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Normal modes of vibration in bovine pancreatic trypsin inhibitor and its mechanical property
Author(s) -
Nishikawa Tetsuo,
Gō Nobuhiro
Publication year - 1987
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340020407
Subject(s) - normal mode , globular protein , dihedral angle , displacement (psychology) , vibration , molecule , chemistry , physics , molecular physics , function (biology) , harmonic , crystallography , molecular vibration , classical mechanics , quantum mechanics , hydrogen bond , biology , psychology , evolutionary biology , psychotherapist
The normal mode analysis of conformational fluctuation is carried out for a small globular protein, bovine pancreatic trypsin inhabitor. Results are analyzed mainly to reveal the mechanical construction of the protein molecule. We take dihedral angles, including peptide ω angles, as independent variables for the normal mode analysis. There are 306 such angles in this molecule. Motions in modes with frequencies lower than 120 cm −1 are showned to involve atoms in the whole protein molecule, and spatial change of displacement vectors is continues, i.e., those of atoms near in space are similar. To quantitate the observation of the continuity, a correlation function of direction vectors of atomic displacement is calculated. From this function we define a Quantity that is interpreted as the wave length of an equivalent elastic plane wave. From this Quantity we deduce eefective young's modulus for each mode. For the mode with the lowest frequency 4.4 cm −1 , it terned out to be 0.8 × 10 9 dyn cm −2 , the value two orders magnitude softer than, for instance, α‐helices. Prompted by this observation, the four lowest frequency modes and also the harmonic motions in the thermal equilibrium are analyzed further mainly to detect relatively rigid structural elements in the molecule. From this analysis emerges a mechanical picture of the protein molecule that is made up of relatively rigid elements held together by very soft parts.