TY - JOUR
T1 - Affinity of small ligands to myoglobin studied by the 3D-RISM theory
AU - Kiyota, Yasuomi
AU - Yoshida, Norio
AU - Hirata, Fumio
N1 - Funding Information:
This work is supported by Grants-in-Aid for Scientific Research on Innovate Areas of ‘Molecular Science of Fluctuations toward Biological Functions’ from the MEXT in Japan. Authors are also grateful to the support by the grant from the Next Generation Supercomputing Project, Nanoscience Program of the Ministry . Molecular graphic images were produced using the UCSF Chimera [23] package and gOpenMol [24,25] . A part of this work is supported by the Research Center for Computational Science (RCCS), Okazaki Research Facilities, National Institutes of Natural Sciences (NINS) .
PY - 2011/2/15
Y1 - 2011/2/15
N2 - The affinity of small ligands including O2, Xe, NO, CO, H 2S, and H2O to myoglobin is studied based on the Three-dimensional Reference Interaction Site Model (3D-RISM) theory, the statistical mechanics of molecular liquids. The affinity is evaluated in terms of the coordination number of ligands in cavities in the protein, or the "Xe site," which can be obtained from the radial distribution function of ligand molecules inside the cavities. It is found that NO, CO, and H 2S show greater affinity to the Xe sites than O2 does, while the affinity of Xe is lower than that of O2. A relevance of the results to the physiological activity of the protein is speculated. The physical origin of the difference in affinity among the ligands is discussed.
AB - The affinity of small ligands including O2, Xe, NO, CO, H 2S, and H2O to myoglobin is studied based on the Three-dimensional Reference Interaction Site Model (3D-RISM) theory, the statistical mechanics of molecular liquids. The affinity is evaluated in terms of the coordination number of ligands in cavities in the protein, or the "Xe site," which can be obtained from the radial distribution function of ligand molecules inside the cavities. It is found that NO, CO, and H 2S show greater affinity to the Xe sites than O2 does, while the affinity of Xe is lower than that of O2. A relevance of the results to the physiological activity of the protein is speculated. The physical origin of the difference in affinity among the ligands is discussed.
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U2 - 10.1016/j.molliq.2010.07.016
DO - 10.1016/j.molliq.2010.07.016
M3 - Article
AN - SCOPUS:79952006302
SN - 0167-7322
VL - 159
SP - 93
EP - 98
JO - Journal of Molecular Liquids
JF - Journal of Molecular Liquids
IS - 1
ER -