Protein Engineering Protocols - Mycobacteriology research center

9Protein Design by Binary Patterningof Polar and Nonpolar Amino AcidsLuke H. Bradley, Yinan Wei, Peter Thumfort, Christine Wurth,and Michael H. HechtSummaryThe design of large libraries of well-folded de novo proteins is a powerful approach towardthe ultimate goal of producing proteins with novel structures and functions for use in industry ormedicine. A method for library design that incorporates both rational design and combinatorialdiversity relies on the “binary patterning” of polar and nonpolar amino acids. Binary patterningis based on the premise that the appropriate arrangement of polar and nonpolar residues can directa polypeptide chain to fold into amphipathic elements of secondary structure that anneal togetherto form a desired tertiary structure. A designed binary pattern exploits the periodicities inherentin protein secondary structure, and allows the identity of the side chain at each polar and nonpolarposition to be varied combinatorially. This chapter provides an overview of the considerationsnecessary to use binary patterning to design libraries of novel proteins.Key Words: Protein design; binary patterning; combinatorial library; de novo proteins; librarydesign.1. IntroductionNumerous studies of natural proteins have demonstrated that protein structuresare remarkably tolerant to amino acid substitutions. Thus, many differentamino acids can encode the information necessary to produce a given threedimensionalstructure (1–7).We have taken advantage of this tolerance to develop a general strategy for proteindesign. The strategy—called “the binary code” strategy—is based on thepremise that the appropriate patterning of polar and nonpolar residues can directa polypeptide chain to fold into elements of secondary structure, while simultaneouslyallowing the burial of nonpolar amino acids in a desired tertiary structure(8–10). A designed binary pattern exploits the periodicities inherent in proteinFrom: Methods in Molecular Biology, vol. 352: Protein Engineering ProtocolsEdited by: K. M. Arndt and K. M. Müller © Humana Press Inc., Totowa, NJ155