Hydration thermodynamics of a protein developed by using Hadwiger theorem

2014 Fiscal Year Final Research Report

• Project/Area Number: 24650158
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Bioinformatics/Life informatics
• Research Institution: Himeji Dokkyo University (2014); Osaka University (2012-2013)
• Principal Investigator: HARANO Yuichi 姫路獨協大学, 薬学部, 准教授 (60456259)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Keywords: 水和熱力学 / Hadwiger定理 / 計算化学

Outline of Final Research Achievements

We have developed a versatile method for calculating solvation thermodynamic quantities for molecules, starting from their atomic coordinates. The contribution of each atom to the thermodynamic quantities is estimated as a linear combination of four fundamental geometric measures of the atomic species, which are defined by Hadwiger’s theorem, and the coefficients reflecting their solvation properties. This treatment enables us to calculate the solvation free energy with high accuracy despite of the limited computational load. The method can readily be applied to macromolecules in an all-atom molecular model, allowing the stability of these molecules’ structures in solution to be evaluated.

Free Research Field

生物物理