loop-sheet polymers is linked to conformational disease and the human serpinopathies. Here we describe the structural and functional dissection of how a unique serpin, the non-histone architectural protein, MENT (Myeloid and Erythroid Nuclear Termination stage-specific protein), participates in DNA and chromatin condensation. Our data suggest that MENT contains at least two distinct DNA-binding sites, consistent with its simultaneous binding to the two closely juxtaposed linker DNA segments on a nucleosome. Remarkably, our studies suggest that the reactive centre loop, a region of the MENT molecule essential for chromatin bridging in vivo and in vitro, is able to mediate formation of a loop-sheet oligomer. These data provide mechanistic insight into chromatin compaction by a non-histone architectural protein and suggest how the structural plasticity of serpins has adapted to mediate physiological, rather than pathogenic, loop-sheet linkages.<br>
DOI: 10.4225/03/57428c5b7f179
title: The structural basis for membrane binding and pore formation by lymphocyte perforin

description: Natural killer cells and cytotoxic T lymphocytes accomplish the critically important function of killing virus-infected and neoplastic cells. They do this by releasing the pore-forming protein perforin and granzyme proteases from cytoplasmic granules into the cleft formed between the abutting killer and target cell membranes. Perforin, a 67-kilodalton multidomain protein, oligomerizes to form pores that deliver the pro-apoptopic granzymes into the cytosol of the target cell. The importance of perforin is highlighted by the fatal consequences of congenital perforin deficiency, with more than 50 different perforin mutations linked to familial haemophagocytic lymphohistiocytosis (type 2 FHL). Here we elucidate the mechanism of perforin pore formation by determining the X-ray crystal structure of monomeric murine perforin, together with a cryo-electron microscopy reconstruction of the entire perforin pore. Perforin is a thin ‘key-shaped’ molecule, comprising an amino-terminal membrane attack complex perforin-like (MACPF)/cholesterol dependent cytolysin (CDC) domain followed by an epidermal growth factor (EGF) domain that, together with the extreme carboxy-terminal sequence, forms a central shelf-like structure. A C-terminal C2 domain mediates initial, Ca2+-dependent membrane binding. Most unexpectedly, however, cryo-electron microscopy reveals that the orientation of the perforin MACPF domain in the pore is inside-out relative to the subunit arrangement in CDCs. These data reveal remarkable flexibility in the mechanism of action of the conserved MACPF/CDC fold and provide new insights into how related immune defence molecules such as complement proteins assemble into pores.
DOI: 10.4225/03/57428c7c8f14c
title: X-ray crystal structure of the fibrinolysis inhibitor {alpha}2-antiplasmin

description: The serpin alpha(2)-antiplasmin (SERPINF2) is the principal inhibitor of plasmin and inhibits fibrinolysis. Accordingly, alpha(2)-antiplasmin deficiency in humans results in uncontrolled fibrinolysis and a bleeding disorder. alpha(2)-antiplasmin is an unusual serpin, in that it contains extensive N- and C-terminal sequences flanking the serpin domain. The N-terminal sequence is crosslinked to fibrin by factor XIIIa, whereas the C-terminal region mediates the initial interaction with plasmin. To understand how this may happen, we have determined the 2.65A X-ray crystal structure of an N-terminal truncated murine alpha(2)-antiplasmin. The structure reveals that part of the C-terminal sequence is tightly associated with the body of the serpin. This would be anticipated to position the flexible plasmin-binding portion of the C-terminus in close proximity to the serpin Reactive Center Loop where it may act as a template to accelerate serpin/protease interactions.<br>
DOI: 10.6084/m9.figshare.3122938
title: A new specimen of <i>Velocisaurus unicus</i> (Theropoda, Abelisauroidea) from the Paso Córdoba locality (Santonian), Río Negro, Argentina

description: Abelisauroids are the most abundant theropods in the Cretaceous beds of Patagonia. They are traditionally subdivided into large-sized Abelisauridae and smaller Noasauridae. Here, we describe a new specimen of the small enigmatic abelisauroid <i>Velocisaurus unicus</i> Bonaparte, 1991, which was previously known from a single incomplete specimen from Neuquén City, Neuquén Province, Patagonia. The new material comes from the Santonian Bajo de la Carpa Formation (Late Cretaceous) at the Paso Córdova locality, Río Negro Province. It comprises an almost complete left hind limb and offers novel information about the anatomy of this poorly known abelisauroid. The new material shows that <i>Velocisaurus</i> is remarkable in having a very short, stout, and anteriorly bowed femur, which has a notably subtriangular cross-section at its proximal end. The tibia is long and slender, and the anterior surface of the distal end is anteroposteriorly flat and transversely expanded, with an enlarged surface for the ascending process of the astragalus. The pes has a stout third metatarsal, rod-like metatarsals II and IV, and highly modified phalanges of digit IV. The unique combination of characters of <i>Velocisaurus</i> indicates that this taxon belongs to a still poorly understood radiation of gracile-limbed abelisauroids. The inclusion of <i>Velocisaurus</i> in a comprehensive phylogenetic analysis recovers a monophyletic Noasauridae, but with only very weak support. Detailed analysis of features supporting the inclusion of <i>Velocisaurus</i> within Noasauridae is discussed, and their implications for abelisauroid phylogeny are revisited. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Brissón Egli, F., F. L. Agnolín, and Fernando Novas. 2016. A new specimen of <i>Velocisaurus unicus</i> (Theropoda, Abelisauroidea) from the Paso Córdoba locality (Santonian), Río Negro, Argentina. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1119156.
DOI: 10.4225/03/57428c1393e72
title: Virulence-associated subtilisin-like proteases that use a novel disulphide-tethered exosite to mediate substrate specificity (3LPA, 3LPC, 3LPD)

description: Many bacterial pathogens produce extracellular proteases that are involved in the degradation of the host extracellular matrix. Dichelobacter nodosus, which causes ovine footrot, is one such pathogen, Mutagenesis and virulence studies revealed that AprV2, one of three secreted subtilisin-like D.¬†nodosus proteases, is required for virulence. Our work challenges the previous hypothesis that the elastase activity of AprV2 is important for disease progression, since aprV2 mutants were virulent when complemented with a variant with impaired elastase activity. These data reveal that an unusual extended disulphide-tethered loop functions as an exosite that governs the ability of AprV2 to degrade insoluble extracellular matrix components. The disulphide bond and Tyr92, located at the exposed end of the loop, were functionally important. Bioinformatics suggests that other pathogens utilize a similar mechanism, providing a new paradigm for understanding the role of proteases in disease.<br>
DOI: 10.6084/m9.figshare.3122938.v1
title: A new specimen of <i>Velocisaurus unicus</i> (Theropoda, Abelisauroidea) from the Paso Córdoba locality (Santonian), Río Negro, Argentina

description: Abelisauroids are the most abundant theropods in the Cretaceous beds of Patagonia. They are traditionally subdivided into large-sized Abelisauridae and smaller Noasauridae. Here, we describe a new specimen of the small enigmatic abelisauroid <i>Velocisaurus unicus</i> Bonaparte, 1991, which was previously known from a single incomplete specimen from Neuquén City, Neuquén Province, Patagonia. The new material comes from the Santonian Bajo de la Carpa Formation (Late Cretaceous) at the Paso Córdova locality, Río Negro Province. It comprises an almost complete left hind limb and offers novel information about the anatomy of this poorly known abelisauroid. The new material shows that <i>Velocisaurus</i> is remarkable in having a very short, stout, and anteriorly bowed femur, which has a notably subtriangular cross-section at its proximal end. The tibia is long and slender, and the anterior surface of the distal end is anteroposteriorly flat and transversely expanded, with an enlarged surface for the ascending process of the astragalus. The pes has a stout third metatarsal, rod-like metatarsals II and IV, and highly modified phalanges of digit IV. The unique combination of characters of <i>Velocisaurus</i> indicates that this taxon belongs to a still poorly understood radiation of gracile-limbed abelisauroids. The inclusion of <i>Velocisaurus</i> in a comprehensive phylogenetic analysis recovers a monophyletic Noasauridae, but with only very weak support. Detailed analysis of features supporting the inclusion of <i>Velocisaurus</i> within Noasauridae is discussed, and their implications for abelisauroid phylogeny are revisited. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Brissón Egli, F., F. L. Agnolín, and Fernando Novas. 2016. A new specimen of <i>Velocisaurus unicus</i> (Theropoda, Abelisauroidea) from the Paso Córdoba locality (Santonian), Río Negro, Argentina. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1119156.
DOI: 10.4225/03/57428bfb1ec91
title: Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase (3EBG, 3EBH, 3EBI)

description: This experiment holds 3EBG, 3EBH and 3EBI.
DOI: 10.6084/m9.figshare.3122941
title: Dielectric anomaly and giant deuteration effect in a H-bond trimeric co-crystal [4, 4'-Bipyridine]<sub>2</sub>[1,4-dihydroxybenzene]

description: Co-crystal [4,4<b>ʹ</b>-bipyridine]<sub>2</sub>[1,4-dihydroxybenzene] (<b>1</b>) was prepared by evaporating methanol solution of 4,4<b>ʹ</b>-bipyridine with 1,4-dihydroxybenzene at 4°C. <b>1</b> shows a fascinating dielectric anomaly with a maximum at ~210 K, which is independent on ac frequency. However, the absence of thermal anomaly and structural phase transition is related to the dielectric anomaly. The co-crystal [4,4<b>ʹ</b>-bipyridine]<sub>2</sub>[1,4-dihydroxybenzene-d<sub>2</sub>] (<b>2</b>) was further obtained via H<sup>+</sup>/D<sup>+</sup> exchange in <b>1</b> and the deuteration gives rise to the maximum shifting to 254 K in the dielectric spectrum of <b>2</b>. The dielectric anomaly corresponds to disorder-to-order transformation of H<sup>+</sup>/D<sup>+</sup> in the O–H/D···N H-bond in <b>1</b> and <b>2</b>.
DOI: 10.6084/m9.figshare.3122920
title: A study on water quality and trophic state of Akgöl Lagoon (Mersin, Turkey)

description: This study aimed to determine the physicochemical characteristics of the water quality and trophic state of Akgöl Lagoon located in the eastern Mediterranean. Cluster analysis clearly revealed the spatial heterogeneity classifying sampling stations as saline and freshwater/brackish water sites. A multivariate analysis of variance followed by principal component analysis supported that salinity was major factor affecting physicochemical water quality variations in the lagoon. As salinity was mainly governed by freshwater inflows depending on agricultural irrigation, it can be proposed that water quality was significantly influenced from freshwater use by human activities. The parameters used as predictors (total nitrogen, total phosphorus, chlorophyll <i>a</i> and Secchi disk transparency) yielded different trophic states for the lagoon. However, as chlorophyll is a better predictor than the other indices, it was concluded that the Akgöl Lagoon is at mesotrophic status.
DOI: 10.6084/m9.figshare.3122941.v2
title: Dielectric anomaly and giant deuteration effect in a H-bond trimeric co-crystal [4, 4'-Bipyridine]<sub>2</sub>[1,4-dihydroxybenzene]

description: Co-crystal [4,4<b>ʹ</b>-bipyridine]<sub>2</sub>[1,4-dihydroxybenzene] (<b>1</b>) was prepared by evaporating methanol solution of 4,4<b>ʹ</b>-bipyridine with 1,4-dihydroxybenzene at 4°C. <b>1</b> shows a fascinating dielectric anomaly with a maximum at ~210 K, which is independent on ac frequency. However, the absence of thermal anomaly and structural phase transition is related to the dielectric anomaly. The co-crystal [4,4<b>ʹ</b>-bipyridine]<sub>2</sub>[1,4-dihydroxybenzene-d<sub>2</sub>] (<b>2</b>) was further obtained via H<sup>+</sup>/D<sup>+</sup> exchange in <b>1</b> and the deuteration gives rise to the maximum shifting to 254 K in the dielectric spectrum of <b>2</b>. The dielectric anomaly corresponds to disorder-to-order transformation of H<sup>+</sup>/D<sup>+</sup> in the O–H/D···N H-bond in <b>1</b> and <b>2</b>.
DOI: 10.6084/m9.figshare.3122920.v1
title: A study on water quality and trophic state of Akgöl Lagoon (Mersin, Turkey)

description: This study aimed to determine the physicochemical characteristics of the water quality and trophic state of Akgöl Lagoon located in the eastern Mediterranean. Cluster analysis clearly revealed the spatial heterogeneity classifying sampling stations as saline and freshwater/brackish water sites. A multivariate analysis of variance followed by principal component analysis supported that salinity was major factor affecting physicochemical water quality variations in the lagoon. As salinity was mainly governed by freshwater inflows depending on agricultural irrigation, it can be proposed that water quality was significantly influenced from freshwater use by human activities. The parameters used as predictors (total nitrogen, total phosphorus, chlorophyll <i>a</i> and Secchi disk transparency) yielded different trophic states for the lagoon. However, as chlorophyll is a better predictor than the other indices, it was concluded that the Akgöl Lagoon is at mesotrophic status.
DOI: 10.6084/m9.figshare.3122941.v1
title: Dielectric anomaly and giant deuteration effect in a H-bond trimeric co-crystal [4, 4’-bipyridine]<sub>2</sub>[1,4-dihydroxybenzene]

description: Co-crystal [4,4’-bipyridine]<sub>2</sub>[1,4-dihydroxybenzene] (<b>1</b>) was prepared by evaporating methanol solution of 4, 4’-bipyridine with 1, 4-dihydroxybenzene at 4 °C. <b>1</b> shows a fascinating dielectric anomaly with a maximum at ca. 210 K, which is independent on ac frequency. However, the absence of thermal anomaly and structural phase transition is related to the dielectric anomaly. The co-crystal [4,4’-bipyridine]<sub>2</sub>[1,4-dihydroxybenzene-d<sub>2</sub>] (<b>2</b>) was further obtained via H<sup>+</sup>/D<sup>+</sup> exchange in <b>1</b> and the deuteration gives rise to the maximum shifting to 254 K in the dielectric spectrum of <b>2</b>. The dielectric anomaly corresponds to disorder-to-order transformation of H<sup>+</sup>/D<sup>+</sup> in the O-H/D…N H-bond in <b>1</b> and <b>2</b>.
DOI: 10.6084/m9.figshare.3122734
title: SCS: Self-Compassion Scale, validation of the French version

description: We validated the French version of the Self-Compassion Scale (SCS) on a community sample. Convergent validity was tested with happiness (Bonh), satisfaction with life (LS), depression (BDI), mindfulness (PLC) and affect (PANAS).<br>
DOI: 10.6084/m9.figshare.3122752
title: Effect of detection heterogeneity on N-mixture models

description: These datasets have compiled results from multiple model runs. They do not contain the raw simulated abundance data from each model run. See the Veech et al. (2016) paper in Methods in Ecology and Evolution for more details.
DOI: 10.6084/m9.figshare.3122713
title: Bilateral retinal hemorrhages following finger pressure against the soft palate (الترفيع) in recessive <i>CRB1</i>-related retinopathy

description: <i>Purpose</i>: To report two siblings with <i>CRB1</i>-related retinopathy who developed retinal hemorrhages following village traditional treatment of upward finger pressure against the soft palate (). <i>Methods</i>: A retrospective case series. <i>Results</i>: Two sisters were clinically diagnosed and genetically confirmed to have recessive <i>CRB1</i>-related retinal dystrophy. The family did not accept the condition as non-treatable and took both sisters for a traditional village therapy, consisting of several sessions of intense upward index finger pressure by the healer against the soft palate for each child. When examined following this therapy, both sisters had bilateral pre-retinal hemorrhages which were not present before the intervention and resolved without sequelae over the next several months. <i>Conclusions</i>: The traditional village therapy may have compromised retinal venous outflow and/or provoked a Valsalva phenomenon, leading to the bilateral retinal hemorrhages. The fact that this occurred bilaterally and in both sisters supports the concept of relative vessel wall incompetence as part of <i>CRB1</i>-related retinopathy.