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Article

Patterns in Protein Flexibility: A Comparison of NMR “Ensembles”, MD Trajectories, and Crystallographic B-Factors

by
Christopher Reinknecht
,
Anthony Riga
,
Jasmin Rivera
and
David A. Snyder
*
Department of Chemistry, College of Science and Health, William Paterson University, 300 Pompton Rd, Wayne, NJ 07470, USA
*
Author to whom correspondence should be addressed.
Molecules 2021, 26(5), 1484; https://doi.org/10.3390/molecules26051484
Submission received: 31 December 2020 / Revised: 18 February 2021 / Accepted: 28 February 2021 / Published: 9 March 2021
(This article belongs to the Special Issue The Conformational Universe of Proteins and Peptides: Tales of Order and Disorder)
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Abstract

Proteins are molecular machines requiring flexibility to function. Crystallographic B-factors and Molecular Dynamics (MD) simulations both provide insights into protein flexibility on an atomic scale. Nuclear Magnetic Resonance (NMR) lacks a universally accepted analog of the B-factor. However, a lack of convergence in atomic coordinates in an NMR-based structure calculation also suggests atomic mobility. This paper describes a pattern in the coordinate uncertainties of backbone heavy atoms in NMR-derived structural “ensembles” first noted in the development of FindCore2 (previously called Expanded FindCore: DA Snyder, J Grullon, YJ Huang, R Tejero, GT Montelione, Proteins: Structure, Function, and Bioinformatics 82 (S2), 219–230) and demonstrates that this pattern exists in coordinate variances across MD trajectories but not in crystallographic B-factors. This either suggests that MD trajectories and NMR “ensembles” capture motional behavior of peptide bond units not captured by B-factors or indicates a deficiency common to force fields used in both NMR and MD calculations.
Keywords: Friedman’s test; backbone atom coordinate variances and uncertainties; superimposition Friedman’s test; backbone atom coordinate variances and uncertainties; superimposition
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MDPI and ACS Style

Reinknecht, C.; Riga, A.; Rivera, J.; Snyder, D.A. Patterns in Protein Flexibility: A Comparison of NMR “Ensembles”, MD Trajectories, and Crystallographic B-Factors. Molecules 2021, 26, 1484. https://doi.org/10.3390/molecules26051484

AMA Style

Reinknecht C, Riga A, Rivera J, Snyder DA. Patterns in Protein Flexibility: A Comparison of NMR “Ensembles”, MD Trajectories, and Crystallographic B-Factors. Molecules. 2021; 26(5):1484. https://doi.org/10.3390/molecules26051484

Chicago/Turabian Style

Reinknecht, Christopher, Anthony Riga, Jasmin Rivera, and David A. Snyder. 2021. "Patterns in Protein Flexibility: A Comparison of NMR “Ensembles”, MD Trajectories, and Crystallographic B-Factors" Molecules 26, no. 5: 1484. https://doi.org/10.3390/molecules26051484

APA Style

Reinknecht, C., Riga, A., Rivera, J., & Snyder, D. A. (2021). Patterns in Protein Flexibility: A Comparison of NMR “Ensembles”, MD Trajectories, and Crystallographic B-Factors. Molecules, 26(5), 1484. https://doi.org/10.3390/molecules26051484

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