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biomoleculesArticleClustering of Aromatic Amino Acid Residues all-around Methionine in ProteinsCurtis A. Gibbs , David S. Weber and Jeffrey J. Warren Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada; [email protected] (C.A.G.); [email protected] (D.S.W.) Correspondence: [email protected] These authors contributed equally.Abstract: Short-range, non-covalent Nav1.4 Molecular Weight interactions between amino acid residues decide protein structures and contribute to protein functions in various strategies. The interactions from the thioether of methionine with all the aromatic rings of tyrosine, tryptophan, and/or phenylalanine has extended been mentioned and this kind of interactions are favorable on the order of one kcal mol-1 . Here, we perform a new bioinformatics survey of known protein structures in which we assay the propensity of 3 aromatic residues to localize about the [-CH2 -S-CH3 ] of methionine. We phrase these groups “3-bridge clusters”. A dataset consisting of 33,819 proteins with under 90 sequence identity was analyzed and this kind of clusters have been discovered in 4093 structures (or 12 in the non-redundant dataset). All sub-classes of enzymes had been represented. A 3D coordinate evaluation demonstrates that most aromatic groups localize near the CH2 and CH3 of methionine. Quantum chemical calculations help that the 3-bridge clusters involve a network of interactions that involve the Met-S, Met-CH2 , Met-CH3 , and the methods of nearby aromatic amino acid residues. Chosen examples of proposed functions of 3-bridge clusters are mentioned. Keyword phrases: methionine; tyrosine; tryptophan; phenylalanine; non-covalent interactions; bioinform
