Highlight

Calculation of lipid-bilayer permeabilities using an average force. Calculations of lipid bilayer permeabilities from first principles, using molecular simulations, would be valuable to rapidly assess the bioavailability of drug candidates, as well as to decipher, at the atomic level, the mechanisms that underlie the translocation of permeants. The most common theoretical approach, the solubility–diffusion model, requires determination of the free energy and the diffusivity as functions of the position of the permeant. Quantitative predictions of permeability have, however, been stymied by acute difficulties in calculating the diffusivity, inadequate sampling, and, most insidiously, systematic biases due to imperfections in the force field, simulation parameters, and the inherent limitations of the diffusive model. In the present work, we combine importance-sampling simulations employing an adaptive biasing force with a Bayesian-inference algorithm to determine the free energy and diffusivity with noteworthy precision and spatial resolution. In multimicrosecond simulations, we probe the sensitivity of the permeability estimates to different aspects of the methodology, including the truncation of short-range interactions, the thermostat, the force-field parameters of the permeant, the time scale over which the diffusivity is estimated, and the size of the simulated system. The force-field parameters and time scale dependence of the diffusivities impose the greatest uncertainties on the permeability estimates. Our simulations highlight the importance of membrane distortion due to the presence of the permeant, which may be partially suppressed if the bilayer patch is not large enough. We suggest that improvements to force fields and more robust kinetic models may be needed to reduce systematic errors below a factor of two. J. Chem. Theory Comput. 2014.

Recent publications

Jo, S.; Chipot, C.; Roux, B.
Efficient determination of relative entropy using combined temperature and Hamiltonian replica-exchange molecular dynamics
J. Chem. Theory Comput.

2015, 11 (5), 2234-2244.
dx.doi.org

Comer, J.; Gumbart, J. C.; Hénin, J.; Lelièvre, T.; Pohorille, A.; Chipot, C.
The adaptive biasing force method: Everything you always wanted to know, but were afraid to ask
J. Phys. Chem. B

2015, 119 (3), 1129-1151.
dx.doi.org

Fu, H.; Comer, J.; Cai, W.; Chipot, C
Sonoporation at small and large length scales. Effect of cavitation bubble collapse on membranes
J. Phys. Chem. Letters

2015, 6 (3), 413-418.
dx.doi.org

News

- An update of ParseFEP is available in the latest version of VMD.
- 新的分子动力学讲义 (Dissemination).

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