Literature DB >> 19237310

Enzyme (re)design: lessons from natural evolution and computation.

John A Gerlt1, Patricia C Babbitt.   

Abstract

The (re)design of enzymes to catalyze 'new' reactions is a topic of considerable practical and intellectual interest. Directed evolution (random mutagenesis followed by screening/selection) has been used widely to identify novel biocatalysts. However, 'rational' approaches using either natural divergent evolution or computational predictions based on chemical principles have been less successful. This review summarizes recent progress in evolution-based and computation-based (re)design.

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Year:  2009        PMID： 19237310      PMCID： PMC2711627          DOI： 10.1016/j.cbpa.2009.01.014

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN： 1367-5931            Impact factor:   8.822


  64 in total

1.  Directed evolution of a (beta alpha)8-barrel enzyme to catalyze related reactions in two different metabolic pathways.

Authors:  C Jürgens; A Strom; D Wegener; S Hettwer; M Wilmanns; R Sterner
Journal:  Proc Natl Acad Sci U S A       Date:  2000-08-29       Impact factor: 11.205

2.  Observation of covalent intermediates in an enzyme mechanism at atomic resolution.

Authors:  A Heine; G DeSantis; J G Luz; M Mitchell; C H Wong; I A Wilson
Journal:  Science       Date:  2001-10-12       Impact factor: 47.728

Review 3.  Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.

Authors:  J A Gerlt; P C Babbitt
Journal:  Annu Rev Biochem       Date:  2001       Impact factor: 23.643

4.  Mimicking natural evolution in vitro: an N-acetylneuraminate lyase mutant with an increased dihydrodipicolinate synthase activity.

Authors:  Andreas C Joerger; Sebastian Mayer; Alan R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2003-04-23       Impact factor: 11.205

5.  Controlling the enantioselectivity of enzymes by directed evolution: practical and theoretical ramifications.

Authors:  Manfred T Reetz
Journal:  Proc Natl Acad Sci U S A       Date:  2004-04-12       Impact factor: 11.205

6.  Crystal structure of an ancient protein: evolution by conformational epistasis.

Authors:  Eric A Ortlund; Jamie T Bridgham; Matthew R Redinbo; Joseph W Thornton
Journal:  Science       Date:  2007-08-16       Impact factor: 47.728

7.  Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase.

Authors:  Eric Wise; Wen Shan Yew; Patricia C Babbitt; John A Gerlt; Ivan Rayment
Journal:  Biochemistry       Date:  2002-03-26       Impact factor: 3.162

8.  Evolutionary potential of (beta/alpha)8-barrels: functional promiscuity produced by single substitutions in the enolase superfamily.

Authors:  Dawn M Z Schmidt; Emily C Mundorff; Michael Dojka; Ericka Bermudez; Jon E Ness; Sridhar Govindarajan; Patricia C Babbitt; Jeremy Minshull; John A Gerlt
Journal:  Biochemistry       Date:  2003-07-22       Impact factor: 3.162

9.  Conversion of a PLP-dependent racemase into an aldolase by a single active site mutation.

Authors:  Florian P Seebeck; Donald Hilvert
Journal:  J Am Chem Soc       Date:  2003-08-27       Impact factor: 15.419

10.  Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases.

Authors:  Paul E O'Maille; Arthur Malone; Nikki Dellas; B Andes Hess; Lidia Smentek; Iseult Sheehan; Bryan T Greenhagen; Joe Chappell; Gerard Manning; Joseph P Noel
Journal:  Nat Chem Biol       Date:  2008-09-07       Impact factor: 15.040
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  46 in total

1.  Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis.

Authors:  Sagar D Khare; Yakov Kipnis; Per Greisen; Ryo Takeuchi; Yacov Ashani; Moshe Goldsmith; Yifan Song; Jasmine L Gallaher; Israel Silman; Haim Leader; Joel L Sussman; Barry L Stoddard; Dan S Tawfik; David Baker
Journal:  Nat Chem Biol       Date:  2012-02-05       Impact factor: 15.040

2.  Distributions of experimental protein structures on coarse-grained free energy landscapes.

Authors:  Kannan Sankar; Jie Liu; Yuan Wang; Robert L Jernigan
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

Review 3.  Expanding P450 catalytic reaction space through evolution and engineering.

Authors:  John A McIntosh; Christopher C Farwell; Frances H Arnold
Journal:  Curr Opin Chem Biol       Date:  2014-03-20       Impact factor: 8.822

Review 4.  Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution.

Authors:  Hans Renata; Z Jane Wang; Frances H Arnold
Journal:  Angew Chem Int Ed Engl       Date:  2015-02-03       Impact factor: 15.336

Review 5.  Resilience of biochemical activity in protein domains in the face of structural divergence.

Authors:  Dapeng Zhang; Lakshminarayan M Iyer; A Maxwell Burroughs; L Aravind
Journal:  Curr Opin Struct Biol       Date:  2014-06-19       Impact factor: 6.809

Review 6.  Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes.

Authors:  Vern L Schramm
Journal:  Annu Rev Biochem       Date:  2011       Impact factor: 23.643

7.  Computational design of an endo-1,4-beta-xylanase ligand binding site.

Authors:  Andrew Morin; Kristian W Kaufmann; Carie Fortenberry; Joel M Harp; Laura S Mizoue; Jens Meiler
Journal:  Protein Eng Des Sel       Date:  2011-02-24       Impact factor: 1.650

8.  Minor modifications of the C-terminal helix reschedule the favored chemical reactions catalyzed by theta class glutathione transferase T1-1.

Authors:  Abeer Shokeer; Bengt Mannervik
Journal:  J Biol Chem       Date:  2009-12-18       Impact factor: 5.157

9.  Phosphodeoxyribosyltransferases, designed enzymes for deoxyribonucleotides synthesis.

Authors:  Pierre Alexandre Kaminski; Gilles Labesse
Journal:  J Biol Chem       Date:  2013-01-16       Impact factor: 5.157

10.  Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole.

Authors:  Daniel A Kraut; Paul A Sigala; Timothy D Fenn; Daniel Herschlag
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-11       Impact factor: 11.205
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