Combinatorial protein design: Strategies for screening protein libraries

Current Opinion in Structural Biology

Volumn 7, Issue 4, 1997, Pages 480-485

  Zhao, Huimin ^a   Arnold, Frances H ^a  

^a Div Chem Chem Eng 210 41 C   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

PRIORITY JOURNAL; PROTEIN STRUCTURE; SHORT SURVEY;

EID: 0030864811     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80110-8     Document Type: Article

References (49)

1. Shao ZX, Arnold FH. Engineering new functions and altering existing functions. Curr Opin Struct Biol. 6:1996;513-518.
2. Warren MS, Benkovic SJ. Combinatorial manipulation of three key active site residues in glycinamide ribonucleotide transformylase. Protein Eng. 10:1997;63-68.
3. Kim B, Hathaway TR, Loeb LA. Human immunodeficiency virus reverse transcriptase - functional mutants obtained by random mutagenesis coupled with genetic selection in Escherichia coli. J Biol Chem. 271:1996;4872-4878.
4. Abelson JN. Combinatorial chemistry. Methods in Enzymology. 267:1996;Academic Press, San Diego.
5. Arnold FH. Directed evolution creating biocatalysts for the future. Chem Eng Sci. 51:1996;5091-5102.
6. Wang C-I, Yang Q, Craik CS. Phage display of proteases and macromolecular inhibitors. Methods Enzymol. 267:1996;52-68.
7. Cole JL. Approaches to high-volume screening assays of viral polymerases and related proteins. of special interest Methods Enzymol. 275:1996;310-328 This review describes several techniques for developing high-volume in vitro screening assays for viral polymerases and related proteins. Several examples are illustrated.
8. Janda KD, Lo LC, Lo CH, Sim MM, Wang R, Wong CH, Lerner RA. Chemical selection for catalysis in combinatorial antibody libraries. Science. 275:1997;945-948.
9. You L, Arnold FH. Directed evolution of subtilisin E in Bacillus subtilis to enhance total activity in aqueous dimethylformamide. of special interest Protein Eng. 9:1996;77-83 This paper discusses the first law of random mutagenesis: you get what you screen for.
10. Crameri A, Whitehorn EA, Tate E, Stemmer WPC. Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat Biotechnol. 14:1996;315-319.
11. Heim R, Tsien RY. Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer. Curr Biol. 6:1996;178-182.
12. Siemering KR, Golbik R, Sever R, Haseloff J. Mutations that suppress the thermosensitivity of green fluorescent protein. Curr Biol. 6:1996;1653-1663.
13. Brunet AP, Huang ES, Huffine ME, Loeb JE, Weltman RJ, Hecht MH. The role of turns in the structure of an α-helical protein. Nature. 364:1993;355-358.
14. Ybe JA, Hecht MH. Sequence replacements in the central β-turn of plastocyanin. Protein Sci. 5:1996;814-824.
15. Hawrani AS, Sessions RB, Moreton KM, Holbrook JJ. Guided evolution of enzymes with new substrate specificities. of special interest J Mol Biol. 264:1996;97-110 The paper describes a systematic approach to screening variants of an NAD-dependent dehydrogenase for several features simultaneously: thermal stability and catalytic activity on various substrates, without substrate inhibition and in the absence of an allosteric activator.
16. Shinkai A, Hirano A, Aisaka K. Substitutions of Ser for Asn-163 and Pro for Leu-264 are important for stabilization of lipase from Pseudomonas aeruginosa. J Biochem. 120:1996;915-921.
17. Sattler A, Kanka S, Maurer KH, Riesner D. Thermostable variants of subtilisin selected by temperature-gradient gel electrophoresis. Electrophoresis. 17:1996;784-792.
18. Zhang JH, Dawes G, Stemmer WPC. Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening. Proc Natl Acad Sci USA. 94:1997;4504-4509.
19. Lama J, Carrasco L. Screening for membrane-permeabilizing mutants of the poliovirus protein 3AB. of special interest J Gen Virol. 77:1996;2109-2119 An in vivo screen, which may be applicable to other eukaryotic proteins known to form pores, is developed to differentiate permeabilizing wild-type 3AB and nonpermeabilizing 3AB mutants.
20. Konopka JB, Margarit SM, Dube P. Mutation of Pro-258 in transmembrane domain 6 constitutively activates the G protein-coupled α-factor receptor. Proc Natl Acad Sci USA. 93:1996;6764-6769.
21. Sidhu SS, Borgford TJ. Selection of Streptomyces griseus protease B mutants with desired alternations in primary specificity using a library screening strategy. J Mol Biol. 257:1996;233-245.
22. Kim JY, Caterina MJ, Milne JLS, Lin KC, Borleis JA, Devreotes PN. Random mutagenesis of the cAMP chemoattractant receptor, cAR1, of Dictyostelium. J Biol Chem. 272:1997;2060-2068.
23. Parent CA, Devreotes PN. Isolation of inactive and G protein-resistant adenylyl cyclase mutants using random mutagenesis. J Biol Chem. 270:1996;22693-22696.
24. Youvan DC, Goldman E, Delagrave S, Yang MM. Digital imaging spectroscopy for massively parallel screening of mutants. Methods Enzymol. 246:1995;732-749.
25. Broach JR, Thorner J. High-throughput screening for drug discovery. of special interest Nature. 384:1996;14-16 This review describes the implementation, limitations and future directions of high-throughput screening for drug discovery. Many of the discussions are applicable to screening protein libraries.
26. Robertson DE, Mathur EJ, Swanson RV, Marrs BL, Short JM. The discovery of new biocatalysts from microbial diversity. SIMS News. 46:1996;3-7.
27. Zhao H, Arnold FH. Functional and non-functional mutations distinguished by random recombination of homologous genes. of special interest Proc Natl Acad Sci. 94:1997;7997-8000 Screening of a randomly recombined gene library allows identification of functional mutations in a laboratory-evolved gene encoding a thermostable subtilisin.
28. Moore JC, Jin H, Kuchner O, Arnold FH. Strategies for the in vitro evolution of protein function: enzyme evolution by random recombination of improved sequences. J Mol Biol. 1997;. in press.
29. Shafikhani S, Siegel RA, Ferrari E, Schellenberger V. Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization. Bio-Techniques. 1997;. in press.
30. Checovich WJ, Bolger RE, Burke T. Fluorescence polarization a new tool for cell and molecular biology. Nature. 375:1995;254-256.
31. Tawfik DS, Green BS, Chap R, Sela M, Eshhar Z. catELISA: a facile general route to catalytic antibodies. Proc Natl Acad Sci USA. 90:1993;373-377.
32. Tawfik DS, Lindner AB, Chap R, Kim SH, Green BS, Eshhar Z. catELISA: ELISA-based detection of catalytic antibodies and enzymes. Immunology Methods Manual. 1997;553-560 Academic Press, San Diego. chapter 8.8.
33. Macbeath G, Hilvert D. Monitoring catalytic activity by immunoassay: implications for screening. J Am Chem Soc. 116:1994;6101-6106.
34. Fenniri H, Janda KD, Lerner RA. Encoded reaction cassette for the highly sensitive detection of the making and breaking of chemical bonds. Proc Natl Acad Sci USA. 92:1995;2278-2282.
35. Janes LE, Kazlauskas RJ. Quick E. A rapid spectrophotometric method to measure the enantioselectivity of hydrolases. of special interest J Org Chem. 1997; A rapid spectrophotometric method is developed to measure the enantioselectivity of hydrolases on the basis of the addition of a chromogenic reference compound to introduce competitive binding for both enantiomers.
36. Moore JC, Arnold FH. Directed evolution of a para-nitrobenzyl esterase for aqueous - organic solvents. of special interest Nat Biotechnol. 14:1996;458-467 This paper describes a rapid screening assay using a chromogenic substrate (an antibiotic p-nitrophenyl ester) which serves as a surrogate for the desired substrate of an esterase (the p-nitrobenzyl ester). The screen is validated against a set of random mutants.
37. Panchal RG, Cusack E, Cheley S, Bayley H. Tumor protease-activated, pore-forming toxins from a combinatorial library. Nat Biotechnol. 14:1996;852-855.
38. 6 HSV-1 TK mutants. Active mutants are then screened for enhanced sensitivity to gancyclovir and/or acyclovir.
39. Christians FC, Loeb LA. Novel human DNA alkyltransferases obtained by random substitution and genetic selection in bacteria. Proc Natl Acad Sci USA. 93:1996;6124-6128.
40. Warren MS, Marolewski AE, Benkovic SJ. A rapid screen of active site mutants in glycinamide ribonucleotide transformylase. Biochemistry. 35:1996;8855-8862.
41. Axe DD, Foster NW, Fersht AR. Active barnase variants with completely random hydrophobic cores. of special interest Proc Natl Acad Sci USA. 93:1996;5590-5594 The autotoxity of barnase is used to identify functional bamases from a mutant library in which 12 hydrophobic core residues are randomly replaced by hydrophobic alternatives. A strikingly high proportion of the mutants are found to retain enzymatic activity in vivo.
42. Jucovic M, Hartley RW. In vivo system for the detection of low level activity barnase mutants. Protein Eng. 8:1995;497-499.
43. Venekei I, Hedstrom L, Rutter WJ. A rapid and effective procedure for screening protease mutants. Protein Eng. 9:1996;85-93.
44. Köhler JM, Schober A, Schwienhorst A. Micromechanical elements for microchemical systems. Exp Tech Phys. 40:1994;35-56.
45. Schober A, Günther R, Schwienhorst A, Döring M, Lindemann BF. Accurate high-speed liquid handling of very small biological samples. Bio-Techniques. 15:1993;324-329.
46. Eigen M, Rigler R. Sorting single molecules: application to diagnostics and evolutionary biotechnology. Proc Natl Acad Sci USA. 91:1994;5740-5747.
47. Rigler R. Fluorescence correlations, single-molecule detection and large number screening applications in biotechnology. J Biotechnol. 41:1995;177-186.
48. Eigen M. The origin of genetic information: viruses as models. Gene. 135:1993;37-47.
49. Georgiou G, Stathopoulos C, Daugherty PS, Nayak AR, Iverson BL, Curtiss R III. Display of heterologous proteins on the surface of microorganisms: from the screening of combinatorial libraries to live recombinant vaccines. of special interest Nat Biotechnol. 15:1997;29-34 This review describes recent progress in the expression and display of heterologous proteins on the surfaces of microorganisms. This approach can be used with cell-sorting techniques for screening large protein libraries.