Residue-Specific Side-Chain Polymorphisms via Particle Belief Propagation

Protein side chains populate diverse conformational ensembles in crystals. Despite much evidence that there is widespread conformational polymorphism in protein side chains, most of the X-ray crystallography data are modeled by single conformations in the Protein Data Bank. The ability to extract or...

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Bibliographic Details
Published in:IEEE/ACM transactions on computational biology and bioinformatics 2014-01, Vol.11 (1), p.33-41
Main Authors: Soltan Ghoraie, Laleh, Burkowski, Forbes, Shuai Cheng Li, Mu Zhu
Format: Article
Language:English
Subjects:
Approximation methods
Belief propagation
Bioinformatics
Computational Biology
Computational modeling
Conformational ensemble
conformational polymorphism
Databases, Protein
Libraries
mixture distribution
Models, Molecular
Optimization
particle belief propagation
Protein Conformation
Proteins
Proteins - chemistry
side-chain prediction
Statistics, Nonparametric
Thermodynamics
von-Mises distribution
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Summary:Protein side chains populate diverse conformational ensembles in crystals. Despite much evidence that there is widespread conformational polymorphism in protein side chains, most of the X-ray crystallography data are modeled by single conformations in the Protein Data Bank. The ability to extract or to predict these conformational polymorphisms is of crucial importance, as it facilitates deeper understanding of protein dynamics and functionality. In this paper, we describe a computational strategy capable of predicting side-chain polymorphisms. Our approach extends a particular class of algorithms for side-chain prediction by modeling the side-chain dihedral angles more appropriately as continuous rather than discrete variables. Employing a new inferential technique known as particle belief propagation, we predict residue-specific distributions that encode information about side-chain polymorphisms. Our predicted polymorphisms are in relatively close agreement with results from a state-of-the-art approach based on X-ray crystallography data, which characterizes the conformational polymorphisms of side chains using electron density information, and has successfully discovered previously unmodeled conformations.
ISSN:1545-5963
1557-9964
DOI:10.1109/TCBB.2013.130