Assessing and refining molecular dynamics simulations of proteins with nuclear magnetic resonance data

Biophysics Reviews
Jane R Allison

Abstract

The sophistication of the force fields, algorithms and hardware used for molecular dynamics (MD) simulations of proteins is continuously increasing. No matter how advanced the methodology, however, it is essential to evaluate the appropriateness of the structures sampled in a simulation by comparison with quantitative experimental data. Solution nuclear magnetic resonance (NMR) data are particularly useful for checking the quality of protein simulations, as they provide both structural and dynamic information on a variety of temporal and spatial scales. Here, various features and implications of using NMR data to validate and bias MD simulations are outlined, including an overview of the different types of NMR data that report directly on structural properties and of relevant simulation techniques. The focus throughout is on how to properly account for conformational averaging, particularly within the context of the assumptions inherent in the relationships that link NMR data to structural properties.

References

Jun 16, 1977·Nature·J A McCammonM Karplus
Nov 20, 1991·Journal of Molecular Biology·D S WishartF M Richards
Jul 5, 1990·Journal of Molecular Biology·A E TordaW F van Gunsteren
Jun 30, 1995·Journal of Molecular Biology·A M Bonvin, A T Brünger
Dec 1, 1994·Journal of Computer-aided Molecular Design·T HuberW F van Gunsteren
Jan 1, 1993·Journal of Biomolecular NMR·A E TordaW F van Gunsteren
Sep 1, 1995·Journal of Biomolecular NMR·J FennenW F van Gunsteren
Mar 29, 2001·Protein Science : a Publication of the Protein Society·H SchwalbeL J Smith
May 24, 2001·Journal of Biomolecular NMR·R BürgiW F van Gunsteren
Jul 19, 2001·Journal of the American Chemical Society·C PérezJ M Schmidt
Apr 25, 2002·Annual Review of Physical Chemistry·Eric Oldfield
Nov 8, 2002·Journal of Molecular Biology·Emanuelel PaciMartin Karplus
Nov 21, 2002·Journal of the American Chemical Society·Yunjun Wang, Oleg Jardetzky
Dec 21, 2002·Protein Science : a Publication of the Protein Society·Ad Bax
Jan 16, 2003·Journal of the American Chemical Society·Phineus R L MarkwickMichael Sattler
May 27, 2003·Journal of Biomolecular NMR·Jens Meiler
May 27, 2003·Journal of Biomolecular NMR·Stephen NealDavid S Wishart
Aug 23, 2003·Journal of Magnetic Resonance·B Hess, R M Scheek
Dec 16, 2003·Chemistry : a European Journal·Christine PeterWilfred F van Gunsteren

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Citations

May 9, 2015·Journal of Computational Chemistry·Justin A Drake, B Montgomery Pettitt
Sep 4, 2013·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Annamária F Ángyán, Zoltán Gáspári
Mar 11, 2016·PLoS Computational Biology·Sarina GrutschMartin Tollinger
Oct 22, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Reinier CárdenasCarlos Amero
Aug 13, 2013·Journal of Chemical Theory and Computation·Martin DračínskýThomas E Exner

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