Exploration of disorder in protein structures by X‐ray restrained molecular dynamics

John Kuriyan, Klara Ösapay, Stephen K. Burley, Axel T. Brünger, Wayne A. Hendrickson, Martin Karplus

Research output: Contribution to journalArticlepeer-review

91 Scopus citations

Abstract

Conformational disorder in crystal structures of ribonuclease‐A and crambin is studied by including two independent structures in least‐squares optimizations against X‐ray data. The optimizations are carried out by X‐ray restrained molecular dynamics (simulated annealing refinement) and by conventional least‐squares optimization. Starting from two identical structures, the optimizations against X‐ray data lead to significant deviations between the two, with rms backbone displacements of 0.45 Å for refinement of ribonuclease at 1.53 Å resolution, and 0.31 Å for crambin at 0.945 Å. More than 15 independent X‐ray restrained molecular dynamics runs have been carried out for ribonuclease, and the displacements between the resulting structures are highly reproducible for most atoms. These include residues with two or more conformations with significant dihedral angle differences and alternative hydrogen bonding, as well as groups of residues that undergo displacements that are suggestive of rigid‐body librations. The crystallographic R‐values obtained are ≈ 13%, as compared to 15.3% for a comparable refinement with a single structure. Least‐squares optimization without an intervening restrained molecular dynamics stage is sufficient to reproduce most of the observed displacements. Similar results are obtained for crambin, where the higher resolution of the X‐ray data allows for refinement of unconstrained individual anisotropic temperature factors. These are shown to be correlated with the displacements in the two‐structure refinements.

Original languageEnglish (US)
Pages (from-to)340-358
Number of pages19
JournalProteins: Structure, Function, and Bioinformatics
Volume10
Issue number4
DOIs
StatePublished - Apr 1991
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Keywords

  • X‐ray refinement
  • conformational disorder
  • crambin
  • protein crystallography
  • ribonuclease A
  • simulated annealing

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