bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient Modeling of An Anatomy‐Based Face and Fast 3D Facial Expression Synthesis
Authors: Zhang Yu , Prakash Edmond C. , Sung Eric 
Published: July 2003

AbstractThis paper presents new methods for efficient modeling and animation of an hierarchical facial model that conforms to the human face anatomy for realistic and fast 3D facial expression synthesis. The facial model has a skin–muscle–skull structure. The deformable skin model directly simulates the nonlinear visco‐elastic behavior of soft tissue and effectively prevents model collapse. The construction of facial muscles is achieved by using an efficient muscle mapping approach. Based on a cylindrical projection of the texture‐mapped facial surface and wire‐frame skin and skull meshes, this approach ensures different muscles to be located at the anatomically correct positions between the skin and skull layers. For computational efficiency, we devise an adaptive simulation algorithm which uses either a semi‐implicit integration scheme or a quasi‐static solver to compute the relaxation by traversing the designed data structures in a breadth‐first order. The algorithm runs in real‐time and has successfully synthesized realistic facial expressions.ACM CSS:I.3.5 Computer Graphics: Computational Geometry and Object Modelling—physically based modelling;I.3.7 Computer Graphics: Three‐Dimensional Graphics and Realism—animation;
Crystal Structure of the YchF Protein Reveals Binding Sites for GTP and Nucleic Acid
Authors: Teplyakov Alexey , Obmolova Galina , Chu Seung Y. , Toedt John , Eisenstein Edward , Howard Andrew J. , Gilliland Gary L. 
Published: July 2003

ABSTRACTThe bacterial protein encoded by the geneychFis 1 of 11 universally conserved GTPases and the only one whose function is unknown. The crystal structure determination of YchF was sought to help with the functional assignment of the protein. The YchF protein fromHaemophilus influenzaewas cloned and expressed, and the crystal structure was determined at 2.4 Å resolution. The polypeptide chain is folded into three domains. The N-terminal domain has a mononucleotide binding fold typical for the P-loop NTPases. An 80-residue domain next to it has a pronounced α-helical coiled coil. The C-terminal domain features a six-stranded half-barrel that curves around an α-helix. The crablike three-domain structure of YchF suggests the binding site for a double-stranded nucleic acid in the cleft between the domains. The structure of the putative GTP-binding site is consistent with the postulated guanine specificity of the protein. Fluorescence measurements have demonstrated the ability of YchF to bind a double-stranded nucleic acid and GTP. Taken together with other experimental data and genomic analysis, these results suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translation factor.
Crystal Structure ofd-Hydantoinase fromBurkholderia pickettiiat a Resolution of 2.7 Angstroms: Insights into the Molecular Basis of Enzyme Thermostability
Authors: Xu Zhen , Liu Yunqing , Yang Yunliu , Jiang Weihong , Arnold Eddy , Ding Jianping 
Published: July 2003

ABSTRACTd-Hydantoinase (d-HYD) is an industrial enzyme that is widely used in the production ofd-amino acids which are precursors for semisynthesis of antibiotics, peptides, and pesticides. This report describes the crystal structure ofd-hydantoinase fromBurkholderia pickettii(HYDBp) at a 2.7-Å resolution. The structure of HYDBpconsists of a core (α/β)8triose phosphate isomerase barrel fold and a β-sheet domain, and the catalytic active site consists of two metal ions and six highly conserved amino acid residues. Although HYDBpshares only moderate sequence similarity withd-HYDs fromThermussp. (HYDTsp) andBacillus stearothermophilus(HYDBst), whose structures have recently been solved, the overall structure and the structure of the catalytic active site are strikingly similar. Nevertheless, the amino acids that compose the substrate-binding site are less conserved and have different properties, which might dictate the substrate specificity. Structural comparison has revealed insights into the molecular basis of the differential thermostability ofd-HYDs. The more thermostable HYDTspcontains more aromatic residues in the interior of the structure than HYDBpand HYDBst. Changes of large aromatic residues in HYDTspto smaller residues in HYDBpor HYDBstdecrease the hydrophobicity and create cavities inside the structure. HYDTsphas more salt bridges and hydrogen-bonding interactions and less oxidation susceptible Met and Cys residues on the protein surface than HYDBpand HYDBst. Besides, HYDTspalso contains more rigid Pro residues. These factors are likely to make major contributions to the varying thermostability of these enzymes. This information could be exploited in helping to engineer more thermostable mesophilic enzymes.
Dimer-Tetramer Transition between Solution and Crystalline States of Streptavidin and Avidin Mutants
Authors: Pazy Yael , Eisenberg-Domovich Yael , Laitinen Olli H. , Kulomaa Markku S. , Bayer Edward A. , Wilchek Meir , Livnah Oded 
Published: July 2003

ABSTRACT

The biotin-binding tetrameric proteins, streptavidin from
Streptomyces avidinii
and chicken egg white avidin, are excellent models for the study of subunit-subunit interactions of a multimeric protein. Efforts are thus being made to prepare mutated forms of streptavidin and avidin, which would form monomers or dimers, in order to examine their effect on quaternary structure and assembly. In the present communication, we compared the crystal structures of binding site W→K mutations in streptavidin and avidin. In solution, both mutant proteins are known to form dimers, but upon crystallization, both formed tetramers with the same parameters as the native proteins. All of the intersubunit bonds were conserved, except for the hydrophobic interaction between biotin and the tryptophan that was replaced by lysine. In the crystal structure, the binding site of the mutated apo-avidin contains 3 molecules of structured water instead of the 5 contained in the native protein. The lysine side chain extends in a direction opposite that of the native tryptophan, the void being partially filled by an adjacent lysine residue. Nevertheless, the binding-site conformation observed for the mutant tetramer is an artificial consequence of crystal packing that would not be maintained in the solution-phase dimer. It appears that the dimer-tetramer transition may be concentration dependent, and the interaction among subunits obeys the law of mass action.
Crystal Structure of a Putative Methyltransferase from
Mycobacterium tuberculosis
: Misannotation of a Genome Clarified by Protein Structural Analysis
Authors: Johnston Jodie M. , Arcus Vickery L. , Morton Craig J. , Parker Michael W. , Baker Edward N. 
Published: July 2003

ABSTRACT

Bioinformatic analyses of whole genome sequences highlight the problem of identifying the biochemical and cellular functions of many gene products that are at present uncharacterized. The open reading frame Rv3853 from
Mycobacterium tuberculosis
has been annotated as
menG
and assumed to encode an
S
-adenosylmethionine (SAM)-dependent methyltransferase that catalyzes the final step in menaquinone biosynthesis. The Rv3853 gene product has been expressed, refolded, purified, and crystallized in the context of a structural genomics program. Its crystal structure has been determined by isomorphous replacement and refined at 1.9 Å resolution to an
R
factor of 19.0% and
R
free
of 22.0%. The structure strongly suggests that this protein is not a SAM-dependent methyltransferase and that the gene has been misannotated in this and other genomes that contain homologs. The protein forms a tightly associated, disk-like trimer. The monomer fold is unlike that of any known SAM-dependent methyltransferase, most closely resembling the phosphohistidine domains of several phosphotransfer systems. Attempts to bind cofactor and substrate molecules have been unsuccessful, but two adventitiously bound small-molecule ligands, modeled as tartrate and glyoxalate, are present on each monomer. These may point to biologically relevant binding sites but do not suggest a function. In silico screening indicates a range of ligands that could occupy these and other sites. The nature of these ligands, coupled with the location of binding sites on the trimer, suggests that proteins of the Rv3853 family, which are distributed throughout microbial and plant species, may be part of a larger assembly binding to nucleic acids or proteins.
Crystal Structure of the Hyperthermophilic Archaeal DNA-Binding Protein Sso10b2 at a Resolution of 1.85 Angstroms
Authors: Chou Chia-Cheng , Lin Ting-Wan , Chen Chin-Yu , Wang Andrew H.-J. 
Published: July 2003

ABSTRACT

The crystal structure of a small, basic DNA binding protein, Sso10b2, from the thermoacidophilic archaeon
Sulfolobus solfataricus
was determined by the Zn multiwavelength anomalous diffraction method and refined to 1.85 Å resolution. The 89-amino-acid protein adopts a βαβαββ topology. The structure is similar to that of Sso10b1 (also called Alba) from the same organism. However, Sso10b2 contains an arginine-rich loop RDRRR motif, which may play an important role in nucleic acid binding. There are two independent Sso10b2 proteins in the asymmetric unit, and a plausible stable dimer could be deduced from the crystal structure. Topology comparison revealed that Sso10b2 is similar to several RNA-binding proteins, including IF3-C, YhhP, and DNase I. Models of the Sso10b2 dimer bound to either B-DNA or A-DNA have been constructed.
A Novel Adenylate Binding Site Confers Phosphopantetheine Adenylyltransferase Interactions with Coenzyme A
Authors: Izard Tina 
Published: July 2003

ABSTRACT

Phosphopantetheine adenylyltransferase (PPAT) regulates the key penultimate step in the essential coenzyme A (CoA) biosynthetic pathway. PPAT catalyzes the reversible transfer of an adenylyl group from Mg
2+
:ATP to 4′-phosphopantetheine to form 3′-dephospho-CoA (dPCoA) and pyrophosphate. The high-resolution crystal structure of PPAT complexed with CoA has been determined. Remarkably, CoA and the product dPCoA bind to the active site in distinct ways. Although the phosphate moiety within the phosphopantetheine arm overlaps, the pantetheine arm binds to the same pocket in two distinct conformations, and the adenylyl moieties of these two ligands have distinct binding sites. Moreover, the PPAT:CoA crystal structure confirms the asymmetry of binding to the two trimers within the hexameric enzyme. Specifically, the pantetheine arm of CoA bound to one protomer within the asymmetric unit displays the dPCoA-like conformation with the adenylyl moiety disordered, whereas CoA binds the twofold-related protomer in an ordered and unique fashion.
Determinants of the Src Homology Domain 3-Like Fold
Authors: D'Aquino J. Alejandro , Ringe Dagmar 
Published: July 2003

ABSTRACTIn eukaryotes, the Src homology domain 3 (SH3) is a very important motif in signal transduction. SH3 domains recognize poly-proline-rich peptides and are involved in protein-protein interactions. Until now, the existence of SH3 domains has not been demonstrated in prokaryotes. However, the structure of the C-terminal domain of DtxR clearly shows that the fold of this domain is very similar to that of the SH3 domain. In addition, there is evidence that the C-terminal domain of DtxR binds to poly-proline-rich regions. Other bacterial proteins have domains that are structurally similar to the SH3 domain but whose functions are unknown or differ from that of the SH3 domain. The observed similarities between the structures of the C-terminal domain of DtxR and the SH3 domain constitute a perfect system to gain insight into their function and information about their evolution. Our results show that the C-terminal domain of DtxR shares a number of conserved key hydrophobic positions not recognizable from sequence comparison that might be responsible for the integrity of the SH3-like fold. Structural alignment of an ensemble of such domains from unrelated proteins shows a common structural core that seems to be conserved despite the lack of sequence similarity. This core constitutes the minimal requirements of protein architecture for the SH3-like fold.
The Purine Repressor of
Bacillus subtilis
: a Novel Combination of Domains Adapted for Transcription Regulation
Authors: Sinha Sangita C. , Krahn Joseph , Shin Byung Sik , Tomchick Diana R. , Zalkin Howard , Smith Janet L. 
Published: July 2003

ABSTRACT

The purine repressor from
Bacillus subtilis
, PurR, represses transcription from a number of genes with functions in the synthesis, transport, and metabolism of purines. The 2.2-Å crystal structure of PurR reveals a two-domain protein organized as a dimer. The larger C-terminal domain belongs to the PRT structural family, in accord with a sequence motif for binding the inducer phosphoribosylpyrophosphate (PRPP). The PRT domain is fused to a smaller N-terminal domain that belongs to the winged-helix family of DNA binding proteins. A positively charged surface on the winged-helix domain likely binds specific DNA sequences in the recognition site. A second positively charged surface surrounds the PRPP site at the opposite end of the PurR dimer. Conserved amino acids in the sequences of PurR homologs in 21 gram-positive bacteria cluster on the proposed recognition surface of the winged-helix domain and around the PRPP binding site at the opposite end of the molecule, supporting a common function of DNA and PRPP binding for all of the proteins. The structure supports a binding mechanism in which extended regions of DNA interact with extensive protein surface. Unlike most PRT proteins, which are phosphoribosyltransferases (PRTases), PurR lacks catalytic activity. This is explained by a tyrosine side chain that blocks the site for a nucleophile cosubstrate in PRTases. Thus,
B. subtilis
has adapted an enzyme fold to serve as an effector-binding domain and has used it in a novel combination with the DNA-binding winged-helix domain as a repressor of purine genes.
Functional Dissection of the
Bacillus subtilis pur
Operator Site
Authors: Bera Aloke Kumar , Zhu Jianghai , Zalkin Howard , Smith Janet L. 
Published: July 2003

ABSTRACT

Bacillus subtilis
PurR represses transcription of several genes involved in purine synthesis, metabolism, and transport and cofactor synthesis. PurR binds specifically to DNAs containing an inverted repeat of a 14-nucleotide “PurBox” located in the upstream control regions of genes in the PurR regulon. Further biochemical investigation of the interaction of PurR with a series of shortened upstream DNA fragments of the
pur
operon determined the minimum length and specificity elements of the operator. The relative affinities of the two PurBoxes differ significantly, such that upstream PurBox1 (−81 to −68 relative to the transcription start site) is designated “strong” and downstream PurBox2 (−49 to −36) is designated “weak.” Two PurBoxes are required for high-affinity PurR binding, and one of these must be strong. The shortest DNA construct with high affinity for PurR is a 74-bp perfect palindrome in which weak PurBox2 and its flanking sequences are replaced by strong PurBox1 and flanking sequences. Two PurR dimers bind to this symmetric construct. Phosphoribosylpyrophosphate (PRPP), the effector molecule that reduces affinity of PurR for DNA, requires one weak PurBox in the DNA construct to inhibit PurR binding. PRPP binds, as expected, to a PRPP-motif in PurR. A tracks outside the central conserved CGAA sequence of the PurBox may facilitate DNA bending, leading to a proposal for strong and weak designations of PurBoxes in the control regions of other genes regulated by PurR.
Structure of a Coenzyme A Pyrophosphatase from
Deinococcus radiodurans
: a Member of the Nudix Family
Authors: Kang Lin-Woo , Gabelli Sandra B. , Bianchet Mario A. , Xu Wen Lian , Bessman Maurice J. , Amzel L. Mario 
Published: July 2003

ABSTRACT

Gene
Dr1184
from
Deinococcus radiodurans
codes for a Nudix enzyme (DR-CoAse) that hydrolyzes the pyrophosphate moiety of coenzyme A (CoA). Nudix enzymes with the same specificity have been found in yeast, humans, and mice. The three-dimensional structure of DR-CoAse, the first of a Nudix hydrolase with this specificity, reveals that this enzyme contains, in addition to the fold observed in other Nudix enzymes, insertions that are characteristic of a CoA-hydrolyzing Nudix subfamily. The structure of the complex of the enzyme with Mg
2+
, its activating cation, reveals the position of the catalytic site. A helix, part of the N-terminal insertion, partially occludes the binding site and has to change its position to permit substrate binding. Comparison of the structure of DR-CoAse to those of other Nudix enzymes, together with the location in the structure of the sequence characteristic of CoAses, suggests a mode of binding of the substrate to the enzyme that is compatible with all available data.
Structure ofMycobacterium tuberculosisMethionine Sulfoxide Reductase A in Complex with Protein-Bound Methionine
Authors: Taylor Alexander B. , Benglis, David M. , Dhandayuthapani Subramanian , Hart P. John 
Published: July 2003

ABSTRACTPeptide methionine sulfoxide reductase (MsrA) repairs oxidative damage to methionine residues arising from reactive oxygen species and reactive nitrogen intermediates. MsrA activity is found in a wide variety of organisms, and it is implicated as one of the primary defenses against oxidative stress. Disruption of the gene encoding MsrA in several pathogenic bacteria responsible for infections in humans results in the loss of their ability to colonize host cells. Here, we present the X-ray crystal structure of MsrA from the pathogenic bacteriumMycobacterium tuberculosisrefined to 1.5 Å resolution. In contrast to the three catalytic cysteine residues found in previously characterized MsrA structures,M. tuberculosisMsrA represents a class containing only two functional cysteine residues. The structure reveals a methionine residue of one MsrA molecule bound at the active site of a neighboring molecule in the crystal lattice and thus serves as an excellent model for protein-bound methionine sulfoxide recognition and repair.
X-Ray Crystal Structure of the Multidomain Endoglucanase Cel9G from
Clostridium cellulolyticum
Complexed with Natural and Synthetic Cello-Oligosaccharides
Authors: Mandelman David , Belaich Anne , Belaich J. P. , Aghajari Nushin , Driguez Hugues , Haser Richard 
Published: July 2003

ABSTRACT

Complete cellulose degradation is the first step in the use of biomass as a source of renewable energy. To this end, the engineering of novel cellulase activity, the activity responsible for the hydrolysis of the β-1,4-glycosidic bonds in cellulose, is a topic of great interest. The high-resolution X-ray crystal structure of a multidomain endoglucanase from
Clostridium cellulolyticum
has been determined at a 1.6-Å resolution. The endoglucanase, Cel9G, is comprised of a family 9 catalytic domain attached to a family III
c
cellulose-binding domain. The two domains together form a flat platform onto which crystalline cellulose is suggested to bind and be fed into the active-site cleft for endolytic hydrolysis. To further dissect the structural basis of cellulose binding and hydrolysis, the structures of Cel9G in the presence of cellobiose, cellotriose, and a DP-10 thio-oligosaccharide inhibitor were resolved at resolutions of 1.7, 1.8, and 1.9 Å, respectively.
The 1.3-Angstrom-Resolution Crystal Structure of β-Ketoacyl-Acyl Carrier Protein Synthase II fromStreptococcus pneumoniae
Authors: Price Allen C. , Rock Charles O. , White Stephen W. 
Published: July 2003

ABSTRACTThe β-ketoacyl-acyl carrier protein synthases are members of the thiolase superfamily and are key regulators of bacterial fatty acid synthesis. As essential components of the bacterial lipid metabolic pathway, they are an attractive target for antibacterial drug discovery. We have determined the 1.3 Å resolution crystal structure of the β-ketoacyl-acyl carrier protein synthase II (FabF) from the pathogenic organismStreptococcus pneumoniae. The protein adopts a duplicated βαβαβαββ fold, which is characteristic of the thiolase superfamily. The two-fold pseudosymmetry is broken by the presence of distinct insertions in the two halves of the protein. These insertions have evolved to bind the specific substrates of this particular member of the thiolase superfamily. Docking of the pantetheine moiety of the substrate identifies the loop regions involved in substrate binding and indicates roles for specific, conserved residues in the substrate binding tunnel. The active site triad of this superfamily is present in spFabF as His 303, His 337, and Cys 164. Near the active site is an ion pair, Glu 346 and Lys 332, that is conserved in the condensing enzymes but is unusual in our structure in being stabilized by an Mg2+ion which interacts with Glu 346. The active site histidines interact asymmetrically with Lys 332, whose positive charge is closer to His 303, and we propose a specific role for the lysine in polarizing the imidazole ring of this histidine. This asymmetry suggests that the two histidines have unequal roles in catalysis and provides new insights into the catalytic mechanisms of these enzymes.
The Crystal Structure of Shikimate Dehydrogenase (AroE) Reveals a Unique NADPH Binding Mode
Authors: Ye Sheng , von Delft Frank , Brooun Alexei , Knuth Mark W. , Swanson Ronald V. , McRee Duncan E. 
Published: July 2003

ABSTRACT

Shikimate dehydrogenase catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. We report the first X-ray structure of shikimate dehydrogenase from
Haemophilus influenzae
to 2.4-Å resolution and its complex with NADPH to 1.95-Å resolution. The molecule contains two domains, a catalytic domain with a novel open twisted α/β motif and an NADPH binding domain with a typical Rossmann fold. The enzyme contains a unique glycine-rich P-loop with a conserved sequence motif, GAGGXX, that results in NADPH adopting a nonstandard binding mode with the nicotinamide and ribose moieties disordered in the binary complex. A deep pocket with a narrow entrance between the two domains, containing strictly conserved residues primarily contributed by the catalytic domain, is identified as a potential 3-dehydroshikimate binding pocket. The flexibility of the nicotinamide mononucleotide portion of NADPH may be necessary for the substrate 3-dehydroshikimate to enter the pocket and for the release of the product shikimate.