1
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Ray D, Das S, Raucci U. Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations. J Chem Inf Model 2024; 64:3953-3958. [PMID: 38607669 DOI: 10.1021/acs.jcim.4c00475] [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: 04/13/2024]
Abstract
The rate constants of enzyme-catalyzed reactions (kcat) are often approximated from the barrier height of the reactive step. We introduce an enhanced sampling QM/MM approach that directly calculates the kinetics of enzymatic reactions, without introducing the transition-state theory assumptions, and takes into account the dynamical equilibrium between the reactive and non-reactive conformations of the enzyme/substrate complex. Our computed kcat values are in order-of-magnitude agreement with the experimental data for two representative enzymatic reactions.
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Affiliation(s)
- Dhiman Ray
- Atomistic Simulations, Italian Institute of Technology, Via Enrico Melen 83, Genova GE 16152, Italy
| | - Sudip Das
- Atomistic Simulations, Italian Institute of Technology, Via Enrico Melen 83, Genova GE 16152, Italy
| | - Umberto Raucci
- Atomistic Simulations, Italian Institute of Technology, Via Enrico Melen 83, Genova GE 16152, Italy
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2
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Agbaglo DA, Summers TJ, Cheng Q, DeYonker NJ. The influence of model building schemes and molecular dynamics sampling on QM-cluster models: the chorismate mutase case study. Phys Chem Chem Phys 2024; 26:12467-12482. [PMID: 38618904 PMCID: PMC11090134 DOI: 10.1039/d3cp06100k] [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] [Indexed: 04/16/2024]
Abstract
Most QM-cluster models of enzymes are constructed based on X-ray crystal structures, which limits comparison to in vivo structure and mechanism. The active site of chorismate mutase from Bacillus subtilis and the enzymatic transformation of chorismate to prephenate is used as a case study to guide construction of QM-cluster models built first from the X-ray crystal structure, then from molecular dynamics (MD) simulation snapshots. The Residue Interaction Network ResidUe Selector (RINRUS) software toolkit, developed by our group to simplify and automate the construction of QM-cluster models, is expanded to handle MD to QM-cluster model workflows. Several options, some employing novel topological clustering from residue interaction network (RIN) information, are evaluated for generating conformational clustering from MD simulation. RINRUS then generates a statistical thermodynamic framework for QM-cluster modeling of the chorismate mutase mechanism via refining 250 MD frames with density functional theory (DFT). The 250 QM-cluster models sampled provide a mean ΔG‡ of 10.3 ± 2.6 kcal mol-1 compared to the experimental value of 15.4 kcal mol-1 at 25 °C. While the difference between theory and experiment is consequential, the level of theory used is modest and therefore "chemical" accuracy is unexpected. More important are the comparisons made between QM-cluster models designed from the X-ray crystal structure versus those from MD frames. The large variations in kinetic and thermodynamic properties arise from geometric changes in the ensemble of QM-cluster models, rather from the composition of the QM-cluster models or from the active site-solvent interface. The findings open the way for further quantitative and reproducible calibration in the field of computational enzymology using the model construction framework afforded with the RINRUS software toolkit.
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Affiliation(s)
- Donatus A Agbaglo
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
| | - Thomas J Summers
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
| | - Qianyi Cheng
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
| | - Nathan J DeYonker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA.
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3
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Choi S, Liu C, Seo DH, Im SW, Kim RM, Jo J, Kim JW, Park GS, Kim M, Brinck T, Nam KT. Kink-Controlled Gold Nanoparticles for Electrochemical Glucose Oxidation. NANO LETTERS 2024; 24:4528-4536. [PMID: 38573311 DOI: 10.1021/acs.nanolett.4c00413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Enzymes in nature efficiently catalyze chiral organic molecules by elaborately tuning the geometrical arrangement of atoms in the active site. However, enantioselective oxidation of organic molecules by heterogeneous electrocatalysts is challenging because of the difficulty in controlling the asymmetric structures of the active sites on the electrodes. Here, we show that the distribution of chiral kink atoms on high-index facets can be precisely manipulated even on single gold nanoparticles; and this enabled stereoselective oxidation of hydroxyl groups on various sugar molecules. We characterized the crystallographic orientation and the density of kink atoms and investigated their specific interactions with the glucose molecule due to the geometrical structure and surface electrostatic potential.
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Affiliation(s)
- Seungwoo Choi
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
- Soft Foundry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chang Liu
- Department of Chemistry, CBH, KTH Royal Institute of Technology; Stockholm SE-10044, Sweden
- Stockholm University, Chemical Physics, Albanova University Center, Stockholm SE-10690, Sweden
| | - Da Hye Seo
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Won Im
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
- Soft Foundry, Seoul National University, Seoul 08826, Republic of Korea
| | - Ryeong Myeong Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaeyeon Jo
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeong Won Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Gyeong-Su Park
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
- Soft Foundry, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Next-Generation Semiconductor Convergence Technology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Miyoung Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Tore Brinck
- Department of Chemistry, CBH, KTH Royal Institute of Technology; Stockholm SE-10044, Sweden
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
- Soft Foundry, Seoul National University, Seoul 08826, Republic of Korea
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4
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Wilkins RS, Lund BA, Isaksen GV, Åqvist J, Brandsdal BO. Accurate Computation of Thermodynamic Activation Parameters in the Chorismate Mutase Reaction from Empirical Valence Bond Simulations. J Chem Theory Comput 2024; 20:451-458. [PMID: 38112329 PMCID: PMC10782440 DOI: 10.1021/acs.jctc.3c01105] [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: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
Chorismate mutase (CM) enzymes have long served as model systems for benchmarking new methods and tools in computational chemistry. Despite the enzymes' prominence in the literature, the extent of the roles that activation enthalpy and entropy play in catalyzing the conversion of chorismate to prephenate is still subject to debate. Knowledge of these parameters is a key piece in fully understanding the mechanism of chorismate mutases. Within this study, we utilize EVB/MD free energy perturbation calculations at a range of temperatures, allowing us to extract activation enthalpies and entropies from an Arrhenius plot of activation free energies of the reaction catalyzed by a monofunctional Bacillus subtilis CM and the promiscuous enzyme isochorismate pyruvate lyase of Pseudomonas aeruginosa. In comparison to the uncatalyzed reaction, our results show that both enzyme-catalyzed reactions exhibit a substantial reduction in activation enthalpy, while the effect on activation entropy is relatively minor, demonstrating that enzyme-catalyzed CM reactions are enthalpically driven. Furthermore, we observe that the monofunctional CM from B. subtilis more efficiently catalyzes this reaction than its promiscuous counterpart. This is supported by a structural analysis of the reaction pathway at the transition state, from which we identified key residues explaining the enthalpically driven nature of the reactions and also the difference in efficiencies between the two enzymes.
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Affiliation(s)
- Ryan Scott Wilkins
- Hylleraas Centre for Quantum Molecular
Sciences, Department of Chemistry, University
of Tromsø, N9037 Tromsø, Norway
| | - Bjarte Aarmo Lund
- Hylleraas Centre for Quantum Molecular
Sciences, Department of Chemistry, University
of Tromsø, N9037 Tromsø, Norway
| | - Geir Villy Isaksen
- Hylleraas Centre for Quantum Molecular
Sciences, Department of Chemistry, University
of Tromsø, N9037 Tromsø, Norway
| | | | - Bjørn Olav Brandsdal
- Hylleraas Centre for Quantum Molecular
Sciences, Department of Chemistry, University
of Tromsø, N9037 Tromsø, Norway
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5
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Jiang Y, Ding N, Shao Q, Stull SL, Cheng Z, Yang ZJ. Substrate Positioning Dynamics Involves a Non-Electrostatic Component to Mediate Catalysis. J Phys Chem Lett 2023; 14:11480-11489. [PMID: 38085952 PMCID: PMC11211065 DOI: 10.1021/acs.jpclett.3c02444] [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: 12/22/2023]
Abstract
Substrate positioning dynamics (SPD) orients the substrate in the active site, thereby influencing catalytic efficiency. However, it remains unknown whether SPD effects originate primarily from electrostatic perturbation inside the enzyme or can independently mediate catalysis with a significant non-electrostatic component. In this work, we investigated how the non-electrostatic component of SPD affects transition state (TS) stabilization. Using high-throughput enzyme modeling, we selected Kemp eliminase variants with similar electrostatics inside the enzyme but significantly different SPD. The kinetic parameters of these mutants were experimentally characterized. We observed a valley-shaped, two-segment linear correlation between the TS stabilization free energy (converted from kinetic parameters) and substrate positioning index (a metric to quantify SPD). The energy varies by approximately 2 kcal/mol. Favorable SPD was observed for the distal mutant R154W, increasing the proportion of reactive conformations and leading to the lowest activation free energy. These results indicate the substantial contribution of the non-electrostatic component of SPD to enzyme catalytic efficiency.
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Affiliation(s)
- Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ning Ding
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Sebastian L. Stull
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zihao Cheng
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zhongyue J. Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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6
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Thorbjørnsrud H, Bressan L, Khatanbaatar T, Carrer M, Würth-Roderer K, Cordara G, Kast P, Cascella M, Krengel U. What Drives Chorismate Mutase to Top Performance? Insights from a Combined In Silico and In Vitro Study. Biochemistry 2023; 62:782-796. [PMID: 36705397 PMCID: PMC9910054 DOI: 10.1021/acs.biochem.2c00635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Unlike typical chorismate mutases, the enzyme from Mycobacterium tuberculosis (MtCM) has only low activity on its own. Remarkably, its catalytic efficiency kcat/Km can be boosted more than 100-fold by complex formation with a partner enzyme. Recently, an autonomously fully active MtCM variant was generated using directed evolution, and its structure was solved by X-ray crystallography. However, key residues were involved in crystal contacts, challenging the functional interpretation of the structural changes. Here, we address these challenges by microsecond molecular dynamics simulations, followed up by additional kinetic and structural analyses of selected sets of specifically engineered enzyme variants. A comparison of wild-type MtCM with naturally and artificially activated MtCMs revealed the overall dynamic profiles of these enzymes as well as key interactions between the C-terminus and the active site loop. In the artificially evolved variant of this model enzyme, this loop is preorganized and stabilized by Pro52 and Asp55, two highly conserved residues in typical, highly active chorismate mutases. Asp55 stretches across the active site and helps to appropriately position active site residues Arg18 and Arg46 for catalysis. The role of Asp55 can be taken over by another acidic residue, if introduced at position 88 close to the C-terminus of MtCM, as suggested by molecular dynamics simulations and confirmed by kinetic investigations of engineered variants.
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Affiliation(s)
- Helen
V. Thorbjørnsrud
- Department
of Chemistry, University of Oslo, Oslo 0315, NO, Norway,Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, NO, Norway
| | - Luca Bressan
- Laboratory
of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Tamjidmaa Khatanbaatar
- Department
of Chemistry, University of Oslo, Oslo 0315, NO, Norway,Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, NO, Norway
| | - Manuel Carrer
- Department
of Chemistry, University of Oslo, Oslo 0315, NO, Norway,Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, NO, Norway
| | | | - Gabriele Cordara
- Department
of Chemistry, University of Oslo, Oslo 0315, NO, Norway,Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, NO, Norway
| | - Peter Kast
- Laboratory
of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland,
| | - Michele Cascella
- Department
of Chemistry, University of Oslo, Oslo 0315, NO, Norway,Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, NO, Norway,
| | - Ute Krengel
- Department
of Chemistry, University of Oslo, Oslo 0315, NO, Norway,Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, NO, Norway,
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7
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Pan X, Van R, Epifanovsky E, Liu J, Pu J, Nam K, Shao Y. Accelerating Ab Initio Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian. J Phys Chem B 2022; 126:10.1021/acs.jpcb.2c02262. [PMID: 35653199 PMCID: PMC9715852 DOI: 10.1021/acs.jpcb.2c02262] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics (MD) simulations employing ab initio quantum mechanical and molecular mechanical (ai-QM/MM) potentials are considered to be the state of the art, but the high computational cost associated with the ai-QM calculations remains a theoretical challenge for their routine application. Here, we present a modified protocol of the multiple time step (MTS) method for accelerating ai-QM/MM MD simulations of condensed-phase reactions. Within a previous MTS protocol [Nam J. Chem. Theory Comput. 2014, 10, 4175], reference forces are evaluated using a low-level (semiempirical QM/MM) Hamiltonian and employed at inner time steps to propagate the nuclear motions. Correction forces, which arise from the force differences between high-level (ai-QM/MM) and low-level Hamiltonians, are applied at outer time steps, where the MTS algorithm allows the time-reversible integration of the correction forces. To increase the outer step size, which is bound by the highest-frequency component in the correction forces, the semiempirical QM Hamiltonian is recalibrated in this work to minimize the magnitude of the correction forces. The remaining high-frequency modes, which are mainly bond stretches involving hydrogen atoms, are then removed from the correction forces. When combined with a Langevin or SIN(R) thermostat, the modified MTS-QM/MM scheme remains robust with an up to 8 (with Langevin) or 10 fs (with SIN(R)) outer time step (with 1 fs inner time steps) for the chorismate mutase system. This leads to an over 5-fold speedup over standard ai-QM/MM simulations, without sacrificing the accuracy in the predicted free energy profile of the reaction.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5251, United States
| | - Richard Van
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5251, United States
| | - Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States
| | - Jian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St., LD326, Indianapolis, Indiana 46202, United States
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5251, United States
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8
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Lawal MM, Vaissier Welborn V. Structural dynamics support electrostatic interactions in the active site of Adenylate Kinase. Chembiochem 2022; 23:e202200097. [PMID: 35303385 DOI: 10.1002/cbic.202200097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Indexed: 11/12/2022]
Abstract
Electrostatic preorganization as well as structural and dynamic heterogeneity are often used to rationalize the remarkable catalytic efficiency of enzymes. However, they are often presented as incompatible because the generation of permanent electrostatic effects implies that the protein structure remains rigid. Here, we use a metric, electric fields, that can treat electrostatic contributions and dynamics effects on equal footing, for a unique perspective on enzymatic catalysis. We find that the residues that contribute the most to electrostatic interactions with the substrate in the active site of Adenylate Kinase (our working example) are also the most flexible residues. Further, entropy-tuning mutations raise flexibility at the picosecond timescale where more conformations can be visited on short time periods, thereby softening the sharp heterogeneity normally visible at the microsecond timescale.
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Affiliation(s)
| | - Valerie Vaissier Welborn
- Virginia Polytechnic Institute and State University, Chemistry, Davidson 421A, 1040 Drillfield Drive, 24073, Blacksburg, UNITED STATES
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9
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Chen D, Li Y, Li X, Hong X, Fan X, Savidge T. Key difference between transition state stabilization and ground state destabilization: increasing atomic charge densities before or during enzyme–substrate binding. Chem Sci 2022; 13:8193-8202. [PMID: 35919436 PMCID: PMC9278421 DOI: 10.1039/d2sc01994a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/20/2022] [Indexed: 11/21/2022] Open
Abstract
The origin of the enormous catalytic power of enzymes has been extensively studied through experimental and computational approaches. Although precise mechanisms are still subject to much debate, enzymes are thought to catalyze reactions by stabilizing transition states (TSs) or destabilizing ground states (GSs). By exploring the catalysis of various types of enzyme–substrate noncovalent interactions, we found that catalysis by TS stabilization and the catalysis by GS destabilization share common features by reducing the free energy barriers (ΔG‡s) of reactions, but are different in attaining the requirement for ΔG‡ reduction. Irrespective of whether enzymes catalyze reactions by TS stabilization or GS destabilization, they reduce ΔG‡s by enhancing the charge densities of catalytic atoms that experience a reduction in charge density between GSs and TSs. Notably, in TS stabilization, the charge density of catalytic atoms is enhanced prior to enzyme–substrate binding; whereas in GS destabilization, the charge density of catalytic atoms is enhanced during the enzyme–substrate binding. Results show that TS stabilization and GS destabilization are not contradictory to each other and are consistent in reducing the ΔG‡s of reactions. The full mechanism of enzyme catalysis includes the mechanism of reducing ΔG‡ and the mechanism of enhancing atomic charge densities. Our findings may help resolve the debate between TS stabilization and GS destabilization and assist our understanding of catalysis and the design of artificial enzymes. Transition state stabilization and ground state destabilization utilize the same molecular mechanism when lowering the free energy barriers (ΔG‡s) of reactions, but differ in achieving the requirement for ΔG‡ reduction.![]()
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Affiliation(s)
- Deliang Chen
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Yibao Li
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Xun Li
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Xuechuan Hong
- State Key Laboratory of Virology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery and Hubei Province, Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Xiaolin Fan
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Tor Savidge
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Microbiome Center, Texas Childrens Hospital, Houston, TX 77030, USA
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10
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Hubrich F, Müller M, Andexer JN. Chorismate- and isochorismate converting enzymes: versatile catalysts acting on an important metabolic node. Chem Commun (Camb) 2021; 57:2441-2463. [PMID: 33605953 DOI: 10.1039/d0cc08078k] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chorismate and isochorismate represent an important branching point connecting primary and secondary metabolism in bacteria, fungi, archaea and plants. Chorismate- and isochorismate-converting enzymes are potential targets for new bioactive compounds, as well as valuable biocatalysts for the in vivo and in vitro synthesis of fine chemicals. The diversity of the products of chorismate- and isochorismate-converting enzymes is reflected in the enzymatic three-dimensional structures and molecular mechanisms. Due to the high reactivity of chorismate and its derivatives, these enzymes have evolved to be accurately tailored to their respective reaction; at the same time, many of them exhibit a fascinating flexibility regarding side reactions and acceptance of alternative substrates. Here, we give an overview of the different (sub)families of chorismate- and isochorismate-converting enzymes, their molecular mechanisms, and three-dimensional structures. In addition, we highlight important results of mutagenetic approaches that generate a broader understanding of the influence of distinct active site residues for product formation and the conversion of one subfamily into another. Based on this, we discuss to what extent the recent advances in the field might influence the general mechanistic understanding of chorismate- and isochorismate-converting enzymes. Recent discoveries of new chorismate-derived products and pathways, as well as biocatalytic conversions of non-physiological substrates, highlight how this vast field is expected to continue developing in the future.
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Affiliation(s)
- Florian Hubrich
- ETH Zurich, Institute of Microbiology, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
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11
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Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review. Catalysts 2020. [DOI: 10.3390/catal10060691] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts.
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12
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Structural basis for stereoselective dehydration and hydrogen-bonding catalysis by the SAM-dependent pericyclase LepI. Nat Chem 2019; 11:812-820. [PMID: 31332284 PMCID: PMC6708486 DOI: 10.1038/s41557-019-0294-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/14/2019] [Indexed: 12/04/2022]
Abstract
LepI is an S-adenosylmethionine (SAM)-dependent pericyclase that catalyzes the formation of 2-pyridone natural product leporin C. Biochemical characterization showed LepI can catalyze the stereoselective dehydration to yield a reactive (E)-quinone methide that can undergo bifurcating intramolecular Diels-Alder (IMDA) and hetero-Diels-Alder (HDA) cyclizations from an ambimodal transition state, as well as a [3,3]-retro-Claisen rearrangement to recycle the IMDA product into leporin C. Here we solved the X-ray crystal structures of SAM-bound LepI and in complex with a substrate analog, the product leporin C, and a retro-Claisen reaction transition-state analog to understand the structural basis for the multitude of reactions. Structural and mutational analysis revealed how Nature evolves a classic methyltransferase active site into one that can serve as a dehydratase and a multifunctional pericyclase. Catalysis of both sets of reactions employs H133 and R295, two active site residues that are not found in canonical methyltransferases. An alternative role of SAM, which is not found to be in direct contact with the substrate, is also proposed.
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13
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Ranaghan KE, Shchepanovska D, Bennie SJ, Lawan N, Macrae SJ, Zurek J, Manby FR, Mulholland AJ. Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution. J Chem Inf Model 2019; 59:2063-2078. [PMID: 30794388 DOI: 10.1021/acs.jcim.8b00940] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly widely utilized in studies of reactions in enzymes and other large systems. Here, we apply a range of QM/MM methods to investigate the Claisen rearrangement of chorismate to prephenate, in solution, and in the enzyme chorismate mutase. Using projector-based embedding in a QM/MM framework, we apply treatments up to the CCSD(T) level. We test a range of density functional QM/MM methods and QM region sizes. The results show that the calculated reaction energetics are significantly more sensitive to the choice of density functional than they are to the size of the QM region in these systems. Projector-based embedding of a wave function method in DFT reduced the 13 kcal/mol spread in barrier heights calculated at the DFT/MM level to a spread of just 0.3 kcal/mol, essentially eliminating dependence on the functional. Projector-based embedding of correlated ab initio methods provides a practical method for achieving high accuracy for energy profiles derived from DFT and DFT/MM calculations for reactions in condensed phases.
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Affiliation(s)
- Kara E Ranaghan
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Darya Shchepanovska
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Simon J Bennie
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Narin Lawan
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Stephen J Macrae
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Jolanta Zurek
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol , U.K. BS8 1TS
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14
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Xie L, Yang M, Chen ZN. Understanding the entropic effect in chorismate mutase reaction catalyzed by isochorismate-pyruvate lyase fromPseudomonas aeruginosa(PchB). Catal Sci Technol 2019. [DOI: 10.1039/c8cy02123f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The substrate preorganization process in the entropically driven PchB-catalyzed chorismate mutase reaction leads to a remarkable apparent entropic effect.
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Affiliation(s)
- Liangxu Xie
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences
- Fuzhou 350002
- China
- Department of Chemistry
| | - Mingjun Yang
- XtalPi Inc. (Shenzhen Jingtai Technology Co., Ltd.)
- Times Science & Tech Mansion E. 20F
- Shenzhen
- China
| | - Zhe-Ning Chen
- State Key Laboratory of Structural Chemistry
- Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences
- Fuzhou 350002
- China
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15
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Hong CM, Bergman RG, Raymond KN, Toste FD. Self-Assembled Tetrahedral Hosts as Supramolecular Catalysts. Acc Chem Res 2018; 51:2447-2455. [PMID: 30272943 DOI: 10.1021/acs.accounts.8b00328] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The field of supramolecular chemistry has its foundation in molecular recognition and selective binding of guest molecules, often with remarkably strong binding affinities. The field evolved to leverage these favorable interactions between the host and its guest to catalyze simple, often biomimetic transformations. Drawing inspiration from these early studies, self-assembled supramolecular hosts continue to capture a significant amount of interest toward their development as catalysts for increasingly complex transformations. Nature often relies on microenvironments, derived from complex tertiary structures and a well-defined active site, to promote reactions with remarkable rate acceleration, substrate specificity, and product selectivity. Similarly, supramolecular chemists have become increasingly intrigued by the prospect that self-assembly of molecular components might generate defined and spatially segregated microenvironments that can catalyze complex transformations. Among the growing palette of supramolecular catalysts, an anionic, water-soluble, tetrahedral metal-ligand coordination host has found a range of applications in catalysis and beyond. Early work focused on characterizing and understanding this host and its various host-guest phenomena, which paved the path for exploiting these features to selectively promote desirable chemistries, including cyclizations, rearrangements, and bimolecular reactions. Although this early work matured into achievements of catalysis with dramatic rate accelerations as well as enantioenrichment, the afforded products were typically identical to those produced by background reactions that occurred outside of the host microenvironment. This Account describes our recent developments in the application of these anionic tetrahedral hosts as catalysts for organic and organometallic transformation. Inspiration from natural systems and unmet synthetic challenges led to supramolecular catalysis displaying unique divergences in reactivity to give products that are inaccessible from bulk solution. Additionally, these tetrahedral assemblies have been shown to catalyze a diverse range of transformations with notable rate acceleration over the uncatalyzed background reaction. The pursuit of complexity beyond supramolecular catalysis has since led to the integration of these tetrahedral catalysts in tandem with natural enzymes, as well as their application to dual catalysis to realize challenging synthetic reactions. Variation in the structure, including size and charge, of these tetrahedral catalysts has enabled recent studies that provide insights into connections between specific structural features of these hosts and their reactivities. These mechanistic studies reveal that the solvent exclusion properties, hydrophobic effects, confinement effects and electrostatic effects play important roles in the observed catalysis. Moreover, these features may be leveraged for the design of supramolecular catalysis beyond those described in this Account. Finally, the supramolecular chemistry detailed in this Account has presented the opportunity to emulate some of the mechanisms nature engages to achieve catalysis; however, this relationship need not be entirely unidirectional, as the examples describe herein can stand as simplified model systems for unravelling more complex biological processes.
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Affiliation(s)
- Cynthia M. Hong
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Robert G. Bergman
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Kenneth N. Raymond
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - F. Dean Toste
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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16
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Freindorf M, Tao Y, Sethio D, Cremer D, Kraka E. New mechanistic insights into the Claisen rearrangement of chorismate – a Unified Reaction Valley Approach study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1530464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Daniel Sethio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
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17
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Grayson KJ, Anderson JR. The ascent of man(made oxidoreductases). Curr Opin Struct Biol 2018; 51:149-155. [PMID: 29754103 PMCID: PMC6227378 DOI: 10.1016/j.sbi.2018.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/24/2018] [Indexed: 11/09/2022]
Abstract
Though established 40 years ago, the field of de novo protein design has recently come of age, with new designs exhibiting an unprecedented level of sophistication in structure and function. With respect to catalysis, de novo enzymes promise to revolutionise the industrial production of useful chemicals and materials, while providing new biomolecules as plug-and-play components in the metabolic pathways of living cells. To this end, there are now de novo metalloenzymes that are assembled in vivo, including the recently reported C45 maquette, which can catalyse a variety of substrate oxidations with efficiencies rivalling those of closely related natural enzymes. Here we explore the successful design of this de novo enzyme, which was designed to minimise the undesirable complexity of natural proteins using a minimalistic bottom-up approach.
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Affiliation(s)
- Katie J Grayson
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD, UK
| | - Jl Ross Anderson
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD, UK; BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, UK.
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18
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Maurer D, Enugala TR, Hamnevik E, Bauer P, Lüking M, Petrović D, Hillier H, Kamerlin SCL, Dobritzsch D, Widersten M. Stereo- and Regioselectivity in Catalyzed Transformation of a 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone by Wild Type and Laboratory Evolved Alcohol Dehydrogenases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01762] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Dirk Maurer
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Thilak Reddy Enugala
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Emil Hamnevik
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Paul Bauer
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
- Biophysics, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
| | - Malin Lüking
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Dušan Petrović
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Heidi Hillier
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Mikael Widersten
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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19
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Infield DT, Lee EEL, Galpin JD, Galles GD, Bezanilla F, Ahern CA. Replacing voltage sensor arginines with citrulline provides mechanistic insight into charge versus shape. J Gen Physiol 2018; 150:1017-1024. [PMID: 29866793 PMCID: PMC6028492 DOI: 10.1085/jgp.201812075] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/08/2018] [Indexed: 01/06/2023] Open
Abstract
Activation of voltage-gated channels results from the outward movement of arginine residues on the S4 segments. Infield et al. use in vivo nonsense suppression to replace Shaker's S4 arginine residues with citrulline and reveal that a positive charge is required on R4 for voltage-dependent deactivation. Voltage-dependent activation of voltage-gated cation channels results from the outward movement of arginine-bearing helices within proteinaceous voltage sensors. The voltage-sensing residues in potassium channels have been extensively characterized, but current functional approaches do not allow a distinction between the electrostatic and steric contributions of the arginine side chain. Here we use chemical misacylation and in vivo nonsense suppression to encode citrulline, a neutral and nearly isosteric analogue of arginine, into the voltage sensor of the Shaker potassium channel. We functionally characterize the engineered channels and compare them with those bearing conventional mutations at the same positions. We observe effects on both voltage sensitivity and gating kinetics, enabling dissection of the roles of residue structure versus positive charge in channel function. In some positions, substitution with citrulline causes mild effects on channel activation compared with natural mutations. In contrast, substitution of the fourth S4 arginine with citrulline causes substantial changes in the conductance–voltage relationship and the kinetics of the channel, which suggests that a positive charge is required at this position for efficient voltage sensor deactivation and channel closure. The encoding of citrulline is expected to enable enhanced precision for the study of arginine residues located in crowded transmembrane environments in other membrane proteins. In addition, the method may facilitate the study of citrullination in vivo.
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Affiliation(s)
- Daniel T Infield
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA.,Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA
| | - Elizabeth E L Lee
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA.,Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA
| | - Grace D Galles
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA.,Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA
| | - Francisco Bezanilla
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA .,Iowa Neuroscience Institute, The University of Iowa, Iowa City, IA
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20
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Rational Discovery of (+) (S) Abscisic Acid as a Potential Antifungal Agent: a Repurposing Approach. Sci Rep 2018; 8:8565. [PMID: 29867091 PMCID: PMC5986790 DOI: 10.1038/s41598-018-26998-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/14/2018] [Indexed: 12/20/2022] Open
Abstract
Fungal infections are spreading widely worldwide, and the types of treatment are limited due to the lack of diverse therapeutic agents and their associated side effects and toxicity. The discovery of new antifungal classes is vital and critical. We discovered the antifungal activity of abscisic acid through a rational drug design methodology that included the building of homology models for fungal chorismate mutases and a pharmacophore model derived from a transition state inhibitor. Ligand-based virtual screening resulted in some hits that were filtered using molecular docking and molecular dynamic simulations studies. Both in silico methods and in vitro antifungal assays were used as tools to select and validate the abscisic acid repurposing. Abscisic acid inhibition assays confirmed the inhibitory effect of abscisic acid on chorismate mutase through the inhibition of phenylpyruvate production. The repositioning of abscisic acid, the well-known and naturally occurring plant growth regulator, as a potential antifungal agent because of its suggested action as an inhibitor to several fungal chorismate mutases was the main result of this work.
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21
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Burschowsky D, Thorbjørnsrud HV, Heim JB, Fahrig-Kamarauskaitė JR, Würth-Roderer K, Kast P, Krengel U. Inter-Enzyme Allosteric Regulation of Chorismate Mutase in Corynebacterium glutamicum: Structural Basis of Feedback Activation by Trp. Biochemistry 2017; 57:557-573. [PMID: 29178787 DOI: 10.1021/acs.biochem.7b01018] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Corynebacterium glutamicum is widely used for the industrial production of amino acids, nucleotides, and vitamins. The shikimate pathway enzymes DAHP synthase (CgDS, Cg2391) and chorismate mutase (CgCM, Cgl0853) play a key role in the biosynthesis of aromatic compounds. Here we show that CgCM requires the formation of a complex with CgDS to achieve full activity, and that both CgCM and CgDS are feedback regulated by aromatic amino acids binding to CgDS. Kinetic analysis showed that Phe and Tyr inhibit CgCM activity by inter-enzyme allostery, whereas binding of Trp to CgDS strongly activates CgCM. Mechanistic insights were gained from crystal structures of the CgCM homodimer, tetrameric CgDS, and the heterooctameric CgCM-CgDS complex, refined to 1.1, 2.5, and 2.2 Å resolution, respectively. Structural details from the allosteric binding sites reveal that DAHP synthase is recruited as the dominant regulatory platform to control the shikimate pathway, similar to the corresponding enzyme complex from Mycobacterium tuberculosis.
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Affiliation(s)
| | | | - Joel B Heim
- Department of Chemistry, University of Oslo , NO-0315 Oslo, Norway
| | | | | | - Peter Kast
- Laboratory of Organic Chemistry, ETH Zurich , CH-8093 Zurich, Switzerland
| | - Ute Krengel
- Department of Chemistry, University of Oslo , NO-0315 Oslo, Norway
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22
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Schwarz H, Shaik S, Li J. Electronic Effects on Room-Temperature, Gas-Phase C-H Bond Activations by Cluster Oxides and Metal Carbides: The Methane Challenge. J Am Chem Soc 2017; 139:17201-17212. [PMID: 29112810 DOI: 10.1021/jacs.7b10139] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This Perspective discusses a story of one molecule (methane), a few metal-oxide cationic clusters (MOCCs), dopants, metal-carbide cations, oriented-electric fields (OEFs), and a dizzying mechanistic landscape of methane activation! One mechanism is hydrogen atom transfer (HAT), which occurs whenever the MOCC possesses a localized oxyl radical (M-O•). Whenever the radical is delocalized, e.g., in [MgO]n•+ the HAT barrier increases due to the penalty of radical localization. Adding a dopant (Ga2O3) to [MgO]2•+ localizes the radical and HAT transpires. Whenever the radical is located on the metal centers as in [Al2O2]•+ the mechanism crosses over to proton-coupled electron transfer (PCET), wherein the positive Al center acts as a Lewis acid that coordinates the methane molecule, while one of the bridging oxygen atoms abstracts a proton, and the negatively charged CH3 moiety relocates to the metal fragment. We provide a diagnostic plot of barriers vs reactants' distortion energies, which allows the chemist to distinguish HAT from PCET. Thus, doping of [MgO]2•+ by Al2O3 enables HAT and PCET to compete. Similarly, [ZnO]•+ activates methane by PCET generating many products. Adding a CH3CN ligand to form [(CH3CN)ZnO]•+ leads to a single HAT product. The CH3CN dipole acts as an OEF that switches off PCET. [MC]+ cations (M = Au, Cu) act by different mechanisms, dictated by the M+-C bond covalence. For example, Cu+, which bonds the carbon atom mostly electrostatically, performs coupling of C to methane to yield ethylene, in a single almost barrier-free step, with an unprecedented atomic choreography catalyzed by the OEF of Cu+.
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Affiliation(s)
- Helmut Schwarz
- Institut für Chemie, Technische Universität Berlin , Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Jilai Li
- Institut für Chemie, Technische Universität Berlin , Straße des 17. Juni 135, 10623 Berlin, Germany.,Institute of Theoretical Chemistry, Jilin University , Changchun 130023, P.R. China
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23
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Mechanisms and Specificity of Phenazine Biosynthesis Protein PhzF. Sci Rep 2017; 7:6272. [PMID: 28740244 PMCID: PMC5524880 DOI: 10.1038/s41598-017-06278-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 06/12/2017] [Indexed: 11/08/2022] Open
Abstract
Phenazines are bacterial virulence and survival factors with important roles in infectious disease. PhzF catalyzes a key reaction in their biosynthesis by isomerizing (2 S,3 S)-2,3-dihydro-3-hydroxy anthranilate (DHHA) in two steps, a [1,5]-hydrogen shift followed by tautomerization to an aminoketone. While the [1,5]-hydrogen shift requires the conserved glutamate E45, suggesting acid/base catalysis, it also shows hallmarks of a sigmatropic rearrangement, namely the suprafacial migration of a non-acidic proton. To discriminate these mechanistic alternatives, we employed enzyme kinetic measurements and computational methods. Quantum mechanics/molecular mechanics (QM/MM) calculations revealed that the activation barrier of a proton shuttle mechanism involving E45 is significantly lower than that of a sigmatropic [1,5]-hydrogen shift. QM/MM also predicted a large kinetic isotope effect, which was indeed observed with deuterated substrate. For the tautomerization, QM/MM calculations suggested involvement of E45 and an active site water molecule, explaining the observed stereochemistry. Because these findings imply that PhzF can act only on a limited substrate spectrum, we also investigated the turnover of DHHA derivatives, of which only O-methyl and O-ethyl DHHA were converted. Together, these data reveal how PhzF orchestrates a water-free with a water-dependent step. Its unique mechanism, specificity and essential role in phenazine biosynthesis may offer opportunities for inhibitor development.
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24
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Burschowsky D, Krengel U, Uggerud E, Balcells D. Quantum chemical modeling of the reaction path of chorismate mutase based on the experimental substrate/product complex. FEBS Open Bio 2017; 7:789-797. [PMID: 28593134 PMCID: PMC5458464 DOI: 10.1002/2211-5463.12224] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 02/26/2017] [Accepted: 03/22/2017] [Indexed: 11/10/2022] Open
Abstract
Chorismate mutase is a well-known model enzyme, catalyzing the Claisen rearrangement of chorismate to prephenate. Recent high-resolution crystal structures along the reaction coordinate of this enzyme enabled computational analyses at unprecedented detail. Using quantum chemical simulations, we investigated how the catalytic reaction mechanism is affected by electrostatic and hydrogen-bond interactions. Our calculations showed that the transition state (TS) was mainly stabilized electrostatically, with Arg90 playing the leading role. The effect was augmented by selective hydrogen-bond formation to the TS in the wild-type enzyme, facilitated by a small-scale local induced fit. We further identified a previously underappreciated water molecule, which separates the negative charges during the reaction. The analysis includes the wild-type enzyme and a non-natural enzyme variant, where the catalytic arginine was replaced with an isosteric citrulline residue.
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Affiliation(s)
- Daniel Burschowsky
- Department of Chemistry University of Oslo Norway.,Present address: Leicester Institute of Structural and Chemical Biology University of Leicester Leicester UK
| | - Ute Krengel
- Department of Chemistry University of Oslo Norway
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25
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Quapp W, Bofill JM, Ribas-Ariño J. Analysis of the Acting Forces in a Theory of Catalysis and Mechanochemistry. J Phys Chem A 2017; 121:2820-2838. [PMID: 28338327 DOI: 10.1021/acs.jpca.7b00022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The theoretical description of a chemical process resulting from the application of mechanical or catalytical stress to a molecule is performed by the generation of an effective potential energy surface (PES). Changes for minima and saddle points by the stress are described by Newton trajectories (NTs) on the original PES. From the analysis of the acting forces we postulate the existence of pulling corridors built by families of NTs that connect the same stationary points. For different exit saddles of different height we discuss the corresponding pulling corridors; mainly by simple two-dimensional surface models. If there are different exit saddles then there can exist saddles of index two, at least, between. Then the case that a full pulling corridor crosses a saddle of index two is the normal case. It leads to an intrinsic hysteresis of such pullings for the forward or the backward reaction. Assuming such relations we can explain some results in the literature. A new finding is the existence of roundabout corridors that can switch between different saddle points by a reversion of the direction. The findings concern the mechanochemistry of molecular systems under a mechanical load as well as the electrostatic force and can be extended to catalytic and enzymatic accelerated reactions. The basic and ground ansatz includes both kinds of forces in a natural way without an extra modification.
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Affiliation(s)
- Wolfgang Quapp
- Mathematisches Institut, Universität Leipzig , PF 100920, D-04009 Leipzig, Germany
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26
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Abstract
Catalysis is common. Rational catalyst design, however, is at the frontier of chemical science. Although the histories of physical organic and synthetic organic chemistry boast key chapters involving [3s,3s] sigmatropic shifts, catalysis of these reactions is much less common than catalysis of ostensibly more complex processes. The comparative dearth of catalysts for sigmatropic shifts is perhaps a result of the perception that transition state structures for these reactions, like their reactants, are nonpolar and therefore not amenable to selective stabilization and its associated barrier lowering. However, as demonstrated in this Account, transition state structures for [3s,3s] sigmatropic shifts can in fact have charge distributions that differ significantly from those of reactants, even for hydrocarbon substrates, allowing for barriers to be decreased and rates increased. In some cases, differences in charge distribution result from the inclusion of heteroatoms at specific positions in reactants, but in other cases differences are actually induced by catalysts. Perhaps surprisingly, strategies for complexation of transition state structures that remain nonpolar are also possible. In general, the strategies for catalysis employed can be characterized as involving either mechanistic intervention, where a catalyst induces a change from the concerted mechanism expected for a [3s,3s] sigmatropic shift to a multistep process (cutting the transformation into halves or smaller pieces) whose overall barrier is decreased relative to the concerted process, or transition state complexation, where a catalyst simply binds (holds) more tightly to the transition state structure for a [3s,3s] sigmatropic shift than to the reactant, leading to a lower barrier in the presence of the catalyst. Both of these strategies can be considered to be biomimetic in that enzymes frequently induce multistep processes and utilize selective transition state stabilization for the steps involved. In addition, transition state complexation was the principle around which catalytic antibodies were originally designed. The field of catalysis of sigmatropic shifts is now ready for rational design. The studies described here all provide evidence for the origins of rate acceleration, derived in large part from the results of quantum chemical calculations, that can now be applied to the design of new catalysts for [3s,3s] and other sigmatropic shifts.
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Affiliation(s)
- Dean J. Tantillo
- University of California—Davis, Davis, California 95616, United States
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27
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Barrozo A, Duarte F, Bauer P, Carvalho ATP, Kamerlin SCL. Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily. J Am Chem Soc 2015; 137:9061-76. [PMID: 26091851 PMCID: PMC4513756 DOI: 10.1021/jacs.5b03945] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
It is becoming widely accepted that catalytic promiscuity, i.e., the ability of a single enzyme to catalyze the turnover of multiple, chemically distinct substrates, plays a key role in the evolution of new enzyme functions. In this context, the members of the alkaline phosphatase superfamily have been extensively studied as model systems in order to understand the phenomenon of enzyme multifunctionality. In the present work, we model the selectivity of two multiply promiscuous members of this superfamily, namely the phosphonate monoester hydrolases from Burkholderia caryophylli and Rhizobium leguminosarum. We have performed extensive simulations of the enzymatic reaction of both wild-type enzymes and several experimentally characterized mutants. Our computational models are in agreement with key experimental observables, such as the observed activities of the wild-type enzymes, qualitative interpretations of experimental pH-rate profiles, and activity trends among several active site mutants. In all cases the substrates of interest bind to the enzyme in similar conformations, with largely unperturbed transition states from their corresponding analogues in aqueous solution. Examination of transition-state geometries and the contribution of individual residues to the calculated activation barriers suggest that the broad promiscuity of these enzymes arises from cooperative electrostatic interactions in the active site, allowing each enzyme to adapt to the electrostatic needs of different substrates. By comparing the structural and electrostatic features of several alkaline phosphatases, we suggest that this phenomenon is a generalized feature driving selectivity and promiscuity within this superfamily and can be in turn used for artificial enzyme design.
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Affiliation(s)
- Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Fernanda Duarte
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Paul Bauer
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24, Uppsala, Sweden
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