1H-NMR stereospecific assignments by conformational data-base searches

Biopolymers. Mar-Apr 1990;29(4-5):813-22. doi: 10.1002/bip.360290415.

Abstract

A search procedure is described for making stereospecific assignments at prochiral centers in proteins on the basis of nuclear Overhauser enhancement and coupling constant data derived from nmr experiments. A data base comprising torsion angles, associated 1H-1H coupling constants and interproton distances is searched by a computer algorithm for sets of values that match the experimental data within specified error limits. Two different data bases are used. The first is a crystallographic data base derived from 34 well-refined crystal structures; the second is a systematic data base derived from conformations of a short peptide fragment with idealized geometry by systematically varying the phi, psi, and chi 1 torsion angles. Both approaches are tested for beta-methylene groups with model data obtained from 20 crystal structures. The results for the two methods are similar though not identical, so that a combination of the two methods appears to be useful. With an appropriate choice of error estimates, around 80% of the beta-methylene groups could be assigned in the test calculations. In addition, results with experimental nmr data indicate that a similar percentage of stereospecific assignments can be made in practical situations.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Cellulose 1,4-beta-Cellobiosidase
  • Glycoside Hydrolases
  • Information Systems*
  • Magnetic Resonance Spectroscopy / methods
  • Protein Conformation*
  • Protons
  • Software
  • Stereoisomerism

Substances

  • Protons
  • Glycoside Hydrolases
  • Cellulose 1,4-beta-Cellobiosidase