An amino acid code for β‐sheet packing structure. Issue 9 (16th April 2014)

• Record Type: Journal Article
• Authors: Joo, Hyun; Tsai, Jerry
• Is Part Of: Proteins. Volume 82:Issue 9(2014)
• Page Start: 2128
• Page End: 2140
• Publication Date: 2014-04-16
• Subjects: Proteins -- Periodicals; Proteins -- Periodicals; 572.6
• DOI: 10.1002/prot.24569
• Languages: English
• ISSNs: 0887-3585

Abstract

<abstract abstract-type="main"> <title>ABSTRACT</title> <p>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 <bold>XY:HG</bold> pocket consists of four residues <italic>i, i</italic>+2 on one strand and <italic>j, j</italic>+2 on the other. Second, characterizing the tertiary packing between β‐sheets, the knob‐socket <bold>XY:H+B</bold> consists of a three‐residue <bold>XY:H</bold> socket (<italic>i, i</italic>+2 on one strand and <italic>j</italic> on the other) packed against a knob <bold>B</bold> residue (residue k distant in sequence). Depending on the packing depth of the knob <bold>B</bold> 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 <bold>XY:HG</bold> pocket clearly shows sequence specificity of amino acids. For tertiary packing, the <bold>XY:H+B</bold> 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. Proteins 2014; 82:2128–2140. © 2014 Wiley Periodicals, Inc.</p> </abstract>