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Application of Hydration Thermodynamics to the Evaluation of Protein Structures and Protein-Ligand Binding

Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
Entropy 2012, 14(8), 1443-1468; https://doi.org/10.3390/e14081443
Received: 28 June 2012 / Revised: 18 July 2012 / Accepted: 2 August 2012 / Published: 7 August 2012
Discovering the mechanism that controls the three-dimensional structures of proteins, which are closely related to their biological functions, remains a challenge in modern biological science, even for small proteins. From a thermodynamic viewpoint, the native structure of a protein can be understood as the global minimum of the free energy landscape of the protein-water system. However, it is still difficult to describe the energetics of protein stability in an effective manner. Recently, our group developed a free energy function with an all-atomic description for a protein that focuses on hydration thermodynamics. The validity of the function was examined using structural decoy sets that provide numerous misfolded “non-native” structures. For all targeted sets, the function was able to identify the experimentally determined native structure as the best structure. The energy function can also be used to calculate the binding free energy of a protein with ligands. I review the physicochemical theories employed in the development of the free energy function and recent studies evaluating protein structure stability and protein-ligand binding affinities that use this function. View Full-Text
Keywords: protein structure stability; binding free energy; hydration thermodynamics; hydration entropy protein structure stability; binding free energy; hydration thermodynamics; hydration entropy
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Harano, Y. Application of Hydration Thermodynamics to the Evaluation of Protein Structures and Protein-Ligand Binding. Entropy 2012, 14, 1443-1468.

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