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Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment

Paper ID Volume ID Publish Year Pages File Format Full-Text
15171 1384 2013 9 PDF Available
Title
Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment
Abstract

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► Similar (CaRMSD < 4 Å) have less than 60% identical packing cliques. ► Structural similarity between packing cliques is generally greater than 70%. ► Primary variation occurs in 2 and 3 body packing cliques. ► Structural similarity generally conserved in packing cliques with 2° structure.

Keywords
Protein packing; Loop modeling; Template-based protein structure prediction; Protein statistical function
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Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 42, February 2013, Pages 40–48
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
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Price was $35.95
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