Enhancement of linear vs. non-linear motions in protein folding

Vojtěch Spiwok

Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague,

Technická 3, 166 28 Prague 6, Czech Republic

spiwokv@vscht.cz

Time scales of molecular simulations are limited by available computational resources. To overcome this obstacle, many enhanced sampling methods have been developed. Metadynamics method disfavors previously visited states of the studied system to improve sampling in directions of selected degrees of freedom. Enhancement of sampling of linear collective motions of a molecule has been tested in the framework of metadynamics. However, atomic motions are not linear. In this project we test enhancement of non-linear collective motions in the simulation of folding of tryptophan cage mini-protein. Several folding-unfolding transitions were observed in 200 ns simulations, despite the fact that significantly longer time scales are necessary to fold this mini-protein in conventional simulations.

This project was supported by COST actions MultiGlycoNano (CM1102, LD13024) and GLISTEN (CM1207, LD14133). Access to computing and storage facilities MetaCentrum (LM2010005) and CERIT-SC (CZ. 1.05/3.2.00/08.0144) is greatly appreciated.