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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. 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 > Centre for Systems Biology |
| Journal or Publication Title: | Biophysical Journal |
| Publisher: | Biophysical Society |
| ISSN: | 0006-3495 |
| Date: | 3 June 2009 |
| Volume: | Vol.96 |
| Number: | No.11 |
| Number of Pages: | 10 |
| Page Range: | pp. 4399-4408 |
| Identification Number: | 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 |
| URI: | http://wrap.warwick.ac.uk/id/eprint/27871 |
Data sourced from Thomson Reuters' Web of Knowledge
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