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Splitting statistical potentials into meaningful scoring functions: Testing the prediction of near-native structures from decoy conformations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We have introduced a method to split knowledge-based potentials and to solve the problem of defining a reference state. The new scores have detected near-native structures as accurately as state-of-art methods and have been successful to identify wrongly modeled regions of many near-native conformations. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - November 16, 2009 Category: Molecular Biology Authors: Patrick AloyBaldo Oliva Source Type: journals

The structural and functional determinants of the Axin and Dishevelled DIX domainsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This report provides the first explanation of the mutant phenotypes caused by non-synonymous substitutions in the Dishevelled and Axin DIX domain by correlating their presumed functional significance with molecular structure. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - November 12, 2009 Category: Molecular Biology Authors: Matthias EhebauerAlfonso Martinez Arias Source Type: journals

Interacting with the biomolecular solvent accessible surface via a haptic feedback deviceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: By using the software, named HaptiMol ISAS (available from www.haptimol.co.uk), one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water accessibility of the biomolecular surface that cannot be so easily attained using conventional molecular graphics software. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - October 27, 2009 Category: Molecular Biology Authors: Matthew StocksSteven HaywardStephen Laycock Source Type: journals

Partially-supervised protein subclass discovery with simultaneous annotation of functional residuesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The partially-supervised clustering revealed biologically meaningful sub-families even for highly heterogeneous domains and the predicted functional residues provide insights into the basis of the different substrate specificities. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - October 26, 2009 Category: Molecular Biology Authors: Benjamin GeorgiJorg SchultzAlexander Schliep Source Type: journals

Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The quaternary structure of Nce103 resembles the typical plant type beta-CAs of known structure, with an N-terminal arm indispensable for the enzymatic activity. Comparative structure analysis enables us to draw a possible tunnel for the substrate to access the active site which is located at the bottom of a funnel-shaped substrate pocket. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - October 23, 2009 Category: Molecular Biology Authors: Yan-Bin TengYong-Liang JiangYong-xing HeWei-Wei HeFu-Ming LianYuxing ChenCong-Zhao Zhou Source Type: journals

Conformational changes and loose packing promote E. coli Tryptophanase cold labilityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We suggest that cold lability of E. coli Trpases is primarily affected by PLP release. The enhanced loss of activity of the three mutants is presumably due to the reduced size of the side chain of the amino acids. This prevents the tight assembly of the active tetramer, making it more susceptible to the cold driven changes in hydrophobic interactions which facilitate PLP release. The hydrophobic interactions along the non catalytic interface overshadow the effect of point mutations and may account for the differences in the dissociation of E. coli Trpase to dimers and P. vulgaris Trpase to monomers. (Source: B...
Source: BMC Structural Biology - Latest articles - October 7, 2009 Category: Molecular Biology Authors: Anna KoganGarik GdalevskyRivka Cohen-LuriaYehuda GoldgurRobert PhillipsAbraham ParolaOrna Almog Source Type: journals

Molecular models for intrastrand DNA G-quadruplexes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Molecular models have been generated for a large number of G_3 X_n1 G_3 X_n2 G_3 X_n3 G_3 sequences. For a given sequence not all topologies are possible with the available repertoire of fragments due to steric hindrance and low superimposability. Since all molecular models are generated by fragments coming from observed quadruplex structures, molecular models are in principle reliable and may be used for interpretation of experimental data. Some examples of applications are given. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - October 6, 2009 Category: Molecular Biology Authors: Federico FogolariHaritha HaridasAlessandra CorazzaPaolo ViglinoDavide Cora'Michele CaselleGennaro EspositoLuigi Xodo Source Type: journals

Structural and functional characteristics of xenavidin, the first frog avidin from Xenopus tropicalisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The novel data reported here provide information about the biochemically and structurally important determinants of biotin binding. This information may facilitate the discovery of novel tools for biotechnology. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - September 28, 2009 Category: Molecular Biology Authors: Juha MaattaSatu HelppolainenVesa HytonenMark JohnsonMarkku KulomaaTomi AirenneHenri Nordlund Source Type: journals

Identification of hemagglutinin structural domain and polymorphisms which may modulate swine H1N1 interactions with human receptorEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results (i) contribute to better understanding of the origin of the novel A/H1N1 influenza virus, (ii) provide a tool for monitoring its molecular evolution (iii) predicts hotspots associated with enhanced infectivity in humans and (iv) identify therapeutic and diagnostic targets for prevention and treatment of A/H1N1 infection. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - September 27, 2009 Category: Molecular Biology Authors: Veljko VeljkovicHenry NimanSanja GlisicNevena VeljkovicVladimir PerovicClaude Muller Source Type: journals

Mirrors in the PDB: left-handed alpha-turns guide design with D-amino acidsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: By examining left-handed -turns containing L-amino acids, new interaction motifs for incorporating D-amino acids into right-handed alpha-helices are identified. These will provide a basis for de novo design of novel heterochiral protein folds. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - September 21, 2009 Category: Molecular Biology Authors: Srinivas AnnavarapuVikas Nanda Source Type: journals

The Sam domain of the lipid phosphatase Ship2 adopts a common model to interact with Arap3-Sam and EphA2-SamEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our studies further clarify the structural features that are relevant for Sam-Sam interactions involving Ship2 and give additional hints that could be used for the identification of new molecules able to selectively inhibit Sam-Sam associations. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - September 17, 2009 Category: Molecular Biology Authors: Marilisa LeoneJason CellittiMaurizio Pellecchia Source Type: journals

Low-resolution structural studies of human Stanniocalcin-1Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our data reveal the first low resolution, structural information for human STC1. Theoretical predictions and circular dichroism spectroscopy both suggested that STC1 has a high content of alpha-helices and SAXS experiments revealed that STC1 is a dimer of slightly elongated shape in solution. The dimerization was confirmed by mass spectrometry as was the highly conserved disulfide pattern, which is similar to that found in fish STC1. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - August 26, 2009 Category: Molecular Biology Authors: Daniel TrindadeJulio SilvaMargareth NavarroIris TorrianiJorg Kobarg Source Type: journals

Initial insight into the function of the lysosomal 66.3 kDa protein from mouse by means of X-ray crystallographyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The 66.3 kDa protein closely resembles conjugated bile acid hydrolase (CBAH) and penicillin V acylase (PVA) suggesting a hydrolytic activity on non-peptide amide bonds. The similarity to these bacterial proteins also implies an autocatalytic maturation of the lysosomal 66.3 kDa protein. Upon cleavage between S248 and C249, a deep pocket becomes solvent accessible, which harbors the putative active site of the 66.3 kDa protein. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - August 24, 2009 Category: Molecular Biology Authors: Kristina LakomekAchim DickmannsMatthias KettwigHenning UrlaubRalf FicnerTorben Luebke Source Type: journals

The crystal structure of Haloferax volcanii proliferating cell nuclear antigen reveals unique surface charge characteristics due to halophilic adaptation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The extent to which individual proteins adapt to halophilic conditions varies, presumably due to their diverse characteristics and roles within the cell. The number of ion pairs observed in the HvPCNA monomer-monomer interface was unexpectedly low. This may reflect the fact that the trimer is intrinsically stable over a wide range of salt concentrations and therefore additional modifications for trimer maintenance in high salt conditions are not required. Halophilic proteins frequently bind anions and cations and in HvPCNA cation binding may compensate for the remarkable reduction in positive charge in the por...
Source: BMC Structural Biology - Latest articles - August 21, 2009 Category: Molecular Biology Authors: Jody WinterPanayiotis ChristofiShaun MorrollKaren Bunting Source Type: journals

The cyanobacterial cell division factor Ftn6 contains an N-terminal DnaD-like domainEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Overall, similarities between FND and DnaD-like domains as well as previously reported observations on Ftn6 suggest that FND may function as a DNA-interacting module thereby providing an as yet missing link between DNA replication and cell division in cyanobacteria. Consistently, we also showed that Ftn6 is involved in tolerance to DNA damages generated by UV rays. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - August 20, 2009 Category: Molecular Biology Authors: Martial MarboutyCyril SaguezFranck Chauvat Source Type: journals

Biochemical and structural characterization of alanine racemase from Bacillus anthracis (Ames)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The chloride ion in AlrBax is functioning effectively as a carbamylated lysine making it an integral and unique part of this structure. Despite differences in space group and crystal form, the two AlrBax structures are very similar, supporting the case that reductive methylation is a valid rescue strategy for proteins recalcitrant to crystallization, and does not, in this case, result in artifacts in the tertiary structure. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - August 19, 2009 Category: Molecular Biology Authors: Rafael CounagoMilya DavlievaUlrich StrychRyan HillKurt Krause Source Type: journals

A Tool for calculating binding-site residues on proteins from PDB StructuresEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The developed tool is very useful for the research on protein binding site analysis and prediction. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - August 2, 2009 Category: Molecular Biology Authors: Jing HuChanghui Yan Source Type: journals

CRYSTALP2: sequence-based protein crystallization propensity predictionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Background: Current protocols yield crystals for (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - July 30, 2009 Category: Molecular Biology Authors: Lukasz KurganAli RazibSara AghakhaniScott DickMarcin MiziantySamad Jahandideh Source Type: journals

A generic method for assignment of reliability scores applied to solvent accessibility predictionsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The performance of the neural networks was evaluated on a commonly used set of sequences known as the CB513 set. An overall Pearson's correlation coefficient of 0.72 was obtained, which is comparable to the performance of the currently best public available method, Real-SPINE. Both methods associate a reliability score with the individual predictions. However, our implementation of reliability scores in the form of a Z-score is shown to be the more informative measure for discriminating good predictions from bad ones in the entire range from completely buried to fully exposed amino acids. This is evident when ...
Source: BMC Structural Biology - Latest articles - July 30, 2009 Category: Molecular Biology Authors: Bent PetersenThomas PetersenPernille AndersenMorten NielsenClaus Lundegaard Source Type: journals

Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosomeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The greater extent of hydrogen bonding and neighbor atom density in the unreactive nucleotide pairs is consistent with reduced flexibility at a majority of the unreactive sites. The reactive photocrosslinking sites are clustered in the 30S subunit and this indicates nonuniform patterns of hydrogen bonding and packing density in the 16S rRNA tertiary structure. Because this analysis addresses inter-nucleotide distances and geometry between nucleotides distant in the primary sequence, the results indicate regional and global flexibility of the rRNA. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - July 29, 2009 Category: Molecular Biology Authors: Wayne HugginsSujit GhoshPaul Wollenzien Source Type: journals

An in silico study of the molecular basis of B-RAF activation and conformational stabilityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Our results showed that the above mechanisms lead to the disruption of the electrostatic interactions between the A-loop and the alpha C-helix in the activating mutants, which presumably contribute to the flipping of the activation segment to an active form. Conversely, in the B-RAFD594V mutant that has impaired kinase activity, and in B-RAFWT these interactions were strong and stabilized the kinase inactive form. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - July 21, 2009 Category: Molecular Biology Authors: Filip FratevSvava Jonsdottir Source Type: journals

Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase familiesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We have provided new insight into the structure and function of the Asp-box motif and of Asp-box beta-propellers, and expect that the classification and analysis presented here will prove helpful in interpreting future data on Asp-box proteins in general and on Asp-box beta-propellers in particular. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - July 12, 2009 Category: Molecular Biology Authors: Esben QuistgaardSoren Thirup Source Type: journals

Amyloidogenic determinants are usually not buriedEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The most significant result of this work is the observation that virtually all, experimentally determined amyloidogenic determinants, to date, and the majority of predicted, but not yet experimentally verified short amyloidogenic stretches, lie 'exposed' on the surface of the relevant amyloidogenic proteins, and also several of them have the ability to act as conformational 'switches'. Experiments, focused on these fragments, should be performed to test this idea. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - July 8, 2009 Category: Molecular Biology Authors: Kimon FrousiosVassiliki IconomidouCarolina-Maria KarletidiStavros Hamodrakas Source Type: journals

Improved estimation of structure predictor qualityEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We find that a constrained regression approach showsconsistently good performance. Although it is not always the absolute best performing scheme, it is always performs on par with the best schemes across multiple datasets. The work presented here provides the basis for the construction of a regression model trained on data from existing structureprediction servers. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - June 29, 2009 Category: Molecular Biology Authors: Kevin DeRonneGeorge Karypis Source Type: journals

Structural and Phylogenetic Analysis of a Conserved Actinobacteria-Specific Protein (ASP1; SCO1997) from Streptomyces coelicolorEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our structural data in combination with sequence analysis supports the idea that two of the 5 actinobacteria-specific proteins, ASP1 and ASP2, mediate similar function. This function is predicted to be novel since the structures of these proteins do not match any known protein with or without known function. Our results suggest that this function could involve divalent metal ion binding/transport. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - June 9, 2009 Category: Molecular Biology Authors: Beile GaoSeiji Sugiman-MarangosMurray JunopRadhey Gupta Source Type: journals

Modelling substrate specificity and enantioselectivity for lipases and esterases by substrate-imprinted dockingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The experimentally observed differences in selectivity and specificity of the enzymes were reproduced with an accuracy of 81%. The method was robust toward small differences in initial structures (different crystallisation conditions or a co-crystallised ligand), although large displacements of catalytic residues often resulted in substrate poses that did not pass the geometric filter criteria. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - June 3, 2009 Category: Molecular Biology Authors: Benjamin JuhlPeter TrodlerSadhna TyagiJurgen Pleiss Source Type: journals

Analysis of proteins with the 'Hot dog' fold: Prediction of function and identification of catalytic residues of hypothetical proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The analysis led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - May 28, 2009 Category: Molecular Biology Authors: Lakshmi PiduguKoustav MaityKarthikeyan RamaswamyNamita SuroliaKaza Suguna Source Type: journals

Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Conformational transitions between the experimentally observed closed and open conformation of the lid were observed by multiple molecular dynamics simulations of B. cepacia lipase. Transitions in both directions occurred without applying restraints or external forces. The opening and closing was driven by the solvent and independent of a bound substrate molecule. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - May 28, 2009 Category: Molecular Biology Authors: Peter TrodlerRolf SchmidJurgen Pleiss Source Type: journals

On the mechanism of autoinhibition of the RhoA-specific nucleotide exchange factor PDZRhoGEFEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results suggest a mechanism for autoinhibition of RGSL family of GEFs, in which the RGSL domain and a unique sequence motif upstream of the DH domain, act cooperatively to reduce the ability of the DH domain to bind the nucleotide free RhoA. The activation mechanism is likely to involve two independent steps, i.e. displacement of the RGSL domain and conformational change involving the autoinhibitory sequence motif containing several negatively charged residues. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - May 21, 2009 Category: Molecular Biology Authors: Meiying ZhengTomasz CierpickiKo MomotaniMykhaylo ArtamonovUrszula DerewendaJohn BushwellerAvril SomlyoZygmunt Derewenda Source Type: journals

Improving protein structure similarity searches using domain boundaries based on conserved sequence informationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Structure similarity searches using domain boundaries based on conserved sequence information can provide an additional method for investigators to identify interesting similarities between proteins with known structures. Because of the improvement in performance of structure similarity searches using sequence domain boundaries, we are in the process of implementing their inclusion into the VAST search and MMDB resources in the NCBI Entrez system. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - May 19, 2009 Category: Molecular Biology Authors: Kenneth Evan Thompson, Yanli Wang, Tom Madej and Stephen H Bryant Source Type: journals

Interaction of perfluorooctanoic acid with human serum albuminEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The present work suggested a characterization method for the intermolecular weak interaction. It is potentially useful for elucidating the toxigenicity of perfluorochemicals when combined with biomolecular function effect, transmembrane transport, toxicological testing and the other experiments. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - May 14, 2009 Category: Molecular Biology Authors: Ling-Ling Wu, Hong-Wen Gao, Nai-Yun Gao, Fang-Fang Chen and Ling Chen Source Type: journals

Prediction of mono- and di- nucleotide specific DNA-binding sites in proteins using neural networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Most residue-nucleotide contacts can be predicted with high accuracy using only sequence and evolutionary information. Major and minor groove contacts, however, depend profoundly on the local structure. Overall, this study takes us a step closer to the ultimate goal of predicting mutual recognition sites in protein and DNA sequences. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - May 13, 2009 Category: Molecular Biology Authors: Munazah Andrabi, Kenji Mizuguchi, Akinori Sarai and Shandar Ahmad Source Type: journals

Three dimensional shape comparison of flexible protein using the local-diameter descriptorEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Our study provides an effective technique to compare the shape of flexible proteins. The experimental results demonstrate the insensitivity of LD descriptor to the protein shape deformation. The demos and supplemental materials are available on https://engineering.purdue.edu/PRECISE/LDD. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - May 12, 2009 Category: Molecular Biology Authors: Yi Fang, Yu-Shen Liu and Karthik Ramani Source Type: journals

Improving consensus contact prediction via server correlation reductionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Reducing server correlation and optimally combining independent latent servers show a significant improvement over the traditional consensus methods. This approach can hopefully provide a powerful tool for protein structure refinement and prediction use. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - May 6, 2009 Category: Molecular Biology Authors: Xin Gao, Dongbo Bu, Jinbo Xu and Ming Li Source Type: journals

Context dependent reference states of solvent accessibility derived from native protein structures and assessed by predictability analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: HOA based normalization of solvent accessibility from native structures is proposed and it shows improvement in sequence-based predictability, as well as enrichment in interface residues on surface. There may still be some difference between the highest possible ASA and highest observed ASA due to an insufficiently covered space of ASA distribution in the PDB, which limit the overall improvement in prediction to a relatively modest degree. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - April 27, 2009 Category: Molecular Biology Authors: Hemajit Singh and Shandar Ahmad Source Type: journals

Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The results illustrate that the free DNA molecule, even in the crystalline state, samples a large amount of conformational space, encompassing both the A and the B-forms, in the absence of any large ligands. A-form as well as some non-A, non-B, distorted geometries are observed for a small number of dinucleotide steps in DNA structures bound to the proteins belonging to a few specific families. However, for most of the bound DNA structures, across a wide variety of protein families, the average step parameters for various dinucleotide sequences as well as backbone torsion angles are observed to be quite close ...
Source: BMC Structural Biology - Latest articles - April 24, 2009 Category: Molecular Biology Authors: Arvind Marathe, Deepti Karandur and Manju Bansal Source Type: journals

Analysis of the impact of solvent on contacts prediction in proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our analysis, despite the complexity of its possible general applicability, opens up that the consideration of water may have an impact on the improvement of the contact predictions obtained by correlated mutations approaches. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - April 15, 2009 Category: Molecular Biology Authors: Sergey A Samsonov, Joan Teyra, Gerd Anders and M. Teresa Pisabarro Source Type: journals

Characterization of conserved properties of hemagglutinin of H5N1 and human influenza viruses: possible consequences for therapy and infection controlEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The presented results may help to better understand the interaction of influenza virus with its receptor(s) and to identify new therapeutic targets for drug development. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - April 7, 2009 Category: Molecular Biology Authors: Veljko Veljkovic, Nevena Veljkovic, Claude P Muller, Sybille Muller, Sanja Glisic, Vladimir Perovic and Heinz Kohler Source Type: journals

Relationship between chemical shift value and accessible surface area for all amino acid atomsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Atoms with zero per-atom ASA have a significantly larger chemical shift dispersion and often have a different chemical shift distribution compared to those that are solvent accessible. With higher per-atom ASA, the chemical shift values also tend towards random coil values. The per-atom ASA, although not the determinant of the chemical shift, thus provides a way to directly correlate chemical shift information to the atomic coordinates. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - April 2, 2009 Category: Molecular Biology Authors: Wim F Vranken and Wolfgang Rieping Source Type: journals

ProteinShader: illustrative rendering of macromoleculesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: By programming to the graphics processor unit, ProteinShader is able to produce high quality images and illustrative rendering effects in real-time. The main feature that distinguishes ProteinShader from other free molecular visualization tools is its use of texture mapping techniques that allow two-dimensional images to be mapped onto the curved three-dimensional surfaces of ribbons and tubes with minimum distortion of the images. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - March 30, 2009 Category: Molecular Biology Authors: Joseph R Weber Source Type: journals

Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power SpectraEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We show that the estimation errors for the CTF detection methodology proposed in \cite{Sorzano2007a} does not show a significant deterioration of the CTF correction capabilities of subsequent algorithms. All together, the methodology described in this paper constitutes a powerful tool for the quantitative analysis of CTF models that can be applied to other models different from the one analyzed here. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - March 26, 2009 Category: Molecular Biology Authors: Carlos Oscar Sanchez Sorzano, Abraham Otero, Estefania M Olmos and Jose Maria Carazo Source Type: journals

Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA - Implications for the catalytic mechanism of parvulinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Detailed structural description of the S. aureus PrsA-PPIase lays the foundation for structure-based design of enzyme inhibitors. The structure resembles hPin1-type parvulins both structurally and regarding substrate preference. Even though a wealth of structural data is available on parvulins, the catalytic mechanism has yet to be resolved. The structure of S. aureus PrsA-PPIase and our findings on the role of the conserved active site histidines help in designing further experiments to solve the detailed catalytic mechanism. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - March 24, 2009 Category: Molecular Biology Authors: Outi Heikkinen, Raili Seppala, Helena Tossavainen, Sami Heikkinen, Harri Koskela, Perttu Permi and Ilkka Kilpelainen Source Type: journals

Structural pattern matching of nonribosomal peptidesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The method has been incorporated into the Norine database, available at http://bioinfo.lifl.fr/norine. Less than one second is needed to search for a pattern in the entire database. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - March 18, 2009 Category: Molecular Biology Authors: Segolene Caboche, Maude Pupin, Valerie Leclere, Philippe Jacques and Gregory Kucherov Source Type: journals

Rational mutagenesis to support structure-based drug design: MAPKAP kinase 2 as a case studyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This set of strategies and automation technologies was used successfully to yield a primary crystal MK2 structure bound to an ATP-competitive inhibitor. The crystal form was an excellent candidate for soaking methods to solve subsequent liganded structures. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - March 18, 2009 Category: Molecular Biology Authors: Maria A Argiriadi, Silvino Sousa, David Banach, Douglas Marcotte, Tao Xiang, Medha J Tomlinson, Megan Demers, Christopher Harris, Silvia Kwak, Jennifer Hardman, Margaret Pietras, Lisa Quinn, Jennifer DiMauro, Baofu Ni, John Mankovich, David W Borhani, Rob Source Type: journals

Implications of the structure of human uridine phosphorylase 1 on the development of novel inhibitors for improving the therapeutic window of fluoropyrimidine chemotherapyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The structural details underlying hUPP1's active site and additional surfaces beyond these catalytic residues, which coordinate binding of BAU and other acyclouridine analogues, suggest avenues for future design of more potent inhibitors of this enzyme. Notably, the loop forming the back wall of the substrate binding pocket is conformationally different and substantially less flexible in hUPP1 than in previously studied microbial homologues. These distinctions can be utilized to discover novel inhibitory compounds specifically optimized for efficacy against the human enzyme as a step toward the development of ...
Source: BMC Structural Biology - Latest articles - March 16, 2009 Category: Molecular Biology Authors: Tarmo P Roosild, Samantha Castronovo, Michael Fabbiani and Giuseppe Pizzorno Source Type: journals

The glycine brace: a component of Rab, Rho, and Ran GTPases associated with hinge regions of guanine- and phosphate-binding loopsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: It is proposed that the two glycine residues function as hinges and that the glycine brace influences guanine nucleotide binding or release by interacting with these hinges. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - March 5, 2009 Category: Molecular Biology Authors: Andrew F Neuwald Source Type: journals

Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: The structure network approach employed in this study for the analysis of dimeric interfaces in LuxS has brought out certain structural details at the side-chain interaction level, which were elusive from the conventional structure comparison methods. The results from this study provide a better understanding of the relation between the luxS gene and its functional role in the prokaryotes. This study also makes it possible to explore the potential direction towards the design of inhibitors of LuxS and thus towards a wide range of antimicrobials. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - February 25, 2009 Category: Molecular Biology Authors: Moitrayee Bhattacharyya and Saraswathi Vishveshwara Source Type: journals

An unexpected phosphate binding site in Glyceraldehyde 3-Phosphate Dehydrogenase: Crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzymeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The structures of the C. parvum GAPDH ternary complex and other GAPDH complexes demonstrate the plasticity of the substrate binding site. We propose that the active site of GAPDH can accommodate the substrate in multiple conformations at multiple locations during the initial encounter. However, the C-3 phosphate group clearly prefers the 'new Pi' site for initial binding in the active site. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - February 25, 2009 Category: Molecular Biology Authors: William J. Cook, Olga Senkovich and Debasish Chattopadhyay Source Type: journals

PDBalert: automatic, recurrent remote homology tracking and protein structure predictionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: PDBalert will accelerate the information flow from the PDB database to all those who can profit from the newly released protein structures for predicting the 3D structure or function of their proteins of interest. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - November 25, 2008 Category: Molecular Biology Authors: Vatsal S Agarwal, Michael Remmert, Andreas Biegert and Johannes Soding Source Type: journals

Ligand-induced conformational changes in a thermophilic ribose-binding proteinEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Although the large-scale ligand-induced changes are mediated through similar regions, and are produced by similar backbone movements in tmRBP and ecRBP, the small-scale ligand-induced structural rearrangements differentiate the mesophile and thermophile. This suggests there are mechanistic differences in the manner by which these two proteins bind their ligands and are an example of how two structurally similar proteins utilize different mechanisms to form a ligand-bound state. (Source: BMC Structural Biology - Latest articles)
Source: BMC Structural Biology - Latest articles - November 19, 2008 Category: Molecular Biology Authors: Matthew J Cuneo, Lorena S Beese and Homme W Hellinga Source Type: journals