Torsion-Angle Molecular Dynamics as a New Efficient Tool for NMR Structure Calculation

Evan G. Stein, Luke M. Rice, Axel T. Brünger

Research output: Contribution to journalArticle

271 Citations (Scopus)

Abstract

Molecular dynamics in torsion-angle space was applied to nuclear magnetic resonance structure calculation using nuclear Overhauser effect-derived distances and J-coupling-constant-derived dihedral angle restraints. Compared to two other commonly used algorithms, molecular dynamics in Cartesian space and metric-matrix distance geometry combined with Cartesian molecular dynamics, the method shows increased computational efficiency and success rate for large proteins, and it shows a dramatically increased radius of convergence for DNA. The torsion-angle molecular dynamics algorithm starts from an extended strand conformation and proceeds in four stages: high-temperature torsion-angle molecular dynamics, slow-cooling torsion-angle molecular dynamics, Cartesian molecular dynamics, and minimization. Tests were carried out using experimental NMR data for protein G, interleukin-8, villin 14T, and a 12 base-pair duplex of DNA, and simulated NMR data for bovine pancreatic trypsin inhibitor. For villin 14T, a monomer consisting of 126 residues, structure determination by torsion-angle molecular dynamics has a success rate of 85%, a more than twofold improvement over other methods. In the case of the 12 base-pair DNA duplex, torsion-angle molecular dynamics had a success rate of 52% while Cartesian molecular dynamics and metric-matrix distance geometry always failed.

Original languageEnglish (US)
Pages (from-to)154-164
Number of pages11
JournalJournal of Magnetic Resonance
Volume124
Issue number1
StatePublished - Jan 1997

Fingerprint

Molecular Dynamics Simulation
Torsional stress
torsion
Molecular dynamics
Nuclear magnetic resonance
molecular dynamics
nuclear magnetic resonance
deoxyribonucleic acid
Base Pairing
DNA
Overhauser effect
interleukins
proteins
trypsin
Aprotinin
Geometry
Dihedral angle
matrices
geometry
Computational efficiency

ASJC Scopus subject areas

  • Molecular Biology
  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Radiology Nuclear Medicine and imaging
  • Condensed Matter Physics

Cite this

Torsion-Angle Molecular Dynamics as a New Efficient Tool for NMR Structure Calculation. / Stein, Evan G.; Rice, Luke M.; Brünger, Axel T.

In: Journal of Magnetic Resonance, Vol. 124, No. 1, 01.1997, p. 154-164.

Research output: Contribution to journalArticle

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