Août 14 2015

Imprimer ce Article

Prediction of protein folding rates from simplified secondary structure alphabet


J Theor Biol. 2015 Aug 4. pii: S0022-5193(15)00369-0. doi: 10.1016/j.jtbi.2015.07.024. [Epub ahead of print]


Huang JT, Wang T, Huang SR, Li X.


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.

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