1
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Schwartz R, Zev S, Major DT. Mechanistic docking in terpene synthases using EnzyDock. Methods Enzymol 2024; 699:265-292. [PMID: 38942507 DOI: 10.1016/bs.mie.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Terpene Synthases (TPS) catalyze the formation of multicyclic, complex terpenes and terpenoids from linear substrates. Molecular docking is an important research tool that can further our understanding of TPS multistep mechanisms and guide enzyme design. Standard docking programs are not well suited to tackle the unique challenges of TPS, like the many chemical steps which form multiple stereo-centers, the weak dispersion interactions between the isoprenoid chain and the hydrophobic region of the active site, description of carbocation intermediates, and finding mechanistically meaningful sets of docked poses. To address these and other unique challenges, we developed the multistate, multiscale docking program EnzyDock and used it to study many TPS and other enzymes. In this review we discuss the unique challenges of TPS, the special features of EnzyDock developed to address these challenges and demonstrate its successful use in ongoing research on the bacterial TPS CotB2.
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Affiliation(s)
- Renana Schwartz
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Shani Zev
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Dan T Major
- Department of Chemistry and Institute for Nanotechnology Advanced Materials, Bar Ilan University, Ramat Gan, Israel.
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2
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Torrence IS, O'Brien TE, Siegel JB, Tantillo DJ. Docking carbocations into terpene synthase active sites using chemically meaningful constraints-The TerDockin approach. Methods Enzymol 2024; 699:231-263. [PMID: 38942505 DOI: 10.1016/bs.mie.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Terpenes are a diverse class of natural products which have long been sought after for their chemical properties as medicine, perfumes, and for food flavoring. Computational docking studies of terpene mechanisms have been a challenge due to the lack of strong directing groups which many docking programs rely on. In this chapter, we dive into our computational method Terdockin (Terpene-Docking) as a successful methodology in modeling terpene synthase mechanisms. This method could also be used as inspiration for any multi-ligand docking project.
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Affiliation(s)
- Ian S Torrence
- Department of Chemistry, University of California Davis, Davis, CA, United States
| | - Terrence E O'Brien
- Discovery Chemistry, Genentech, Inc., South San Francisco, CA, United States
| | - Justin B Siegel
- Department of Chemistry, University of California Davis, Davis, CA, United States; Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, CA, United States; Genome Center, University of California Davis, Davis, CA, Untied States.
| | - Dean J Tantillo
- Department of Chemistry, University of California Davis, Davis, CA, United States
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3
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Matsuyama T, Togashi K, Nakano M, Sato H, Uchiyama M. Revision of the Peniroquesine Biosynthetic Pathway by Retro-Biosynthetic Theoretical Analysis: Ring Strain Controls the Unique Carbocation Rearrangement Cascade. JACS AU 2023; 3:1596-1603. [PMID: 37388688 PMCID: PMC10301677 DOI: 10.1021/jacsau.3c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 07/01/2023]
Abstract
Peniroquesine, a sesterterpenoid featuring a unique 5/6/5/6/5 fused pentacyclic ring system, has been known for a long time, but its biosynthetic pathway/mechanism remains elusive. Based on isotopic labeling experiments, a plausible biosynthetic pathway to peniroquesines A-C and their derivatives was recently proposed, in which the characteristic peniroquesine-type 5/6/5/6/5 pentacyclic skeleton is synthesized from geranyl-farnesyl pyrophosphate (GFPP) via a complex concerted A/B/C-ring formation, repeated reverse-Wagner-Meerwein alkyl shifts, three successive secondary (2°) carbocation intermediates, and a highly distorted trans-fused bicyclo[4.2.1]nonane intermediate. However, our density functional theory calculations do not support this mechanism. By applying a retro-biosynthetic theoretical analysis strategy, we were able to find a preferred pathway for peniroquesine biosynthesis, involving a multistep carbocation cascade including triple skeletal rearrangements, trans-cis isomerization, and 1,3-H shift. This pathway/mechanism is in good agreement with all of the reported isotope-labeling results.
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Affiliation(s)
- Taro Matsuyama
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ko Togashi
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Moe Nakano
- Interdisciplinary
Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Hajime Sato
- Interdisciplinary
Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
| | - Masanobu Uchiyama
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Research
Initiative for Supra-Materials (RISM), Shinshu
University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
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4
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The propensity of terpenes to invoke concerted reactions in their biosynthesis. ADVANCES IN QUANTUM CHEMISTRY 2022. [DOI: 10.1016/bs.aiq.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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5
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Zev S, Gupta PK, Pahima E, Major DT. A Benchmark Study of Quantum Mechanics and Quantum Mechanics-Molecular Mechanics Methods for Carbocation Chemistry. J Chem Theory Comput 2021; 18:167-178. [PMID: 34905380 DOI: 10.1021/acs.jctc.1c00746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Carbocations play key roles in classical organic reactions and have also been implicated in several enzyme families. A hallmark of carbocation chemistry is multitudes of competing reaction pathways, and to be able to distinguish between pathways with quantum chemical calculations, it is necessary to approach chemical accuracy for relative energies between carbocations. Here, we present an extensive study of the performance of selected density functional theory (DFT) methods in describing the thermochemistry and kinetics of carbocations and their corresponding neutral alkenes both in the gas-phase and within a hybrid quantum mechanics-molecular mechanics (QM/MM) framework. The density functionals are benchmarked against accurate ab initio methods such as CBS-QB3 and DLPNO-CCSD(T). Based on the findings in the gas-phase calculations of carbocations and alkenes, the best functionals are chosen and tested further for non-covalent interactions in model systems using QM and QM/MM methods. We compute the interaction energies between a model carbocation/alkane and model π, dipole, and hydrophobic systems using DFT and QM(DFT)/MM and compare with DLPNO-CCSD(T). These latter model systems are representative of side chains of amino acids such as phenylalanine/tyrosine, tryptophan, asparagine/glutamine, serine/threonine, methionine, and other hydrophobic groups. The Lennard-Jones parameters of the QM atoms in QM(DFT)/MM calculations are modified to obtain an optimal fit with the QM energies. Finally, a selected carbocation reaction is studied in the gas phase and in implicit chloroform solvent using QM and in explicit chloroform solvent using QM/MM and umbrella sampling simulations. This study highlights the highest accuracy possible with selected density functionals and QM/MM methods but also some limitations in using QM/MM methods for carbocation systems.
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Affiliation(s)
- Shani Zev
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Prashant Kumar Gupta
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Efrat Pahima
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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6
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Raz K, Levi S, Gupta PK, Major DT. Enzymatic control of product distribution in terpene synthases: insights from multiscale simulations. Curr Opin Biotechnol 2020; 65:248-258. [PMID: 32679412 DOI: 10.1016/j.copbio.2020.06.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 11/25/2022]
Abstract
In this opinion, we review some recent work on terpene biosynthesis using multiscale simulation approaches, with special focus on contributions from our group. Terpene synthases generate terpenes employing rich carbocation chemistry, including highly specific ring formations, proton, hydride, methyl, and methylene migrations, followed by reaction quenching. In these enzymes, the main catalytic challenge is not rate enhancement, but rather control of intrinsically reactive carbocations and the resulting product distribution. Herein, we review multiscale simulations of selected mono-, sesqui-, and diterpene synthases. We point to the many tools adopted by terpene synthases to achieve correct substrate fold, carbocation formation, carbocation reaction environment, and reaction quenching. A better understanding of the toolbox employed by terpene synthases is expected to aid in the search for new enzymatic and biomimetic synthetic routes to natural and unnatural terpenes.
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Affiliation(s)
- Keren Raz
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Shani Levi
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Prashant Kumar Gupta
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel.
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7
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Diao H, Chen N, Wang K, Zhang F, Wang YH, Wu R. Biosynthetic Mechanism of Lanosterol: A Completed Story. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hongjuan Diao
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
| | - Nanhao Chen
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Kai Wang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
| | - Fan Zhang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
| | - Yong-Heng Wang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, People’s Republic of China
| | - Ruibo Wu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
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8
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Quilez Del Moral JF, Domingo V, Pérez Á, Martínez Andrade KA, Enríquez L, Jaraiz M, López-Pérez JL, Barrero AF. Mimicking Halimane Synthases: Monitoring a Cascade of Cyclizations and Rearrangements from Epoxypolyprenes. J Org Chem 2019; 84:13764-13779. [PMID: 31559826 DOI: 10.1021/acs.joc.9b01996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have developed and rationalized a biomimetic transformation mimicking halimane synthases based on a Lewis acid-catalyzed cascade of cyclizations and rearrangements of epoxypolyprenes. Two rings, three stereogenic centers, and a new double bond were generated in a single chemical operation. Based on this cascade transformation, we achieved a unified strategy toward the stereoselective total syntheses of halimene-type terpenoids and analogues as a proof-of-concept study. This method has been applied to the rapid synthesis of diterpene isotuberculosinol, a virulence factor of Mycobacterium tuberculosis as a representative example.
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Affiliation(s)
- José F Quilez Del Moral
- Department of Organic Chemistry, Institute of Biotechnology , University of Granada , 18071 Granada , Spain
| | - Victoriano Domingo
- Department of Organic Chemistry, Institute of Biotechnology , University of Granada , 18071 Granada , Spain
| | - Álvaro Pérez
- Department of Organic Chemistry, Institute of Biotechnology , University of Granada , 18071 Granada , Spain
| | - Kevin A Martínez Andrade
- Department of Organic Chemistry, Institute of Biotechnology , University of Granada , 18071 Granada , Spain
| | - Lourdes Enríquez
- Department of Electronics , University of Valladolid , 47011 Valladolid , Spain
| | - Martín Jaraiz
- Department of Electronics , University of Valladolid , 47011 Valladolid , Spain
| | - José Luis López-Pérez
- Department of Pharmaceutical Sciences, IBSAL-CIETUS , University of Salamanca , 37007 Salamanca , Spain.,Department of Pharmacology, Faculty of Medicine , University of Panama , 3366 Panama , Republic of Panama
| | - Alejandro F Barrero
- Department of Organic Chemistry, Institute of Biotechnology , University of Granada , 18071 Granada , Spain
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9
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Elkin M, Scruse AC, Turlik A, Newhouse TR. Computational and Synthetic Investigation of Cationic Rearrangement in the Putative Biosynthesis of Justicane Triterpenoids. Angew Chem Int Ed Engl 2019; 58:1025-1029. [PMID: 30575223 PMCID: PMC6499374 DOI: 10.1002/anie.201810566] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/30/2018] [Indexed: 02/06/2023]
Abstract
A biomimetic cationic structural rearrangement of the oleanolic acid framework is reported for the gram-scale synthesis and structural reassignment of justicioside E aglycone. The mechanism of the putative biosynthetic rearrangement is investigated with kinetic, computational, and synthetic approaches. The precursor to rearrangement was accessed through two strategic advancements: (1) synthesis of a 1,3-diketone via oxidation of a β-silyl enone, and (2) diastereoselective 1,3-diketone reduction to form a syn-1,3-diol using SmI2 with PhSH as a key additive.
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Affiliation(s)
- Masha Elkin
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 20817, New Haven, CT, 06511, USA
| | - Anthony C Scruse
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 20817, New Haven, CT, 06511, USA
| | - Aneta Turlik
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 20817, New Haven, CT, 06511, USA
| | - Timothy R Newhouse
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 20817, New Haven, CT, 06511, USA
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10
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Elkin M, Scruse AC, Turlik A, Newhouse TR. Computational and Synthetic Investigation of Cationic Rearrangement in the Putative Biosynthesis of Justicane Triterpenoids. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Masha Elkin
- Department of ChemistryYale University 225 Prospect Street, PO Box 20817 New Haven CT 06511 USA
| | - Anthony C. Scruse
- Department of ChemistryYale University 225 Prospect Street, PO Box 20817 New Haven CT 06511 USA
| | - Aneta Turlik
- Department of ChemistryYale University 225 Prospect Street, PO Box 20817 New Haven CT 06511 USA
| | - Timothy R. Newhouse
- Department of ChemistryYale University 225 Prospect Street, PO Box 20817 New Haven CT 06511 USA
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11
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Ideno N, Umeyama S, Watanabe T, Nakajima M, Sato T, Hoshino T. Alicyclobacillus acidocaldarius
Squalene‐Hopene Cyclase: The Critical Role of Steric Bulk at Ala306 and the First Enzymatic Synthesis of Epoxydammarane from 2,3‐Oxidosqualene. Chembiochem 2018; 19:1873-1886. [DOI: 10.1002/cbic.201800281] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Natsumi Ideno
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Shikou Umeyama
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Takashi Watanabe
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Mami Nakajima
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Tsutomu Sato
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
| | - Tsutomu Hoshino
- Graduate School of Science and Technology andDepartment of Applied Biological ChemistryFaculty of AgricultureNiigata University Ikarashi 2–8050, Nishi-ku Niigata 950–2181 Japan
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12
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Ansbacher T, Freud Y, Major DT. Slow-Starter Enzymes: Role of Active-Site Architecture in the Catalytic Control of the Biosynthesis of Taxadiene by Taxadiene Synthase. Biochemistry 2018; 57:3773-3779. [DOI: 10.1021/acs.biochem.8b00452] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tamar Ansbacher
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
- Hadassah Academic College, 7 Hanevi’im Street, Jerusalem 9101001, Israel
| | - Yehoshua Freud
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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13
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Yao J, Chen F, Guo H. QM/MM free energy simulations of the reaction catalysed by (4S)-limonene synthase involving linalyl diphosphate (LPP) substrate. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1447106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Jianzhuang Yao
- School of Biological Science and Technology, University of Jinan , Jinan, P.R. China
| | - Feng Chen
- Department of Plant Sciences, University of Tennessee , Knoxville, TN, USA
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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14
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Eriksson A, Kürten C, Syrén P. Protonation-Initiated Cyclization by a Class II Terpene Cyclase Assisted by Tunneling. Chembiochem 2017; 18:2301-2305. [PMID: 28980755 PMCID: PMC5725671 DOI: 10.1002/cbic.201700443] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Indexed: 02/03/2023]
Abstract
Terpenes represent one of the most diversified classes of natural products with potent biological activities. The key to the myriad of polycyclic terpene skeletons with crucial functions in organisms from all kingdoms of life are terpene cyclase enzymes. These biocatalysts enable stereospecific cyclization of relatively simple, linear, prefolded polyisoprenes by highly complex, partially concerted, electrophilic cyclization cascades that remain incompletely understood. Herein, additional mechanistic light is shed on terpene biosynthesis by kinetic studies in mixed H2 O/D2 O buffers of a class II bacterial ent-copalyl diphosphate synthase. Mass spectrometry determination of the extent of deuterium incorporation in the bicyclic product, reminiscent of initial carbocation formation by protonation, resulted in a large kinetic isotope effect of up to seven. Kinetic analysis at different temperatures confirmed that the isotope effect was independent of temperature, which is consistent with hydrogen tunneling.
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Affiliation(s)
- Adam Eriksson
- School of Chemical Science and EngineeringKTH Royal Institute of Technology100 44StockholmSweden
| | - Charlotte Kürten
- Science for Life LaboratoryKTH Royal Institute of TechnologySchool of BiotechnologyDivision of Proteomics171 21StockholmSweden
| | - Per‐Olof Syrén
- School of Chemical Science and EngineeringKTH Royal Institute of Technology100 44StockholmSweden
- Science for Life LaboratoryKTH Royal Institute of TechnologySchool of BiotechnologyDivision of Proteomics171 21StockholmSweden
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15
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Gustafsson C, Vassiliev S, Kürten C, Syrén PO, Brinck T. MD Simulations Reveal Complex Water Paths in Squalene-Hopene Cyclase: Tunnel-Obstructing Mutations Increase the Flow of Water in the Active Site. ACS OMEGA 2017; 2:8495-8506. [PMID: 31457386 PMCID: PMC6645472 DOI: 10.1021/acsomega.7b01084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/20/2017] [Indexed: 06/10/2023]
Abstract
Squalene-hopene cyclase catalyzes the cyclization of squalene to hopanoids. A previous study has identified a network of tunnels in the protein, where water molecules have been indicated to move. Blocking these tunnels by site-directed mutagenesis was found to change the activation entropy of the catalytic reaction from positive to negative with a concomitant lowering of the activation enthalpy. As a consequence, some variants are faster and others are slower than the wild type (wt) in vitro under optimal reaction conditions for the wt. In this study, molecular dynamics (MD) simulations have been performed for the wt and the variants to investigate how the mutations affect the protein structure and the water flow in the enzyme, hypothetically influencing the activation parameters. Interestingly, the tunnel-obstructing variants are associated with an increased flow of water in the active site, particularly close to the catalytic residue Asp376. MD simulations with the substrate present in the active site indicate that the distance for the rate-determining proton transfer between Asp376 and the substrate is longer in the tunnel-obstructing protein variants than in the wt. On the basis of the previous experimental results and the current MD results, we propose that the tunnel-obstructing variants, at least partly, could operate by a different catalytic mechanism, where the proton transfer may have contributions from a Grotthuss-like mechanism.
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Affiliation(s)
- Camilla Gustafsson
- Applied
Physical Chemistry, School of Chemical Science and Engineering, KTH Royal Institute of Technology, Teknikringen 36, 100 44 Stockholm, Sweden
| | - Serguei Vassiliev
- Department
of Biological Sciences, Brock University, Mackenzie Chown F 234, 1812 Sir
Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Charlotte Kürten
- Science
for Life Laboratory, Stockholm—School of Biotechnology, Division
of Proteomics and Nanobiotechnology, KTH
Royal Institute of Technology, Tomtebodavägen 23a, 171 65 Solna, Sweden
| | - Per-Olof Syrén
- Applied
Physical Chemistry, School of Chemical Science and Engineering, KTH Royal Institute of Technology, Teknikringen 36, 100 44 Stockholm, Sweden
- Science
for Life Laboratory, Stockholm—School of Biotechnology, Division
of Proteomics and Nanobiotechnology, KTH
Royal Institute of Technology, Tomtebodavägen 23a, 171 65 Solna, Sweden
| | - Tore Brinck
- Applied
Physical Chemistry, School of Chemical Science and Engineering, KTH Royal Institute of Technology, Teknikringen 36, 100 44 Stockholm, Sweden
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16
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Dixit M, Weitman M, Gao J, Major DT. Comment on "Substrate Folding Modes in Trichodiene Synthase: A Determinant of Chemo- and Stereoselectivity". ACS Catal 2017; 8:1371-1375. [PMID: 29805842 DOI: 10.1021/acscatal.7b02823] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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.
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Affiliation(s)
- Mudit Dixit
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Michal Weitman
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Jiali Gao
- Department
of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Theoretical
Chemistry Institute, Jilin University, Changchun 130023, P.R. China
| | - Dan T. Major
- Department
of Chemistry and the Lise Meitner-Minerva Center of Computational
Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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17
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Affiliation(s)
- Dan T. Major
- Department of Chemistry and
the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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18
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Dixit M, Weitman M, Gao J, Major DT. Chemical Control in the Battle against Fidelity in Promiscuous Natural Product Biosynthesis: The Case of Trichodiene Synthase. ACS Catal 2017; 7:812-818. [PMID: 29399379 PMCID: PMC5793923 DOI: 10.1021/acscatal.6b02584] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Terpene cyclases catalyze the highly stereospecific molding of polyisoprenes into terpenes, which are precursors to most known natural compounds. The isoprenoids are formed via intricate chemical cascades employing rich, yet highly erratic, carbocation chemistry. It is currently not well understood how these biocatalysts achieve chemical control. Here, we illustrate the catalytic control exerted by trichodiene synthase, and in particular, we discover two features that could be general catalytic tools adopted by other terpenoid cyclases. First, to avoid formation of byproducts, the enzyme raises the energy of bisabolyl carbocation, which is a general mechanistic branching point in many sesquiterpene cyclases, resulting in an essentially concerted cyclization cascade. Second, we identify a sulfur-carbocation dative bonding interaction that anchors the bisabolyl cation in a reactive conformation, avoiding tumbling and premature deprotonation. Specifically, Met73 acts as a chameleon, shifting from an initial sulfur-π interaction in the Michaelis complex to a sulfur-carbocation complex during catalysis.
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Affiliation(s)
- Mudit Dixit
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Michal Weitman
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Jiali Gao
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Theoretical Chemistry Institute, Jilin University, Changchun 130023, P.R. China
| | - Dan T. Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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19
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Hess BA. Computational studies on the cyclization of squalene to the steroids and hopenes. Org Biomol Chem 2017; 15:2133-2145. [DOI: 10.1039/c7ob00222j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A review of computational studies of the related biosyntheses of steroids and hopenes reported during the last two decades is presented.
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Affiliation(s)
- B. Andes Hess
- Department of Chemistry
- Vanderbilt University
- Nashville
- USA
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20
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Zhang X, Chung LW. Alternative Mechanistic Strategy for Enzyme Catalysis in a Ni-Dependent Lactate Racemase (LarA): Intermediate Destabilization by the Cofactor. Chemistry 2016; 23:3623-3630. [DOI: 10.1002/chem.201604893] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Xiaoyong Zhang
- Department of Chemistry; South University of Science and Technology of China; Shenzhen 518055 P. R. China
| | - Lung W. Chung
- Department of Chemistry; South University of Science and Technology of China; Shenzhen 518055 P. R. China
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21
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Das S, Dixit M, Major DT. First principles model calculations of the biosynthetic pathway in selinadiene synthase. Bioorg Med Chem 2016; 24:4867-4870. [DOI: 10.1016/j.bmc.2016.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 06/30/2016] [Accepted: 07/02/2016] [Indexed: 11/29/2022]
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22
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From hopanoids to cholesterol: Molecular clocks of pentameric ligand-gated ion channels. Prog Lipid Res 2016; 63:1-13. [DOI: 10.1016/j.plipres.2016.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 03/22/2016] [Accepted: 03/24/2016] [Indexed: 11/21/2022]
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23
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Liu Z, Zhou J, Wu R, Xu J. Mechanism of Assembling Isoprenoid Building Blocks 1. Elucidation of the Structural Motifs for Substrate Binding in Geranyl Pyrophosphate Synthase. J Chem Theory Comput 2015; 10:5057-67. [PMID: 26584386 DOI: 10.1021/ct500607n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Terpenes (isoprenoids) represent the most functionally and structurally diverse group of natural products. Terpenes are assembled from two building blocks, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP or DPP), by prenyltransferases (PTSs). Geranyl pyrophosphate synthase (GPPS) is the enzyme that assembles DPP and IPP in the first step of chain elongation during isoprenoid biosynthesis. The mechanism by which GPPS assembles the terpene precursor remains unknown; elucidating this mechanism will help in development of new technology to generate novel natural product-like scaffolds. With classic and QM/MM MD simulations, an "open-closed" conformation change of the catalytic pocket was observed in the GPPS active site at its large subunit (LSU), and a critical salt bridge between Asp91(in loop 1) and Lys239(in loop 2) was identified. The salt bridge is responsible for opening or closing the catalytic pocket. Meanwhile, the small subunit (SSU) regulates the size and shape of the hydrophobic pocket to flexibly host substrates with different shapes and sizes (DPP/GPP/FPP, C5/C10/C15). Further QM/MM MD simulations were carried out to explore the binding modes for the different substrates catalyzed by GPPS. Our simulations suggest that the key residues (Asp91, Lys239, and Gln156) are good candidates for site-directed mutagenesis and may help in protein engineering.
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Affiliation(s)
- Zhihong Liu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University , 132 East Circle at University City, Guangzhou 510006, China
| | - Jingwei Zhou
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University , 132 East Circle at University City, Guangzhou 510006, China
| | - Ruibo Wu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University , 132 East Circle at University City, Guangzhou 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University , 132 East Circle at University City, Guangzhou 510006, China
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24
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Hong YJ, Tantillo DJ. Tension between Internal and External Modes of Stabilization in Carbocations Relevant to Terpene Biosynthesis: Modulating Minima Depth via C–H···π Interactions. Org Lett 2015; 17:5388-91. [DOI: 10.1021/acs.orglett.5b02740] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Young J. Hong
- Department
of Chemistry, Univeristy of California—Davis, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department
of Chemistry, Univeristy of California—Davis, Davis, California 95616, United States
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25
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Zhou J, Wang X, Kuang M, Wang L, Luo HB, Mo Y, Wu R. Protonation-Triggered Carbon-Chain Elongation in Geranyl Pyrophosphate Synthase (GPPS). ACS Catal 2015. [DOI: 10.1021/acscatal.5b00947] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingwei Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Xiaoming Wang
- Program in Public Health, College of Healthy Sciences, University of California—Irvine, Irvine, California 92697,United States
| | - Ming Kuang
- Institute of Chinese Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Laiyou Wang
- Institute of Chinese Medical Sciences, Guangdong Pharmaceutical University, Guangzhou 510006, P.R. China
| | - Hai-Bin Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
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26
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Review of computer simulations of isotope effects on biochemical reactions: From the Bigeleisen equation to Feynman's path integral. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1782-94. [PMID: 25936775 DOI: 10.1016/j.bbapap.2015.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/13/2015] [Accepted: 04/22/2015] [Indexed: 12/18/2022]
Abstract
Enzymatic reactions are integral components in many biological functions and malfunctions. The iconic structure of each reaction path for elucidating the reaction mechanism in details is the molecular structure of the rate-limiting transition state (RLTS). But RLTS is very hard to get caught or to get visualized by experimentalists. In spite of the lack of explicit molecular structure of the RLTS in experiment, we still can trace out the RLTS unique "fingerprints" by measuring the isotope effects on the reaction rate. This set of "fingerprints" is considered as a most direct probe of RLTS. By contrast, for computer simulations, oftentimes molecular structures of a number of TS can be precisely visualized on computer screen, however, theoreticians are not sure which TS is the actual rate-limiting one. As a result, this is an excellent stage setting for a perfect "marriage" between experiment and theory for determining the structure of RLTS, along with the reaction mechanism, i.e., experimentalists are responsible for "fingerprinting", whereas theoreticians are responsible for providing candidates that match the "fingerprints". In this Review, the origin of isotope effects on a chemical reaction is discussed from the perspectives of classical and quantum worlds, respectively (e.g., the origins of the inverse kinetic isotope effects and all the equilibrium isotope effects are purely from quantum). The conventional Bigeleisen equation for isotope effect calculations, as well as its refined version in the framework of Feynman's path integral and Kleinert's variational perturbation (KP) theory for systematically incorporating anharmonicity and (non-parabolic) quantum tunneling, are also presented. In addition, the outstanding interplay between theory and experiment for successfully deducing the RLTS structures and the reaction mechanisms is demonstrated by applications on biochemical reactions, namely models of bacterial squalene-to-hopene polycyclization and RNA 2'-O-transphosphorylation. For all these applications, we used our recently-developed path-integral method based on the KP theory, called automated integration-free path-integral (AIF-PI) method, to perform ab initio path-integral calculations of isotope effects. As opposed to the conventional path-integral molecular dynamics (PIMD) and Monte Carlo (PIMC) simulations, values calculated from our AIF-PI path-integral method can be as precise as (not as accurate as) the numerical precision of the computing machine. Lastly, comments are made on the general challenges in theoretical modeling of candidates matching the experimental "fingerprints" of RLTS. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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27
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Tian BX, Wallrapp FH, Holiday GL, Chow JY, Babbitt PC, Poulter CD, Jacobson MP. Predicting the functions and specificity of triterpenoid synthases: a mechanism-based multi-intermediate docking approach. PLoS Comput Biol 2014; 10:e1003874. [PMID: 25299649 PMCID: PMC4191879 DOI: 10.1371/journal.pcbi.1003874] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/25/2014] [Indexed: 11/18/2022] Open
Abstract
Terpenoid synthases construct the carbon skeletons of tens of thousands of natural products. To predict functions and specificity of triterpenoid synthases, a mechanism-based, multi-intermediate docking approach is proposed. In addition to enzyme function prediction, other potential applications of the current approach, such as enzyme mechanistic studies and enzyme redesign by mutagenesis, are discussed. The rapid growth in the number of protein sequences presents challenges for enzyme function assignment. Computational methods, such as bioinformatics, homology modeling and docking, are becoming increasingly important for predicting of enzyme functions from protein sequences. Terpenoids are one of largest classes of natural products, and many drugs (e.g. taxol) consist of terpenoids or terpenoid derivatives. Understanding the biosynthesis of the terpenoids is of great interest. Terpenoid synthases catalyze the key cyclization steps of the biosynthesis of terpenoids via carbocation rearrangements, generating numerous multiple-ring carbon skeletons. Triterpenoid synthases, as an important class of terpenoid synthases, catalyze the cyclization of either squalene or oxido-squalene into cyclized products such as sterols (e.g. lanosterol). In this work, we propose a computational approach that can be used to predict product specificity of the triterpenoid synthases. Our approach provides insight into the ‘design principles’ of these fascinating enzymes, and may become a practical approach for function prediction and enzyme engineering.
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Affiliation(s)
- Bo-Xue Tian
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
| | - Frank H. Wallrapp
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
| | - Gemma L. Holiday
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Jeng-Yeong Chow
- Department of Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Patricia C. Babbitt
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - C. Dale Poulter
- Department of Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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28
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Catalytic control in terpenoid cyclases: multiscale modeling of thermodynamic, kinetic, and dynamic effects. Curr Opin Chem Biol 2014; 21:25-33. [DOI: 10.1016/j.cbpa.2014.03.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 03/09/2014] [Indexed: 02/08/2023]
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29
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Bis-pyrene carbocations for chromogenic and fluorogenic dual-detection of fluoride anion in situ. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.03.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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30
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Grishko VV, Nogovitsina YM, Ivshina IB. Bacterial transformation of terpenoids. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n04abeh004396] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Doron D, Weitman M, Vardi-Kilshtain A, Azuri A, Engel H, Major DT. Multiscale Quantum-Classical Simulations of Enzymes. Isr J Chem 2014. [DOI: 10.1002/ijch.201400026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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32
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Syrén PO, Hammer SC, Claasen B, Hauer B. Entropy is Key to the Formation of Pentacyclic Terpenoids by Enzyme-Catalyzed Polycyclization. Angew Chem Int Ed Engl 2014; 53:4845-9. [DOI: 10.1002/anie.201402087] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 02/21/2014] [Indexed: 01/13/2023]
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33
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Syrén PO, Hammer SC, Claasen B, Hauer B. Entropy is Key to the Formation of Pentacyclic Terpenoids by Enzyme-Catalyzed Polycyclization. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Chen N, Zhou J, Li J, Xu J, Wu R. Concerted Cyclization of Lanosterol C-Ring and D-Ring Under Human Oxidosqualene Cyclase Catalysis: An ab Initio QM/MM MD Study. J Chem Theory Comput 2014; 10:1109-20. [PMID: 26580186 DOI: 10.1021/ct400949b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Nanhao Chen
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Jingwei Zhou
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Jiabo Li
- Schrödinger, LLC., 120 West 45th Street,
17th Floor, New York, New York, 10036 United States
| | - Jun Xu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Ruibo Wu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
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35
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Sokol JG, Cochrane NA, Becker JJ, Gagné MR. Catalytic platinum-initiated cation-olefin reactions with alkene terminating groups. Chem Commun (Camb) 2013; 49:5046-8. [PMID: 23619982 DOI: 10.1039/c3cc41699b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of phosphine-Pt(2+)-catalysts is reported, which enable the oxidative cascade cyclization of poly-alkene substrates. When the terminus is appropriately arranged and a catalyst reoxidation mediator is included, several polycyclic all carbon skeletons can be obtained. In one example, a chiral P2Pt(+2) catalyst provides up to 79% ee.
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Affiliation(s)
- Joseph G Sokol
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA
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36
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Tian BX, Eriksson LA. Catalytic Mechanism and Product Specificity of Oxidosqualene-Lanosterol Cyclase: A QM/MM Study. J Phys Chem B 2012; 116:13857-62. [DOI: 10.1021/jp3091396] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Bo-Xue Tian
- School of Chemistry, National University of Ireland—Galway, Galway,
Ireland
| | - Leif A. Eriksson
- Department of Chemistry
and
Molecular Biology, University of Gothenburg, 412 96 Göteborg, Sweden
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37
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Major DT, Weitman M. Electrostatically guided dynamics--the root of fidelity in a promiscuous terpene synthase? J Am Chem Soc 2012; 134:19454-62. [PMID: 23101787 DOI: 10.1021/ja308295p] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Terpene cyclases are responsible for the initial cyclization cascade in the multistep synthesis of more than 60,000 known natural products. This abundance of compounds is generated using a very limited pool of substrates based on linear isoprenoids. The astounding chemodiversity obtained by terpene cyclases suggests a tremendous catalytic challenge to these often promiscuous enzymes. In the current study we present a detailed mechanistic view of the biosynthesis of the monoterpene bornyl diphosphate (BPP) from geranyl diphosphate by BPP synthase using state of the art simulation methods. We identify the bornyl cation as an enzyme-induced bifurcation point on the multidimensional free energy surface, connecting between the product BPP and the side product camphene. Chemical dynamics simulations suggest that the active site diphosphate moiety steers reaction trajectories toward product formation. Nonetheless, chemical dynamics is not precise enough for exclusive product formation, providing a rationale for the lack of fidelity in this promiscuous terpene cyclase.
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Affiliation(s)
- Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel.
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38
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Godeau J, Fontaine-Vive F, Antoniotti S, Duñach E. Experimental and theoretical studies on the bismuth-triflate-catalysed cycloisomerisation of 1,6,10-trienes and aryl polyenes. Chemistry 2012; 18:16815-22. [PMID: 23143886 DOI: 10.1002/chem.201202263] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/01/2012] [Indexed: 11/07/2022]
Abstract
Cycloisomerisation of polyenes such as diethyl geranylprenylmalonate [(E)-1 a], diethyl geranylphenylmalonate [(E)-2 a] and diethyl cinnamylgeranylmalonate [(E,E)-3 a] catalysed by bismuth triflate was studied from experimental and theoretical viewpoints. Several intermediates were isolated and characterised, and calculated transition-state structures are proposed for the three reactions. The diastereoselectivity observed during the reaction of (E)- or (Z)-2 a in favour of the formation of trans-fused bicyclic products is discussed in detail. The nature of the active catalytic species derived from bismuth triflate was also investigated, and the formation of a hybrid Lewis acid/Brønsted acid catalyst with water molecules is proposed, supported by experimental and theoretical data.
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Affiliation(s)
- Julien Godeau
- Institut de Chimie de Nice, UMR, Université de Nice Sophia Antipolis-CNRS, France
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39
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Abstract
Hopanoids and sterols are members of a large group of cyclic triterpenoic compounds that have important functions in many prokaryotic and eukaryotic organisms. They are biochemically synthesized from linear precursors (squalene, 2,3-oxidosqualene) in only one enzymatic step that is catalyzed by squalene-hopene cyclase (SHC) or oxidosqualene cyclase (OSC). SHCs and OSCs are related in amino acid sequences and probably are derived from a common ancestor. The SHC reaction requires the formation of five ring structures, 13 covalent bonds, and nine stereo centers and therefore is one of the most complex one-step enzymatic reactions. We summarize the knowledge of the properties of triterpene cyclases and details of the reaction mechanism of Alicyclobacillus acidocaldarius SHC. Properties of other SHCs are included.
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Affiliation(s)
| | - Dieter Jendrossek
- Institute for Microbiology, University of Stuttgart, Stuttgart, Germany
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40
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Sokol JG, Korapala CS, White PS, Becker JJ, Gagné MR. Terminating platinum-initiated cation-olefin reactions with simple alkenes. Angew Chem Int Ed Engl 2011; 50:5658-61. [PMID: 21574222 DOI: 10.1002/anie.201100463] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Joseph G Sokol
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA
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41
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Sokol JG, Korapala CS, White PS, Becker JJ, Gagné MR. Terminating Platinum-Initiated Cation-Olefin Reactions with Simple Alkenes. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100463] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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42
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Tantillo DJ. Biosynthesis via carbocations: theoretical studies on terpene formation. Nat Prod Rep 2011; 28:1035-53. [PMID: 21541432 DOI: 10.1039/c1np00006c] [Citation(s) in RCA: 281] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review describes applications of quantum chemical calculations in the field of terpene biosynthesis, with a focus on insights into the mechanisms of terpene-forming carbocation rearrangements arising from theoretical studies.
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43
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Hong YJ, Tantillo DJ. How Many Secondary Carbocations Are Involved in the Biosynthesis of Avermitilol? Org Lett 2011; 13:1294-7. [DOI: 10.1021/ol103079v] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Young J. Hong
- Department of Chemistry, University of California−Davis, One Shields Avenue, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department of Chemistry, University of California−Davis, One Shields Avenue, Davis, California 95616, United States
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44
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Smentek L, Hess BA. Compelling Computational Evidence for the Concerted Cyclization of the ABC Rings of Hopene from Protonated Squalene. J Am Chem Soc 2010; 132:17111-7. [DOI: 10.1021/ja1039133] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lidia Smentek
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - B. Andes Hess
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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45
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Weitman M, Major DT. Challenges posed to bornyl diphosphate synthase: diverging reaction mechanisms in monoterpenes. J Am Chem Soc 2010; 132:6349-60. [PMID: 20394387 DOI: 10.1021/ja910134x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The simplest form of terpenoid chemistry is found for the monoterpenes, which give plants fragrance, flavor, and medicinal properties. Monoterpene synthases employ geranyl diphosphate as a substrate to generate an assortment of cyclic products. In the current study we present a detailed analysis of the multiple gas-phase reaction pathways in the synthesis of bornyl cation from geranyl diphosphate. Additionally, the fate of the proposed bornyl cation intermediate in the bornyl diphosphate synthase reaction is investigated by molecular dynamics simulations. We employ accurate density functional theory (DFT) methods after careful validation against high-level ab initio data for a set of model carbocations. The gas-phase results for the monoterpene reactions indicate a diverging reaction mechanism with multiple products in the absence of enzymatic control. This complex potential energy surface includes several possible bifurcation points due to the presence of secondary cations. Additionally, the suggested bornyl cation intermediate in the bornyl diphosphate synthase reaction is studied by molecular dynamics simulations employing a hybrid quantum mechanics (DFT)-molecular mechanics potential energy function. The simulations suggest that the bornyl cation is a transient species as in the gas phase and that electrostatic steering directs the formation of the final product, bornyl diphosphate.
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Affiliation(s)
- Michal Weitman
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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Li S, Zhang X, Wang W. Cluster formation of anchored proteins induced by membrane-mediated interaction. Biophys J 2010; 98:2554-63. [PMID: 20513399 PMCID: PMC2877327 DOI: 10.1016/j.bpj.2010.02.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Revised: 01/16/2010] [Accepted: 02/17/2010] [Indexed: 11/16/2022] Open
Abstract
Computer simulations were used to study the cluster formation of anchored proteins in a membrane. The rate and extent of clustering was found to be dependent upon the hydrophobic length of the anchored proteins embedded in the membrane. The cluster formation mechanism of anchored proteins in our work was ascribed to the different local perturbations on the upper and lower monolayers of the membrane and the intermonolayer coupling. Simulation results demonstrated that only when the penetration depth of anchored proteins was larger than half the membrane thickness, could the structure of the lower monolayer be significantly deformed. Additionally, studies on the local structures of membranes indicated weak perturbation of bilayer thickness for a shallowly inserted protein, while there was significant perturbation for a more deeply inserted protein. The origin of membrane-mediated protein-protein interaction is therefore due to the local perturbation of the membrane thickness, and the entropy loss-both of which are caused by the conformation restriction on the lipid chains and the enhanced intermonolayer coupling for a deeply inserted protein. Finally, in this study we addressed the difference of cluster formation mechanisms between anchored proteins and transmembrane proteins.
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Affiliation(s)
| | - Xianren Zhang
- Division of Molecular and Materials Simulation, Key Laboratory for Nanomaterials, Ministry of Education, Beijing University of Chemical Technology, Beijing, China
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Hong YJ, Tantillo DJ. Formation of Beyerene, Kaurene, Trachylobane, and Atiserene Diterpenes by Rearrangements That Avoid Secondary Carbocations. J Am Chem Soc 2010; 132:5375-86. [DOI: 10.1021/ja9084786] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Young J. Hong
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616
| | - Dean J. Tantillo
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616
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Tantillo DJ. The carbocation continuum in terpene biosynthesis—where are the secondary cations? Chem Soc Rev 2010; 39:2847-54. [DOI: 10.1039/b917107j] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Raptis C, Lykakis I, Tsangarakis C, Stratakis M. Acid-Catalyzed Cyclization of Terpenes Under Homogeneous and Heterogeneous Conditions as Probed Through Stereoisotopic Studies: A Concerted Process with Competing Preorganized Chair and Boat Transition States. Chemistry 2009; 15:11918-27. [DOI: 10.1002/chem.200901563] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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