DOI: 10.1209/epl/i2003-00165-4
Europhys. Lett., 61 (4) , pp. 561-566 (2003)

Mean first-passage time analysis reveals rate-limiting steps, parallel pathways and dead ends in a simple model of protein folding

M. A. Micheelsen¹, C. Rischel^{1, 2}, J. Ferkinghoff-Borg^{1, 3}, R. Guerois³ and L. Serrano<sup>3

1</sup>  Complexity Lab., Niels Bohr Institute, University of Copenhagen Blegdamsvej 17, DK-2100 København Ø, Denmark
²  Department of Mathematics and Physics Royal Veterinary and Agricultural University Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
³  EMBL Heidelberg - Meyerhofstrasse 1, D-69117 Heidelberg, Germany

rischel@nbi.dk

(Received 2 July 2002; accepted in final form 9 December 2002)

Abstract
We have analyzed dynamics on the complex free-energy landscape of protein folding in the FOLD-X model, by calculating for each state of the system the mean first-passage time to the folded state. The resulting kinetic map of the folding process shows that it proceeds in jumps between well-defined, local free-energy minima. Closer analysis of the different local minima allows us to reveal secondary, parallel pathways as well as dead ends.

PACS
87.15.Aa - Theory and modeling; computer simulation.
82.20.Fd - Collision theories; trajectory models.

© EDP Sciences 2003