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Title: Local dynamics of proteins and DNA evaluated from crystallographic B factors

Abstract

Distributions of scaled B factors from 704 protein–DNA complexes reflect primarily the neighbourhood of amino-acid and nucleotide residues: their flexibility grows from the protein core to protein–protein and protein–DNA interfaces, to solvent-exposed residues. Some of the findings clearly observed at higher resolution structures can no longer be observed for structures at low resolution indicating problems in refinement protocols. The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein–DNA crystal structures were analyzed [Schneider et al. (2014 ▶), Nucleic Acids Res.42, 3381–3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein–protein or protein–DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but alsomore » revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified.« less

Authors:
 [1]; ;  [2];  [3];  [4];  [3];  [1]
  1. Institute of Biotechnology AS CR, Videnska 1083, 142 20 Prague (Czech Republic)
  2. INSERM, U1134, DSIMB, 75739 Paris (France)
  3. (France)
  4. (INTS), 75739 Paris (France)
Publication Date:
OSTI Identifier:
22347750
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 70; Journal Issue: Pt 9; Other Information: PMCID: PMC4157449; PMID: 25195754; PUBLISHER-ID: dz5328; OAI: oai:pubmedcentral.nih.gov:4157449; Copyright (c) Schneider et al. 2014; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ATOMS; CHAINS; CRYSTAL STRUCTURE; CRYSTALS; DIFFRACTION; DISTRIBUTION; FLEXIBILITY; FLUCTUATIONS; IMAGES; INTERFACES; MOLECULES; PROTEINS; RESOLUTION; WATER

Citation Formats

Schneider, Bohdan, E-mail: bohdan.schneider@gmail.com, Gelly, Jean-Christophe, Brevern, Alexandre G. de, Université Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, 75739 Paris, Institut National de la Transfusion Sanguine, Laboratoire d’Excellence GR-Ex, 75739 Paris, and Černý, Jiří. Local dynamics of proteins and DNA evaluated from crystallographic B factors. Denmark: N. p., 2014. Web. doi:10.1107/S1399004714014631.
Schneider, Bohdan, E-mail: bohdan.schneider@gmail.com, Gelly, Jean-Christophe, Brevern, Alexandre G. de, Université Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, 75739 Paris, Institut National de la Transfusion Sanguine, Laboratoire d’Excellence GR-Ex, 75739 Paris, & Černý, Jiří. Local dynamics of proteins and DNA evaluated from crystallographic B factors. Denmark. doi:10.1107/S1399004714014631.
Schneider, Bohdan, E-mail: bohdan.schneider@gmail.com, Gelly, Jean-Christophe, Brevern, Alexandre G. de, Université Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, 75739 Paris, Institut National de la Transfusion Sanguine, Laboratoire d’Excellence GR-Ex, 75739 Paris, and Černý, Jiří. Mon . "Local dynamics of proteins and DNA evaluated from crystallographic B factors". Denmark. doi:10.1107/S1399004714014631.
@article{osti_22347750,
title = {Local dynamics of proteins and DNA evaluated from crystallographic B factors},
author = {Schneider, Bohdan, E-mail: bohdan.schneider@gmail.com and Gelly, Jean-Christophe and Brevern, Alexandre G. de and Université Paris Diderot, Sorbonne Paris Cité, UMR-S 1134, 75739 Paris and Institut National de la Transfusion Sanguine and Laboratoire d’Excellence GR-Ex, 75739 Paris and Černý, Jiří},
abstractNote = {Distributions of scaled B factors from 704 protein–DNA complexes reflect primarily the neighbourhood of amino-acid and nucleotide residues: their flexibility grows from the protein core to protein–protein and protein–DNA interfaces, to solvent-exposed residues. Some of the findings clearly observed at higher resolution structures can no longer be observed for structures at low resolution indicating problems in refinement protocols. The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-called B factors. To find out how the crystal-derived B factors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaled B factors from a carefully curated data set of over 700 protein–DNA crystal structures were analyzed [Schneider et al. (2014 ▶), Nucleic Acids Res.42, 3381–3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e. forming the protein core) or lying at protein–protein or protein–DNA interfaces; the backbone and side-chain atoms were analyzed separately. The B factors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids have B factors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of the B factors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified.},
doi = {10.1107/S1399004714014631},
journal = {Acta Crystallographica. Section D: Biological Crystallography},
number = Pt 9,
volume = 70,
place = {Denmark},
year = {Mon Sep 01 00:00:00 EDT 2014},
month = {Mon Sep 01 00:00:00 EDT 2014}
}
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