Prediction of nitroxide spin label EPR spectra from MD trajectories: application to myoglobin

Kuprusevicius, Egidijus, White, Gaye and Oganesyan, Vasily (2011) Prediction of nitroxide spin label EPR spectra from MD trajectories: application to myoglobin. Faraday Discussions, 148. p. 283.

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Abstract

We report the prediction of motional EPR spectra of the metalloprotein sperm whale myoglobin spin labelled with nitroxide directly from Molecular Dynamics (MD) simulations at the atomistic scale. We show that an accurate simulation of EPR spectra can be achieved from a single MD trajectory which is in excellent agreement with experiment. Simulations have been carried out using a general method reported previously by us for the simulation of EPR spectra form single dynamical trajectories. Our calculations demonstrate the complex nature of the dynamics of a spin label which is a superposition of the fast librational motions around dihedral states, of slow conformational flips among different rotameric states and of the slow rotational diffusion of the protein itself. The MD-EPR methodology reported does not require any additional stochastic modelling using adjustable parameters and opens, for the first time, the prospect of the simulation of EPR spectra entirely from single MD trajectories. Such a technique not only simplifies the interpretation and analysis of EPR spectra but also opens the possibility, for example, of “computer engineering” of spin-labelled proteins with the desired properties prior to actual EPR experiment.

Item Type: Article
Faculty \ School: Faculty of Science > School of Biological Sciences
Faculty of Science > School of Chemistry
Related URLs:
Depositing User: Rachel Smith
Date Deposited: 23 Mar 2011 15:13
Last Modified: 21 Apr 2020 16:48
URI: https://ueaeprints.uea.ac.uk/id/eprint/27053
DOI: 10.1039/C004855K

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