Prediction of nitroxide spin label EPR spectra from MD trajectories: Application to myoglobin
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...
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ftuniveastangl:oai:ueaeprints.uea.ac.uk:27053 2023-08-27T04:12:14+02:00 Prediction of nitroxide spin label EPR spectra from MD trajectories: Application to myoglobin Kuprusevicius, Egidijus White, Gaye Oganesyan, Vasily S. 2011 https://ueaeprints.uea.ac.uk/id/eprint/27053/ https://doi.org/10.1039/C004855K unknown Kuprusevicius, Egidijus, White, Gaye and Oganesyan, Vasily S. (2011) Prediction of nitroxide spin label EPR spectra from MD trajectories: Application to myoglobin. Faraday Discussions, 148. pp. 283-298. doi:10.1039/C004855K Article PeerReviewed 2011 ftuniveastangl https://doi.org/10.1039/C004855K 2023-08-10T22:32:10Z 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. Article in Journal/Newspaper Sperm whale University of East Anglia: UEA Digital Repository Faraday Discuss. 148 283 298 |
institution |
Open Polar |
collection |
University of East Anglia: UEA Digital Repository |
op_collection_id |
ftuniveastangl |
language |
unknown |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Kuprusevicius, Egidijus White, Gaye Oganesyan, Vasily S. |
spellingShingle |
Kuprusevicius, Egidijus White, Gaye Oganesyan, Vasily S. Prediction of nitroxide spin label EPR spectra from MD trajectories: Application to myoglobin |
author_facet |
Kuprusevicius, Egidijus White, Gaye Oganesyan, Vasily S. |
author_sort |
Kuprusevicius, Egidijus |
title |
Prediction of nitroxide spin label EPR spectra from MD trajectories: Application to myoglobin |
title_short |
Prediction of nitroxide spin label EPR spectra from MD trajectories: Application to myoglobin |
title_full |
Prediction of nitroxide spin label EPR spectra from MD trajectories: Application to myoglobin |
title_fullStr |
Prediction of nitroxide spin label EPR spectra from MD trajectories: Application to myoglobin |
title_full_unstemmed |
Prediction of nitroxide spin label EPR spectra from MD trajectories: Application to myoglobin |
title_sort |
prediction of nitroxide spin label epr spectra from md trajectories: application to myoglobin |
publishDate |
2011 |
url |
https://ueaeprints.uea.ac.uk/id/eprint/27053/ https://doi.org/10.1039/C004855K |
genre |
Sperm whale |
genre_facet |
Sperm whale |
op_relation |
Kuprusevicius, Egidijus, White, Gaye and Oganesyan, Vasily S. (2011) Prediction of nitroxide spin label EPR spectra from MD trajectories: Application to myoglobin. Faraday Discussions, 148. pp. 283-298. doi:10.1039/C004855K |
op_doi |
https://doi.org/10.1039/C004855K |
container_title |
Faraday Discuss. |
container_volume |
148 |
container_start_page |
283 |
op_container_end_page |
298 |
_version_ |
1775356165406851072 |