Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling.
In recent work, we demonstrated that it is possible to obtain approximate representations of high-dimensional free energy surfaces with variationally enhanced sampling ( Shaffer, P.; Valsson, O.; Parrinello, M. Proc. Natl. Acad. Sci. , 2016 , 113 , 17 ). The high-dimensional spaces considered in that work were the set of backbone dihedral angles of a small peptide, Chignolin, and the high-dimensional free energy surface was approximated as the sum of many two-dimensional terms plus an additional term which represents an initial estimate. In this paper, we build on that work and demonstrate that we can calculate high-dimensional free energy surfaces of very high accuracy by incorporating additional terms. The additional terms apply to a set of collective variables which are more coarse than the base set of collective variables. In this way, it is possible to build hierarchical free energy surfaces, which are composed of terms that act on different length scales. We test the accuracy of these free energy landscapes for the proteins Chignolin and Trp-cage by constructing simple coarse-grained models and comparing results from the coarse-grained model to results from atomistic simulations. The approach described in this paper is ideally suited for problems in which the free energy surface has important features on different length scales or in which there is some natural hierarchy.
Department of Chemistry and Applied Biosciences, ETH Zurich , 8092 Zurich, Switzerland.
Patrick
P
Shaffer
Department of Chemistry and Applied Biosciences, ETH Zurich , 8092 Zurich, Switzerland.
Omar
O
Valsson
Department of Chemistry and Applied Biosciences, ETH Zurich , 8092 Zurich, Switzerland.
Michele
M
Parrinello
D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
D009842:Oligopeptides; C506175:chignolin