| Budget Amount *help |
¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Fiscal Year 2014: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2012: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
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| Outline of Final Research Achievements |
In this study, development of an analyzing method for the interaction between biomolecules and their ligands, considering the function of water inside the molecules were performed. The theoretical features of the glycan ligand-protein interactions in the HIV-1 antibody 2G12 as well as a lection called Siglec-7 were clarified in detail by ab initio Fragment Molecular Orbital calculations and classical molecular dynamics simulations. The dynamics of the protein-ligand's complexes was shown to play an important role in the ligand recognition mechanism. Calculated interaction energies agreed well with the experimentally observed ligands' affinities. The water molecules inside the biomolecules stabilized the ligand’s conformation and its binding site, which was notably observed in the system with neutral glycan ligands.
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