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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
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: |
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| 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 |
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