Conformation of 3'CMP bound to RNase A using TrNOESY.

Academic Article

Abstract

  • The conditions for accurately determining distance constraints from TrNOESY data on a small ligand (3'CMP) bound to a small protein (RNase A, <14 kDa) are described. For small proteins, normal TrNOESY conditions of 10:1 ligand:protein or greater can lead to inaccurate structures for the ligand-bound conformation due to the contribution of the free ligand to the TrNOESY signals. By using two ligand:protein ratios (2:1 and 5:1), which give the same distance constraints, a conformation of 3'CMP bound to RNase A was determined (glycosidic torsion angle, chi=-166 degrees ; pseudorotational phase angle, 0 degrees < or = P < or =36 degrees ). Ligand-protein NOESY cross peaks were also observed and used to dock 3'CMP into the binding pocket of the apo-protein (7rsa). After energy minimization, the conformation of the 3'CMP:RNase A complex was similar to the X-ray structure (1 rpf) except that a C3'-endo conformation for the ribose ring (rather than C2'-exo conformation) was found in the TrNOESY structure.
  • Keywords

  • Computer Simulation, Cytidine Monophosphate, Electron Spin Resonance Spectroscopy, Models, Molecular, Molecular Conformation, Ribonuclease, Pancreatic
  • Digital Object Identifier (doi)

    Author List

  • Lee Y-C; Jackson PL; Jablonsky MJ; Muccio DD
  • Start Page

  • 37
  • End Page

  • 46
  • Volume

  • 463
  • Issue

  • 1