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Combined use of homo‐ and heteronuclear coupling constants as restraints in molecular dynamics simulations
Author(s) -
Mierke Dale F.,
Kessler Horst
Publication year - 1992
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360321003
Subject(s) - dihedral angle , heteronuclear molecule , chemistry , molecular dynamics , coupling constant , scalar (mathematics) , coupling (piping) , computational chemistry , nuclear overhauser effect , molecular physics , function (biology) , constant (computer programming) , crystallography , thermodynamics , chemical physics , nuclear magnetic resonance , physics , molecule , stereochemistry , nuclear magnetic resonance spectroscopy , quantum mechanics , geometry , materials science , organic chemistry , mathematics , hydrogen bond , biology , computer science , programming language , evolutionary biology , metallurgy
A penalty function for scalar coupling constants has been applied in molecular dynamics simulations as an experimental constraint. The function is based on the difference between the coupling constant calculated from the dihedral angle and the experimentally measured coupling constant. The method is illustrated on a model cyclic pentapeptide for which 3 J HN‐Hα and 3 J HN‐Cβ , both about the ϕ backbone dihedral angle, have been measured. The function is efficient in producing structures consistent with the scalar couplings, but removed from the conformation observed in solution. This arises from the lack of J restraints for the ψ dihedral angle. Simulation with both nuclear Overhauser effect (NOE) and J ‐coupling restraints illustrates small but significant differences from simulations using only NOEs. © 1992 John Wiley & Sons, Inc.