The dynamical contact order: Protein folding rate parameters based on quantum conformational transitions

Abstract

Protein folding is regarded as a quantum transition between the torsion states of a polypeptide chain. According to the quantum theory of conformational dynamics, we propose the dynamical contact order (DCO) defined as a characteristic of the contact described by the moment of inertia and the torsion potential energy of the polypeptide chain between contact residues. Consequently, the protein folding rate can be quantitatively studied from the point of view of dynamics. By comparing theoretical calculations and experimental data on the folding rate of 80 proteins, we successfully validate the view that protein folding is a quantum conformational transition. We conclude that (i) a correlation between the protein folding rate and the contact inertial moment exists; (ii) multi-state protein folding can be regarded as a quantum conformational transition similar to that of two-state proteins but with an intermediate delay. We have estimated the order of magnitude of the time delay; (iii) folding can be classified into two types, exergonic and endergonic. Most of the two-state proteins with higher folding rate are exergonic and most of the multi-state proteins with low folding rate are endergonic. The folding speed limit is determined by exergonic folding. © 2011 The Author(s).