Schedule Jun 06, 2012
A Novel Coarse-grained Force Field for Unbiased Protein- Membrane Simulations
Markus Deserno (Carnegie Mellon Univ.)

Many biophysical processes involving the interaction of proteins with lipid membranes operate at length- and time-scales that are currently unattainable by atomistic computer simulations. In this talk I will introduce a new coarse-grained (CG) force field for protein- lipid interactions. Its main features include: (i) a solvent-free representation; (ii) unconstrained protein structure formation; (iii) accurate bilayer structural properties; and (iv) transferability over amino acid sequences and lipid types. The cross-parametrization is achieved by reproducing the free energy of insertion of single amino acids into a bilayer as a function of insertion depth. As a validation I will show various structural properties of simple transmembrane proteins, such as fluctuations, tilt angle, and helix-helix distance. To illustrate its efficiency, I show two possible applications: First, the folding and insertion of WALP peptides in a membrane environment; and second, membrane pore formation mediated by the cooperative action of eight antimicrobial peptides (magainin).

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