Abstract
The design of large libraries of well-folded de novo proteins is a powerful approach toward the ultimate goal of producing proteins with novel structures and functions for use in industry or medicine. A method for library design that incorporates both rational design and combinatorial diversity relies on the “binary patterning” of polar and nonpolar amino acids. Binary patterning is based on the premise that the appropriate arrangement of polar and nonpolar residues can direct a polypeptide chain to fold into amphipathic elements of secondary structure that anneal together to form a desired tertiary structure. A designed binary pattern exploits the periodicities inherent in protein secondary structure, and allows the identity of the side chain at each polar and nonpolar position to be varied combinatorially. This chapter provides an overview of the considerations necessary to use binary patterning to design libraries of novel proteins.
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References
Lim, W. A. and Sauer, R. T. (1989) Alternative packing arrangements in the hydrophobic core of lambda repressor. Nature 339, 31–36.
Bowie, J. U., Reidhaar-Olson, J. F., Lim, W. A., and Sauer, R. T. (1990) Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science 247, 1306–1310.
Axe, D. D., Foster, N. W., and Fersht, A. R. (1996) Active barnase variants with completely random hydrophobic cores. Proc. Natl. Acad. Sci. USA 93, 5590–5594.
Gassner, N. C., Baase, W. A., and Matthews, B. W. (1996) A test of the “jigsaw puzzle” model for protein folding by multiple methionine substitutions within the core of T4 lysozyme. Proc. Natl. Acad. Sci. USA 93, 12,155–12,158.
Riddle, D. S., Santiago, J. V., Bray-Hall, S. T., et al. (1997) Functional rapidly folding proteins from simplified amino acid sequences. Nat. Struct. Biol. 4, 805–809.
Silverman, J. A., Balakrishnan, R., and Harbury, P. B. (2001) Reverse engineering the (β/α)8 barrel fold. Proc. Natl. Acad. Sci. USA 98, 3092–3097.
Lau, K. F. and Dill, K. A. (1990) Theory for protein mutability and biogenesis. Proc. Natl. Acad. Sci. USA 87, 638–642.
Kamtekar, S., Schiffer, J. M., Xiong, H., Babik, J. M., and Hecht, M. H. (1993) Protein design by binary patterning of polar and nonpolar amino acids. Science 262, 1680–1685.
West, M. W., Wang, W., Patterson, J., Mancias, J. D., Beasley, J. R., and Hecht, M. H. (1999) De novo amyloid proteins from designed combinatorial libraries. Proc. Natl. Acad. Sci. USA 96, 11,211–11,216.
Xiong, H., Buckwalter, B. L., Shieh, H. M., and Hecht, M. H. (1995) Periodicity of polar and nonpolar amino acids is the major determinant of secondary structure in self-assembling oligomeric peptides. Proc. Natl. Acad. Sci. USA 92, 6349–6353.
Moffet, D. A. and Hecht, M. H. (2001) De novo proteins from combinatorial libraries. Chem. Rev. 101, 3191–3203.
Hecht, M. H., Das, A., Go, A., Bradley, L. H., and Wei, Y. (2004) De novo proteins from designed combinatorial libraries. Protein Sci. 13, 1711–1723.
Taylor, S. V., Walter, K. U., Kast, P., and Hilvert, D. (2001) Searching sequence space for protein catalysts. Proc. Natl. Acad. Sci. USA 98, 10,596–10,601.
Roy, S., Ratnaswamy, G., Boice, J. A., Fairman, F., McLendon, G., and Hecht, M. H. (1997) A protein designed by binary patterning of polar and nonpolar amino acids displays native-like properties. J. Am. Chem. Soc. 119, 5302–5306.
Roy, S., Helmer, K. J., and Hecht, M. H. (1997) Detecting native-like properties in combinatorial libraries of de novo proteins. Folding Des. 2, 89–92.
Roy, S. and Hecht, M. H. (2000) Cooperative thermal denaturation of proteins designed by binary patterning of polar and nonpolar amino acids. Biochemistry 39, 4603–4607.
Rosenbaum, D. M., Roy, S., and Hecht, M. H. (1999) Screening combinatorial libraries of de novo proteins by hydrogen-deuterium exchange and electrospray mass spectrometry. J. Am. Chem. Soc. 121, 9509–9513.
Wei, Y., Liu, T. I. P., Sazinsky, S. L., Moffet, D. A., and Hecht, M. H. (2003) Well folded de novo proteins from a designed combinatorial library. Protein Sci. 12, 92–102.
Xu, G., Wang, W., Groves, J. T., and Hecht, M. H. (2001) Self-assembled monolayers from a designed combinatorial library of de novo β-sheet proteins. Proc. Natl. Acad. Sci. USA 98, 3652–3657.
Brown, C. L., Aksay, I. A., Saville, D. A., and Hecht, M. H. (2002) Template-directed assembly of a de novo designed protein. J. Am. Chem. Soc. 124, 6846–6848.
Richardson, J. S. and Richardson, D. C. (1988) Amino acid preferences for specific locations at the ends of alpha helices. Science 240, 1648–1652.
Hutchinson, E. G. and Thornton, J. M. (1994) A revised set of potentials for β-turn formation in proteins. Protein Sci. 3, 2207–2216.
Hirel, P. H., Schmitter, M. J., Dessen, P., Fayat, G., and Blanquet, S. (1989) Extent of N-terminal methionine excision from Escherichia coli proteins is governed by the side-chain length of the penultimate amino acid. Proc. Natl. Acad. Sci. USA 86, 8247–8251.
Dalboge, H., Bayne, S., and Pedersen, J. (1990) In vivo processing of N-terminal methionine in E. coli. FEBS Lett. 266, 1–3.
Tsunasawa, S., Stewart, J. W., and Sherman, F. (1985) Amino-terminal processing of mutant forms of yeast iso-1-cytochrome c. The specificities of methionine aminopeptidase and acetyltransferase. J. Biol. Chem. 260, 5382–5391.
Huang, S., Elliott, R. C., Liu, P. S., et al. (1987) Specificity of cotranslational amino-terminal processing of proteins in yeast. Biochemistry 26, 8242–8246.
Bowie, J. U. and Sauer, R. T. (1989) Identification of C-terminal extensions that protect proteins from intracellular proteolysis. J. Biol. Chem. 264, 7596–7602.
Parsell, D. A., Silber, K. R., and Sauer, R. T. (1990) Carboxy-terminal determinants of intracellular protein degradation. Genes Dev. 4, 277–286.
Milla, M. E., Brown, B. M., and Sauer, R. T. (1993) P22 Arc repressor: enhanced expression of unstable mutants by addition of polar C-terminal sequences. Protein Sci. 2, 2198–2205.
Shoemaker, K. R., Kim, P. S., York, E. J., Stewart, J. M., and Baldwin, R. L. (1987) Tests of the helix dipole model for stabilization of alpha-helices. Nature 326, 563–567.
Wei, Y., Kim, S., Fela, D., and Hecht, M. H. (2003) Solution structure of a de novo protein from a designed combinatorial library. Proc. Natl. Acad. Sci. USA 100, 13,270–13,273.
Chou, P. Y. and Fasman, G. D. (1978) Empirical predictions of protein conformation. Annu. Rev. Biochem. 47, 251–276.
Fasman, G. D. (1989) Prediction of Protein Structure and the Principles of Protein Conformation. Plenum, New York, NY.
Creighton, T. E. (1993) Proteins: Structures and Molecular Properties. 2nd ed., Freeman, New York, NY.
Pace, C. N. and Scholtz, J. M. (1998) A helix propensity scale based on experimental studies of peptides and proteins. Biophys. J. 75, 422–427.
DeBoer, H. A. and Kastelein, R. A. (1986) in Maximizing Gene Expression (Rezinikoff, W. and Gold, L., eds.), Butterworth, Stoneham, MA, pp. 225–285.
Kane, J. F. (1995) Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Curr. Opin. Biotechnol. 6, 494–500.
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Bradley, L.H., Wei, Y., Thumfort, P., Wurth, C., Hecht, M.H. (2007). Protein Design by Binary Patterning of Polar and Nonpolar Amino Acids. In: Arndt, K.M., Müller, K.M. (eds) Protein Engineering Protocols. Methods in Molecular Biology™, vol 352. Humana Press. https://doi.org/10.1385/1-59745-187-8:155
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DOI: https://doi.org/10.1385/1-59745-187-8:155
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