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Conformational Preferences of π-π Stacking Between Ligand and Protein, Analysis Derived from Crystal Structure Data Geometric Preference of π-π Interaction

Zhao, Yuan and Li, Jue and Gu, Hui and Wei, DongQing and Fu, Wei and Yu, Zhengtian (2015) Conformational Preferences of π-π Stacking Between Ligand and Protein, Analysis Derived from Crystal Structure Data Geometric Preference of π-π Interaction. Interdisciplinary sciences, computational life sciences, 7 (3). pp. 211-220. ISSN 1867-1462

Abstract

π-π Interaction is a direct attractive non-covalent interaction between aromatic moieties, playing an important role in DNA stabilization, drug intercalation, etc. Aromatic rings interact through several different conformations including face-to-face, T-shaped, and offset stacked conformation. Previous quantum calculations indicated that T-shaped and offset stacked conformations are preferred for their smaller electron repulsions. However, substitution group on aromatic ring could have a great impact on π-π interaction by changing electron repulsion force between two rings. To investigate π-π interaction between ligand and aromatic side chain of protein, Brookhaven Protein Data Bank was analyzed. We extracted isolated dimer pairs with the aim of excluding multiple π-π stacking effects and found that T-shaped conformation is prevalent among aromatic interaction between phenyl ring of ligand and protein, which corresponds with the phenomenon of Phe-Phe interactions in small peptide. Specifically, for the non-substitution model, both Phe-Phe and Phenyl-Phe exhibit a favored T-shaped conformation whose dihedral angle is around 50°-70° and centroid distance is between 5.0 and 5.6 Å. However, it could be changed by substituent effect. The hydroxyl group could contact in the case of Tyr-Tyr pairs, while they point away from phenyl plane in Phe-Tyr pairs.

Item Type: Article
Keywords: Geometric preference Multiple π–π interaction Parallel conformation Substitution effect T-shaped conformation π–π interaction
Date Deposited: 13 Mar 2018 00:45
Last Modified: 25 Jan 2019 00:46
URI: https://oak.novartis.com/id/eprint/5695

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