Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids.
Recent progress in the theory of molecular recognition in biomolecules is reviewed, which has been made based on the statistical mechanics of liquids or the RISM/3D-RISM theory during the last five years in the authors' group. The method requires just the structure of protein and the potential energy parameters for the biomolecules and solutions as inputs. The calculation is carried out in two steps. The first step is to obtain the pair correlation functions for solutions consisting of water and ligands based on the RISM theory. Then, given the pair correlation functions prepared in the first step, we calculate the 3D-distribution functions of water and ligands around and inside protein based on the 3D-RISM theory. The molecular recognition of a ligand by the protein is realized by the 3D-distribution functions: if one finds some conspicuous peaks in the distribution of a ligand inside protein, then the ligand is regarded as "recognized" by the protein. Some biochemical processes are investigated, which are intimately related to the molecular recognition of small ligands including water, noble gases, and ions by a protein.
Yoshida
Norio
N
Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan.
Imai
Takashi
T
Phongphanphanee
Saree
S
Kovalenko
Andriy
A
Hirata
Fumio
F
D006801:Humans; D007477:Ions; D008958:Models, Molecular; D008968:Molecular Conformation; D008970:Molecular Weight; D009113:Muramidase / Q000737:chemistry*; D010100:Oxygen / Q000032:analysis / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics; D014961:X-Ray Diffraction / Q000379:methods; D014978:Xenon / Q000737:chemistry
D007477:Ions; D011506:Proteins; D014978:Xenon; D009113:Muramidase; D010100:Oxygen