Literature DB >> 25651000

Enantioselective enzymes by computational design and in silico screening.

Hein J Wijma1, Robert J Floor, Sinisa Bjelic, Siewert J Marrink, David Baker, Dick B Janssen.   

Abstract

Computational enzyme design holds great promise for providing new biocatalysts for synthetic chemistry. A strategy to design small mutant libraries of complementary enantioselective epoxide hydrolase variants for the production of highly enantioenriched (S,S)-diols and (R,R)-diols is developed. Key features of this strategy (CASCO, catalytic selectivity by computational design) are the design of mutations that favor binding of the substrate in a predefined orientation, the introduction of steric hindrance to prevent unwanted substrate binding modes, and ranking of designs by high-throughput molecular dynamics simulations. Using this strategy we obtained highly stereoselective mutants of limonene epoxide hydrolase after experimental screening of only 37 variants. The results indicate that computational methods can replace a substantial amount of laboratory work when developing enantioselective enzymes.
© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Entities:  

Keywords:  biocatalysis; computational design; epoxide hydrolase; screening; stereoselectivity

Mesh:

Substances:

Year:  2015        PMID: 25651000     DOI: 10.1002/anie.201411415

Source DB:  PubMed          Journal:  Angew Chem Int Ed Engl        ISSN: 1433-7851            Impact factor:   15.336


  21 in total

Review 1.  Rational and Semirational Protein Design.

Authors:  Ivan V Korendovych
Journal:  Methods Mol Biol       Date:  2018

2.  Biocatalysis in the Pharmaceutical Industry: The Need for Speed.

Authors:  Matthew D Truppo
Journal:  ACS Med Chem Lett       Date:  2017-04-18       Impact factor: 4.345

3.  Learning epistatic interactions from sequence-activity data to predict enantioselectivity.

Authors:  Julian Zaugg; Yosephine Gumulya; Alpeshkumar K Malde; Mikael Bodén
Journal:  J Comput Aided Mol Des       Date:  2017-12-12       Impact factor: 3.686

4.  Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin.

Authors:  Justin T Biel; Michael C Thompson; Christian N Cunningham; Jacob E Corn; James S Fraser
Journal:  Structure       Date:  2017-04-13       Impact factor: 5.006

5.  Origins of stereoselectivity in evolved ketoreductases.

Authors:  Elizabeth L Noey; Nidhi Tibrewal; Gonzalo Jiménez-Osés; Sílvia Osuna; Jiyong Park; Carly M Bond; Duilio Cascio; Jack Liang; Xiyun Zhang; Gjalt W Huisman; Yi Tang; Kendall N Houk
Journal:  Proc Natl Acad Sci U S A       Date:  2015-12-07       Impact factor: 11.205

6.  Automated Design of Efficient and Functionally Diverse Enzyme Repertoires.

Authors:  Olga Khersonsky; Rosalie Lipsh; Ziv Avizemer; Yacov Ashani; Moshe Goldsmith; Haim Leader; Orly Dym; Shelly Rogotner; Devin L Trudeau; Jaime Prilusky; Pep Amengual-Rigo; Victor Guallar; Dan S Tawfik; Sarel J Fleishman
Journal:  Mol Cell       Date:  2018-09-27       Impact factor: 17.970

Review 7.  Step-by-step design of proteins for small molecule interaction: A review on recent milestones.

Authors:  José M Pereira; Maria Vieira; Sérgio M Santos
Journal:  Protein Sci       Date:  2021-05-10       Impact factor: 6.993

8.  Using molecular dynamics simulations to evaluate active designs of cephradine hydrolase by molecular mechanics/Poisson-Boltzmann surface area and molecular mechanics/generalized Born surface area methods.

Authors:  Jing Xue; Xiaoqiang Huang; Yushan Zhu
Journal:  RSC Adv       Date:  2019-05-07       Impact factor: 3.361

9.  Extending enzyme molecular recognition with an expanded amino acid alphabet.

Authors:  Claire L Windle; Katie J Simmons; James R Ault; Chi H Trinh; Adam Nelson; Arwen R Pearson; Alan Berry
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-14       Impact factor: 11.205

10.  Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes.

Authors:  Beat A Amrein; Paul Bauer; Fernanda Duarte; Åsa Janfalk Carlsson; Agata Naworyta; Sherry L Mowbray; Mikael Widersten; Shina C L Kamerlin
Journal:  ACS Catal       Date:  2015-08-17       Impact factor: 13.084

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