2026-03-15T15:26:34Z https://kanazawa-u.repo.nii.ac.jp/oai

oai:kanazawa-u.repo.nii.ac.jp:00049555 2024-05-08T01:55:25Z 934:941:943:3790

Molecular dynamics study of free energy profile for dissociation of ligand from CA I active site Molecular dynamics study of free energy profile for dissociation of ligand from CA I active site 90402429 川口, 一朋 30291892 長尾, 秀実 Arwansyah, MS Kodama, Koichi Kurniawan, Isman Kataoka, Tatsuki 90402429 Kawaguchi, Kazutomo 30291892 Nagao, Hidemi CA I active site ligand molecule force field parameters free energy profile free energy surface We investigate the binding/dissociation process of ligand molecule from carbonic anhydrase (CA) I carbonic anhydrase (CA) I enzyme by using all-atom molecular dynamics simulation. The force field parameters of zinc ion in the CA I active site are estimated by quantum chemical calculations and are summarized in this paper. The free energy profile for binding/dissociation process of ligand from CA I active site is calculated by the thermodynamic integration combined with the all-atom molecular dynamics simulation. The binding free energy as a function of the distance between the center of mass positions of CA I active site and the ligand molecule is estimated. The radial distribution function of the CA I-ligand complex is calculated from the trajectory of all-atom molecular dynamics (MD) simulation. We estimate the free energy surface from the radial distribution function. We can obtain the bond constant of the equilibrium state from the value of the free energy surface. We discuss the binding/dissociation process of ligand molecule by calculating the free energy profile to know the stability of the CA I-ligand complex with some thermodynamic properties such as the binding free energy, the equilibrium state of the free energy surface and so on. 2019 Institute of Science and Engineering, Kanazawa University 2019 2019-10-21 eng departmental bulletin paper VoR https://doi.org/10.24517/00055867 http://hdl.handle.net/2297/00055867 https://kanazawa-u.repo.nii.ac.jp/records/49555 10.24517/00055867 http://scirep.w3.kanazawa-u.ac.jp/ http://scirep.w3.kanazawa-u.ac.jp/ 2433-040X The Science Reports of Kanazawa University The Science Reports of Kanazawa University 63 15 28 https://kanazawa-u.repo.nii.ac.jp/record/49555/files/Sci_Rep63-002.pdf application/pdf 1.9 MB 2019-10-21