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The Amounts of Thermal Vibrations and Static Disorder in Protein X-ray Crystallographic B-factors
  • Hyuntae Na,
  • Konrad Hinsen,
  • Guang Song
Hyuntae Na
Penn State Harrisburg
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Konrad Hinsen
CNRS
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Guang Song
Iowa State University
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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 with the well-known CHARMM force field, we obtain computationally the magnitudes of thermal vibrations of nearly 1,000 structures. Our key findings are: (i) the magnitude of thermal vibrations, surprisingly, is nearly protein-independent, as a corollary to the universality in 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 status:ACCEPTED

18 Sep 2020Submitted to PROTEINS: Structure, Function, and Bioinformatics
22 Sep 2020Submission Checks Completed
22 Sep 2020Assigned to Editor
18 Oct 2020Reviewer(s) Assigned
10 Dec 2020Review(s) Completed, Editorial Evaluation Pending
12 Dec 2020Editorial Decision: Revise Minor
20 Dec 20201st Revision Received
21 Dec 2020Submission Checks Completed
21 Dec 2020Assigned to Editor
20 Jan 2021Reviewer(s) Assigned
08 Feb 2021Review(s) Completed, Editorial Evaluation Pending
04 Mar 2021Editorial Decision: Revise Minor
29 Mar 20212nd Revision Received
30 Mar 2021Submission Checks Completed
30 Mar 2021Assigned to Editor
05 Apr 2021Reviewer(s) Assigned
07 May 2021Review(s) Completed, Editorial Evaluation Pending
14 May 2021Editorial Decision: Revise Minor
31 May 20213rd Revision Received
01 Jun 2021Submission Checks Completed
01 Jun 2021Assigned to Editor
05 Jun 2021Review(s) Completed, Editorial Evaluation Pending
06 Jun 2021Editorial Decision: Accept