Tohoku University · Biochemistry, Genetics and Molecular Biology
Professor Kaori Fukuzawa's research lab specializes in the theoretical and computational investigation of molecular interactions in biological and astrochemical systems. The lab focuses on applying advanced quantum mechanical methods—particularly the fragment molecular orbital (FMO) approach—to study biomolecular recognition, protein-ligand interactions, and the electronic origins of binding affinities in estrogen receptors and other macromolecular complexes. Additionally, the lab explores the mechanisms of neutral-neutral reactions in interstellar environments, aiming to understand the formation pathways of complex organic molecules such as cyanopolyynes and cyanoacetylenes. Their work bridges computational chemistry, structural biology, and astrochemistry through high-accuracy ab initio calculations and the development of public databases for data sharing and analysis.
Figures are computed from collected data and may differ slightly.
We have theoretically examined the relative binding affinities (RBA) of typical ligands, 17beta-estradiol (EST), 17alpha-estradiol (ESTA), genistein (GEN), raloxifene (RAL), 4-hydroxytamoxifen (OHT), tamoxifen (TAM), clomifene (CLO), 4-hydroxyclomifene (OHC), diethylstilbestrol (DES), bisphenol A (BISA), and bisphenol F (BISF), to the alpha-subtype of the human estrogen receptor ligand-binding domain (hERalpha LBD), by calculating their binding energies. The ab initio fragment molecular orbital
The ab initio fragment molecular orbital calculations were performed for molecular interactions of the whole estrogen receptor (ER) ligand-binding domain with a natural ligand, 17beta-estradiol (EST). The interaction energies of the ligand at the residue level were calculated using HF and MP2 methods with several basis sets. The charge-transfer (CT) interactions were also analyzed based on configuration analysis for fragment interaction. Strong electrostatic interactions were observed between th
The ab initio fragment molecular orbital (FMO) calculations were performed for the cAMP receptor protein (CRP) complexed with a cAMP and DNA duplex to elucidate their sequence-specific binding and the stability of the DNA duplex, as determined by analysis of their inter- and intramolecular interactions. Calculations were performed with the AMBER94 force field and at the HF and MP2 levels with several basis sets. The interfragment interaction energies (IFIEs) were analyzed for interactions of CRP
The ab initio molecular orbital method is applied to explore the possibility that neutral-neutral reactions lead to the formation of cyanoacetylene and its isomers HCCNC and HNCCC in inter-HC 3 N stellar space. Potential energy surfaces for the formation of the molecule are examined HC 3 N theoretically for the reactions of the CN radical with acetylene and the radical with HCN and C 2 H HNC. The calculated result shows that it is possible for HCCCN to be formed from and C 2 H 2 ] CN because the
We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy de
Ab initio molecular quantum-mechanical methods have been applied to explore the possibility of neutral-neutral reactions leading to the formation of cyanopolyynes and polyacetylenes in interstellar cloud. Potential energy surfaces for the reactions between the CN radical and polyacetylenes indicate that all reactions, (n \ 14), which form molecules, are exothermic and have no C 2n H 2 ] CN HC 2n`1 N energy barriers. We have also examined the possibility of the various product channels from the r
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