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Published on: May 10, 2021
Hybrid Solvation Model for Analyzing the Binding of Yttrium and Calcium Cations to the Lanmodulin Protein Using the
Dmitri G Fedorov1, Yoongkee Choe1
1Materials DX Research Center (MDX), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba305-8568, Japan.
Abstract:
A hybrid solvation model combining microsolvation with continuum solvent is proposed to analyze the binding of calcium and yttrium cations to the lanmodulin protein (PDB: 6MI5), using the fragment molecular orbital method combined with partition analysis. The contributions of protein deformation, metal ion desolvation, and the formation of a water cluster from desolvated metal ions, as well as protein-ion and water-ion interactions are quantified. The binding energy for each of the three binding sites is evaluated, and the most potent site is identified.
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