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Secondary Structure, Mechanical Stability, and Location of Transition State of Proteins

Institute of Physics, Polish Academy of Sciences, Warsaw, Poland

Correspondence: Address reprint requests to Mai Suan Li, E-mail: masli{at}ifpan.edu.pl.

It is well known that the unfolding times of proteins, _u, scales with the external mechanical force f as where x_u is the location of the average transition state along the reaction coordinate given by the end-to-end distance. Using the off-lattice Go-like models, we have shown that in terms of x_u, proteins may be divided into two classes. The first class, which includes ß- and ß/-proteins, has x_u 2–5 Å whereas the second class of -proteins has x_u about three times larger than that of the first class, x_u 7–15 Å. These results are in good agreement with the experimental data. The secondary structure is found to play the key role in determining the shape of the free energy landscape. Namely, the distance between the native state and the transition state depends on the helix content linearly. It is shown that x_u has a strong correlation with mechanical stability of proteins. Defining the unfolding force, f_u, from the constant velocity pulling measurements as a measure of the mechanical stability, we predict that x_u decays with f_u by a power law, where the exponent µ 0.4. We have demonstrated that the unfolding force correlates with the helix content of a protein. The contact order, which is a measure of fraction of local contacts, was found to strongly correlate with the mechanical stability and the distance between the transition state and native state. Our study reveals that x_u and f_u might be estimated using either the helicity or the contact order.