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A new constraint potential for the structure refinement of biomolecules in solution using experimental nuclear overhauser effect intensity
Author(s) -
Stawarz Bernard,
Genest Monique,
Genest Daniel
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.360320606
Subject(s) - nuclear overhauser effect , chemistry , biomolecule , constraint (computer aided design) , intensity (physics) , inverse , molecular dynamics , function (biology) , potential energy , chemical physics , biological system , statistical physics , molecule , computational chemistry , atomic physics , physics , quantum mechanics , biochemistry , geometry , mathematics , organic chemistry , biology , mechanical engineering , evolutionary biology , engineering
A new constraint potential is proposed for the refinement of the three‐dimensional structure of biomolecules in solution from nmr data. It is based on the nuclear Overhauser effect (NOE) intensity calculations, taking into account the spin diffusion phenomenon. For restrained energy minimization or molecular dynamics techniques, a constraint potential term expressed as a function of the negative inverse of the sixth power of the NOE intensities (NOE −1/6 ) is added to the classical potential energy function. The properties of this new NOE constraint potential are discussed and compared to those of a harmonic NOE intensity potential. The method integrated in the molecular modeling program GROMOS is tested on the regular α‐helical structure of a decaglycylpeptide.