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For: Raz K, Driller R, Dimos N, Ringel M, Brück T, Loll B, Major DT. The Impression of a Nonexisting Catalytic Effect: The Role of CotB2 in Guiding the Complex Biosynthesis of Cyclooctat-9-en-7-ol. J Am Chem Soc 2020;142:21562-21574. [PMID: 33289561 DOI: 10.1021/jacs.0c11348] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Number Cited by Other Article(s)
1
Schwartz R, Hadar-Volk A, Nam K, Major DT. Template-Based Docking Using Automated Maximum Common Substructure Identification with EnzyDock: Mechanistic and Inhibitor Docking. J Chem Inf Model 2025. [PMID: 40388499 DOI: 10.1021/acs.jcim.5c00201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2025]
2
Wei X, DeSnoo W, Li Z, Ning W, Kong WY, Nafie J, Tantillo DJ, Rudolf JD. Avoidance of Secondary Carbocations, Unusual Deprotonation, and Nonstatistical Dynamic Effects in the Cyclization Mechanism of Tetraisoquinane. J Am Chem Soc 2025;147:16293-16300. [PMID: 40299714 PMCID: PMC12105118 DOI: 10.1021/jacs.5c01828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2025]
3
Nakano M, Hiasa K, Sato-Shimizu S, Sato H. Seven-Membered Ring Formation in Triterpene Biosynthesis: A Key Cyclopropane Rearrangement in Ilelic Acid Biosynthesis. J Org Chem 2025;90:2907-2914. [PMID: 39960431 DOI: 10.1021/acs.joc.4c02541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2025]
4
Suh D, Schwartz R, Gupta PK, Zev S, Major DT, Im W. CHARMM-GUI EnzyDocker for Protein-Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes. J Chem Theory Comput 2025;21:2118-2128. [PMID: 39950957 PMCID: PMC11866752 DOI: 10.1021/acs.jctc.4c01691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Revised: 01/23/2025] [Accepted: 01/28/2025] [Indexed: 02/26/2025]
5
Li T, Shu D, Lei L, Li Z, Luo D, Yang J, Wang Y, Hou X, Wang H, Tan H. Molecular Insight into the Catalytic Mechanism of the Sesquiterpene Cyclase BcABA3. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025;73:835-846. [PMID: 39689351 DOI: 10.1021/acs.jafc.4c07116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2024]
6
Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, Deng Y, Devereux M, Ding X, Feig MF, Gao J, Glowacki DR, Gonzales JE, Hamaneh MB, Harder ED, Hayes RL, Huang J, Huang Y, Hudson PS, Im W, Islam SM, Jiang W, Jones MR, Käser S, Kearns FL, Kern NR, Klauda JB, Lazaridis T, Lee J, Lemkul JA, Liu X, Luo Y, MacKerell AD, Major DT, Meuwly M, Nam K, Nilsson L, Ovchinnikov V, Paci E, Park S, Pastor RW, Pittman AR, Post CB, Prasad S, Pu J, Qi Y, Rathinavelan T, Roe DR, Roux B, Rowley CN, Shen J, Simmonett AC, Sodt AJ, Töpfer K, Upadhyay M, van der Vaart A, Vazquez-Salazar LI, Venable RM, Warrensford LC, Woodcock HL, Wu Y, Brooks CL, Brooks BR, Karplus M. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. J Phys Chem B 2024;128:9976-10042. [PMID: 39303207 PMCID: PMC11492285 DOI: 10.1021/acs.jpcb.4c04100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/15/2024] [Accepted: 08/22/2024] [Indexed: 09/22/2024]
7
Zhang W, Wang X, Zhu G, Zhu B, Peng K, Hsiang T, Zhang L, Liu X. Function Switch of a Fungal Sesterterpene Synthase through Molecular Dynamics Simulation Assisted Alteration of an Aromatic Residue Cluster in the Active Pocket of PfNS. Angew Chem Int Ed Engl 2024;63:e202406246. [PMID: 38934471 DOI: 10.1002/anie.202406246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024]
8
Schwartz R, Zev S, Major DT. Differential Substrate Sensing in Terpene Synthases from Plants and Microorganisms: Insight from Structural, Bioinformatic, and EnzyDock Analyses. Angew Chem Int Ed Engl 2024;63:e202400743. [PMID: 38556463 DOI: 10.1002/anie.202400743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
9
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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
10
Nam K, Shao Y, Major DT, Wolf-Watz M. Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS OMEGA 2024;9:7393-7412. [PMID: 38405524 PMCID: PMC10883025 DOI: 10.1021/acsomega.3c09084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
11
Xu H, Köllner TG, Chen F, Dickschat JS. Mechanistic characterisation of a sesquiterpene synthase for asterisca-1,6-diene from the liverwort Radula lindenbergiana and implications for pentalenene biosynthesis. Org Biomol Chem 2024;22:1360-1364. [PMID: 38240688 DOI: 10.1039/d3ob02088f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
12
Whitehead J, Leferink NGH, Johannissen LO, Hay S, Scrutton NS. Decoding Catalysis by Terpene Synthases. ACS Catal 2023;13:12774-12802. [PMID: 37822860 PMCID: PMC10563020 DOI: 10.1021/acscatal.3c03047] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/31/2023] [Indexed: 10/13/2023]
13
Zhang F, Zeng T, Wu R. QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis. J Chem Inf Model 2023;63:5018-5034. [PMID: 37556841 DOI: 10.1021/acs.jcim.3c00779] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
14
Spencer TA, Ditchfield R. Tryptophan Stabilization of a Biochemical Carbocation Evaluated by Analysis of π Complexes of 3-Ethylindole with the t-Butyl Cation. ACS OMEGA 2023;8:26497-26507. [PMID: 37521644 PMCID: PMC10373456 DOI: 10.1021/acsomega.3c03259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023]
15
Major DT, Gupta PK, Gao J. Origin of Catalysis by Nitroalkane Oxidase. J Phys Chem B 2023;127:151-162. [PMID: 36580021 DOI: 10.1021/acs.jpcb.2c07357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
16
Biosynthesis of fusicoccane-type diterpenoids featuring a 5–8–5 tricyclic carbon skeleton. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.154224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
17
Whitehead JN, Leferink NGH, Komati Reddy G, Levy CW, Hay S, Takano E, Scrutton NS. How a 10-epi-Cubebol Synthase Avoids Premature Reaction Quenching to Form a Tricyclic Product at High Purity. ACS Catal 2022;12:12123-12131. [PMID: 36249875 PMCID: PMC9552170 DOI: 10.1021/acscatal.2c03155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/02/2022] [Indexed: 11/29/2022]
18
Xing B, Xu H, Li A, Lou T, Xu M, Wang K, Xu Z, Dickschat JS, Yang D, Ma M. Crystal Structure Based Mutagenesis of Cattleyene Synthase Leads to the Generation of Rearranged Polycyclic Diterpenes. Angew Chem Int Ed Engl 2022;61:e202209785. [PMID: 35819825 PMCID: PMC9543850 DOI: 10.1002/anie.202209785] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Indexed: 11/08/2022]
19
Zev S, Ringel M, Driller R, Loll B, Brück T, Major DT. Understanding the competing pathways leading to hydropyrene and isoelisabethatriene. Beilstein J Org Chem 2022;18:972-978. [PMID: 35965858 PMCID: PMC9359192 DOI: 10.3762/bjoc.18.97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022]  Open
20
Xing B, Xu H, Li A, Lou T, Xu M, Wang K, Xu Z, Dickschat JS, Yang D, Ma M. Crystal Structure Based Mutagenesis of Cattleyene Synthase Leads to the Generation of Rearranged Polycyclic Diterpenes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
21
Fordjour E, Mensah EO, Hao Y, Yang Y, Liu X, Li Y, Liu CL, Bai Z. Toward improved terpenoids biosynthesis: strategies to enhance the capabilities of cell factories. BIORESOUR BIOPROCESS 2022;9:6. [PMID: 38647812 PMCID: PMC10992668 DOI: 10.1186/s40643-022-00493-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 02/22/2023]  Open
22
Schafer JW, Chen X, Schwartz SD. Engineered Tryptophan Synthase Balances Equilibrium Effects and Fast Dynamic Effects. ACS Catal 2022;12:913-922. [PMID: 35719741 PMCID: PMC9202816 DOI: 10.1021/acscatal.1c03913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
23
Tsutsumi H, Moriwaki Y, Terada T, Shimizu K, Shin‐ya K, Katsuyama Y, Ohnishi Y. Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6‐Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6‐Methyltransferase. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
24
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: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
25
Tsutsumi H, Moriwaki Y, Terada T, Shimizu K, Shin-Ya K, Katsuyama Y, Ohnishi Y. Structural and Molecular Basis of the Catalytic Mechanism of Geranyl Pyrophosphate C6-Methyltransferase: Creation of an Unprecedented Farnesyl Pyrophosphate C6-Methyltransferase. Angew Chem Int Ed Engl 2021;61:e202111217. [PMID: 34626048 DOI: 10.1002/anie.202111217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Indexed: 11/11/2022]
26
Huang ZY, Ye RY, Yu HL, Li AT, Xu JH. Mining methods and typical structural mechanisms of terpene cyclases. BIORESOUR BIOPROCESS 2021;8:66. [PMID: 38650244 PMCID: PMC10992375 DOI: 10.1186/s40643-021-00421-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/24/2021] [Indexed: 12/13/2022]  Open
27
Xu H, Goldfuss B, Dickschat JS. 1,2- or 1,3-Hydride Shifts: What Controls Guaiane Biosynthesis? Chemistry 2021;27:9758-9762. [PMID: 33929065 PMCID: PMC8362104 DOI: 10.1002/chem.202101371] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Indexed: 12/19/2022]
28
Srivastava PL, Escorcia AM, Huynh F, Miller DJ, Allemann RK, van der Kamp MW. Redesigning the Molecular Choreography to Prevent Hydroxylation in Germacradien-11-ol Synthase Catalysis. ACS Catal 2021;11:1033-1041. [PMID: 33614194 PMCID: PMC7886051 DOI: 10.1021/acscatal.0c04647] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/26/2020] [Indexed: 12/04/2022]
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