Conformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR-Relaxation-Theory and Molecular-Dynamics-Simulation Approaches.
Related Articles Conformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR-Relaxation-Theory and Molecular-Dynamics-Simulation Approaches.
J Phys Chem B. 2020 Sep 26;:
Authors: Mendelman N, Zerbetto M, Buck M, Meirovitch E
Abstract
A new method for determining conformational entropy in proteins is reported. Proteins prevail as conformational ensembles, p ? exp(-u). By selecting a bond-vector (e.g., N-H) as conformation representative, MD simulations can provide (relative to a reference structure) p as approximate Boltzmann probability density and u as N-H Potential of Mean Force (POMF). The latter is as accurate as the force-field but statistical in character; this limits the insight it can provide, and its utilization. Conformational entropy is given exclusively by u. Deriving it from POMFs renders it accurate but statistical in character. Previously we devised explicit (i.e., analytical but not exact) potentials made of Wigner functions, DL0K, with L