http://www.biomedcentral.com/bmcstructbiol/ The latest research articles published by BMC Structural Biology 2009-10-27T00:00:00Z This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ Background: From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results: A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion: By using the software, named HaptiMol ISAS (available from http://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. http://www.biomedcentral.com/1472-6807/9/69 Matthew Stocks Steven Hayward Stephen Laycock BMC Structural Biology 2009, 9:69 2009-10-27T00:00:00Z doi:10.1186/1472-6807-9-69 BMC Structural Biology 1472-6807 9 69 2009-10-27T00:00:00Z XML Background: The study of functional sub-families of protein domain families and the identification of the residues which determine substrate specificity is an important question in the analysis of protein domains. One way to address this question is the use of clustering methods for protein sequence data and approaches to predict functional residues based on such clusterings. The locations of putative functional residues in known protein structures provide insights into how different substrate specificities are reflected on the protein structure level. Results: We have developed an extension of the context-specific independence mixture model clustering framework which allows for the integration of experimental data. As these are usually known only for a few proteins, our algorithm implements a partially-supervised learning approach. We discover domain sub-families and predict functional residues for four protein domain families: phosphatases, pyridoxal dependent decarboxylases, WW and SH3 domains to demonstrate the usefulness of our approach. 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. http://www.biomedcentral.com/1472-6807/9/68 Benjamin Georgi Jorg Schultz Alexander Schliep BMC Structural Biology 2009, 9:68 2009-10-26T00:00:00Z doi:10.1186/1472-6807-9-68 BMC Structural Biology 1472-6807 9 68 2009-10-26T00:00:00Z PDF Background: The carbonic anhydrases (CAs) are involved in inorganic carbon utilization. They have been classified into six evolutionary and structural families: α-, β-, γ-, δ-, ε-, ζ- CAs, with β-CAs present in higher plants, algae and prokaryotes. The yeast Saccharomyces cerevisiae encodes a single copy of β-CA Nce103/YNL036W. Results: We determined the crystal structure of Nce103 in complex with a substrate analog at 2.04 Å resolution. It assembles as a homodimer, with the active site located at the interface between two monomers. At the bottom of the substrate pocket, a zinc ion is coordinated by the three highly conserved residues Cys57, His112 and Cys115 in addition to a water molecule. Residues Asp59, Arg61, Gly111, Leu102, Val80, Phe75 and Phe97 form a tunnel to the bottom of the active site which is occupied by a molecule of the substrate analog acetate. Activity assays of full length and two truncated versions of Nce103 indicated that the N-terminal arm is indispensable. Conclusion: The quaternary structure of Nce103 resembles the typical plant type β-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. http://www.biomedcentral.com/1472-6807/9/67 Yan-Bin Teng Yong-Liang Jiang Yong-xing He Wei-Wei He Fu-Ming Lian Yuxing Chen Cong-Zhao Zhou BMC Structural Biology 2009, 9:67 2009-10-24T00:00:00Z doi:10.1186/1472-6807-9-67 BMC Structural Biology 1472-6807 9 67 2009-10-24T00:00:00Z XML Background: Computational prediction of protein stability change due to single-site amino acid substitutions is of interest in protein design and analysis. We consider the following four ways to improve the performance of the currently available predictors: (1) We include additional sequence- and structure-based features, namely, the amino acid substitution likelihoods, the equilibrium fluctuations of the alpha- and beta-carbon atoms, and the packing density. (2) By implementing different machine learning integration approaches, we combine information from different features or representations. (3) We compare classification vs. regression methods to predict the sign vs. the output of stability change. (4) We allow a reject option for doubtful cases where the risk of misclassification is high. Results: We investigate three different approaches: early, intermediate and late integration, which respectively combine features, kernels over feature subsets, and decisions. We perform simulations on two data sets: (1) S1615 is used in previous studies, (2) S2783 is the updated version (as of July 2, 2009) extracted also from ProTherm. For S1615 data set, our highest accuracy using both sequence and structure information is 0.842 on cross-validation and 0.904 on testing using early integration. Newly added features, namely, local compositional packing and the mobility extent of the mutated residues, improve accuracy significantly with intermediate integration. For S2783 data set, we also train regression methods to estimate not only the sign but also the amount of stability change and apply risk-based classification to reject when the learner has low confidence and the loss of misclassification is high. The highest accuracy is 0.835 on cross-validation and 0.832 on testing using only sequence information. The percentage of false positives can be decreased to less than 0.005 by rejecting 10 per cent using late integration. Conclusions: We find that in both early and late integration, combining inputs or decisions is useful in increasing accuracy. Intermediate integration allows assessing the contributions of individual features by looking at the assigned weights. Overall accuracy of regression is not better than that of classification but it has less false positives, especially when combined with the reject option. The server for stability prediction for three integration approaches and the data sets are available at http://www.prc.boun.edu.tr/appserv/prc/mlsta. http://www.biomedcentral.com/1472-6807/9/66 Aysegul Ozen Mehmet Gonen Ethem Alpaydin Turkan Haliloglu BMC Structural Biology 2009, 9:66 2009-10-19T00:00:00Z doi:10.1186/1472-6807-9-66 BMC Structural Biology 1472-6807 9 66 2009-10-19T00:00:00Z PDF Background: Oligomeric enzymes can undergo a reversible loss of activity at low temperatures. One such enzyme is tryptophanase (Trpase) from Escherichia coli. Trpase is a pyridoxal phosphate (PLP)-dependent tetrameric enzyme with a Mw of 210 kD. PLP is covalently bound through an enamine bond to Lys270 at the active site. The incubation of holo E. coli Trpases at 2°C for 20 h results in breaking this enamine bond and PLP release, as well as a reversible loss of activity and dissociation into dimers. This sequence of events is termed cold lability and its understanding bears relevance to protein stability and shelf life. Results: We studied the reversible cold lability of E. coli Trpase and its Y74F, C298S and W330F mutants. In contrast to the holo E. coli Trpase all apo forms of Trpase dissociated into dimers already at 25°C and even further upon cooling to 2°C. The crystal structures of the two mutants, Y74F and C298S in their apo form were determined at 1.9Å resolution. These apo mutants were found in an open conformation compared to the closed conformation found for P. vulgaris in its holo form. This conformational change is further supported by a high pressure study. Conclusion: 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. http://www.biomedcentral.com/1472-6807/9/65 Anna Kogan Garik Gdalevsky Rivka Cohen-Luria Yehuda Goldgur Robert Phillips Abraham Parola Orna Almog BMC Structural Biology 2009, 9:65 2009-10-08T00:00:00Z doi:10.1186/1472-6807-9-65 BMC Structural Biology 1472-6807 9 65 2009-10-08T00:00:00Z XML Background: Independent surveys of human gene promoter regions have demonstrated an overrepresentation of G3Xn1G3Xn2G3Xn3G3 motifs which are known to be capable of forming intrastrand quadruple helix structures. In spite of the widely recognized importance of G-quadruplex structures in gene regulation and growing interest around this unusual DNA structure, there are at present only few such structures available in the Nucleic Acid Database. In the present work we generate by molecular modeling feasible G-quadruplex structures which may be useful for interpretation of experimental data. Results: We have used all quadruplex DNA structures deposited in the Nucleic Acid Database in order to select a list of fragments entailing a strand of three adjacent G's paired with another strand of three adjacent G's separated by a loop of one to four residues. These fragments were further clustered and representative fragments were finally selected. Further fragments were generated by assemblying the two strands of each fragment with loops from different fragments whenever the anchor G's were superimposable. The fragments were used to assemble G quadruplex based on a superimposability criterion. Conclusion: Molecular models have been generated for a large number of G3Xn1G3Xn2G3Xn3G3 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. http://www.biomedcentral.com/1472-6807/9/64 Federico Fogolari Haritha Haridas Alessandra Corazza Paolo Viglino Davide Cora' Michele Caselle Gennaro Esposito Luigi Xodo BMC Structural Biology 2009, 9:64 2009-10-07T00:00:00Z doi:10.1186/1472-6807-9-64 BMC Structural Biology 1472-6807 9 64 2009-10-07T00:00:00Z XML Background: Avidins are proteins with extraordinarily high ligand-binding affinity, a property which is used in a wide array of life science applications. Even though useful for biotechnology and nanotechnology, the biological function of avidins is not fully understood. Here we structurally and functionally characterise a novel avidin named xenavidin, which is to our knowledge the first reported avidin from a frog. Results: Xenavidin was identified from an EST sequence database for Xenopus tropicalis and produced in insect cells using a baculovirus expression system. The recombinant xenavidin was found to be homotetrameric based on gel filtration analysis. Biacore sensor analysis, fluorescently labelled biotin and radioactive biotin were used to evaluate the biotin-binding properties of xenavidin - it binds biotin with high affinity though less tightly than do chicken avidin and bacterial streptavidin. X-ray crystallography revealed structural conservation around the ligand-binding site, while some of the loop regions have a unique design. The location of structural water molecules at the entrance and/or within the ligand-binding site may have a role in determining the characteristic biotin-binding properties of xenavidin. Conclusion: 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. http://www.biomedcentral.com/1472-6807/9/63 Juha Maatta Satu Helppolainen Vesa Hytonen Mark Johnson Markku Kulomaa Tomi Airenne Henri Nordlund BMC Structural Biology 2009, 9:63 2009-09-29T00:00:00Z doi:10.1186/1472-6807-9-63 BMC Structural Biology 1472-6807 9 63 2009-09-29T00:00:00Z XML Background: The novel A/H1N1 influenza virus, which recently emerged in North America is most closely related to North American H1N1/N2 swine viruses. Until the beginning of 2009, North American swine H1N1/N2 viruses have only sporadically infected humans as dead-end hosts. In 2009 the A/H1N1 virus acquired the capacity to spread efficiently by human to human transmission. The novel A/H1N1 influenza virus has struck thousands of people in more than 70 countries and killed more than 140, representing a public health emergency of international concern. Here we have studied properties of hemagglutinin of A/H1N1 which may modulate virus/receptor interaction. Results: Analyses by ISM bioinformatics platform of the HA1 protein of North American swine H1N1/N2 viruses and the new A/H1N1 showed that both groups of viruses differed in conserved characteristics that reflect a distinct propensity of these viruses to undergo a specific interaction with swine or human host proteins or receptors. Swine H1N1/N2 viruses that sporadically infected humans featured both the swine and the human interaction pattern. Substitutions F71S, T128S, E302K, M314L in HA1 of swine H1N1 viruses from North America are identified as critical for the human interaction pattern of A/H1N1 and residues D94, D196 and D274 are predicted to be "hot-spots" for polymorphisms which could increase infectivity of A/H1N1 virus. At least one of these residues has already emerged in the A/H1N1 isolates from Spain, Italy and USA. The domain 286-326 was identified to be involved in virus/receptor interaction. Conclusion: 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. http://www.biomedcentral.com/1472-6807/9/62 Veljko Veljkovic Henry Niman Sanja Glisic Nevena Veljkovic Vladimir Perovic Claude Muller BMC Structural Biology 2009, 9:62 2009-09-28T00:00:00Z doi:10.1186/1472-6807-9-62 BMC Structural Biology 1472-6807 9 62 2009-09-28T00:00:00Z XML Background: Incorporating variable amino acid stereochemistry in molecular design has the potential to improve existing protein stability and create new topologies inaccessible to homochiral molecules. The Protein Data Bank has been a reliable, rich source of information on molecular interactions and their role in protein stability and structure. D-amino acids rarely occur naturally, making it difficult to infer general rules for how they would be tolerated in proteins through an analysis of existing protein structures. However, protein elements containing short left-handed turns and helices turn out to contain useful information. Molecular mechanisms used in proteins to stabilize left-handed elements by L-amino acids are structurally enantiomeric to potential synthetic strategies for stabilizing right-handed elements with D-amino acids. Results: Propensities for amino acids to occur in contiguous αL helices correlate with published thermodynamic scales for incorporation of D-amino acids into αR helices. Two backbone rules for terminating a left-handed helix are found: an αR conformation is disfavored at the amino terminus, and a βR conformation is disfavored at the carboxy terminus. Helix capping sidechain-backbone interactions are found which are unique to αL helices including an elevated propensity for L-Asn, and L-Thr at the amino terminus and L-Gln, L-Thr and L-Ser at the carboxy terminus. Conclusion: By examining left-handed α-turns containing L-amino acids, new interaction motifs for incorporating D-amino acids into right-handed α-helices are identified. These will provide a basis for de novo design of novel heterochiral protein folds. http://www.biomedcentral.com/1472-6807/9/61 Srinivas Annavarapu Vikas Nanda BMC Structural Biology 2009, 9:61 2009-09-22T00:00:00Z doi:10.1186/1472-6807-9-61 BMC Structural Biology 1472-6807 9 61 2009-09-22T00:00:00Z XML Background: Classification of newly resolved protein structures is important in understanding their architectural, evolutionary and functional relatedness to known protein structures. Among various efforts to improve the database of Structural Classification of Proteins (SCOP), automation has received particular attention. Herein, we predict the deepest SCOP structural level that an unclassified protein shares with classified proteins with an equal number of secondary structure elements (SSEs). Results: We compute a coefficient of dissimilarity (Ω) between proteins, based on structural and sequence-based descriptors characterising the respective constituent SSEs. For a set of 1,661 pairs of proteins with sequence identity up to 35%, the performance of Ω in predicting shared Class, Fold and Super-family levels is comparable to that of DaliLite Z score and shows a greater than four-fold increase in the true positive rate (TPR) for proteins sharing the Family level. On a larger set of 600 domains representing 200 families, the performance of Z score improves in predicting a shared Family, but still only achieves about half of the TPR of Ω. The TPR for structures sharing a Super-family is lower than in the first dataset, but Ω performs slightly better than Z score. Overall, the sensitivity of Ω in predicting common Fold level is higher than that of the DaliLite Z score. Conclusion: Classification to a deeper level in the hierarchy is specific and difficult. So the efficiency of Ω may be attractive to the curators and the end-users of SCOP. We suggest Ω may be a better measure for structure classification than the DaliLite Z score, with the caveat that currently we are restricted to comparing structures with equal number of SSEs. http://www.biomedcentral.com/1472-6807/9/60 Pooja Jain Jonathan Hirst BMC Structural Biology 2009, 9:60 2009-09-19T00:00:00Z doi:10.1186/1472-6807-9-60 BMC Structural Biology 1472-6807 9 60 2009-09-19T00:00:00Z XML