Coupling between properties of the protein shape and the rate of protein folding

Abstract

There are several important questions on the coupling between properties of the protein shape and the rate of protein folding. We have studied a series of structural descriptors intended for describing protein shapes (the radius of gyration, the radius of cross-section, and the coefficient of compactness) and their possible connection with folding behavior, either rates of folding or the emergence of folding intermediates, and compared them with classical descriptors, protein chain length and contact order. It has been found that when a descriptor is normalized to eliminate the influence of the protein size (the radius of gyration normalized to the radius of gyration of a ball of equal volume, the coefficient of compactness defined as the ratio of the accessible surface area of a protein to that of an ideal ball of equal volume, and relative contact order) it completely looses its ability to predict folding rates. On the other hand, when a descriptor correlates well with protein size (the radius of cross-section and absolute contact order in our consideration) then it correlates well with the logarithm of folding rates and separates reasonably well two-state folders from multi-state ones. The critical control for the performance of new descriptors demonstrated that the radius of cross-section has a somewhat higher predictive power (the correlation coefficient is 20.74) than size alone (the correlation coefficient is 20.65). So, we have shown that the numerical descriptors of the overall shape-geometry of protein structures are one of the important determinants of the protein-folding rate and mechanism. © 2009 Ivankov et al.