Implicit solvation models ranging from simple but efficient surface-dependent contributions to generalized Born or boundary element solver of the Poisson equation [Totrov, 2002] were developed within the context of the Internal Coordinate Mechanics method (ICM) for structure prediction.  Recently the atomic solvent accessible surface method was extended to the two environment models with water, membrane, and a continuous transition between the two [Bordner et al., 2011].  The new model predicts accurate placement and conformations of peptides at the water membrane interface.  Similar models based on the local desolvation energies were applied to predict protein-protein and protein-membrane interaction interfaces with a method called MODA (membrane optimal desolvation areas).  ReferencesTotrov  M., R. Abagyan.  2001.   Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide.    Biopolymers, (60):124-33.  PMID:1145554Bordner A.J., B. Zorman, R. Abagyan. 2011. Efficient molecular mechanics simulations of the folding, orientation, and assembly of peptides in lipid bilayers using an implicit atomic solvation model. J Comput Aided Mol Des. 2011 Oct;25(10):895-911 PMID:21904908

Implicit solvation models inside pockets and membranes

244th National Meeting (2012)

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