The quest for molecular quasi-species in ligand-activity space and its application to directed enzyme evolution

FEBS Letters

Volumn 584, Issue 12, 2010, Pages 2565-2571

  Mannervik, Bengt ^a   Runarsdottir, Arna ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Activity space; Enzyme evolution; Glutathione transferase; Ligand space; Multivariate analysis; Quasi species

Indexed keywords

DNA; ENZYME VARIANT; GLUTATHIONE TRANSFERASE;

CATALYSIS; DIRECTED MOLECULAR EVOLUTION; DNA SEQUENCE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ENGINEERING; ENZYME KINETICS; ENZYME STRUCTURE; ENZYME SUBSTRATE; GENE MUTATION; GENETIC VARIABILITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; REVIEW;

DIRECTED MOLECULAR EVOLUTION; ENZYMES; EVOLUTION, MOLECULAR; GENETIC VARIATION; LIGANDS; MODELS, BIOLOGICAL; PROTEIN ENGINEERING; SUBSTRATE SPECIFICITY;

EID: 77953128777     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2010.04.024     Document Type: Review

References (28)

1. Romero P.A., Arnold F.H. Exploring protein fitness landscapes by directed evolution. Nat. Rev. Mol. Cell Biol. 2009, 10:866-876.
2. Gerlt J.A., Babbitt P.C. Enzyme (re)design: lessons from natural evolution and computation. Curr. Opin. Chem. Biol. 2009, 13:10-18.
3. Arnold F.H. Evolutionary protein design. Adv. Protein Chem. 2001, 55:1-438.
4. Enzyme Functionality: Design, Engineering, and Screening 2004, Marcel Dekker, Inc., New York. A. Svendsen (Ed.).
5. Hegazy U., Mannervik B. Semi-synthetic enzymes. Amino Acids, Peptides and Proteins in Organic Chemistry 2009, 379-431. Wiley-VCH, New York. A.B. Hughes (Ed.).
6. Pettersson P.L., Johansson A.-S., Mannervik B. Transmutation of human glutathione transferase A2-2 with peroxidase activity into an efficient steroid isomerase. J. Biol. Chem. 2002, 277:30019-30022.
7. Tars K., Olin B., Mannervik B. Structural basis for featuring of steroid isomerase activity in alpha class glutathione transferases. J. Mol. Biol. 2010, 397:332-340.
8. Nilsson L.O., Gustafsson A., Mannervik B. Redesign of substrate-selectivity determining modules of glutathione transferase A1-1 installs high catalytic efficiency with toxic alkenal products of lipid peroxidation. Proc. Natl. Acad. Sci. USA 2000, 97:9408-9412.
9. Balogh L.M., Le Trong I., Kripps K.A., Tars K., Stenkamp R.E., Mannervik B., Atkins W.M. Structural analysis of a glutathione transferase A1-1 mutant tailored for high catalytic efficiency with toxic alkenals. Biochemistry 2009, 48:7698-7704.
10. Jensen R.A. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 1976, 30:409-425.
11. O'Brien P.J., Herschlag D. Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol. 1999, 6:R91-R105.
12. Copley S.D. Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr. Opin. Chem. Biol. 2003, 7:265-272.
13. Khersonsky O., Roodveldt C., Tawfik D.S. Enzyme promiscuity: evolutionary and mechanistic aspects. Curr. Opin. Chem. Biol. 2006, 10:498-508.
14. Matsumura I., Ellington A.D. In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates. J. Mol. Biol. 2001, 305:331-339.
15. Tracewell C.A., Arnold F.H. Directed enzyme evolution: climbing fitness peaks one amino acid at a time. Curr. Opin. Chem. Biol. 2009, 13:3-9.
16. Nobeli I., Favia A.D., Thornton J.M. Protein promiscuity and its implications for biotechnology. Nat. Biotechnol. 2009, 27:157-167.
17. Pocker Y., Stone J.T. The catalytic versatility of erythrocyte carbonic anhydrase. 3. Kinetic studies of the enzyme-catalyzed hydrolysis of p-nitrophenyl acetate. Biochemistry 1967, 6:668-678.
18. Kurtovic S., Shokeer A., Mannervik B. Emergence of novel enzyme quasi-species depends on the substrate matrix. J. Mol. Biol. 2008, 382:136-153.
19. Emrén L.O., Kurtovic S., Runarsdottir A., Larsson A.-K., Mannervik B. Functionally diverging molecular quasi-species evolve by crossing two enzymes. Proc. Natl. Acad. Sci. USA 2006, 103:10866-10870.
20. Fersht A. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding 1999, W.H. Freeman, New York, pp. 349-376.
21. Ivarsson Y., Mackey A.J., Edalat M., Pearson W.R., Mannervik B. Identification of residues in glutathione transferase capable of driving functional diversification in evolution. A novel approach to protein redesign. J. Biol. Chem. 2003, 278:8733-8738.
22. Kurtovic S., Runarsdottir A., Emrén L.O., Larsson A.-K., Mannervik B. Multivariate-activity mining for molecular quasi-species in a glutathione transferase mutant library. Protein Eng. Des. Sel. 2007, 20:243-256.
23. Krzanowski W.J. Principles of Multivariate Analysis - A Users's Perspective 2000, Oxford University Press, Inc., New York.
24. Gabriel K.R. The biplot graphic display of matrices with application to principal component analysis. Biometrika 1971, 58:453-467.
25. Mannervik B., Runarsdottir A., Kurtovic S. Multi-substrate-activity space and quasi-species in enzyme evolution: Ohno's dilemma, promiscuity and functional orthogonality. Biochem. Soc. Trans. 2009, 37:740-744.
26. Darwin C. The Origin of Species by Means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life 1859, The New American Library of World Literature, Inc., New York.
27. Eigen M., McCaskill J., Schuster P. Molecular quasi-species. J. Phys. Chem. 1988, 92:6881-6891.
28. Hansson L.O., Bolton-Grob R., Massoud T., Mannervik B. Evolution of differential substrate specificities in Mu class glutathione transferases probed by DNA shuffling. J. Mol. Biol. 1999, 287:265-276.