The aim of our laboratory is to elucidate the relationship between structures and functions of biological macromolecules and their mutual interactions by strutural bioinformatics using protein 3D structures, which were given by PDBj (Protein Data Bank Japan: http://www.pdbj.org/) in our institute, and molecular simulations including hybrid-QM/MM computations to analyze the electronic structures.
Current Research Programs
Bioinformatics studies focused on protein structures and protein-protein interactions
Development of new algorithms for simulations to examine free energy landscapes of biomolecular systems and their electronic structures by a hybrid-QM/MM method
Composite structural motifs of binding sites for delineating biological functions of proteins. Kinjo, A. R., Nakamura, H. (2012) PLoS One 7:e31437.
Electronic structures of the [4Fe-4S] cluster in dark-operative protochlorophyllide oxidoreductase (DPOR). Takano, Y., Yonezawa, Y., Fujita, Y., Kurisu, G., Nakamura, H. (2012) Chem. Phys. Lett. 503: 296.
A Free-Energy Landscape for Coupled Folding and Binding of an Intrinsically Disordered Protein in Explicit Solvent from D etailed All-Atom Computations. Higo J., Nishimura, Y., Nakamura, H. (2011) J. Ame. Chem. Soc. 133: 10448.
Molecular dynamics scheme for precise estimation of electrostatic interaction via zero-dipole summation principle. Fukuda , I., Yonezawa, Y., Nakamura, H. (2011) J. Chem. Phys. 134: 164107.
Intra- and Intermolecular Interaction Inducing Pyramidalization on both sides of a Proline Di-peptide during Isomerizatio n: an ab Initio QM/MM Molecular Dynamics Simulation Study in explicit water. Yonezawa, Y., Nakata, K., Sakakura, K., Takada, T., Nakamura, H. (2009) J. Am. Chem. Soc. 131: 4535.