title: A highly efficient hybrid method for calculating the hydration free energy of a protein.
abstract: We develop a new method for calculating the hydration free energy (HFE) of a protein with any net charge. The polar part of the energetic component in the HFE is expressed as a linear combination of four geometric measures (GMs) of the protein structure and the generalized Born (GB) energy plus a constant. The other constituents in the HFE are expressed as linear combinations of the four GMs. The coefficients (including the constant) in the linear combinations are determined using the three-dimensional reference interaction site model (3D-RISM) theory applied to sufficiently many protein structures. Once the coefficients are determined, the HFE and its constituents of any other protein structure are obtained simply by calculating the four GMs and GB energy. Our method and the 3D-RISM theory give perfectly correlated results. Nevertheless, the computation time required in our method is over four orders of magnitude shorter.
authors.affiliation: Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.
authors.forename: Hiraku
authors.initials: H
authors.lastname: Oshima
authors.affiliation: Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Kinoshita
mesh_terms: D000818:Animals; D030562:Databases, Protein; D006801:Humans; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D055672:Static Electricity; D013816:Thermodynamics; D025801:Ubiquitin / Q000737:chemistry; D014867:Water / Q000737:chemistry*
chemical_list: D011506:Proteins; D025801:Ubiquitin; D014867:Water
keywords: generalized Born energy; hydration free energy; integral equation theory; morphometric approach; protein