Tohoku University · 생화학·유전·분자생물학
카오리 후쿠자와 교수의 연구실은 생체분자 간의 상호작용을 정밀하게 해석하기 위해 고도화된 분자 궤도 이론 기반의 FMO(Fragment Molecular Orbital) 계산 방법을 개발하고 응용합니다. 주로 에스트로겐 수용체, cAMP 수용체 등 생물학적 막대분자 시스템의 결합 에너지와 전자적 상호작용을 정량적으로 분석하며, 특히 전자기적 상호작용, 양자역학적 전이, 반응 경로 분석을 통해 생체분자 간의 특이적 결합 원리를 규명합니다. 또한, 천체배경에서의 유기분자 형성 메커니즘에 이르기까지 다양한 스케일의 분자 상호작용을 이론적으로 연구하고 있습니다.
표시된 성과는 수집된 데이터 기준으로 산출되며, 일부 차이가 있을 수 있습니다.
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
