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Quasi‐harmonic method for studying very low frequency modes in proteins
Author(s) -
Levy R. M.,
Srinivasan A. R.,
Olson W. K.,
McCammon J. A.
Publication year - 1984
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.360230610
Subject(s) - anharmonicity , chemistry , normal mode , force constant , eigenvalues and eigenvectors , vibration , harmonic , quadratic equation , low frequency , force field (fiction) , molecular dynamics , computational chemistry , classical mechanics , molecular physics , physics , molecule , acoustics , quantum mechanics , geometry , mathematics , organic chemistry , astronomy
A quasi‐harmonic approximation is described for studying very low frequency vibrations and flexible paths in proteins. The force constants of the empirical potential function are quadratic approximations to the potentials of mean force; they are evaluated from a molecular dynamics simulation of a protein based on a detailed anharmonic potential. The method is used to identify very low frequency (∼1 cm −1 ) normal modes for the protein pancreatic trypsin inhibitor. A simplified model for the protein is used, for which each residue is represented by a single interaction center. The quasi‐harmonic force constants of the virtual internal coordinates are evaluated and the normal‐mode frequencies and eigenvectors are obtained. Conformations corresponding to distortions along selected low‐frequency modes are analyzed.