Prediction of protein folding rates from simplified secondary structure alphabet
- PMID: 26247139
- DOI: 10.1016/j.jtbi.2015.07.024
Prediction of protein folding rates from simplified secondary structure alphabet
Abstract
Protein folding is a very complicated and highly cooperative dynamic process. However, the folding kinetics is likely to depend more on a few key structural features. Here we find that secondary structures can determine folding rates of only large, multi-state folding proteins and fails to predict those for small, two-state proteins. The importance of secondary structures for protein folding is ordered as: extended β strand > α helix > bend > turn > undefined secondary structure>310 helix > isolated β strand > π helix. Only the first three secondary structures, extended β strand, α helix and bend, can achieve a good correlation with folding rates. This suggests that the rate-limiting step of protein folding would depend upon the formation of regular secondary structures and the buckling of chain. The reduced secondary structure alphabet provides a simplified description for the machine learning applications in protein design.
Keywords: Key secondary structures; Kinetic prediction; Protein folding mechanism; Reduced alphabet of secondary structures.
Copyright © 2015 Elsevier Ltd. All rights reserved.
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