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Prediction of folding transition‐state position (βT) of small, two‐state proteins from local secondary structure content

Folding kinetics of proteins is governed by the free energy and position of transition states. But attempts to predict the position of folding transition state on reaction pathway from protein structure have been met with only limited success, unlike the folding‐rate prediction. Here, we find that the folding transition‐state position is related to the secondary structure content of native two‐state proteins. We present a simple method for predicting the transition‐state position from their α‐helix, turn and polyproline secondary structures. The method achieves 81% correlation with experiment over 24 small, two‐state proteins, suggesting that the local secondary structure content, especially for content of α‐helix, is a determinant of the solvent accessibility of the transition state ensemble and size of folding nucleus. Proteins 2007. © 2007 Wiley‐Liss, Inc.