Unification of the folding mechanisms of non-two-state and two-state proteins.
We have collected the kinetic folding data for non-two-state and two-state globular proteins reported in the literature, and investigated the relationships between the folding kinetics and the native three-dimensional structure of these proteins. The rate constants of formation of both the intermediate and the native state of non-two-state folders were found to be significantly correlated with protein chain length and native backbone topology, which is represented by the absolute contact order and sequence-distant native pairs. The folding rate of two-state folders, which is known to be correlated with the native backbone topology, apparently does not correlate significantly with protein chain length. On the basis of a comparison of the folding rates of the non-two-state and two-state folders, it was found that they are similarly dependent on the parameters that reflect the native backbone topology. This suggests that the mechanisms behind non-two-state and two-state folding are essentially identical. The present results lead us to propose a unified mechanism of protein folding, in which folding occurs in a hierarchical manner, reflecting the hierarchy of the native three-dimensional structure, as embodied in the case of non-two-state folding with an accumulation of the intermediate. Apparently, two-state folding is merely a simplified version of hierarchical folding caused either by an alteration in the rate-limiting step of folding or by destabilization of the intermediate.
Kamagata
Kiyoto
K
Department of Physics, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Arai
Munehito
M
Kuwajima
Kunihiro
K
D007700:Kinetics; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000145:classification
D011506:Proteins