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 foldingM. A. Micheelsen1, C. Rischel1, 2, J. Ferkinghoff-Borg1, 3, R. Guerois3 and L. Serrano3
1 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
(Received 2 July 2002; accepted in final form 9 December 2002)
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.
87.15.Aa - Theory and modeling; computer simulation.
82.20.Fd - Collision theories; trajectory models.
© EDP Sciences 2003