Journal
JOURNAL OF MOLECULAR BIOLOGY
Volume 339, Issue 4, Pages 951-965Publisher
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2004.04.015
Keywords
protein folding; topology; contact order; chain length; intermediate
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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. (C) 2004 Elsevier Ltd. All rights reserved.
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