An easy way to include weak alignment constraints into NMR structure calculations

H. J. Sass, G. Musco, S. J. Stahl, P. T. Wingfield, S. Grzesiek

Research output: Contribution to journalArticlepeer-review

Abstract

We have recently shown that an energy penalty for the incorporation of residual tensorial constraints into molecular structure calculations can be formulated without the explicit knowledge of the Saupe orientation tensor (Moltke and Grzesiek, J. Biomol. NMR, 1999, 15, 77-82). Here we report the implementation of such an algorithm into the program X-PLOR. The new algorithm is easy to use and has good convergence properties. The algorithm is used for the structure refinement of the HIV-1 Nef protein using 252 dipolar coupling restraints. The approach is compared to the conventional penalty function with explicit knowledge of the orientation tensor's amplitude and rhombicity. No significant differences are found with respect to speed, Ramachandran core quality or coordinate precision.

Original languageEnglish
Pages (from-to)275-280
Number of pages6
JournalJournal of Biomolecular NMR
Volume21
Issue number3
DOIs
Publication statusPublished - 2001

Keywords

  • Orientation
  • Protein
  • Pseudo-inverse
  • Residual tensorial coupling
  • Structure calculation

ASJC Scopus subject areas

  • Spectroscopy
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry

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