Protein folding with the adaptive tempering Monte Carlo method

Abstract

Characterization of the folding transition in a model protein was achieved with the recent multicanonical tempering method implemented with Monte Carlo the adaptive tempering Monte Carlo (ATMC) (X. Dong and E. Blaisten-Barojas. Adaptive tempering Monte Carlo method. J. Comput. Theor. Nanosci., 3, p. 118 2006). The folding transition temperature was successfully determined and a spread of states was observed around the interface between native and folded regions. Energy states collected from all tempering events in a series of parallel runs were used in the calculation of the free energy, internal energy, order parameter and radius of gyration as a function of temperature through the weighted histogram method. Not only the calculated thermodynamic properties are in good agreement with results from Langevin dynamics simulations (D. K. Klimov and D. Thirumalai. Native topology determines forced-induced pathways in global proteins. Proc. Natl. Acad. Sci. USA. 97, p. 7254 2000), but also this multicanonical approach is noticeably more efficient because of the adaptive manner in which the system visits states near a transition in the interface between two phases. Additionally, the ATMC is advantageous for protein simulation over regular single canonical ensemble methods because it accelerates the hopping between local energy minima on the potential energy surface.