Kinetics of α-helix formation as diffusion on a one-dimensional free energy surface

• Published in: Chemical physics Vol. 307; no. 2; pp. 129 - 136
• Main Authors: Doshi, Urmi, Muñoz, Victor
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 27-12-2004
• ISSN: 0301-0104
• DOI: 10.1016/j.chemphys.2004.05.022

A question of great interest is whether Kramers-rate theory can be used to describe the highly complex conformational dynamics of biopolymers. In this paper we investigate this question in the context of the kinetics of the helix–coil transition. The formation of α-helices is possibly the dynamic process related to protein folding for which there is a better mechanistic understanding. Using a master equation-based model of the helix–coil transition we calculate the relaxation kinetics of α-helix forming peptides after perturbations induced by `instantaneous' jumps in temperature. These calculations successfully simulate the results of recent laser-induced temperature-jump experiments. We compare the time courses generated by such detailed model with the relaxation kinetics obtained by diffusion on a one-dimensional free energy surface derived from the projection of the free energy of the helix–coil transition onto the order parameter
H (i.e., number of helical peptide bonds). The diffusive kinetics calculated with a constant effective diffusion coefficient of ∼0.6
×
10
9 pb
2 s
−1 are in very good agreement with the results of the detailed kinetic model, indicating that
H is an appropriate reaction coordinate for α-helix formation.