Issue 37, 2010

Colored noise, folding rates and departure from Kramers’ behavior

Abstract

Recent experiments have shown that, for several proteins, the dependence of folding and unfolding rates on solvent viscosity does not obey Kramers’ theory. Such a departure from standard Kramers’ behavior is often attributed to the existence of internal friction, related to the structure of a polypeptide chain. In this paper, we propose an entirely different mechanism leading to violation of Kramers’ theory. Using the generalized Langevin equation with time-dependent friction and a Cα-Go model, we demonstrate that this effect may be caused by the colored Gaussian noise which is characterized by correlation time τ. Surprisingly, the dependence of folding time tf on τ is non-trivial: the plot tfvs τ exhibits two minima at low and intermediate values of τ. The appearance of one more additional minimum is in sharp contrast to one dimensional barrier crossing dynamics. We argue that it is a generic signature of entropy of activation in a multidimensional problem.

Graphical abstract: Colored noise, folding rates and departure from Kramers’ behavior

Article information

Article type
Paper
Submitted
10 Mar 2010
Accepted
29 Jun 2010
First published
20 Aug 2010

Phys. Chem. Chem. Phys., 2010,12, 11753-11762

Colored noise, folding rates and departure from Kramers’ behavior

B. Chandra Bag, C. Hu and M. Suan Li, Phys. Chem. Chem. Phys., 2010, 12, 11753 DOI: 10.1039/C004113K

To request permission to reproduce material from this article, please go to the Copyright Clearance Center request page.

If you are an author contributing to an RSC publication, you do not need to request permission provided correct acknowledgement is given.

If you are the author of this article, you do not need to request permission to reproduce figures and diagrams provided correct acknowledgement is given. If you want to reproduce the whole article in a third-party publication (excluding your thesis/dissertation for which permission is not required) please go to the Copyright Clearance Center request page.

Read more about how to correctly acknowledge RSC content.

Social activity

Spotlight

Advertisements