Comparison of Different Torsion Angle Approaches for NMR Structure Determination

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In this Subject: <a title="Anatomy & Physiology" href="/content/subcat?j_subject=157&j_availability=">Anatomy & Physiology ,&nbsp; <a title="Analytical Chemistry" href="/content/subcat?j_subject=164&j_availability=">Analytical Chemistry ,&nbsp; Internal Medicine
By this author: Bardiaux, Benjamin ;&nbsp; Malliavin, Th&#233;r&#232;se ;&nbsp; Nilges, Michael ;&nbsp; Mazur, Alexey

Authors: Bardiaux, Benjamin; Malliavin, Thérèse; Nilges, Michael; Mazur, Alexey

Source: Journal of Biomolecular NMR, Volume 34, Number 3, March 2006 , pp. 153-166(14)

Publisher: Springer

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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 Φ, ψ distributions. The new method is more computationally demanding although the overall load is reasonable.

Keywords: BMRB; cis peptides; CNS; CYANA; ICMD; NMR; RECOORD; ribosomal protein; structure calculation; torsion angle space; XPLOR-NIH