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Reconstruction and stability of secondary structure elements in the context of protein structure prediction

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Podtelezhnikov, Alexei A. and Wild, David L. (2009) Reconstruction and stability of secondary structure elements in the context of protein structure prediction. Biophysical Journal, Vol.96 (No.11). pp. 4399-4408. doi:10.1016/j.bpj.2009.02.057 ISSN 0006-3495.

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Official URL: http://dx.doi.org/10.1016/j.bpj.2009.02.057

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Abstract

Efficient and accurate reconstruction of secondary structure elements in the context of protein structure prediction is the major focus of this work. We present a novel approach capable of reconstructing alpha-helices and beta-sheets in atomic detail. The method is based on Metropolis Monte Carlo simulations in a force field of empirical potentials that are designed to stabilize secondary structure elements in room-temperature simulations. Particular attention is paid to lateral side-chain interactions in beta-sheets and between the turns of alpha-helices, as well as backbone hydrogen bonding. The force constants are optimized using contrastive divergence, a novel machine learning technique, from a data set of known structures. Using this approach, we demonstrate the applicability of the framework to the problem of reconstructing the overall protein fold for a number of commonly studied small proteins, based on only predicted secondary structure and contact map. For protein G and chymotrypsin inhibitor 2, we are able to reconstruct the secondary structure elements in atomic detail and the overall protein folds with a root mean-square deviation of <10 angstrom. For cold-shock protein and the SH3 domain, we accurately reproduce the secondary structure elements and the topology of the 5-stranded beta-sheets, but not the barrel structure. The importance of high-quality secondary structure and contact map prediction is discussed.

Item Type: Journal Article
Subjects: Q Science > QH Natural history > QH301 Biology
Divisions: Faculty of Science, Engineering and Medicine > Research Centres > Warwick Systems Biology Centre
Journal or Publication Title: Biophysical Journal
Publisher: Biophysical Society
ISSN: 0006-3495
Official Date: 3 June 2009
Dates:
DateEvent
3 June 2009Published
Volume: Vol.96
Number: No.11
Number of Pages: 10
Page Range: pp. 4399-4408
DOI: 10.1016/j.bpj.2009.02.057
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access
Funder: National Institutes of Health
Grant number: 1 P01 GM63208

Data sourced from Thomson Reuters' Web of Knowledge

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