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Issue 10, 2018
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Cation–π interactions in protein–ligand binding: theory and data-mining reveal different roles for lysine and arginine

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Abstract

We have studied the cation–π interactions of neutral aromatic ligands with the cationic amino acid residues arginine, histidine and lysine using ab initio calculations, symmetry adapted perturbation theory (SAPT), and a systematic meta-analysis of all available Protein Data Bank (PDB) X-ray structures. Quantum chemical potential energy surfaces (PES) for these interactions were obtained at the DLPNO-CCSD(T) level of theory and compared against the empirical distribution of 2012 unique protein–ligand cation–π interactions found in X-ray crystal structures. We created a workflow to extract these structures from the PDB, filtering by interaction type and residue pKa. The gas phase cation–π interaction of lysine is the strongest by more than 10 kcal mol−1, but the empirical distribution of 582 X-ray structures lies away from the minimum on the interaction PES. In contrast, 1381 structures involving arginine match the underlying calculated PES with good agreement. SAPT analysis revealed that underlying differences in the balance of electrostatic and dispersion contributions are responsible for this behavior in the context of the protein environment. The lysine–arene interaction, dominated by electrostatics, is greatly weakened by a surrounding dielectric medium and causes it to become essentially negligible in strength and without a well-defined equilibrium separation. The arginine–arene interaction involves a near equal mix of dispersion and electrostatic attraction, which is weakened to a much smaller degree by the surrounding medium. Our results account for the paucity of cation–π interactions involving lysine, even though this is a more common residue than arginine. Aromatic ligands are most likely to interact with cationic arginine residues as this interaction is stronger than for lysine in higher polarity surroundings.

Graphical abstract: Cation–π interactions in protein–ligand binding: theory and data-mining reveal different roles for lysine and arginine

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Supplementary files

Article information


Submitted
15 Nov 2017
Accepted
20 Jan 2018
First published
31 Jan 2018

This article is Open Access
All publication charges for this article have been paid for by the Royal Society of Chemistry

Chem. Sci., 2018,9, 2655-2665
Article type
Edge Article

Cation–π interactions in protein–ligand binding: theory and data-mining reveal different roles for lysine and arginine

K. Kumar, S. M. Woo, T. Siu, W. A. Cortopassi, F. Duarte and R. S. Paton, Chem. Sci., 2018, 9, 2655
DOI: 10.1039/C7SC04905F

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