title: An amino acid code for β-sheet packing structure.
abstract: To understand the relationship between protein sequence and structure, this work extends the knob-socket model in an investigation of β-sheet packing. Over a comprehensive set of β-sheet folds, the contacts between residues were used to identify packing cliques: sets of residues that all contact each other. These packing cliques were then classified based on size and contact order. From this analysis, the two types of four-residue packing cliques necessary to describe β-sheet packing were characterized. Both occur between two adjacent hydrogen bonded β-strands. First, defining the secondary structure packing within β-sheets, the combined socket or XY:HG pocket consists of four residues i, i+2 on one strand and j, j+2 on the other. Second, characterizing the tertiary packing between β-sheets, the knob-socket XY:H+B consists of a three-residue XY:H socket (i, i+2 on one strand and j on the other) packed against a knob B residue (residue k distant in sequence). Depending on the packing depth of the knob B residue, two types of knob-sockets are found: side-chain and main-chain sockets. The amino acid composition of the pockets and knob-sockets reveal the sequence specificity of β-sheet packing. For β-sheet formation, the XY:HG pocket clearly shows sequence specificity of amino acids. For tertiary packing, the XY:H+B side-chain and main-chain sockets exhibit distinct amino acid preferences at each position. These relationships define an amino acid code for β-sheet structure and provide an intuitive topological mapping of β-sheet packing.
authors.affiliation: Department of Chemistry, University of the Pacific, Stockton, California, 95212.
authors.forename: Hyun
authors.initials: H
authors.lastname: Joo
authors.forename: Jerry
authors.initials: J
authors.lastname: Tsai
mesh_terms: D000595:Amino Acid Sequence; D006860:Hydrogen Bonding; D008958:Models, Molecular; D017510:Protein Folding; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000378:metabolism*
chemical_list: D011506:Proteins
keywords: amino acid code; packing topology; secondary structure packing; tertiary structure; β-sheet packing