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Issue 13, 2011
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Exploring the free-energy landscapes of biological systems with steered molecular dynamics

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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

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Publication details

The article was received on 06 Dec 2010, accepted on 27 Jan 2011 and first published on 25 Feb 2011


Article type: Paper
DOI: 10.1039/C0CP02799E
Citation: Phys. Chem. Chem. Phys., 2011,13, 6176-6183
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    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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