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Protein structure calculation with data imputation: the use of substitute restraints


Abstract The amount of experimental restraints e.g., NOEs is often too small for calculating high quality three-dimensional structures by restrained molecular dynamics. Considering this as a typical missing value problem we propose here a model based data imputation technique that should lead to an improved estimation of the correct structure. The novel automated method implemented in AUREMOL makes a more efficient use of the experimental information to obtain NMR structures with higher accuracy. It creates a large set of substitute restraints that are used either alone or together with the experimental restraints. The new approach was successfully tested on three examples: firstly, the Ras-binding domain of Byr2 from Schizosaccharomyces pombe, the mutant HPr (H15A) from Staphylococcus aureus, and a X-ray structure of human ubiquitin. In all three examples, the quality of the resulting final bundles was improved considerably by the use of additional substitute restraints, as assessed quantitatively by the calculation of RMSD values to the â??trueâ?? structure and NMR R-factors directly calculated from the original NOESY spectra or the published diffraction data.

• Content Type Journal Article
• Pages 397-411
• DOI 10.1007/s10858-009-9379-y
• Authors
  • Carolina Cano, University of Regensburg Institut für Biophysik und physikalische Biochemie Universitätstr. 31 93053 Regensburg Germany
  • Konrad Brunner, University of Regensburg Institut für Biophysik und physikalische Biochemie Universitätstr. 31 93053 Regensburg Germany
  • Kumaran Baskaran, University of Regensburg Institut für Biophysik und physikalische Biochemie Universitätstr. 31 93053 Regensburg Germany
  • Ralph Elsner, University of Regensburg Institut für Biophysik und physikalische Biochemie Universitätstr. 31 93053 Regensburg Germany
  • Claudia E. Munte, University of Regensburg Institut für Biophysik und physikalische Biochemie Universitätstr. 31 93053 Regensburg Germany
  • Hans Robert Kalbitzer, University of Regensburg Institut für Biophysik und physikalische Biochemie Universitätstr. 31 93053 Regensburg Germany

• • Journal Journal of Biomolecular NMR
  • Online ISSN 1573-5001
  • Print ISSN 0925-2738
  • Journal Volume Volume 45
  • Journal Issue Volume 45, Number 4

Source: Journal of Biomolecular NMR