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© Research
Publication : Journal of biomolecular NMR

Comparison of different torsion angle approaches for NMR structure determination

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Journal of biomolecular NMR - 01 Mar 2006

Bardiaux B, Malliavin TE, Nilges M, Mazur AK

Link to Pubmed [PMID] – 16604424

J. Biomol. NMR 2006 Mar;34(3):153-66

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.

http://www.ncbi.nlm.nih.gov/pubmed/16604424