A refined, efficient mean solvation force model that includes the interior volume contribution

TitleA refined, efficient mean solvation force model that includes the interior volume contribution
Publication TypeJournal Article
Year of Publication2011
AuthorsAllison, JR, Boguslawski K, Fraternali F, van Gunsteren WF
Volume115
Pagination4547-4557
Abstract

A refined implicit aqueous solvation model is proposed for the simulation of biomolecules without the explicit inclusion of the solvent degrees of freedom. The mean force due to solvation is approximated by the derivative of a simple analytic function of the solvent accessible surface area combined with two atomic solvation parameters, as described previously, with the addition of a novel term to account for the interaction of the interior atoms of the solute with the solvent. The extended model is parametrized by comparing the structural properties and energies computed from simulations of six test proteins of varying sizes and shapes using the new solvation energy term with the corresponding values obtained from simulations in vacuum, using the original implicit solvent model and in explicit water, and from the X-ray or NMR model structures. The mean solvation model proposed here improves the structural properties relative to vacuum simulations and relative to the simpler model that neglects the volume contribution, while remaining significantly more efficient than simulations in explicit water.

URLhttp://dx.doi.org/10.1021/jp2017117

Publications by Jane Allison

Allison, JR, Riniker S, van Gunsteren WF. 2012. Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol. The Journal of Chemical Physics. 136: 054505-11
Kunz, A-PE, Allison JR, Geerke DP, Horta BAC, Hünenberger PH, Riniker S, Schmid N, van Gunsteren WF. 2012. New functionalities in the GROMOS biomolecular simulation software. Journal of Computational Chemistry. 33: 340-353
Allison, JR, Bergeler M, Hansen N, van Gunsteren WF. 2011. Current computer modeling cannot explain why two highly similar sequences fold into different structures. Biochemistry. 50: 10965-10973
Allison, JR, Boguslawski K, Fraternali F, van Gunsteren WF. 2011. A refined, efficient mean solvation force model that includes the interior volume contribution. The Journal of Physical Chemistry B. 115: 4547-4557
Eichenberger, AP, Allison JR, Dolenc J, Geerke DP, Horta BAC, Meier K, Oostenbrink C, Schmid N, Steiner D, Wang D et al.. 2011. GROMOS++ software for the analysis of biomolecular simulation trajectories. Journal of Chemical Theory and Computation. 7: 3379-3390
Schmid, N, Allison J, Dolenc J, Eichenberger A, Kunz A-P, van Gunsteren W. 2011. Biomolecular structure refinement using the GROMOS simulation software. Journal of Biomolecular NMR. 51: 265-281