Abstract
Protein combinatorial libraries have become a platform technology for exploring protein sequence space for novel molecules for use in research, synthetic biology, biotechnology, and medicine. To expedite the isolation of proteins with novel/desired functions using screens and selections, high-quality approaches that generate protein libraries rich in folded and soluble structures are desirable for this goal. The binary patterning approach is a protein library design method that incorporates elements of both rational design and combinatorial diversity to specify the arrangement of polar and nonpolar amino acid residues in the context of a desired, folded tertiary structure template. An overview of the considerations necessary to design and construct binary patterned libraries of de novo and natural proteins is presented.
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Mandecki W (1990) A method for construction of long randomized open reading frames and polypeptides. Protein Eng 3:221–226
Davidson AR, Lumb KJ, Sauer RT (1995) Cooperatively folded proteins in random sequence libraries. Nat Struct Biol 2:856–864
Prijambada ID, Yomo T, Tanaka F, Kawama T, Yamamoto K, Hasegawa A et al (1996) Solubility of artificial proteins with random sequences. FEBS Lett 382:21–25
Yamauchi A, Yomo T, Tanaka F, Prijambada ID, Ohhashi S, Yamamoto K et al (1998) Characterization of soluble artificial proteins with random sequences. FEBS Lett 421: 147–151
Keefe AD, Szostak JW (2001) Functional proteins from a random-sequence library. Nature 410:715–718
Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH (1993) Protein design by binary patterning of polar and nonpolar amino acids. Science 262:1680–1685
West MW, Wang W, Patterson J, Mancias JD, Beasley JR, Hecht MH (1999) De novo amyloid proteins from designed combinatorial libraries. Proc Natl Acad Sci U S A 96: 11211–11216
Moffet DA, Hecht MH (2001) De novo proteins from combinatorial libraries. Chem Rev 101:3191–3203
Hecht MH, Das A, Go A, Bradley LH, Wei Y (2004) De novo proteins from designed combinatorial libraries. Protein Sci 13:1711–1723
Cherny I, Korolev M, Koehler AN, Hecht MH (2012) Proteins from an unevolved library of de novo designed sequences bind a range of small molecules. ACS Synth Biol 1:130–138
Fisher MA, McKinley KL, Bradley LH, Viola SR, Hecht MH (2011) De novo designed proteins from a library of artificial sequences function in Escherichia coli and enable cell growth. PLoS One 6:e15364
Taylor SV, Walter KU, Kast P, Hilvert D (2001) Searching sequence space for protein catalysts. Proc Natl Acad Sci U S A 98: 10596–10601
Bradley LH, Bricken ML, Randle C (2011) Expression, purification, and characterization of proteins from high-quality combinatorial libraries of the mammalian calmodulin central linker. Protein Expr Purif 75:186–191
Sexton T, Hitchcook LJ, Rodgers DW, Bradley LH, Hersh LB (2012) Active site mutations change the cleavage specificity of neprilysin. PLoS One 7:10
Magnani R, Chaffin B, Dick E, Bricken ML, Houtz RL, Bradley LH (2012) Utilization of a calmodulin lysine methyltransferase co-expression system for the generation of a combinatorial library of post-translationally modified proteins. Protein Expr Purif 86:83–88
Bradley LH, Thumfort PP, Hecht MH (2006) De novo proteins from binary-patterned combinatorial libraries. In: Guerois R, López de la Paz M (eds) Protein design: methods and applications, vol 340, Methods in molecular biology. Humana Press, Totowa, NJ, pp 53–69
Bradley LH, Wei Y, Thumfort P, Wurth C, Hecht MH (2007) Protein design by binary patterning of polar and nonpolar amino acids. In: Arndt K, Mueller KM (eds) Protein engineering protocols, vol 352, Methods in molecular biology. Humana Press, Totowa, NJ, pp 155–166
Matsuura T, Ernst A, Pluckthun A (2002) Construction and characterization of protein libraries composed of secondary structure modules. Protein Sci 11:2631–2643
Wei Y, Liu T, Sazinsky SL, Moffet DA, Pelczer I, Hecht MH (2003) Stably folded de novo proteins from a designed combinatorial library. Protein Sci 12:92–102
Bradley LH, Kleiner RE, Wang AF, Hecht MH, Wood DW (2005) An intein-based genetic selection allows the construction of a high-quality library of binary patterned de novo protein sequences. Protein Eng Des Sel 18:201–207
Rosenbaum DM, Roy S, Hecht MH (1999) Screening combinatorial libraries of de novo proteins by hydrogen-deuterium exchange and electrospray mass spectrometry. J Am Chem Soc 121:9509–9513
Roy S, Ratnaswamy G, Boice JA, Fairman R, McLendon G, Hecht MH (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, Hecht MH (2000) Cooperative thermal denaturation of proteins designed by binary patterning of polar and nonpolar amino acids. Biochemistry 39:4603–4607
Wei Y, Kim S, Fela D, Baum J, Hecht MH (2003) Solution structure of a de novo protein from a designed combinatorial library. Proc Natl Acad Sci U S A 100:13270–13273
Go A, Kim S, Baum J, Hecht MH (2008) Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles. Protein Sci 17:821–832
Wang W, Hecht MH (2002) Rationally designed mutations convert de novo amyloid-like fibrils into monomeric beta-sheet proteins. Proc Natl Acad Sci U S A 99:2760–2765
Xiong HY, Buckwalter BL, Shieh HM, Hecht MH (1995) Periodicity of polar and nonpolar amino-acids is the major determinant of secondary structure in self-assembling oligomeric peptides. Proc Natl Acad Sci U S A 92:6349–6353
Brown CL, Aksay IA, Saville DA, Hecht MH (2002) Template-directed assembly of a de novo designed protein. J Am Chem Soc 124:6846–6848
Xu G, Wang W, Groves JT, Hecht MH (2001) Self-assembled monolayers from a designed combinatorial library of de novo beta-sheet proteins. Proc Natl Acad Sci U S A 98: 3652–3657
Hirel PH, Schmitter JM, Dessen P, Fayat G, 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 U S A 86:8247–8251
Dalboge H, Bayne S, Pedersen J (1990) In vivo processing of N-terminal methionine in Escherichia coli. FEBS Lett 266:1–3
Tsunasawa S, Stewart JW, 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 RC, Liu PS, Koduri RK, Weickmann JL, Lee JH et al (1987) Specificity of cotranslational amino-terminal processing of proteins in yeast. Biochemistry 26: 8242–8246
Bowie JU, Sauer RT (1989) Identification of C-terminal extensions that protect proteins from intracellular proteolysis. J Biol Chem 264:7596–7602
Parsell DA, Silber KR, Sauer RT (1990) Carboxy-terminal determinants of intracellular protein-degradation. Genes Dev 4:277–286
Shoemaker KR, Kim PS, York EJ, Stewart JM, Baldwin RL (1987) Tests of the helix dipole model for stabilization of alpha-helices. Nature 326:563–567
Richardson JS, Richardson DC (1988) Amino-acid preferences for specific locations at the ends of alpha-helices. Science 240:1648–1652
Hutchinson EG, Thornton JM (1994) A revised set of potentials for beta-turn formation in proteins. Protein Sci 3:2207–2216
Arai R, Kobayashi N, Kimura A, Sato T, Matsuo K, Wang AF et al (2012) Domain-swapped dimeric structure of a stable and functional de novo four-helix bundle protein WA20. J Phys Chem B 116:6789–6797
Cornish-Bowden A (1985) Nomenclature for incompletely specified bases in nucleic-acid sequences—recommendations 1984. Nucleic Acids Res 13:3021–3030
Chou PY, Fasman GD (1978) Empirical predictions of protein conformation. Annu Rev Biochem 47:251–276
Pace CN, Scholtz JM (1998) A helix propensity scale based on experimental studies of peptides and proteins. Biophys J 75:422–427
Gouy M, Gautier C (1982) Codon usage in bacteria—correlation with gene expressivity. Nucleic Acids Res 10:7055–7074
Kane JF (1995) Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Curr Opin Biotechnol 6:494–500
Virnekas B, Ge L, Pluckthun A, Schneider KC, Wellnhofer G, Moroney SE (1994) Trinucleotide phosphoramidites: ideal reagents for the synthesis of mixed oligonucleotides for random mutagenesis. Nucleic Acids Res 22: 5600–5607
Babu YS, Sack JS, Greenhough TJ, Bugg CE, Means AR, Cook WJ (1985) Three-dimensional structure of calmodulin. Nature 315:37–40
Babu YS, Bugg CE, Cook WJ (1988) Structure of calmodulin refined at 2.2 A resolution. J Mol Biol 204:191–204
Acknowledgements
Support was obtained from the following sources: a pilot project grant from the NIH National Center for Research Resources (NCRR) Grant P20 RR020171, the Kentucky Science and Engineering Foundation (Grant Agreement # KSEF-148-502-207-201 with the Kentucky Science and Technology Corporation), the University of Kentucky Office of the Vice President of Research, and the University of Kentucky College of Medicine Startup funds.
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Bradley, L.H. (2014). High-Quality Combinatorial Protein Libraries Using the Binary Patterning Approach. In: Köhler, V. (eds) Protein Design. Methods in Molecular Biology, vol 1216. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1486-9_6
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DOI: https://doi.org/10.1007/978-1-4939-1486-9_6
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