Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data.

ABSTRACT: We present an approach for incorporating solvent accessibility data from electron paramagnetic resonance experiments in the structural refinement of membrane proteins through restrained molecular dynamics simulations. The restraints have been parameterized from oxygen (PiO(2)) and nickel-ethylenediaminediacetic acid (PiNiEdda) collision frequencies, as indicators of lipid or aqueous exposed spin-label sites. These are enforced through interactions between a pseudoatom representation of the covalently attached Nitroxide spin-label and virtual "solvent" particles corresponding to O(2) and NiEdda in the surrounding environment. Interactions were computed using an empirical potential function, where the parameters have been optimized to account for the different accessibilities of the spin-lab

SUBMITTER: Sompornpisut P 

PROVIDER: S-EPMC2586578 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature