2017 Fiscal Year Final Research Report
Binding free energy calculation based on various protonation states
| Project/Area Number |
15K16084
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| Research Category |
Grant-in-Aid for Young Scientists (B)
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| Allocation Type | Multi-year Fund |
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| Research Field |
Life / Health / Medical informatics
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| Research Institution | Tottori University |
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Principal Investigator |
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| Research Collaborator |
AMISAKI Takashi
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| Project Period (FY) |
2015-04-01 – 2018-03-31
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| Keywords | 結合自由エネルギー / 分子動力学 / タンパク質 / リガンド / プロトン化状態 / pH / MM/GBSA |
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| Outline of Final Research Achievements |
Information on binding affinity is important for understanding the functions of protein-ligand binding. Although various computational approaches have been used to predict binding free energy, accurate prediction remains difficult. To improve the quality of molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy calculations, we here propose the use of trajectory data on protonation states along with the coordinates generated by constant pH molecular dynamics simulations. Compared with the conventional method using fixed protonation states, the inclusion of information pertaining to flexible protonation states markedly lowered the calculated binding free energies of the hMTH1-8-oxo-dGMP complex. This study demonstrated an approach to calculating the binding free energy based on reasonable protonation states of amino acids at various pH values.
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| Free Research Field |
生命分子計算
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