Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Moscow Region

Annotation.The problem of protein self-organization is one of the most important problems of molecular biology nowadays. Despite the recent success in understanding general principles of protein folding, details of this process is yet to be elucidated. That is why the search for the factors influencing protein folding kinetics is going on. We check in this study the hypothesis that more spherical proteins should fold more slowly than elongated ones. To this aim we analyze a number of structural determinants, designed for description protein shape, as well as their relationship with rates of protein folding and unfolding. We show here that dimensionless structural parameters describing protein shape have low correlation with protein folding and unfolding rates. At the same time structural determinants taking into account both protein shape and its size show good agreement with experimentally observed rates of protein folding and unfolding.

Key words: compactness, radius of gyration, radius of cross-section, simple mechanism of folding “all-or-none”, complex mechanism of folding with accumulation of intermediate state.