Comparison of different torsion angle approaches for NMR structure determination

J Biomol NMR. 2006 Mar;34(3):153-66. doi: 10.1007/s10858-006-6889-8.

Abstract

A new procedure for NMR structure determination, based on the Internal Coordinate Molecular Dynamics (ICMD) approach, is presented. The method finds biopolymer conformations that satisfy usual NMR-derived restraints by using high temperature dynamics in torsion angle space. A variable target function algorithm gradually increases the number of NOE-based restraints applied, with the treatment of ambiguous and floating restraints included. This soft procedure allows combining artificially high temperature with a general purpose force-field including Coulombic and Lennard-Jones non-bonded interactions, which improves the quality of the ensemble of conformations obtained in the gas-phase. The new method is compared to existing algorithms by using the structures of eight ribosomal proteins earlier obtained with state-of-the-art procedures and included into the RECOORD database [Nederveen, A., Doreleijers, J., Vranken, W., Miller, Z., Spronk, C., Nabuurs, S., Guntert, P., Livny, M., Markley, M., Nilges, M., Ulrich, E., Kaptein, R. and Bonvin, A.M. (2005) Proteins, 59, 662-672]. For the majority of tested proteins, the ICMD algorithm shows similar convergence and somewhat better quality Z scores for the phi, psi distributions. The new method is more computationally demanding although the overall load is reasonable.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Computer Simulation
  • Databases, Protein
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Protein Conformation*
  • Proteins / chemistry*

Substances

  • Proteins