Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme.

ABSTRACT: DEER (double electron-electron resonance) is a powerful pulsed ESR (electron spin resonance) technique allowing the determination of distance histograms between pairs of nitroxide spin-labels linked to a protein in a native-like solution environment. However, exploiting the huge amount of information provided by ESR/DEER histograms to refine structural models is extremely challenging. In this study, a restrained ensemble (RE) molecular dynamics (MD) simulation methodology is developed to address this issue. In RE simulation, the spin-spin distance distribution histograms calculated from a multiple-copy MD simulation are enforced, via a global ensemble-based energy restraint, to match those obtained from ESR/DEER experiments. The RE simulation is applied to 51 ESR/DEER distance histogram da

SUBMITTER: Islam SM 

PROVIDER: S-EPMC3684008 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature