A computational insight into the interaction of methylated lysines with aromatic amino acid cages. (10th October 2016)

• Record Type: Journal Article
• Authors: Yildiz, Ibrahim
• Is Part Of: Journal of physical organic chemistry. Volume 30:Number 8(2017)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2016-10-10
• Subjects: cation‐π interaction -- DFT -- histone proteins -- M06‐2X functional -- reader proteins; Chemistry, Physical organic -- Periodicals; 547.1
• DOI: 10.1002/poc.3660
• Languages: English
• ISSNs: 0894-3230

Abstract

Abstract: Posttranslational lysine methylations in histone proteins are recognized by specific reader proteins. The interaction proceeds through the binding of methylated lysine to the aromatic cages created by the combinations of tryptophan and/or tyrosine and/or phenylalanine, and it is specific to the degree of methylation of lysine residue. The chemical recognition is based on cation‐π interaction between positively charged lysine and the π system of the aromatic groups. In this study, the energetics of the binding of model methylated Lys to the model aromatic amino acids as well as aromatic cages are investigated with density functional theory calculations. Molecular orbitals corresponding to the bound complexes and separate lysine and aromatic amino acid components are analyzed. Finally, using single‐point energy calculations, the feasibility of comparing binding energies/affinities of methylated lysines with different methylation degrees is shown, using available crystal structures of the bound model complexes. Abstract : A density functional theory functional, M06‐2X, is used to gain insight into the interactions of methylated lysines with different aromatic amino acids. Furthermore, aromatic cages composed of different amino acids are constructed to model and understand the energetics and interactions. Finally, single‐point calculations are employed to probe the feasibility of using density functional theory models to investigate histone reader proteins with different methylation degrees.