TY - JOUR
T1 - Statistical mechanics theory of molecular recognition and pharmaceutical design
AU - Yoshida, Norio
AU - Kiyota, Yasuomi
AU - Phongphanphanee, Saree
AU - Maruyama, Yutaka
AU - Imai, Takashi
AU - Hirata, Fumio
N1 - Funding Information:
This study is supported by Grants-in-Aid for Scientific Research on Innovate Areas of Molecular Science of Fluctuations towards Biological Functions from the MEXT in Japan. Authors are also supported by the Next Generation Super Computing Project, Nanoscience Program, a Grant-in-Aid for Scientific Research. T. Imai acknowledges the support from HPCI STRATEGIC PROGRAM Computational Life Science and Application in Drug Discovery and Medical Development, and Research and Development of the Next-Generation Integrated Simulation of Living Matter, a part of the Development and Use of the Next-Generation Supercomputer Project of MEXT. Molecular graphics images were produced using the UCSF Chimera package and VMD [82,83]. A part of this study was carried out by a supercomputer in the Research Center for Computational Science (RCCS), Okazaki Research Facilities, National Institutes of Natural Sciences (NINS).
PY - 2011/10
Y1 - 2011/10
N2 - Molecular recognition (MR) is an essential elementary process allowing biomolecules to perform their function. MR can be defined as a molecular process in which one or several guest molecules are bound with a high probability at a particular site such as a cleft or a cavity, of a host molecule in a particular orientation. It is a thermodynamic process which is characterised by the difference of the free energies between two states of a host-guest system, bound and unbound. The process features an extremely heterogeneous atomic-environment around binding sites, which has turned away challenges by the conventional statistical mechanics of liquids, e.g. a mean field theory. We have been developing a new theory for MR in biomolecular systems, based on the statistical mechanics of liquids, or the 3D-reference interaction site model (RISM)/RISM theory. The theory has demonstrated its amazing capability of predicting the process from the first principle. In this article, we review our recent works on MR concerning protein and deoxyribonucleic acid. Some applications of the method to drug design are also presented.
AB - Molecular recognition (MR) is an essential elementary process allowing biomolecules to perform their function. MR can be defined as a molecular process in which one or several guest molecules are bound with a high probability at a particular site such as a cleft or a cavity, of a host molecule in a particular orientation. It is a thermodynamic process which is characterised by the difference of the free energies between two states of a host-guest system, bound and unbound. The process features an extremely heterogeneous atomic-environment around binding sites, which has turned away challenges by the conventional statistical mechanics of liquids, e.g. a mean field theory. We have been developing a new theory for MR in biomolecular systems, based on the statistical mechanics of liquids, or the 3D-reference interaction site model (RISM)/RISM theory. The theory has demonstrated its amazing capability of predicting the process from the first principle. In this article, we review our recent works on MR concerning protein and deoxyribonucleic acid. Some applications of the method to drug design are also presented.
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U2 - 10.1080/0144235X.2011.648755
DO - 10.1080/0144235X.2011.648755
M3 - Review article
AN - SCOPUS:84856772205
SN - 0144-235X
VL - 30
SP - 445
EP - 478
JO - International Reviews in Physical Chemistry
JF - International Reviews in Physical Chemistry
IS - 4
ER -