Literature DB >> 20647463

Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.

Justin B Siegel1, Alexandre Zanghellini, Helena M Lovick, Gert Kiss, Abigail R Lambert, Jennifer L St Clair, Jasmine L Gallaher, Donald Hilvert, Michael H Gelb, Barry L Stoddard, Kendall N Houk, Forrest E Michael, David Baker.   

Abstract

The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry.

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Year:  2010        PMID: 20647463      PMCID: PMC3241958          DOI: 10.1126/science.1190239

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  11 in total

1.  Biomimetic Reactions Catalyzed by Cyclodextrins and Their Derivatives.

Authors:  Ronald Breslow; Steven D. Dong
Journal:  Chem Rev       Date:  1998-07-30       Impact factor: 60.622

2.  Native protein sequences are close to optimal for their structures.

Authors:  B Kuhlman; D Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2000-09-12       Impact factor: 11.205

3.  Experimental determination of the absolute enantioselectivity of an antibody-catalyzed Diels-Alder reaction and theoretical explorations of the origins of stereoselectivity.

Authors:  Carina E Cannizzaro; Jon A Ashley; K D Janda; K N Houk
Journal:  J Am Chem Soc       Date:  2003-03-05       Impact factor: 15.419

4.  Insight into a natural Diels-Alder reaction from the structure of macrophomate synthase.

Authors:  Toyoyuki Ose; Kenji Watanabe; Takashi Mie; Mamoru Honma; Hiromi Watanabe; Min Yao; Hideaki Oikawa; Isao Tanaka
Journal:  Nature       Date:  2003-03-13       Impact factor: 49.962

5.  New algorithms and an in silico benchmark for computational enzyme design.

Authors:  Alexandre Zanghellini; Lin Jiang; Andrew M Wollacott; Gong Cheng; Jens Meiler; Eric A Althoff; Daniela Röthlisberger; David Baker
Journal:  Protein Sci       Date:  2006-12       Impact factor: 6.725

6.  Kemp elimination catalysts by computational enzyme design.

Authors:  Daniela Röthlisberger; Olga Khersonsky; Andrew M Wollacott; Lin Jiang; Jason DeChancie; Jamie Betker; Jasmine L Gallaher; Eric A Althoff; Alexandre Zanghellini; Orly Dym; Shira Albeck; Kendall N Houk; Dan S Tawfik; David Baker
Journal:  Nature       Date:  2008-03-19       Impact factor: 49.962

7.  Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect.

Authors:  M I Page; W P Jencks
Journal:  Proc Natl Acad Sci U S A       Date:  1971-08       Impact factor: 11.205

8.  Control of the exo and endo pathways of the Diels-Alder reaction by antibody catalysis.

Authors:  V E Gouverneur; K N Houk; B de Pascual-Teresa; B Beno; K D Janda; R A Lerner
Journal:  Science       Date:  1993-10-08       Impact factor: 47.728

9.  The origins of noncovalent catalysis of intermolecular Diels-Alder reactions by cyclodextrins, self-assembling capsules, antibodies, and RNAses.

Authors:  Susanna P Kim; Andrew G Leach; K N Houk
Journal:  J Org Chem       Date:  2002-06-14       Impact factor: 4.354

10.  The putative Diels-Alderase macrophomate synthase is an efficient aldolase.

Authors:  Jörg M Serafimov; Dennis Gillingham; Simon Kuster; Donald Hilvert
Journal:  J Am Chem Soc       Date:  2008-05-31       Impact factor: 15.419

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  223 in total

1.  Mapping the reaction coordinates of enzymatic defluorination.

Authors:  Peter W Y Chan; Alexander F Yakunin; Elizabeth A Edwards; Emil F Pai
Journal:  J Am Chem Soc       Date:  2011-04-21       Impact factor: 15.419

2.  Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers.

Authors:  James P Allen; Tien L Olson; Paul Oyala; Wei-Jen Lee; Aaron A Tufts; JoAnn C Williams
Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-30       Impact factor: 11.205

3.  Iterative approach to computational enzyme design.

Authors:  Heidi K Privett; Gert Kiss; Toni M Lee; Rebecca Blomberg; Roberto A Chica; Leonard M Thomas; Donald Hilvert; Kendall N Houk; Stephen L Mayo
Journal:  Proc Natl Acad Sci U S A       Date:  2012-02-22       Impact factor: 11.205

4.  Protein design: A metalloenzyme reloaded.

Authors:  Birte Höcker
Journal:  Nat Chem Biol       Date:  2012-02-15       Impact factor: 15.040

5.  Molecular engineering: Unnatural design.

Authors:  Allison Doerr
Journal:  Nat Methods       Date:  2010-09       Impact factor: 28.547

6.  An exciting but challenging road ahead for computational enzyme design.

Authors:  David Baker
Journal:  Protein Sci       Date:  2010-10       Impact factor: 6.725

7.  Evaluation and ranking of enzyme designs.

Authors:  Gert Kiss; Daniela Röthlisberger; David Baker; K N Houk
Journal:  Protein Sci       Date:  2010-09       Impact factor: 6.725

Review 8.  Converting a protein into a switch for biosensing and functional regulation.

Authors:  Margaret M Stratton; Stewart N Loh
Journal:  Protein Sci       Date:  2011-01       Impact factor: 6.725

9.  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

Review 10.  Computer aided enzyme design and catalytic concepts.

Authors:  Maria P Frushicheva; Matthew J L Mills; Patrick Schopf; Manoj K Singh; Ram B Prasad; Arieh Warshel
Journal:  Curr Opin Chem Biol       Date:  2014-05-08       Impact factor: 8.822

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