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Issue 21, 2020
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On the polarization of ligands by proteins

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Abstract

Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we use a quantum mechanics/molecular mechanics (QM/MM) approach, in which the ligand is the QM region, to compute the ligand polarization energy of 286 protein–ligand complexes from the PDBBind Core Set (release 2016). Calculations were performed both with and without implicit solvent based on the domain decomposition Conductor-like Screening Model. We observe that the ligand polarization energy is linearly correlated with the magnitude of the electric field acting on the ligand, the magnitude of the induced dipole moment, and the classical polarization energy. The influence of protein and cation charges on the ligand polarization diminishes with the distance and is below 2 kcal mol−1 at 9 Å and 1 kcal mol−1 at 12 Å. Compared to these embedding field charges, implicit solvent has a relatively minor effect on ligand polarization. Considering both polarization and solvation appears essential to computing negative binding energies in some crystallographic complexes. Solvation, but not polarization, is essential for achieving moderate correlation with experimental binding free energies.

Graphical abstract: On the polarization of ligands by proteins

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Supplementary files

Article information


Submitted
22 Jan 2020
Accepted
01 May 2020
First published
18 May 2020

This article is Open Access

Phys. Chem. Chem. Phys., 2020,22, 12044-12057
Article type
Paper

On the polarization of ligands by proteins

S. Y. Willow, B. Xie, J. Lawrence, R. S. Eisenberg and D. D. L. Minh, Phys. Chem. Chem. Phys., 2020, 22, 12044
DOI: 10.1039/D0CP00376J

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