Literature DB >> 29805842

Comment on "Substrate Folding Modes in Trichodiene Synthase: A Determinant of Chemo- and Stereoselectivity".

Mudit Dixit1, Michal Weitman1, Jiali Gao2,3, Dan T Major1.   

Abstract

Wang et al. recently reported an in silico study of the trichodiene synthase (TDS) conversion of farnesyl diphosphate (FPP) to trichodiene (TD) (Wang et al., ACS Catal. 2017, 7, 5841-5846). Although the methods and level of theory used in that work are nearly identical to our own recent work on this system (Dixit et al., ACS Catal. 2017, 7, 812-818), Wang et al. reach rather different conclusions. The authors claimed to obtain a "very credible" mechanism for the biosynthesis of TD and optimized the optimal folding mode of FPP in the 1,6-ring closure in TDS. However, the folding mode of the FPP substrate that was presented contradicts well-established NMR and mass spectrometry data. Moreover, the authors make numerous incorrect statements regarding our earlier work.

Entities:  

Year:  2017        PMID: 29805842      PMCID: PMC5968826          DOI: 10.1021/acscatal.7b02823

Source DB:  PubMed          Journal:  ACS Catal            Impact factor:   13.084


  25 in total

1.  Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase.

Authors:  N Wu; Y Mo; J Gao; E F Pai
Journal:  Proc Natl Acad Sci U S A       Date:  2000-02-29       Impact factor: 11.205

2.  Pre-steady-state kinetic analysis of the trichodiene synthase reaction pathway.

Authors:  D E Cane; H T Chiu; P H Liang; K S Anderson
Journal:  Biochemistry       Date:  1997-07-08       Impact factor: 3.162

3.  Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction.

Authors:  Dan T Major; Annie Heroux; Allen M Orville; Michael P Valley; Paul F Fitzpatrick; Jiali Gao
Journal:  Proc Natl Acad Sci U S A       Date:  2009-11-19       Impact factor: 11.205

4.  Dispersion-Corrected Mean-Field Electronic Structure Methods.

Authors:  Stefan Grimme; Andreas Hansen; Jan Gerit Brandenburg; Christoph Bannwarth
Journal:  Chem Rev       Date:  2016-04-14       Impact factor: 60.622

Review 5.  Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions.

Authors:  M Dixit; S Das; A R Mhashal; R Eitan; D T Major
Journal:  Methods Enzymol       Date:  2016-07-01       Impact factor: 1.600

6.  Chemical Control in the Battle against Fidelity in Promiscuous Natural Product Biosynthesis: The Case of Trichodiene Synthase.

Authors:  Mudit Dixit; Michal Weitman; Jiali Gao; Dan T Major
Journal:  ACS Catal       Date:  2016-12-02       Impact factor: 13.084

7.  Synthetic efficiency in enzyme mechanisms involving carbocations: aristolochene synthase.

Authors:  Rudolf K Allemann; Neil J Young; Shuhua Ma; Donald G Truhlar; Jiali Gao
Journal:  J Am Chem Soc       Date:  2007-10-05       Impact factor: 15.419

8.  The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations.

Authors:  Kin-Yiu Wong; Jiali Gao
Journal:  Biochemistry       Date:  2007-10-30       Impact factor: 3.162

Review 9.  Catalytic control in terpenoid cyclases: multiscale modeling of thermodynamic, kinetic, and dynamic effects.

Authors:  Dan Thomas Major; Yehoshua Freud; Michal Weitman
Journal:  Curr Opin Chem Biol       Date:  2014-04-14       Impact factor: 8.822

10.  Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase.

Authors:  Mireia Garcia-Viloca; Donald G Truhlar; Jiali Gao
Journal:  Biochemistry       Date:  2003-11-25       Impact factor: 3.162

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  1 in total

1.  Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases-Bornyl Diphosphate Synthase as a Representative Case.

Authors:  Terrence E O'Brien; Steven J Bertolani; Yue Zhang; Justin B Siegel; Dean J Tantillo
Journal:  ACS Catal       Date:  2018-03-08       Impact factor: 13.084

  1 in total

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