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A novel method for visualizing the electrostatic complementarity of protein-protein interaction based on fragment molecular orbital method
  • Takeshi Ishikawa
Takeshi Ishikawa
Kagoshima Daigaku
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Abstract

Here, the development of a method for visualizing the electrostatic complementarity of protein-protein interactions (PPIs) using fully quantum mechanical electron density (EDN) and electrostatic potential (ESP) is described. For this method, the partial EDN (pEDN) and partial ESP (pESP) of each protein were newly defined based on equations used for the fragment molecular orbital method. To demonstrate the efficacy of the method, calculations were performed for the complex of programmed cell death-1 (PD-1) and its ligand (PD-L1). The results showed that the interface between PD-1 and PD-L1 was appropriately determined by the pEDN, and that the electrostatic complementarity of the PPI was clearly represented by visualizing the pESP. Further analysis of the pESP revealed that additional electrostatic complementarity induced by charge transfer or polarization due to complex formation was non-negligible and, therefore, considered important for binding between the proteins. These findings suggest the efficacy of this method for chemical and biological studies.