July 26, Thu 2012
10:00 am, MRB 200 Conference Room
Department of Biochemistry & Molecular Biology, Michigan State University
Implicit solvent membrane with adaptive thickness
Molecular dynamics simulation of proteins embedded in membrane bilayer has remained a challenging task throughout the years. One of the possibilities to reduce the computational cost is to employ a mean field approximation in the form of implicit membrane models. However, these models normally do not allow for membrane deformation in response to the presence of a biomolecules which limits their ability to accurately model the insertion energy of a charged particle or hydrophobic mismatch.
In a new implicit membrane model, we are allowing the membrane thickness to fluctuate dynamically. In this model, the membrane thickness is represented through additional degrees of freedom that are coupled via an extended Hamiltonian to the standard simulation formalism. The membrane deformation energy is obtained from elasticity equation and the solvation free energies are calculated using the heterogeneous dielectric Generalized Born (HDGB) model with dielectric profiles that are adjusted dynamically to account for local thickness variations. The flexible implicit membrane model is tested by comparing insertion profiles of side-chain amino acid analogs with explicit bilayer simulations. Furthermore, the adaptation of the membrane geometry to helical test peptides to optimize hydrophobic matching is tested.