Issue 13, 2011

Exploring the free-energy landscapes of biological systems with steered molecular dynamics

Abstract

We perform steered molecular dynamics (SMD) simulations and use the Brownian dynamics fluctuation-dissipation-theorem (BD-FDT) to accurately compute the free-energy profiles for several biophysical processes of fundamental importance: hydration of methane and cations, binding of benzene to T4-lysozyme L99A mutant, and permeation of water through aquaglyceroporin. For each system, the center-of-mass of the small molecule (methane, ion, benzene, and water, respectively) is steered (pulled) at a given speed over a period of time, during which the system transitions from one macroscopic state/conformation (State A) to another one (State B). The mechanical work of pulling the system is measured during the process, sampling a forward pulling path. Then the reverse pulling is conducted to sample a reverse path from B back to A. Sampling a small number of forward and reverse paths, we are able to accurately compute the free-energy profiles for all the afore-listed systems that represent various important aspects of biological physics. The numerical results are in excellent agreement with the experimental data and/or other computational studies available in the literature.

Graphical abstract: Exploring the free-energy landscapes of biological systems with steered molecular dynamics

Article information

Article type
Paper
Submitted
06 Dec 2010
Accepted
27 Jan 2011
First published
25 Feb 2011

Phys. Chem. Chem. Phys., 2011,13, 6176-6183

Exploring the free-energy landscapes of biological systems with steered molecular dynamics

L. Y. Chen, Phys. Chem. Chem. Phys., 2011, 13, 6176 DOI: 10.1039/C0CP02799E

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