This title appears in the Scientific Report : 2014 

Extension of the FACTS Implicit Solvation Model to Membranes
Carballo-Pacheco, Martín
Vancea, Ioan / Strodel, Birgit (Corresponding Author)
Strukturbiochemie ; ICS-6
Journal of chemical theory and computation, 10 (2014) 8, S. 3163 - 3176
Washington, DC American Chemical Society (ACS) 2014
Journal Article
Structural Biology
Please use the identifier: in citations.
The generalized Born (GB) formalism can be used to model water as a dielectric continuum. Among the different implicit solvent models using the GB formalism, FACTS is one of the fastest. Here, we extend FACTS so that it can represent a membrane environment. This extension is accomplished by considering a position dependent dielectric constant and empirical surface tension parameter. For the calculation of the effective Born radii in different dielectric environments we present a parameter-free approximation to Kirkwood’s equation, which uses the Born radii obtained with FACTS for the water environment as input. This approximation is tested for the calculation of self-free energies, pairwise interaction energies in solution and solvation free energies of complete protein conformations. The results compare well to those from the finite difference Poisson method. The new implicit membrane model is applied to estimate free energy insertion profiles of amino acid analogues and in molecular dynamics simulations of melittin, WALP23 and KALP23, glycophorin A, bacteriorhodopsin, and a Clc channel dimer. In all cases, the results agree qualitatively with experiments and explicit solvent simulations. Moreover, the implicit membrane model is only six times slower than a vacuum simulation.