A general approach for prediction of motional EPR spectra from Molecular Dynamics (MD) simulations: application to spin labelled protein

Oganesyan, V. S. ORCID: https://orcid.org/0000-0002-8738-1146 (2011) A general approach for prediction of motional EPR spectra from Molecular Dynamics (MD) simulations: application to spin labelled protein. Physical Chemistry Chemical Physics, 13 (10). pp. 4724-4737. ISSN 1463-9076

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Abstract

A general approach for the prediction of EPR spectra directly and completely from single dynamical trajectories generated from Molecular Dynamics (MD) simulations is described. The approach is applicable to an arbitrary system of electron and nuclear spins described by a general form of the spin-Hamiltonian for the entire motional range. It is shown that for a reliable simulation of motional EPR spectra only a single truncated dynamical trajectory generated until the point when correlation functions of rotational dynamics are completely relaxed is required. The simulation algorithm is based on a combination of the propagation of the spin density matrix in the Liouville space for this initial time interval and the use of well defined parameters calculated entirely from the dynamical trajectory for prediction of the evolution of the spin density matrix at longer times. A new approach is illustrated with the application to a nitroxide spin label MTSL attached to the protein sperm whale myoglobin. It is shown that simulation of the EPR spectrum, which is in excellent agreement with experiment, can be achieved from a single MD trajectory. Calculations reveal the complex nature of the dynamics of a spin label which is a superposition of the fast librational motions within dihedral states, of slow rotameric dynamics among different conformational states of the nitroxide tether and of the slow rotational diffusion of the protein itself. The significance of the slow rotameric dynamics of the nitroxide tether on the overall shape of the EPR spectrum is analysed and discussed.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Chemistry (former - to 2024)
UEA Research Groups:	Faculty of Science > Research Groups > Biophysical Chemistry (former - to 2017) Faculty of Science > Research Groups > Chemistry of Light and Energy Faculty of Science > Research Groups > Chemistry of Life Processes Faculty of Science > Research Centres > Centre for Molecular and Structural Biochemistry Faculty of Science > Research Groups > Centre for Photonics and Quantum Science
Depositing User:	Rachel Smith
Date Deposited:	31 May 2011 15:44
Last Modified:	24 Sep 2024 09:05
URI:	https://ueaeprints.uea.ac.uk/id/eprint/31637
DOI:	10.1039/c0cp01068e

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