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Romero-Téllez S, Cruz A, Masgrau L, González-Lafont À, Lluch JM. Accounting for the instantaneous disorder in the enzyme-substrate Michaelis complex to calculate the Gibbs free energy barrier of an enzyme reaction. Phys Chem Chem Phys 2021; 23:13042-13054. [PMID: 34100037 DOI: 10.1039/d1cp01338f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Many enzyme reactions present instantaneous disorder. These dynamic fluctuations in the enzyme-substrate Michaelis complexes generate a wide range of energy barriers that cannot be experimentally observed, but that determine the measured kinetics of the reaction. These individual energy barriers can be calculated using QM/MM methods, but then the problem is how to deal with this dispersion of energy barriers to provide kinetic information. So far, the most usual procedure has implied the so-called exponential average of the energy barriers. In this paper, we discuss the foundations of this method, and we use the free energy perturbation theory to derive an alternative equation to get the Gibbs free energy barrier of the enzyme reaction. In addition, we propose a practical way to implement it. We have chosen four enzyme reactions as examples. In particular, we have studied the hydrolysis of a glycosidic bond catalyzed by the enzyme Thermus thermophilus β-glycosidase, and the mutant Y284P Ttb-gly, and the hydrogen abstraction reactions from C13 and C7 of arachidonic acid catalyzed by the enzyme rabbit 15-lipoxygenase-1.
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Affiliation(s)
- Sonia Romero-Téllez
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain and Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Alejandro Cruz
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Laura Masgrau
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain and Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain and Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain.
| | - Àngels González-Lafont
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain and Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain and Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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2
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Wu L, Qin L, Nie Y, Xu Y, Zhao YL. Computer-aided understanding and engineering of enzymatic selectivity. Biotechnol Adv 2021; 54:107793. [PMID: 34217814 DOI: 10.1016/j.biotechadv.2021.107793] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 12/26/2022]
Abstract
Enzymes offering chemo-, regio-, and stereoselectivity enable the asymmetric synthesis of high-value chiral molecules. Unfortunately, the drawback that naturally occurring enzymes are often inefficient or have undesired selectivity toward non-native substrates hinders the broadening of biocatalytic applications. To match the demands of specific selectivity in asymmetric synthesis, biochemists have implemented various computer-aided strategies in understanding and engineering enzymatic selectivity, diversifying the available repository of artificial enzymes. Here, given that the entire asymmetric catalytic cycle, involving precise interactions within the active pocket and substrate transport in the enzyme channel, could affect the enzymatic efficiency and selectivity, we presented a comprehensive overview of the computer-aided workflow for enzymatic selectivity. This review includes a mechanistic understanding of enzymatic selectivity based on quantum mechanical calculations, rational design of enzymatic selectivity guided by enzyme-substrate interactions, and enzymatic selectivity regulation via enzyme channel engineering. Finally, we discussed the computational paradigm for designing enzyme selectivity in silico to facilitate the advancement of asymmetric biosynthesis.
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Affiliation(s)
- Lunjie Wu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Lei Qin
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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3
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Sheng X, Himo F. Mechanisms of metal-dependent non-redox decarboxylases from quantum chemical calculations. Comput Struct Biotechnol J 2021; 19:3176-3186. [PMID: 34141138 PMCID: PMC8187880 DOI: 10.1016/j.csbj.2021.05.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 11/18/2022] Open
Abstract
Quantum chemical calculations are today an extremely valuable tool for studying enzymatic reaction mechanisms. In this mini-review, we summarize our recent work on several metal-dependent decarboxylases, where we used the so-called cluster approach to decipher the details of the reaction mechanisms, including elucidation of the identity of the metal cofactors and the origins of substrate specificity. Decarboxylases are of growing potential for biocatalytic applications, as they can be used in the synthesis of novel compounds of, e.g., pharmaceutical interest. They can also be employed in the reverse direction, providing a strategy to synthesize value‐added chemicals by CO2 fixation. A number of non-redox metal-dependent decarboxylases from the amidohydrolase superfamily have been demonstrated to have promiscuous carboxylation activities and have attracted great attention in the recent years. The computational mechanistic studies provide insights that are important for the further modification and utilization of these enzymes in industrial processes. The discussed enzymes are: 5‐carboxyvanillate decarboxylase, γ‐resorcylate decarboxylase, 2,3‐dihydroxybenzoic acid decarboxylase, and iso-orotate decarboxylase.
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Key Words
- 2,3-DHBD, 2,3‐dihydroxybenzoic acid decarboxylase
- 2,6-DHBD, 2,6‐dihydroxybenzoic acid decarboxylase
- 2-NR, 2-nitroresorcinol
- 5-CV, 5-carboxyvanillate
- 5-NV, 5-nitrovanillate
- 5caU, 5-carboxyuracil
- AHS, amidohydrolase superfamily
- Biocatalysis
- Decarboxylase
- Density functional theory
- IDCase, iso-orotate decarboxylase
- LigW, 5‐carboxyvanillate decarboxylase
- MIMS, membrane inlet mass spectrometry
- QM/MM, quantum mechanics/molecular mechanics
- Reaction mechanism
- Transition state
- γ-RS, γ-resorcylate
- γ-RSD, γ‐resorcylate decarboxylase
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Affiliation(s)
- Xiang Sheng
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, and National Technology Innovation Center for Synthetic Biology, Tianjin 300308, PR China
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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4
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Waheed S, Ramanan R, Chaturvedi SS, Lehnert N, Schofield CJ, Christov CZ, Karabencheva-Christova TG. Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair. ACS CENTRAL SCIENCE 2020; 6:795-814. [PMID: 32490196 PMCID: PMC7256942 DOI: 10.1021/acscentsci.0c00312] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Indexed: 05/08/2023]
Abstract
AlkB and its human homologue AlkBH2 are Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases that repair alkylated DNA bases occurring as a consequence of reactions with mutagenic agents. We used molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) methods to investigate how structural dynamics influences the selectivity and mechanisms of the AlkB- and AlkBH2-catalyzed demethylation of 3-methylcytosine (m3C) in single (ssDNA) and double (dsDNA) stranded DNA. Dynamics studies reveal the importance of the flexibility in both the protein and DNA components in determining the preferences of AlkB for ssDNA and of AlkBH2 for dsDNA. Correlated motions, including of a hydrophobic β-hairpin, are involved in substrate binding in AlkBH2-dsDNA. The calculations reveal that 2OG rearrangement prior to binding of dioxygen to the active site Fe is preferred over a ferryl rearrangement to form a catalytically productive Fe(IV)=O intermediate. Hydrogen atom transfer proceeds via a σ-channel in AlkBH2-dsDNA and AlkB-dsDNA; in AlkB-ssDNA, there is a competition between σ- and π-channels, implying that the nature of the complexed DNA has potential to alter molecular orbital interactions during the substrate oxidation. Our results reveal the importance of the overall protein-DNA complex in determining selectivity and how the nature of the substrate impacts the mechanism.
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Affiliation(s)
- Sodiq
O. Waheed
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Rajeev Ramanan
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Shobhit S. Chaturvedi
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Nicolai Lehnert
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Christopher J. Schofield
- The
Chemistry Research Laboratory, The Department of Chemistry, Mansfield
Road, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christo Z. Christov
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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5
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Sheng X, Kazemi M, Planas F, Himo F. Modeling Enzymatic Enantioselectivity using Quantum Chemical Methodology. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00983] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Masoud Kazemi
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Ferran Planas
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
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6
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Dasgupta S, Herbert JM. Using Atomic Confining Potentials for Geometry Optimization and Vibrational Frequency Calculations in Quantum-Chemical Models of Enzyme Active Sites. J Phys Chem B 2020; 124:1137-1147. [PMID: 31986049 DOI: 10.1021/acs.jpcb.9b11060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Quantum-chemical studies of enzymatic reaction mechanisms sometimes use truncated active-site models as simplified alternatives to mixed quantum mechanics molecular mechanics (QM/MM) procedures. Eliminating the MM degrees of freedom reduces the complexity of the sampling problem, but the trade-off is the need to introduce geometric constraints in order to prevent structural collapse of the model system during geometry optimizations that do not contain a full protein backbone. These constraints may impair the efficiency of the optimization, and care must be taken to avoid artifacts such as imaginary vibrational frequencies. We introduce a simple alternative in which terminal atoms of the model system are placed in soft harmonic confining potentials rather than being rigidly constrained. This modification is simple to implement and straightforward to use in vibrational frequency calculations, unlike iterative constraint-satisfaction algorithms, and allows the optimization to proceed without constraint even though the practical result is to fix the anchor atoms in space. The new approach is more efficient for optimizing minima and transition states, as compared to the use of fixed-atom constraints, and also more robust against unwanted imaginary frequencies. We illustrate the method by application to several enzymatic reaction pathways where entropy makes a significant contribution to the relevant reaction barriers. The use of confining potentials correctly describes reaction paths and facilitates calculation of both vibrational zero-point and finite-temperature entropic corrections to barrier heights.
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Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - John M Herbert
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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7
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Abstract
The urea functionality is inherent to numerous bioactive compounds, including a variety of clinically approved therapies. Urea containing compounds are increasingly used in medicinal chemistry and drug design in order to establish key drug-target interactions and fine-tune crucial drug-like properties. In this perspective, we highlight physicochemical and conformational properties of urea derivatives. We provide outlines of traditional reagents and chemical procedures for the preparation of ureas. Also, we discuss newly developed methodologies mainly aimed at overcoming safety issues associated with traditional synthesis. Finally, we provide a broad overview of urea-based medicinally relevant compounds, ranging from approved drugs to recent medicinal chemistry developments.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Margherita Brindisi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Excellence of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
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8
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Calixto AR, Ramos MJ, Fernandes PA. Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway. Chem Sci 2019; 10:7212-7221. [PMID: 31588289 PMCID: PMC6677113 DOI: 10.1039/c9sc01464k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/10/2019] [Indexed: 02/04/2023] Open
Abstract
The role of conformational diversity in enzyme catalysis has been a matter of analysis in recent studies. Pre-organization of the active site has been pointed out as the major source for enzymes' catalytic power. Following this line of thought, it is becoming clear that specific, instantaneous, non-rare enzyme conformations that make the active site perfectly pre-organized for the reaction lead to the lowest activation barriers that mostly contribute to the macroscopically observed reaction rate. The present work is focused on exploring the relationship between structure and catalysis in HIV-1 protease (PR) with an adiabatic mapping method, starting from different initial structures, collected from a classical MD simulation. The first, rate-limiting step of the HIV-1 PR catalytic mechanism was studied with the ONIOM QM/MM methodology (B3LYP/6-31G(d):ff99SB), with activation and reaction energies calculated at the M06-2X/6-311++G(2d,2p):ff99SB level of theory, in 19 different enzyme:substrate conformations. The results showed that the instantaneous enzyme conformations have two independent consequences on the enzyme's chemistry: they influence the barrier height, something also observed in the past in other enzymes, and they also influence the specific reaction pathway, which is something unusual and unexpected, challenging the "one enzyme-one substrate-one reaction mechanism" paradigm. Two different reaction mechanisms, with similar reactant probabilities and barrier heights, lead to the same gem-diol intermediate. Subtle nanosecond-timescale rearrangements in the active site hydrogen bonding network were shown to determine which reaction the enzyme follows. We named this phenomenon chemical disorder. The results make us realize the unexpected mechanistic consequences of conformational diversity in enzymatic reactivity.
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Affiliation(s)
- Ana Rita Calixto
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
| | - Maria João Ramos
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
| | - Pedro Alexandrino Fernandes
- UCIBIO@REQUIMTE , Departamento de Química e Bioquímica , Faculdade de Ciências Universidade do Porto , Rua do Campo Alegre s/n , 4169-007 Porto , Portugal .
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9
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Mitusińska K, Magdziarz T, Bzówka M, Stańczak A, Gora A. Exploring Solanum tuberosum Epoxide Hydrolase Internal Architecture by Water Molecules Tracking. Biomolecules 2018; 8:biom8040143. [PMID: 30424576 PMCID: PMC6315908 DOI: 10.3390/biom8040143] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/05/2018] [Accepted: 11/08/2018] [Indexed: 11/17/2022] Open
Abstract
Several different approaches are used to describe the role of protein compartments and residues in catalysis and to identify key residues suitable for the modification of the activity or selectivity of the desired enzyme. In our research, we applied a combination of molecular dynamics simulations and a water tracking approach to describe the water accessible volume of Solanum tuberosum epoxide hydrolase. Using water as a molecular probe, we were able to identify small cavities linked with the active site: (i) one made up of conserved amino acids and indispensable for the proper positioning of catalytic water and (ii) two others in which modification can potentially contribute to enzyme selectivity and activity. Additionally, we identified regions suitable for de novo tunnel design that could also modify the catalytic properties of the enzyme. The identified hot-spots extend the list of the previously targeted residues used for modification of the regioselectivity of the enzyme. Finally, we have provided an example of a simple and elegant process for the detailed description of the network of cavities and tunnels, which can be used in the planning of enzyme modifications and can be easily adapted to the study of any other protein.
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Affiliation(s)
- Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, Poland.
- Faculty of Chemistry, Silesian University of Technology, ks. Marcina Strzody 9, 44-100 Gliwice, Poland.
| | - Tomasz Magdziarz
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, Poland.
| | - Maria Bzówka
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, Poland.
- Faculty of Chemistry, Silesian University of Technology, ks. Marcina Strzody 9, 44-100 Gliwice, Poland.
| | - Agnieszka Stańczak
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, Poland.
- Faculty of Chemistry, Silesian University of Technology, ks. Marcina Strzody 9, 44-100 Gliwice, Poland.
| | - Artur Gora
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, Poland.
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10
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Planas F, Sheng X, McLeish MJ, Himo F. A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism. Front Chem 2018; 6:205. [PMID: 29998094 PMCID: PMC6028569 DOI: 10.3389/fchem.2018.00205] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/18/2018] [Indexed: 01/27/2023] Open
Abstract
Density functional theory calculations are used to investigate the detailed reaction mechanism of benzoylformate decarboxylase, a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the nonoxidative decarboxylation of benzoylformate yielding benzaldehyde and carbon dioxide. A large model of the active site is constructed on the basis of the X-ray structure, and it is used to characterize the involved intermediates and transition states and evaluate their energies. There is generally good agreement between the calculations and available experimental data. The roles of the various active site residues are discussed and the results are compared to mutagenesis experiments. Importantly, the calculations identify off-cycle intermediate species of the ThDP cofactor that can have implications on the kinetics of the reaction.
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Affiliation(s)
- Ferran Planas
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Xiang Sheng
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Michael J McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden
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11
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Rinaldi S, Van der Kamp MW, Ranaghan KE, Mulholland AJ, Colombo G. Understanding Complex Mechanisms of Enzyme Reactivity: The Case of Limonene-1,2-Epoxide Hydrolases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00863] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Silvia Rinaldi
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Via Mario Bianco 9, 20131 Milano, Italy
| | - Marc W. Van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
| | - Kara E. Ranaghan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Via Mario Bianco 9, 20131 Milano, Italy
- Dipartimento di Chimica, Università degli Studi di Pavia, Via Taramelli 12, 27100 Pavia, Italy
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12
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Schramm VL, Schwartz SD. Promoting Vibrations and the Function of Enzymes. Emerging Theoretical and Experimental Convergence. Biochemistry 2018; 57:3299-3308. [PMID: 29608286 DOI: 10.1021/acs.biochem.8b00201] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A complete understanding of enzyme catalysis requires knowledge of both transition state features and the detailed motions of atoms that cause reactant molecules to form and traverse the transition state. The seeming intractability of the problem arises from the femtosecond lifetime of chemical transition states, preventing most experimental access. Computational chemistry is admirably suited to short time scale analysis but can be misled by inappropriate starting points or by biased assumptions. Kinetic isotope effects provide an experimental approach to transition state structure and a method for obtaining transition state analogues but, alone, do not inform how that transition state is reached. Enzyme structures with transition state analogues provide computational starting points near the transition state geometry. These well-conditioned starting points, combined with the unbiased computational method of transition path sampling, provide realistic atomistic motions involved in transition state formation and passage. In many, but not all, enzymatic systems, femtosecond local protein motions near the catalytic site are linked to transition state formation. These motions are not inherently revealed by most approaches of transition state theory, because transition state theory replaces dynamics with the statistics of the transition state. Experimental and theoretical convergence of the link between local catalytic site vibrational modes and catalysis comes from heavy atom ("Born-Oppenheimer") enzymes. Fully labeled and catalytic site local heavy atom labels perturb the probability of finding enzymatic transition states in ways that can be analyzed and predicted by transition path sampling. Recent applications of these experimental and computational approaches reveal how subpicosecond local catalytic site protein modes play important roles in creating the transition state.
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Affiliation(s)
- Vern L Schramm
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
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13
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Zaugg J, Gumulya Y, Bodén M, Mark AE, Malde AK. Effect of Binding on Enantioselectivity of Epoxide Hydrolase. J Chem Inf Model 2018; 58:630-640. [DOI: 10.1021/acs.jcim.7b00353] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Julian Zaugg
- School of Chemistry and Molecular Biosciences, University of Queensland, 4072 Brisbane, Australia
| | - Yosephine Gumulya
- School of Chemistry and Molecular Biosciences, University of Queensland, 4072 Brisbane, Australia
| | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, University of Queensland, 4072 Brisbane, Australia
- Institute for Molecular Bioscience, University of Queensland, 4072 Brisbane, Australia
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences, University of Queensland, 4072 Brisbane, Australia
- Institute for Molecular Bioscience, University of Queensland, 4072 Brisbane, Australia
| | - Alpeshkumar K. Malde
- School of Chemistry and Molecular Biosciences, University of Queensland, 4072 Brisbane, Australia
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14
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Ainsley J, Lodola A, Mulholland AJ, Christov CZ, Karabencheva-Christova TG. Combined Quantum Mechanics and Molecular Mechanics Studies of Enzymatic Reaction Mechanisms. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 113:1-32. [PMID: 30149903 DOI: 10.1016/bs.apcsb.2018.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The combined quantum mechanics/molecular mechanics (QM/MM) methods have become a valuable tool in computational biochemistry and received versatile applications for studying the reaction mechanisms of enzymes. The approach combines the calculations of the electronic structure of the active site by QM, with modeling of the protein environment using MM force field, which allows the long-range electrostatics and steric effects on the enzyme reactivity to be accounted for. In this review, we review some key theoretical and computational aspects of the method and we also present some applications to particular enzymatic reactions such as tryptophan-7-halogenase, cyclooxygenase-1, and the epidermal growth factor receptor.
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Affiliation(s)
- Jon Ainsley
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Christo Z Christov
- Department of Chemistry, Michigan Technological University, Houghton, MI, United States.
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15
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Ryde U. How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging. J Chem Theory Comput 2017; 13:5745-5752. [DOI: 10.1021/acs.jctc.7b00826] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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16
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Abstract
The quantum chemical cluster approach is a powerful method for investigating enzymatic reactions. Over the past two decades, a large number of highly diverse systems have been studied and a great wealth of mechanistic insight has been developed using this technique. This Perspective reviews the current status of the methodology. The latest technical developments are highlighted, and challenges are discussed. Some recent applications are presented to illustrate the capabilities and progress of this approach, and likely future directions are outlined.
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Affiliation(s)
- Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University , SE-106 91 Stockholm, Sweden
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17
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Saenz-Méndez P, Katz A, Pérez-Kempner ML, Ventura ON, Vázquez M. Structural insights into human microsomal epoxide hydrolase by combined homology modeling, molecular dynamics simulations, and molecular docking calculations. Proteins 2017; 85:720-730. [DOI: 10.1002/prot.25251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/07/2016] [Accepted: 12/18/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Patricia Saenz-Méndez
- Computational Chemistry and Biology Group; Facultad de Química; UdelaR, Isidoro de María 1614 Montevideo 11800 Uruguay
- Department of Chemistry and Molecular Biology; University of Gothenburg; Göteborg 405 30 Sweden
| | - Aline Katz
- Computational Chemistry and Biology Group; Facultad de Química; UdelaR, Isidoro de María 1614 Montevideo 11800 Uruguay
| | - María Lucía Pérez-Kempner
- Pharmaceutical Science Department; Facultad de Química; UdelaR, General Flores 2124 Montevideo 11800 Uruguay
| | - Oscar N. Ventura
- Computational Chemistry and Biology Group; Facultad de Química; UdelaR, Isidoro de María 1614 Montevideo 11800 Uruguay
| | - Marta Vázquez
- Pharmaceutical Science Department; Facultad de Química; UdelaR, General Flores 2124 Montevideo 11800 Uruguay
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18
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Lind MES, Himo F. Quantum Chemical Modeling of Enantioconvergency in Soluble Epoxide Hydrolase. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01562] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Maria E. S. Lind
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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19
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Lee KSS, Henriksen NM, Ng CJ, Yang J, Jia W, Morisseau C, Andaya A, Gilson MK, Hammock BD. Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase. Arch Biochem Biophys 2016; 613:1-11. [PMID: 27983948 DOI: 10.1016/j.abb.2016.10.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 11/30/2022]
Abstract
Soluble epoxide hydrolase (sEH) is an important therapeutic target of many diseases, such as chronic obstructive pulmonary disease (COPD) and diabetic neuropathic pain. It acts by hydrolyzing and thus regulating specific bioactive long chain polyunsaturated fatty acid epoxides (lcPUFA), like epoxyeicosatrienoic acids (EETs). To better predict which epoxides could be hydrolyzed by sEH, one needs to dissect the important factors and structural requirements that govern the binding of the substrates to sEH. This knowledge allows further exploration of the physiological role played by sEH. Unfortunately, a crystal structure of sEH with a substrate bound has not yet been reported. In this report, new photoaffinity mimics of a sEH inhibitor and EET regioisomers were prepared and used in combination with peptide sequencing and computational modeling, to identify the binding orientation of different regioisomers and enantiomers of EETs into the catalytic cavity of sEH. Results indicate that the stereochemistry of the epoxide plays a crucial role in dictating the binding orientation of the substrate.
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Affiliation(s)
- Kin Sing Stephen Lee
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0736, La Jolla, CA 92093, USA
| | - Connie J Ng
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jun Yang
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Weitao Jia
- Campus Mass Spectrometry Facilities, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Christophe Morisseau
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Armann Andaya
- Campus Mass Spectrometry Facilities, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0736, La Jolla, CA 92093, USA
| | - Bruce D Hammock
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.
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20
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Kearns FL, Hudson PS, Boresch S, Woodcock HL. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis. Methods Enzymol 2016; 577:75-104. [PMID: 27498635 DOI: 10.1016/bs.mie.2016.05.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples.
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Affiliation(s)
- F L Kearns
- University of South Florida, Tampa, FL, United States
| | - P S Hudson
- University of South Florida, Tampa, FL, United States
| | - S Boresch
- Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - H L Woodcock
- University of South Florida, Tampa, FL, United States.
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21
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Bauer P, Carlsson ÅJ, Amrein BA, Dobritzsch D, Widersten M, Kamerlin SCL. Conformational diversity and enantioconvergence in potato epoxide hydrolase 1. Org Biomol Chem 2016; 14:5639-51. [PMID: 27049844 PMCID: PMC5315018 DOI: 10.1039/c6ob00060f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 03/31/2016] [Indexed: 01/11/2023]
Abstract
Potato epoxide hydrolase 1 (StEH1) is a biocatalytically important enzyme that exhibits rich enantio- and regioselectivity in the hydrolysis of chiral epoxide substrates. In particular, StEH1 has been demonstrated to enantioconvergently hydrolyze racemic mixes of styrene oxide (SO) to yield (R)-1-phenylethanediol. This work combines computational, crystallographic and biochemical analyses to understand both the origins of the enantioconvergent behavior of the wild-type enzyme, as well as shifts in activities and substrate binding preferences in an engineered StEH1 variant, R-C1B1, which contains four active site substitutions (W106L, L109Y, V141K and I155V). Our calculations are able to reproduce both the enantio- and regioselectivities of StEH1, and demonstrate a clear link between different substrate binding modes and the corresponding selectivity, with the preferred binding modes being shifted between the wild-type enzyme and the R-C1B1 variant. Additionally, we demonstrate that the observed changes in selectivity and the corresponding enantioconvergent behavior are due to a combination of steric and electrostatic effects that modulate both the accessibility of the different carbon atoms to the nucleophilic side chain of D105, as well as the interactions between the substrate and protein amino acid side chains and active site water molecules. Being able to computationally predict such subtle effects for different substrate enantiomers, as well as to understand their origin and how they are affected by mutations, is an important advance towards the computational design of improved biocatalysts for enantioselective synthesis.
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Affiliation(s)
- P. Bauer
- Science for Life Laboratory , Department of Cell and Molecular Biology , Uppsala University , BMC Box 596 , S-751 24 Uppsala , Sweden .
| | - Å. Janfalk Carlsson
- Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden . ;
| | - B. A. Amrein
- Science for Life Laboratory , Department of Cell and Molecular Biology , Uppsala University , BMC Box 596 , S-751 24 Uppsala , Sweden .
| | - D. Dobritzsch
- Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden . ;
| | - M. Widersten
- Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden . ;
| | - S. C. L. Kamerlin
- Science for Life Laboratory , Department of Cell and Molecular Biology , Uppsala University , BMC Box 596 , S-751 24 Uppsala , Sweden .
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22
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Manickam M, Pillaiyar T, Boggu P, Venkateswararao E, Jalani HB, Kim ND, Lee SK, Jeon JS, Kim SK, Jung SH. Discovery of enantioselectivity of urea inhibitors of soluble epoxide hydrolase. Eur J Med Chem 2016; 117:113-24. [PMID: 27092411 DOI: 10.1016/j.ejmech.2016.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 01/12/2023]
Abstract
Soluble epoxide hydrolase (sEH) hydrolyzes epoxyeicosatrienoic acids (EETs) in the metabolic pathway of arachidonic acid and has been considered as an important therapeutic target for chronic diseases such as hypertension, diabetes and inflammation. Although many urea derivatives are known as sEH inhibitors, the enantioselectivity of the inhibitors is not highlighted in spite of the stereoselective hydrolysis of EETs by sEH. In an effort to explore the importance of enantioselectivity in the urea scaffold, a series of enantiomers with the stereocenter adjacent to the urea nitrogen atom were prepared. The selectivity of enantiomers of 1-(α-alkyl-α-phenylmethyl)-3-(3-phenylpropyl)ureas showed wide range differences up to 125 fold with the low IC50 value up to 13 nM. The S-configuration with planar phenyl and small alkyl groups at α-position is crucial for the activity and selectivity. However, restriction of the free rotation of two α-groups with indan-1-yl or 1,2,3,4-tetrahydronaphthalen-1-yl moiety abolishes the selectivity between the enantiomers, despite the increase in activity up to 13 nM. The hydrophilic group like sulfonamido group at para position of 3-phenylpropyl motif of 1-(α-alkyl-α-phenylmethyl-3-(3-phenylpropyl)urea improves the activity as well as enantiomeric selectivity. All these ureas are proved to be specific inhibitor of sEH without inhibition against mEH.
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Affiliation(s)
- Manoj Manickam
- College of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| | - Thanigaimalai Pillaiyar
- College of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| | - PullaReddy Boggu
- College of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| | - Eeda Venkateswararao
- College of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| | - Hitesh B Jalani
- College of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| | - Nam-Doo Kim
- DGMIF, New Drug Development Center, 80, Cheombok-ro, Dong-gu, Daegu 41061, South Korea
| | - Seul Ki Lee
- College of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| | - Jang Su Jeon
- College of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| | - Sang Kyum Kim
- College of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea
| | - Sang-Hun Jung
- College of Pharmacy and Institute of Drug Research and Development, Chungnam National University, Daejeon 34134, South Korea.
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23
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Epoxide hydrolase-catalyzed enantioselective conversion of trans -stilbene oxide: Insights into the reaction mechanism from steady-state and pre-steady-state enzyme kinetics. Arch Biochem Biophys 2016; 591:66-75. [DOI: 10.1016/j.abb.2015.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 11/18/2022]
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24
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Amrein BA, Bauer P, Duarte F, Janfalk Carlsson Å, Naworyta A, Mowbray SL, Widersten M, Kamerlin SCL. Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes. ACS Catal 2015; 5:5702-5713. [PMID: 26527505 PMCID: PMC4613740 DOI: 10.1021/acscatal.5b01639] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 08/15/2015] [Indexed: 11/30/2022]
Abstract
Potato epoxide hydrolase 1 exhibits rich enantio- and regioselectivity in the hydrolysis of a broad range of substrates. The enzyme can be engineered to increase the yield of optically pure products as a result of changes in both enantio- and regioselectivity. It is thus highly attractive in biocatalysis, particularly for the generation of enantiopure fine chemicals and pharmaceuticals. The present work aims to establish the principles underlying the activity and selectivity of the enzyme through a combined computational, structural, and kinetic study using the substrate trans-stilbene oxide as a model system. Extensive empirical valence bond simulations have been performed on the wild-type enzyme together with several experimentally characterized mutants. We are able to computationally reproduce the differences between the activities of different stereoisomers of the substrate and the effects of mutations of several active-site residues. In addition, our results indicate the involvement of a previously neglected residue, H104, which is electrostatically linked to the general base H300. We find that this residue, which is highly conserved in epoxide hydrolases and related hydrolytic enzymes, needs to be in its protonated form in order to provide charge balance in an otherwise negatively charged active site. Our data show that unless the active-site charge balance is correctly treated in simulations, it is not possible to generate a physically meaningful model for the enzyme that can accurately reproduce activity and selectivity trends. We also expand our understanding of other catalytic residues, demonstrating in particular the role of a noncanonical residue, E35, as a "backup base" in the absence of H300. Our results provide a detailed view of the main factors driving catalysis and regioselectivity in this enzyme and identify targets for subsequent enzyme design efforts.
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Affiliation(s)
- Beat A. Amrein
- 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
| | - Fernanda Duarte
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Åsa Janfalk Carlsson
- Department
of Chemistry-BMC, Uppsala University, BMC Box 576, SE-751 23 Uppsala, Sweden
| | - Agata Naworyta
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Sherry L. Mowbray
- Science
for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC
Box 596, SE-751 24 Uppsala, Sweden
| | - Mikael Widersten
- Department
of Chemistry-BMC, Uppsala University, BMC Box 576, SE-751 23 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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25
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Is Promiscuous CALB a Good Scaffold for Designing New Epoxidases? Molecules 2015; 20:17789-806. [PMID: 26404218 PMCID: PMC6331936 DOI: 10.3390/molecules201017789] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/10/2015] [Accepted: 09/11/2015] [Indexed: 12/23/2022] Open
Abstract
Candida Antarctica lipase B (CALB) is a well-known enzyme, especially because of its promiscuous activity. Due to its properties, CALB was widely used as a benchmark for designing new catalysts for important organic reactions. The active site of CALB is very similar to that of soluble epoxide hydrolase (sEH) formed by a nucleophile-histidine-acid catalytic triad and an oxyanion hole typical for molecular structures derived from processes of α/β hydrolases. In this work we are exploring these similarities and proposing a Ser105Asp variant of CALB as a new catalyst for epoxide hydrolysis. In particular, the hydrolysis of the trans-diphenylpropene oxide (t-DPPO) is studied by means of quantum cluster models mimicking the active site of both enzymes. Our results, based on semi-empirical and DFT calculations, suggest that mutant Ser105Asp CALB is a good protein scaffold to be used for the bio-synthesis of chiral compounds.
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26
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Raunio H, Kuusisto M, Juvonen RO, Pentikäinen OT. Modeling of interactions between xenobiotics and cytochrome P450 (CYP) enzymes. Front Pharmacol 2015; 6:123. [PMID: 26124721 PMCID: PMC4464169 DOI: 10.3389/fphar.2015.00123] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/29/2015] [Indexed: 01/01/2023] Open
Abstract
The adverse effects to humans and environment of only few chemicals are well known. Absorption, distribution, metabolism, and excretion (ADME) are the steps of pharmaco/toxicokinetics that determine the internal dose of chemicals to which the organism is exposed. Of all the xenobiotic-metabolizing enzymes, the cytochrome P450 (CYP) enzymes are the most important due to their abundance and versatility. Reactions catalyzed by CYPs usually turn xenobiotics to harmless and excretable metabolites, but sometimes an innocuous xenobiotic is transformed into a toxic metabolite. Data on ADME and toxicity properties of compounds are increasingly generated using in vitro and modeling (in silico) tools. Both physics-based and empirical modeling approaches are used. Numerous ligand-based and target-based as well as combined modeling methods have been employed to evaluate determinants of CYP ligand binding as well as predicting sites of metabolism and inhibition characteristics of test molecules. In silico prediction of CYP–ligand interactions have made crucial contributions in understanding (1) determinants of CYP ligand binding recognition and affinity; (2) prediction of likely metabolites from substrates; (3) prediction of inhibitors and their inhibition potency. Truly predictive models of toxic outcomes cannot be created without incorporating metabolic characteristics; in silico methods help producing such information and filling gaps in experimentally derived data. Currently modeling methods are not mature enough to replace standard in vitro and in vivo approaches, but they are already used as an important component in risk assessment of drugs and other chemicals.
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Affiliation(s)
- Hannu Raunio
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland Kuopio, Finland
| | - Mira Kuusisto
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland Kuopio, Finland ; Computational Bioscience Laboratory, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä Jyväskylä, Finland
| | - Risto O Juvonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland Kuopio, Finland
| | - Olli T Pentikäinen
- Computational Bioscience Laboratory, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä Jyväskylä, Finland
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27
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Abstract
Drug metabolism can produce metabolites with physicochemical and pharmacological properties that differ substantially from those of the parent drug, and consequently has important implications for both drug safety and efficacy. To reduce the risk of costly clinical-stage attrition due to the metabolic characteristics of drug candidates, there is a need for efficient and reliable ways to predict drug metabolism in vitro, in silico and in vivo. In this Perspective, we provide an overview of the state of the art of experimental and computational approaches for investigating drug metabolism. We highlight the scope and limitations of these methods, and indicate strategies to harvest the synergies that result from combining measurement and prediction of drug metabolism.
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28
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Xu M, Hao H, Jiang L, Long F, Wei Y, Ji H, Sun B, Peng Y, Wang G, Ju W, Li P. In vitro inhibitory effects of ethanol extract of Danshen (Salvia miltiorrhiza) and its components on the catalytic activity of soluble epoxide hydrolase. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2015; 22:444-51. [PMID: 25925966 DOI: 10.1016/j.phymed.2015.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/17/2014] [Accepted: 02/20/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND Soluble epoxide hydrolase (sEH) has been demonstrated to be a key enzyme involved in the pathologic development of several cardiovascular diseases and inflammation, and inhibition of sEH is therefore very helpful or crucial for the treatment of ischemia-reperfusion injury, cardiac hypertrophy, hypertension and inflammation. Danshen, the dried root of Salvia miltiorrhiza (Fam. Labiatae), has been used for the treatment of cardiovascular and cerebrovascular diseases in China and other countries for hundreds of years. Recent studies indicated that Danshen and its preparations also have potential for the management of inflammation. However, little information is available about the possibility of Danshen and its components on sEH inhibition. PURPOSE AND METHODS Danshen extracts and its constituents were tested for sEH inhibition using its physiological substrate, 8,9-EET, based on a LC-MS/MS assay in this study. RESULTS Among the tested 15 compounds, tanshinone IIA and cryptotanshinone were found to be the potent (Ki = 0.87 μM) and medium (Ki = 6.7 μM) mixed-type inhibitors of sEH, respectively. Salvianolic acid C (Ki = 8.6 μM) was proved to be a moderate noncompetitive sEH inhibitor. In consistent with the inhibition results of the pure compounds, the 75% ethanol extract of Danshen (EE, IC50 = 86.5 μg/ml) which contained more tanshinone IIA and cryptotanshinone exhibited more potent inhibition on sEH than the water extract (WE, IC50 > 200 μg/ml) or 1 M NaHCO3 (BE, IC50 > 200 μg/ml) extract. CONCLUSION These data indicated that using the ethanol fraction of Danshen and increasing the amounts of tanshinone IIA, cryptotanshinone and salvianolic acid C, especially the contents of tanshinone IIA in Danshen extract or preparations to enhance the inhibitory effects on sEH might be efficient ways to improve its cardiovascular protective and anti-inflammatory effects, and that herbal medicines could be an untapped reservoir for sEH-inhibition agents and developing sEH inhibitors from the cardiovascular protective and anti-inflammatory herbs is a promising approach.
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Affiliation(s)
- Meijuan Xu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China; Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, No. 155 Hanzhong Road, Nanjing 210029, China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Lifeng Jiang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Fang Long
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Yidan Wei
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Hui Ji
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Bingting Sun
- Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, No. 155 Hanzhong Road, Nanjing 210029, China
| | - Ying Peng
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Guangji Wang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China
| | - Wenzheng Ju
- Department of Clinical Pharmacology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, No. 155 Hanzhong Road, Nanjing 210029, China.
| | - Ping Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 24 Tongjia Lane, Nanjing 210009, China.
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29
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Kaiyawet N, Lonsdale R, Rungrotmongkol T, Mulholland AJ, Hannongbua S. High-level QM/MM calculations support the concerted mechanism for Michael addition and covalent complex formation in thymidylate synthase. J Chem Theory Comput 2015; 11:713-22. [PMID: 26579604 DOI: 10.1021/ct5005033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thymidylate synthase (TS) is a promising cancer target, due to its crucial function in thymine synthesis. It performs the reductive methylation of 2'-deoxyuridine-5'-phosphate (dUMP) to thymidine-5'-phosphate (dTMP), using N-5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) as a cofactor. After the formation of the dUMP/mTHF/TS noncovalent complex, and subsequent conformational activation, this complex has been proposed to react via nucleophilic attack (Michael addition) by Cys146, followed by methylene-bridge formation to generate the ternary covalent intermediate. Herein, QM/MM (B3LYP-D/6-31+G(d)-CHARMM27) methods are used to model the formation of the ternary covalent intermediate. A two-dimensional potential energy surface reveals that the methylene-bridged intermediate is formed via a concerted mechanism, as indicated by a single transition state on the minimum energy pathway and the absence of a stable enolate intermediate. A range of different QM methods (B3LYP, MP2 and SCS-MP2, and different basis sets) are tested for the calculation of the activation energy barrier for the formation of the methylene-bridged intermediate. We test convergence of the QM/MM results with respect to size of the QM region. Inclusion of Arg166, which interacts with the nucleophilic thiolate, in the QM region is important for reliable results; the MM model apparently does not reproduce energies for distortion of the guanidinium side chain correctly. The spin component scaled-Møller-Plessett perturbation theory (SCS-MP2) approach was shown to be in best agreement (within 1.1 kcal/mol) while the results obtained with MP2 and B3LYP also yielded acceptable values (deviating by less than 3 kcal/mol) compared with the barrier derived from experiment. Our results indicate that using a dispersion-corrected DFT method, or a QM method with an accurate treatment of electron correlation, increases the agreement between the calculated and experimental activation energy barriers, compared with the semiempirical AM1 method. These calculations provide important insight into the reaction mechanism of TS and may be useful in the design of new TS inhibitors.
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Affiliation(s)
| | - Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol, BS8 1TS, United Kingdom
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol, BS8 1TS, United Kingdom
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Krámos B, Oláh J. The mechanism of human aromatase (CYP 19A1) revisited: DFT and QM/MM calculations support a compound I-mediated pathway for the aromatization process. Struct Chem 2014. [DOI: 10.1007/s11224-014-0545-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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31
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Cooper AM, Kästner J. Averaging Techniques for Reaction Barriers in QM/MM Simulations. Chemphyschem 2014; 15:3264-9. [DOI: 10.1002/cphc.201402382] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/29/2014] [Indexed: 12/28/2022]
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Recent advances in QM/MM free energy calculations using reference potentials. Biochim Biophys Acta Gen Subj 2014; 1850:954-965. [PMID: 25038480 PMCID: PMC4547088 DOI: 10.1016/j.bbagen.2014.07.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/06/2014] [Accepted: 07/07/2014] [Indexed: 01/02/2023]
Abstract
Background Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. Scope of review Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. Major conclusions The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. General significance As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. We present some of the advances to accelerate high-level QM/MM calculations. Quantitative limitations of low-level methods can be overcome by these approaches. Reference potentials make free energy simulations feasible for large systems. Automated fitting reduces the need of expensive sampling of high-level approaches. Application of reference potentials can be extended to a wide range of processes.
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Lonsdale R, Rouse SL, Sansom MSP, Mulholland AJ. A multiscale approach to modelling drug metabolism by membrane-bound cytochrome P450 enzymes. PLoS Comput Biol 2014; 10:e1003714. [PMID: 25033460 PMCID: PMC4102395 DOI: 10.1371/journal.pcbi.1003714] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/28/2014] [Indexed: 01/30/2023] Open
Abstract
Cytochrome P450 enzymes are found in all life forms. P450s play an important role in drug metabolism, and have potential uses as biocatalysts. Human P450s are membrane-bound proteins. However, the interactions between P450s and their membrane environment are not well-understood. To date, all P450 crystal structures have been obtained from engineered proteins, from which the transmembrane helix was absent. A significant number of computational studies have been performed on P450s, but the majority of these have been performed on the solubilised forms of P450s. Here we present a multiscale approach for modelling P450s, spanning from coarse-grained and atomistic molecular dynamics simulations to reaction modelling using hybrid quantum mechanics/molecular mechanics (QM/MM) methods. To our knowledge, this is the first application of such an integrated multiscale approach to modelling of a membrane-bound enzyme. We have applied this protocol to a key human P450 involved in drug metabolism: CYP3A4. A biologically realistic model of CYP3A4, complete with its transmembrane helix and a membrane, has been constructed and characterised. The dynamics of this complex have been studied, and the oxidation of the anticoagulant R-warfarin has been modelled in the active site. Calculations have also been performed on the soluble form of the enzyme in aqueous solution. Important differences are observed between the membrane and solution systems, most notably for the gating residues and channels that control access to the active site. The protocol that we describe here is applicable to other membrane-bound enzymes.
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Affiliation(s)
- Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Sarah L. Rouse
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail: (MSPS); (AJM)
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
- * E-mail: (MSPS); (AJM)
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Plotnikov NV. Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model. J Chem Theory Comput 2014; 10:2987-3001. [PMID: 25136268 PMCID: PMC4132848 DOI: 10.1021/ct500109m] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Indexed: 12/21/2022]
Abstract
![]()
Proposed
in this contribution is a protocol for calculating fine-physics
(e.g., ab initio QM/MM) free-energy surfaces at a high level of accuracy
locally (e.g., only at reactants and at the transition state for computing
the activation barrier) from targeted fine-physics sampling and extensive
exploratory coarse-physics sampling. The full free-energy surface
is still computed but at a lower level of accuracy from coarse-physics
sampling. The method is analytically derived in terms of the umbrella
sampling and the free-energy perturbation methods which are combined
with the thermodynamic cycle and the targeted sampling strategy of
the paradynamics approach. The algorithm starts by computing low-accuracy
fine-physics free-energy surfaces from the coarse-physics sampling
in order to identify the reaction path and to select regions for targeted
sampling. Thus, the algorithm does not rely on the coarse-physics
minimum free-energy reaction path. Next, segments of high-accuracy
free-energy surface are computed locally at selected regions from
the targeted fine-physics sampling and are positioned relative to
the coarse-physics free-energy shifts. The positioning is done by
averaging the free-energy perturbations computed with multistep linear
response approximation method. This method is analytically shown to
provide results of the thermodynamic integration and the free-energy
interpolation methods, while being extremely simple in implementation.
Incorporating the metadynamics sampling to the algorithm is also briefly
outlined. The application is demonstrated by calculating the B3LYP//6-31G*/MM
free-energy barrier for an enzymatic reaction using a semiempirical
PM6/MM reference potential. These modifications allow computing the
activation free energies at a significantly reduced computational
cost but at the same level of accuracy compared to computing full
potential of mean force.
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Affiliation(s)
- Nikolay V Plotnikov
- Department of Chemistry, Stanford University , 333 Campus Drive, Mudd Building 121, MB 88, Stanford, California 94305, United States
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35
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Jitonnom J, Limb MAL, Mulholland AJ. QM/MM free-energy simulations of reaction in Serratia marcescens Chitinase B reveal the protonation state of Asp142 and the critical role of Tyr214. J Phys Chem B 2014; 118:4771-83. [PMID: 24730355 DOI: 10.1021/jp500652x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Serratia marcescens Chitinase B (ChiB), belonging to the glycosidase family 18 (GH18), catalyzes the hydrolysis of β-1,4-glycosidic bond, with retention of configuration, via an unusual substrate-assisted mechanism, in which the substrate itself acts as an intramolecular nucleophile. Here, both elementary steps (glycosylation and deglycosylation) of the ChiB-catalyzed reaction are investigated by means of combined quantum mechanics/molecular mechanics (QM/MM) umbrella sampling molecular dynamics (MD) simulations at the SCC-DFTB/CHARMM22 level of theory. We examine the influence of the Asp142 protonation state on the reaction and the role that this residue performs in the reaction. Our simulations show that reaction with a neutral Asp142 is preferred and demonstrate that this residue provides electrostatic stabilization of the oxazolinium ion intermediate formed in the reaction. Insight into the conformational itinerary ((1,4)B↔(4)H5↔(4)C1) adopted by the substrate (bound in subsite -1) along the preferred reaction pathway is also provided by the simulations. The relative energies of the stationary points found along the reaction pathway calculated with SCC-DFTB and B3LYP were compared. The results suggest that SCC-DFTB is an accurate method for estimating the relative barriers for both steps of the reaction; however, it was found to overestimate the relative energy of an intermediate formed in the reaction when compared with the higher level of theory. Glycosylation is suggested to be a rate-determining step in the reaction with calculated overall reaction free-energy barrier of 20.5 kcal/mol, in a reasonable agreement with the 16.1 kcal/mol barrier derived from the experiment. The role of Tyr214 in catalysis was also investigated with the results, indicating that the residue plays a critical role in the deglycosylation step of the reaction. Simulations of the enzyme-product complex were also performed with an unbinding event suggested to have been observed, affording potential new mechanistic insight into the release of the product of ChiB.
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Affiliation(s)
- Jitrayut Jitonnom
- Division of Chemistry, School of Science, University of Phayao , Phayao 56000, Thailand
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König G, Hudson PS, Boresch S, Woodcock HL. Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes. J Chem Theory Comput 2014; 10:1406-1419. [PMID: 24803863 PMCID: PMC3985817 DOI: 10.1021/ct401118k] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Indexed: 11/28/2022]
Abstract
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The reliability of free energy simulations
(FES) is limited by
two factors: (a) the need for correct sampling and (b) the accuracy
of the computational method employed. Classical methods (e.g., force
fields) are typically used for FES and present a myriad of challenges,
with parametrization being a principle one. On the other hand, parameter-free
quantum mechanical (QM) methods tend to be too computationally expensive
for adequate sampling. One widely used approach is a combination of
methods, where the free energy difference between the two end states
is computed by, e.g., molecular mechanics (MM), and the end states
are corrected by more accurate methods, such as QM or hybrid QM/MM
techniques. Here we report two new approaches that significantly improve
the aforementioned scheme; with a focus on how to compute corrections
between, e.g., the MM and the more accurate QM calculations. First,
a molecular dynamics trajectory that properly samples relevant conformational
degrees of freedom is generated. Next, potential energies of each
trajectory frame are generated with a QM or QM/MM Hamiltonian. Free
energy differences are then calculated based on the QM or QM/MM energies
using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann
free energy perturbation (NB-FEP). Both approaches are applied to
calculate relative and absolute solvation free energies in explicit
and implicit solvent environments. Solvation free energy differences
(relative and absolute) between ethane and methanol in explicit solvent
are used as the initial test case for QM-NBB. Next, implicit solvent
methods are employed in conjunction with both QM-NBB and NB-FEP to
compute absolute solvation free energies for 21 compounds. These compounds
range from small molecules such as ethane and methanol to fairly large,
flexible solutes, such as triacetyl glycerol. Several technical aspects
were investigated. Ultimately some best practices are suggested for
improving methods that seek to connect MM to QM (or QM/MM) levels
of theory in FES.
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Affiliation(s)
- Gerhard König
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Phillip S Hudson
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
| | - Stefan Boresch
- Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna , Währingerstraße 17, A-1090 Vienna, Austria
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida , 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620-5250, United States
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Rungrotmongkol T, Mulholland AJ, Hannongbua S. QM/MM simulations indicate that Asp185 is the likely catalytic base in the enzymatic reaction of HIV-1 reverse transcriptase. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00319a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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38
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. ENTROPY 2013. [DOI: 10.3390/e16010163] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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39
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Lonsdale R, Houghton KT, Żurek J, Bathelt CM, Foloppe N, de Groot MJ, Harvey JN, Mulholland AJ. Quantum mechanics/molecular mechanics modeling of regioselectivity of drug metabolism in cytochrome P450 2C9. J Am Chem Soc 2013; 135:8001-15. [PMID: 23641937 PMCID: PMC3670427 DOI: 10.1021/ja402016p] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
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Cytochrome P450 enzymes (P450s) are
important in drug metabolism
and have been linked to adverse drug reactions. P450s display broad
substrate reactivity, and prediction of metabolites is complex. QM/MM
studies of P450 reactivity have provided insight into important details
of the reaction mechanisms and have the potential to make predictions
of metabolite formation. Here we present a comprehensive study of
the oxidation of three widely used pharmaceutical compounds (S-ibuprofen, diclofenac, and S-warfarin)
by one of the major drug-metabolizing P450 isoforms, CYP2C9. The reaction
barriers to substrate oxidation by the iron-oxo species (Compound
I) have been calculated at the B3LYP-D/CHARMM27 level for different
possible metabolism sites for each drug, on multiple pathways. In
the cases of ibuprofen and warfarin, the process with the lowest activation
energy is consistent with the experimentally preferred metabolite.
For diclofenac, the pathway leading to the experimentally observed
metabolite is not the one with the lowest activation energy. This
apparent inconsistency with experiment might be explained by the two
very different binding modes involved in oxidation at the two competing
positions. The carboxylate of diclofenac interacts strongly with the
CYP2C9 Arg108 side chain in the transition state for formation of
the observed metabolite—but not in that for the competing pathway.
We compare reaction barriers calculated both in the presence and in
the absence of the protein and observe a marked improvement in selectivity
prediction ability upon inclusion of the protein for all of the substrates
studied. The barriers calculated with the protein are generally higher
than those calculated in the gas phase. This suggests that active-site
residues surrounding the substrate play an important role in controlling
selectivity in CYP2C9. The results show that inclusion of sampling
(particularly) and dispersion effects is important in making accurate
predictions of drug metabolism selectivity of P450s using QM/MM methods.
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Affiliation(s)
- Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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40
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van der Kamp MW, Mulholland AJ. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry 2013; 52:2708-28. [PMID: 23557014 DOI: 10.1021/bi400215w] [Citation(s) in RCA: 399] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Computational enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications. We outline some practical considerations for such simulations. Further, we highlight applications that show how QM/MM methods can contribute to the practical development and application of enzymology, e.g., in the interpretation and prediction of the effects of mutagenesis and in drug and catalyst design.
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Affiliation(s)
- Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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41
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Lind MES, Himo F. Quantum chemistry as a tool in asymmetric biocatalysis: limonene epoxide hydrolase test case. Angew Chem Int Ed Engl 2013; 52:4563-7. [PMID: 23512539 PMCID: PMC3734700 DOI: 10.1002/anie.201300594] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Indexed: 12/24/2022]
Affiliation(s)
- Maria E S Lind
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
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42
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Lind MES, Himo F. Quantum Chemistry as a Tool in Asymmetric Biocatalysis: Limonene Epoxide Hydrolase Test Case. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300594] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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43
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Liao RZ, Thiel W. Determinants of Regioselectivity and Chemoselectivity in Fosfomycin Resistance Protein FosA from QM/MM Calculations. J Phys Chem B 2013; 117:1326-36. [DOI: 10.1021/jp4002719] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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44
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Abstract
Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, 'Why Nature Chose Phosphate' (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that nature really chose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.
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45
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Ram Prasad B, Kamerlin SCL, Florián J, Warshel A. Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1288-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Barrozo A, Borstnar R, Marloie G, Kamerlin SCL. Computational protein engineering: bridging the gap between rational design and laboratory evolution. Int J Mol Sci 2012. [PMID: 23202907 PMCID: PMC3497281 DOI: 10.3390/ijms131012428] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts for a whole host of processes, from chemical synthesis to the generation of novel biofuels. For them to be more amenable to the needs of biotechnology, however, it is often necessary to be able to manipulate their physico-chemical properties in an efficient and streamlined manner, and, ideally, to be able to train them to catalyze completely new reactions. Recent years have seen an explosion of interest in different approaches to achieve this, both in the laboratory, and in silico. There remains, however, a gap between current approaches to computational enzyme design, which have primarily focused on the early stages of the design process, and laboratory evolution, which is an extremely powerful tool for enzyme redesign, but will always be limited by the vastness of sequence space combined with the low frequency for desirable mutations. This review discusses different approaches towards computational enzyme design and demonstrates how combining newly developed screening approaches that can rapidly predict potential mutation “hotspots” with approaches that can quantitatively and reliably dissect the catalytic step can bridge the gap that currently exists between computational enzyme design and laboratory evolution studies.
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Affiliation(s)
- Alexandre Barrozo
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
| | - Rok Borstnar
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gaël Marloie
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
| | - Shina Caroline Lynn Kamerlin
- Department of Cell and Molecular Biology, Uppsala Biomedical Center (BMC), Uppsala University, Box 596, S-751 24 Uppsala, Sweden; E-Mails: (A.B.); (R.B.); (G.M.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +46-18-471-4423; Fax: +46-18-530-396
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47
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Carlsson ÅJ, Bauer P, Ma H, Widersten M. Obtaining optical purity for product diols in enzyme-catalyzed epoxide hydrolysis: contributions from changes in both enantio- and regioselectivity. Biochemistry 2012; 51:7627-37. [PMID: 22931287 DOI: 10.1021/bi3007725] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzyme variants of the plant epoxide hydrolase StEH1 displaying improved stereoselectivities in the catalyzed hydrolysis of (2,3-epoxypropyl)benzene were generated by directed evolution. The evolution was driven by iterative saturation mutagenesis in combination with enzyme activity screenings where product chirality was the decisive selection criterion. Analysis of the underlying causes of the increased diol product ratios revealed two major contributing factors: increased enantioselectivity for the corresponding epoxide enantiomer(s) and, in some cases, a concomitant change in regioselectivity in the catalyzed epoxide ring-opening half-reaction. Thus, variant enzymes that catalyzed the hydrolysis of racemic (2,3-epoxypropyl)benzene into the R-diol product in an enantioconvergent manner were isolated.
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Affiliation(s)
- Åsa Janfalk Carlsson
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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48
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Lonsdale R, Harvey JN, Mulholland AJ. Effects of Dispersion in Density Functional Based Quantum Mechanical/Molecular Mechanical Calculations on Cytochrome P450 Catalyzed Reactions. J Chem Theory Comput 2012; 8:4637-45. [PMID: 26605619 DOI: 10.1021/ct300329h] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional theory (DFT) based quantum mechanical/molecular mechanical (QM/MM) calculations have provided valuable insight into the reactivity of the cytochrome P450 family of enzymes (P450s). A failure of commonly used DFT methods, such as B3LYP, is the neglect of dispersion interactions. An empirical dispersion correction has been shown to improve the accuracy of gas phase DFT calculations of P450s. The current work examines the effect of the dispersion correction in QM/MM calculations on P450s. The hydrogen abstraction from camphor, and hydrogen abstraction and C-O addition of cyclohexene and propene by P450cam have been modeled, along with the addition of benzene to Compound I in CYP2C9, at the B3LYP-D2/CHARMM27 level of theory. Single point energy calculations were also performed at the B3LYP-D3//B3LYP-D2/CHARMM27 level. The dispersion corrections lower activation energy barriers significantly (by ∼5 kcal/mol), as seen for gas phase calculations, but has a small effect on optimized geometries.These effects are likely to be important in modeling reactions catalyzed by other enzymes also. Given the low computational cost of including such dispersion corrections, we recommend doing so in all B3LYP based QM/MM calculations.
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Affiliation(s)
- Richard Lonsdale
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Jeremy N Harvey
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
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49
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Plotnikov NV, Warshel A. Exploring, refining, and validating the paradynamics QM/MM sampling. J Phys Chem B 2012; 116:10342-56. [PMID: 22853800 DOI: 10.1021/jp304678d] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The performance of the paradynamics (PD) reference potential approach in QM/MM calculations is examined. It is also clarified that, in contrast to some possible misunderstandings, this approach provides a rigorous strategy for QM/MM free energy calculations. In particular, the PD approach provides a gradual and controlled way of improving the evaluation of the free energy perturbation associated with moving from the EVB reference potential to the target QM/MM surface. This is achieved by moving from the linear response approximation to the full free energy perturbation approach in evaluating the free energy changes. We also present a systematic way of improving the reference potential by using Gaussian-based correction potentials along a reaction coordinate. In parallel, we review other recent adaptations of the reference potential approach, emphasizing and demonstrating the advantage of using the EVB potential as a reference potential, relative to semiempirical QM/MM molecular orbital potentials. We also compare the PD results to those obtained by direct calculations of the potentials of the mean force (PMF). Additionally, we propose a way of accelerating the PMF calculations by using Gaussian-based negative potentials along the reaction coordinate (which are also used in the PD refinement). Finally, we discuss performance of the PD and the metadynamics approaches in ab initio QM/MM calculations and emphasize the advantage of using the PD approach.
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Affiliation(s)
- Nikolay V Plotnikov
- Department of Chemistry (SGM418), University of Southern California , 3620 McClintock Avenue, Los Angeles CA-90089, United States
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Heimdal J, Ryde U. Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations. Phys Chem Chem Phys 2012; 14:12592-604. [PMID: 22797613 DOI: 10.1039/c2cp41005b] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lately, there has been great interest in performing free-energy perturbation (FEP) at the combined quantum mechanics and molecular mechanics (QM/MM) level, e.g. for enzyme reactions. Such calculations require extensive sampling of phase space, which typically is prohibitive with density-functional theory or ab initio methods. Therefore, such calculations have mostly been performed with semiempirical QM (SQM) methods, or by using a thermodynamic cycle involving sampling at the MM level and perturbations between the MM and QM/MM levels of theory. However, the latter perturbations typically have convergence problems, unless the QM system is kept fixed during the simulations, because the MM and QM/MM descriptions of the internal degrees of freedom inside the QM system are too dissimilar. We have studied whether the convergence of the MM → QM/MM perturbation can be improved by using a thoroughly parameterised force field or by using SQM/MM methods. As a test case we use the first half-reaction of haloalkane dehalogenase and the QM calculations are performed with the PBE, B3LYP, and TPSSH density-functional methods. We show that the convergence can be improved with a tailored force field, but only locally around the parameterised state. Simulations based on SQM/MM methods using the MNDO, AM1, PM3, RM1, PDDG-MNDO, and PDDG-PM3 Hamiltonians have slightly better convergence properties, but very long simulations are still needed (~10 ns) and convergence is obtained only if electrostatic interactions between the QM system and the surroundings are ignored. This casts some doubts on the common practice to base QM/MM FEPs on semiempirical simulations without any reweighting of the trajectories.
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Affiliation(s)
- Jimmy Heimdal
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
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