Exposing relationships using directed evolution

Trends in Biotechnology

Volumn 22, Issue 5, 2004, Pages 203-205

  Miller, Oliver J ^a   Dalby, Paul A ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SYSTEMS; MUTAGENESIS; PROTEINS; RNA;

BINDING REGION; FUNCTIONAL SEQUENCES;

BIOTECHNOLOGY;

PROTEIN; ROP PROTEIN; UNCLASSIFIED DRUG;

EVOLUTION; PROTEIN;

AB INITIO CALCULATION; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; BINDING AFFINITY; BIOINFORMATICS; DIRECTED MOLECULAR EVOLUTION; DNA RNA HYBRIDIZATION; ENANTIOSELECTIVITY; ENZYME ACTIVITY; ENZYME REGULATION; ENZYME STABILITY; GROWTH RATE; HYDROGEN BOND; LACTOSE OPERON; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN ENGINEERING; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; PROTEIN VARIANT; REPORTER GENE; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE HOMOLOGY; SHORT SURVEY; STRUCTURAL HOMOLOGY;

BACTERIAL PROTEINS; DATABASES, GENETIC; DIRECTED MOLECULAR EVOLUTION; MUTATION; PROTEIN ENGINEERING; PROTEIN STRUCTURE, TERTIARY; RNA-BINDING PROTEINS; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN; VALINE-TRNA LIGASE;

EID: 1942470089     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2004.03.003     Document Type: Short Survey

References (25)

1. Berg J.M., et al. Exploring evolution. 5th edn Biochemistry. 2002;Freeman, New York. pp. 179-180.
2. Riddle D.S., et al. Functional rapidly folding proteins from simplified amino acid sequences. Nat. Struct. Biol. 4:1997;805-809.
3. Baker D., Sali A. Protein structure prediction and structural genomics. Science. 294:2001;93-96.
4. Christ D., Winter G. Identification of functional similarities between proteins using directed evolution. Proc. Natl. Acad. Sci. U. S. A. 100:2003;13184-13189.
5. Hoess R.H. Protein design and phage display. Chem. Rev. 101:2001;3205-3218.
6. Dalby P.A. Optimising enzyme function by directed evolution. Curr. Opin. Struct. Biol. 13:2003;500-505.
7. Goud G.N., et al. Specific glycosidase activity isolated from a random phage display antibody library. Biotechnol. Prog. 17:2001;197-202.
8. Lowman H.B., et al. Selecting high-affinity binding proteins by monovalent phage display. Biochemistry. 30:1991;10832-10838.
9. Smith G.P., et al. Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage. J. Mol. Biol. 277:1998;317-332.
10. Dalby P.A., et al. Evolution of binding affinity in a WW domain probed by phage display. Protein Sci. 9:2000;2366-2376.
11. Stemmer W.P.C. Rapid evolution of a protein in vitro by DNA shuffling. Nature. 370:1994;389-391.
12. Chen K., Arnold F.H. Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. Proc. Natl. Acad. Sci. U. S. A. 90:1993;5618-5622.
13. Flores H., Ellington A.D. Increasing the thermal stability of an oligomeric protein, β-glucuronidase. J. Mol. Biol. 315:2002;325-337.
14. Pedersen J.S., et al. Directed evolution of barnase stability using proteolytic selection. J. Mol. Biol. 323:2002;115-123.
15. Matsumura I., Ellington A.D. In vitro evolution of β-glucuronidase into a β-galactosidase proceeds through non-specific intermediates. J. Mol. Biol. 305:2001;331-339.
16. Raillard S., et al. Novel enzyme activities and functional plasticity revealed by recombining highly homologous enzymes. Chem. Biol. 8:2001;891-898.
17. Zha D.X., et al. Complete reversal of enantioselectivity of an enzyme-catalyzed reaction by directed evolution. Chem. Comm. 2001;2664-2665.
18. Lin Z., et al. Functional expression of horseradish peroxidase in E. coli by directed evolution. Biotechnol. Prog. 15:1999;467-471.
19. Zhou H.X., et al. In vitro evolution of thermodynamically stable turns. Nat. Struct. Biol. 3:1996;446-451.
20. Salamone P.R., et al. Directed molecular evolution of ADP-glucose pyrophosphorylase. Proc. Natl. Acad. Sci. U. S. A. 99:2002;1070-1075.
21. O'Neil K.T., et al. Identification of novel peptide antagonists for GPIIb/IIIa from a conformationally constrained phage peptide library. Proteins. 14:1992;509-515.
22. Li R.H., et al. Use of phage display to probe the evolution of binding specificity and affinity in integrins. Protein Eng. 16:2003;65-72.
23. Kasanov J., et al. Characterizing class I WW domains defines key specificity determinants and generates mutant domains with novel specificities. Chem. Biol. 8:2004;231-241.
24. Tong A.H.Y., et al. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science. 295:2002;321-324.
25. Kleywegt G.J. Recognition of spatial motifs in protein structures. J. Mol. Biol. 285:1999;1887-1897.