An amino acid code for irregular and mixed protein packing. Issue 12 (5th October 2015)

• Record Type: Journal Article
• Authors: Joo, Hyun; Chavan, Archana G.; Fraga, Keith J.; Tsai, Jerry
• Is Part Of: Proteins. Volume 83:Issue 12(2015)
• Page Start: 2147
• Page End: 2161
• Publication Date: 2015-10-05
• Subjects: knob‐socket motif -- helix‐sheet packing -- coil packing -- protein 3° structure; Proteins -- Periodicals; Proteins -- Periodicals; 572.6
• DOI: 10.1002/prot.24929
• Languages: English
• ISSNs: 0887-3585

Abstract

ABSTRACT: To advance our understanding of protein tertiary structure, the development of the knob‐socket model is completed in an analysis of the packing in irregular coil and turn secondary structure packing as well as between mixed secondary structure. The knob‐socket model simplifies packing based on repeated patterns of two motifs: a three‐residue socket for packing within secondary (2°) structure and a four‐residue knob‐socket for tertiary (3°) packing. For coil and turn secondary structure, knob‐sockets allow identification of a correlation between amino acid composition and tertiary arrangements in space. Coil contributes almost as much as α‐helices to tertiary packing. In irregular sockets, Gly, Pro, Asp, and Ser are favored, while in irregular knobs, the preference order is Arg, Asp, Pro, Asn, Thr, Leu, and Gly. Cys, His, Met, and Trp are not favored in either. In mixed packing, the knob amino acid preferences are a function of the socket that they are packing into, whereas the amino acid composition of the sockets does not depend on the secondary structure of the knob. A unique motif of a coil knob with anXYZ β‐sheet socket may potentially function to inhibit β‐sheet extension. In addition, analysis of the preferred crossing angles for strands within a β‐sheet and mixed α‐helice/β‐sheet identifies canonical packing patterns useful in protein design. Lastly, the knob‐socket model abstracts the complexity of protein tertiary structure into an intuitive packing surface topology map. Proteins 2015; 83:2147–2161. © 2015 Wiley Periodicals, Inc.