Premium
Importance of CH/π hydrogen bonds in recognition of the core motif in proline‐recognition domains: An Ab initio fragment molecular orbital study
Author(s) -
Ozawa Tomonaga,
Okazaki Kosuke,
Kitaura Kazuo
Publication year - 2011
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21857
Subject(s) - fragment molecular orbital , chemistry , hydrogen bond , ab initio , proline , protein ligand , ligand (biochemistry) , stereochemistry , molecular recognition , molecular orbital , molecule , crystallography , amino acid , receptor , biochemistry , organic chemistry
We examined CH/π hydrogen bonds in protein/ligand complexes involving at least one proline residue using the ab initio fragment molecular orbital (FMO) method and the program CHPI. FMO calculations were carried out at the Hartree–Fock (HF)/6‐31G*, HF/6‐31G**, second‐order Møller–Plesset perturbation (MP2)/6‐31G*, and MP2/6‐31G** levels for three Src homology 3 (SH3) domains and five proline‐recognition domains (PRDs) complexed with their corresponding ligand peptides. PRDs use a conserved set of aromatic residues to recognize proline‐rich sequences of specific ligands. Many CH/π hydrogen bonds were identified in these complexes. CH/π hydrogen bonds occurred, in particular, in the central part of the proline‐rich motifs. Our results suggest that CH/π hydrogen bonds are important in the recognition of SH3 and PRDs by their ligand peptides and play a vital role in the signal transduction system. Combined use of the FMO method and CHPI analysis is a valuable tool for the study of protein/protein and protein/ligand interactions and may be useful in rational drug design. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011