TY - JOUR
T1 - Torsion-Angle Molecular Dynamics as a New Efficient Tool for NMR Structure Calculation
AU - Stein, Evan G.
AU - Rice, Luke M.
AU - Brünger, Axel T.
N1 - Funding Information:
We thank G. Warren, A. Bonvin, P. Adams, T. Burling, and W. DeLano for valuable discussions, and G. M. Clore for providing the NMR data of interleukin 8 and the DNA dodecamer, and M. Nilges for the BPTI test case. We also thank M. A. Markus and G. Wagner for providing the data on villin 14T. This work was supported by a grant of the National Science Foundation to A.T.B. (ASC93181159). L.M.R. is an HHMI predoctoral fellow.
PY - 1997/1
Y1 - 1997/1
N2 - 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.
AB - 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.
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U2 - 10.1006/jmre.1996.1027
DO - 10.1006/jmre.1996.1027
M3 - Article
C2 - 9424305
AN - SCOPUS:0030621858
SN - 1090-7807
VL - 124
SP - 154
EP - 164
JO - Journal of Magnetic Resonance
JF - Journal of Magnetic Resonance
IS - 1
ER -