BMC Structural Biology

K2D2: estimation of protein secondary structure from circular dichroism spectra.

Publication Date: 2008 May 13 PMID: 18477405
Authors: Perez-Iratxeta, C. - Andrade-Navarro, M. A.
Journal: BMC Struct Biol

ABSTRACT: BACKGROUND: Circular dichroism spectroscopy is a widely used technique to analyze the secondary structure of proteins in solution. Predictive methods use the circular dichroism spectra from proteins of known tertiary structure to assess the secondary structure contents of a protein with unknown structure given its circular dichroism spectrum. RESULTS: We developed K2D2, a method with an associated web server to estimate protein secondary structure from circular dichroism spectra. The method uses a self-organized map of spectra from proteins with known structure to deduce a map of protein secondary structure that is used to do the predictions. CONCLUSIONS: The K2D2 server is publicly accessible at http://www.ogic.ca/projects/k2d2/. It accepts as input a circular dichroism spectrum and outputs the estimated secondary structure content (alpha-helix and beta-strand) of the corresponding protein, as well as an estimated measure of error.

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Improving the accuracy of template-based predictions by mixing and matching between initial models.

Publication Date: 2008 May 5 PMID: 18457597
Authors: Liu, T. - Guerquin, M. - Samudrala, R.
Journal: BMC Struct Biol

ABSTRACT: BACKGROUND: Comparative modeling is a technique to predict the three dimensional structure of a given protein sequence based primarily on its alignment to one or more proteins with experimentally determined structures. A major bottleneck of current comparative modeling methods is the lack of methods to accurately refine a starting initial model so that it approaches the resolution of the corresponding experimental structure. We investigate the effectiveness of a graph-theoretic clique finding approach to solve this problem. RESULTS: Our refinement method takes into account the information presented in multiple templates/alignments at the three-dimensional level by mixing and matching regions between different initial comparative models. This method enables us to obtain an optimized conformation ensemble representing the best combination of secondary structures, resulting in the refined models of higher quality. In addition, the process of refinement accumulates near-native conformations, resulting in discriminating the native-like conformation in a more effective manner. In the CASP7 experiment, the refined models produced are more accurate than the starting initial models. CONCLUSIONS: This novel approach can be applied without any manual intervention to improve the quality of comparative predictions where multiple template/alignment combinations are available for modeling, producing conformational models of higher quality than the starting initial predictions.

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Exploring Allosteric Coupling in the alpha-Subunit of Heterotrimeric G Proteins Using Evolutionary and Ensemble-Based Approaches.

Publication Date: 2008 May 2 PMID: 18454845
Authors: Sayar, K. - Ugur, O. - Liu, T. - Hilser, V. J. - Onaran, O.
Journal: BMC Struct Biol

ABSTRACT: BACKGROUND: Allosteric coupling, which can be defined as propagation of a perturbation at one region of the protein molecule (such as ligand binding) to distant sites in the same molecule, constitutes the most general mechanism of regulation of protein function. However, unlike molecular details of ligand binding, structural elements involved in allosteric effects are difficult to diagnose. Here, we used two different approaches that utilize fundamentally different and independent information to identify allosteric linkages in the alpha-subunits of heterotrimeric G proteins, which were evolved to transmit membrane receptor signals by allosteric mechanisms. RESULTS: We analyzed: 1) correlated mutations in the G protein alpha-subunits family, and 2) cooperativity of the native state ensemble of the Galpha-i1 or transducin. The combination of these approaches not only recovered already-known details such as the switch regions that change conformation upon nucleotide exchange, and those regions that are involved in receptor, effector or G-beta-gamma interactions (indicating that the predictions of the analyses can be viewed with a measure of confidence), but also predicted new sites that are potentially involved in allosteric communication among different regions of the G-alpha protein. A summary of the new sites found in the present analysis, which were not apparent in crystallographic data, are given along with known functional and structural information, and implications of the results are discussed. CONCLUSIONS: A set of residues and/or structural elements that are potentially involved in allosteric communication in G-alpha is presented. This information can be used as a guide to structural, spectroscopic, mutational, and theoretical studies on the allosteric network in G-alpha proteins, which will provide a better understanding of G protein-mediated signal transduction.

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Structural insights on the pamoic acid and the 8 kDa domain of DNA polymerase beta complex: towards the design of higher-affinity inhibitors.

Publication Date: 2008 PMID: 18416825
Authors: Hazan, C. - Boudsocq, F. - Gervais, V. - Saurel, O. - Ciais, M. - Cazaux, C. - Czaplicki, J. - Milon, A.
Journal: BMC Struct Biol

BACKGROUND: DNA polymerase beta (pol beta), the error-prone DNA polymerase of single-stranded DNA break repair as well as base excision repair pathways, is overexpressed in several tumors and takes part in chemotherapeutic agent resistance, like that of cisplatin, through translesion synthesis. For this reason pol beta has become a therapeutic target. Several inhibitors have been identified, but none of them presents a sufficient affinity and specificity to become a drug. The fragment-based inhibitor design allows an important improvement in affinity of small molecules. The initial and critical step for setting up the fragment-based strategy consists in the identification and structural characterization of the first fragment bound to the target. RESULTS: We have performed docking studies of pamoic acid, a 9 micromolar pol beta inhibitor, and found that it binds in a single pocket at the surface of the 8 kDa domain of pol beta. However, docking studies provided five possible conformations for pamoic acid in this site. NMR experiments were performed on the complex to select a single conformation among the five retained. Chemical Shift Mapping data confirmed pamoic acid binding site found by docking while NOESY and saturation transfer experiments provided distances between pairs of protons from the pamoic acid and those of the 8 kDa domain that allowed the identification of the correct conformation. CONCLUSION: Combining NMR experiments on the complex with docking results allowed us to build a three-dimensional structural model. This model serves as the starting point for further structural studies aimed at improving the affinity of pamoic acid for binding to DNA polymerase beta.

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