COMP 386 |
| Implicit models of biological membranes are attractive for simulations of membrane-bound peptides and proteins because they greatly reduce the complexity of the simulated systems. However, a key question remains to what extent implicit models without any explicit lipids can accurately represent all of the physics involved in protein-lipid interactions. A heterogeneous dielectric model describes membranes as layers of low- and high-dielectric environments. In combination with a non-polar contribution that varies as a function of membrane insertion such a model can provide a realistic account of most of the underlying physics. The extension of such a model to include van der Waals interactions, an anisotropic cost of cavity formation, and a response of the modeled bilayer thickness to the presence of a protein or peptide is presented. First tests of the model in simulations with the Generalized Born formalism are presented for peptide-membrane insertion and helix-helix association applications. |
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Current Techniques in Molecular Simulation of Biological Systems
9:00 AM-11:55 AM, Wednesday, August 22, 2007 BCEC -- 156B, Oral
Division of Computers in Chemistry |