Unification of the folding mechanisms of non-two-state and two-state proteins

Kiyoto Kamagata, Munehito Arai, Kunihiro Kuwajima

Research output: Contribution to journalArticle

80 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)951-965
Number of pages15
JournalJournal of Molecular Biology
Volume339
Issue number4
DOIs
Publication statusPublished - 2004 Jun 11
Externally publishedYes

Keywords

  • ACO, absolute contact order
  • RCO, relative contact order
  • chain length
  • contact order
  • intermediate
  • protein folding
  • topology
  • ΔG , the change in free energy of unfolding in the absent of a denaturant

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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