Anisotropic local motions and location of amide protons in proteins

J Am Chem Soc. 2005 Apr 13;127(14):5180-5. doi: 10.1021/ja043575v.

Abstract

A new method has been developed to obtain dynamic and structural information about peptide planes in proteins by a combination of measurements of weak short-range cross-correlation rates R(H(N)N/NC') that are due to concerted fluctuations of the H(N)-N and N-C' dipole-dipole interactions and stronger long-range cross-correlation rates R(C'H(N)/H(N)N) and R(NH(N)/H(N)C(alpha)). The rates were interpreted using the axially symmetric Gaussian axial fluctuation model (GAF). The oscillation amplitudes as well as the positions of H(N) atoms with respect to peptide planes in ubiquitin were determined. Most N-H(N) bonds were found not to lie exactly along the bisector of the N-C' and N-C(alpha) bonds but to be slightly tilted toward the carbon-terminal side of the peptide.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amides / chemistry*
  • Anisotropy
  • Computer Simulation
  • Models, Chemical
  • Proteins / chemistry*
  • Protons
  • Quantum Theory
  • Ubiquitin / chemistry

Substances

  • Amides
  • Proteins
  • Protons
  • Ubiquitin