Premium
Conformational deformation in deoxymyoglobin by hydrostatic pressure
Author(s) -
Yamato Takahisa,
Higo Jun'ichi,
Seno Yasunobu,
Gō Nobuhiro
Publication year - 1993
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.340160403
Subject(s) - compressibility , hydrostatic pressure , volume (thermodynamics) , chemistry , deformation (meteorology) , thermodynamics , root mean square , hydrostatic equilibrium , molecule , displacement (psychology) , crystallography , materials science , physics , psychology , organic chemistry , quantum mechanics , composite material , psychotherapist
Pressure effect on the equilibrium conformation in sperm whale deoxymyoglobin and its volume fluctuation are studied by the normal mode analysis and strain tensor analysis. The pressure‐induced deformation of interhelix regions are found to be remarkably more compressed than the other parts of the molecule. The intrahelix compressibility is shown to be relatively small. We also calculate the compressibility of the three hydrophobic clusters, located at the bottom, distal, and proximal side of the heme. Its value is found to decrease in the indicated order. The average compressibility of these hydrophobic clusters is less than the average interhelix compressibility, even though there are large cavities in these clusters. In order to study overall deformation, we define a linear compressibility and calculate it for all pairs of C α atoms. The pressure‐induced deformation is observed to be heterogeneous also in this analysis. The calculated root‐mean‐square displacement of the constituent atoms in the equilibrium conformation at 1,000 atm from those at 0 atm is 0.12 Å, which is much smaller in magnitude than the average value of the atomic fluctuations at room temperature. In the water solvent, the volume excluded by the protein molecule in the equilibrium conformation is reduced by 0.9%, when the pressure is raised from 0 to 1,000 atm. The calculated magnitude of the root‐mean‐square volume fluctuation is 0.3% of the excluded volume at room temperature. The square of the volume fluctuation is given as a sum of contributions from individual normal modes. Contributions from low frequency normal modes are found to dominate over those from higher frequency normal modes. The estimated value of the isothermal compressibility of deoxymyoglobin is 9.37 × 10 −12 cm 2 /dyn. © 1993 Wiley‐Liss, Inc.