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Lu Y, Sen K, Yong C, Gunn DSD, Purton JA, Guan J, Desmoutier A, Abdul Nasir J, Zhang X, Zhu L, Hou Q, Jackson-Masters J, Watts S, Hanson R, Thomas HN, Jayawardena O, Logsdail AJ, Woodley SM, Senn HM, Sherwood P, Catlow CRA, Sokol AA, Keal TW. Multiscale QM/MM modelling of catalytic systems with ChemShell. Phys Chem Chem Phys 2023; 25:21816-21835. [PMID: 37097706 DOI: 10.1039/d3cp00648d] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.
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Affiliation(s)
- You Lu
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Kakali Sen
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Chin Yong
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - David S D Gunn
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - John A Purton
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Jingcheng Guan
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Alec Desmoutier
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Jamal Abdul Nasir
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Xingfan Zhang
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Lei Zhu
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Qing Hou
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Joe Jackson-Masters
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Sam Watts
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Rowan Hanson
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Harry N Thomas
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Omal Jayawardena
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Andrew J Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Scott M Woodley
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Hans M Senn
- School of Chemistry, University of Glasgow, Joseph Black Building, Glasgow G12 8QQ, UK
| | - Paul Sherwood
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - C Richard A Catlow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Alexey A Sokol
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Thomas W Keal
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
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2
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Canyelles-Niño M, González-Lafont À, Lluch JM. Hydroperoxidation of Docosahexaenoic Acid by Human ALOX12 and pigALOX15-mini-LOX. Int J Mol Sci 2023; 24:ijms24076064. [PMID: 37047037 PMCID: PMC10094721 DOI: 10.3390/ijms24076064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
Human lipoxygenase 12 (hALOX12) catalyzes the conversion of docosahexaenoic acid (DHA) into mainly 14S-hydroperoxy-4Z,7Z,10Z,12E,16Z,19Z-docosahexaenoic acid (14S-H(p)DHA). This hydroperoxidation reaction is followed by an epoxidation and hydrolysis process that finally leads to maresin 1 (MaR1), a potent bioactive specialized pro-resolving mediator (SPM) in chronic inflammation resolution. By combining docking, molecular dynamics simulations, and quantum mechanics/molecular mechanics calculations, we have computed the potential energy profile of DHA hydroperoxidation in the active site of hALOX12. Our results describe the structural evolution of the molecular system at each step of this catalytic reaction pathway. Noteworthy, the required stereospecificity of the reaction leading to MaR1 is explained by the configurations adopted by DHA bound to hALOX12, along with the stereochemistry of the pentadienyl radical formed after the first step of the mechanism. In pig lipoxygenase 15 (pigALOX15-mini-LOX), our calculations suggest that 14S-H(p)DHA can be formed, but with a stereochemistry that is inadequate for MaR1 biosynthesis.
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Affiliation(s)
- Miquel Canyelles-Niño
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Arquebio SL, Carrer de Álava 51, 08005 Barcelona, Spain
| | - Àngels González-Lafont
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
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3
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Sardar A, Abid OUR, Daud S, Ali Shah B, Shahid W, Ashraf M, fatima M, ezzine S, Wadood A, Shareef A, Al-Ghulikah HA, Alissa SA. Identification of novel diclofenac acid and naproxen bearing hydrazones as 15-LOX inhibitors: Design, Synthesis, In vitro evaluation, cytotoxicity, and In silico studies. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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4
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Cebrián-Prats A, Pinto A, González-Lafont À, Fernandes PA, Lluch JM. The role of acetylated cyclooxygenase-2 in the biosynthesis of resolvin precursors derived from eicosapentaenoic acid. Org Biomol Chem 2022; 20:1260-1274. [PMID: 35067692 DOI: 10.1039/d1ob01932e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Specialized pro-resolving lipid mediators (SPMs) are natural bioactive agents actively involved in inflammation resolution. SPMs act when uncontrolled inflammatory processes are developed, for instance, in patients of COVID-19 or other diseases. The so-called resolution pharmacology aims at developing new treatments based on the use of SPMs as agonists, which promote inflammation resolution without unwanted side effects. It has been shown that the biosynthesis of SPMs called eicosapentaenoic acid (EPA)-derived E-series resolvins is initiated by aspirin-acetylated COX-2 from EPA, leading to 18-hydroperoxy-eicosapentaenoic acid (18-HpEPE). However, there are many open questions concerning the intriguing role of aspirin in the molecular mechanism of resolvin formation. Our MD simulations, combined with QM/MM calculations, show that the potential energy barriers for the H16-abstraction from EPA, required for forming 18-HpEPE, are higher than for the H13-abstraction, thus explaining why 18-HpEPE is a marginal product of COX-2 catalysis. By contrast, in the aspirin-acetylated COX-2/EPA complex, the H16proS-abstraction energy barriers are somewhat lower than the H13proS energy barriers and much smaller than the H16-transfer barriers in the wild type COX-2/EPA system. Those results agree with the experimental observation that aspirin favours the synthesis of several SPMs known as aspirin-triggered resolvins. In the following step of the catalytic mechanism, the calculated O2 addition to C18 is preferred versus the addition to C14 which also agrees with 18R-HEPE and 18S-HEPE being the main products from EPA in aspirin-acetylated COX-2.
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Affiliation(s)
- Anna Cebrián-Prats
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | - Alexandre Pinto
- LAQV-Requimte, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, Porto, Portugal.
| | - Àngels González-Lafont
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. .,Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Pedro A Fernandes
- LAQV-Requimte, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, Porto, Portugal.
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. .,Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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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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6
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Ivanov I, Cruz A, Zhuravlev A, Di Venere A, Nicolai E, Stehling S, Lluch JM, González-Lafont À, Kuhn H. Conformational Heterogeneity and Cooperative Effects of Mammalian ALOX15. Int J Mol Sci 2021; 22:ijms22063285. [PMID: 33807076 PMCID: PMC8004969 DOI: 10.3390/ijms22063285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 12/19/2022] Open
Abstract
Arachidonic acid lipoxygenases (ALOXs) have been suggested to function as monomeric enzymes, but more recent data on rabbit ALOX15 indicated that there is a dynamic monomer-dimer equilibrium in aqueous solution. In the presence of an active site ligand (the ALOX15 inhibitor RS7) rabbit ALOX15 was crystalized as heterodimer and the X-ray coordinates of the two monomers within the dimer exhibit subtle structural differences. Using native polyacrylamide electrophoresis, we here observed that highly purified and predominantly monomeric rabbit ALOX15 and human ALOX15B are present in two conformers with distinct electrophoretic mobilities. In silico docking studies, molecular dynamics simulations, site directed mutagenesis experiments and kinetic measurements suggested that in aqueous solutions the two enzymes exhibit motional flexibility, which may impact the enzymatic properties.
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Affiliation(s)
- Igor Ivanov
- Lomonosov Institute of Fine Chemical Technologies, MIREA—Russian Technological University, Vernadskogo pr. 86, 119571 Moscow, Russia; (I.I.); (A.Z.)
| | - Alejandro Cruz
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; (A.C.); (J.M.L.); (À.G.-L.)
| | - Alexander Zhuravlev
- Lomonosov Institute of Fine Chemical Technologies, MIREA—Russian Technological University, Vernadskogo pr. 86, 119571 Moscow, Russia; (I.I.); (A.Z.)
| | - Almerinda Di Venere
- Department of Experimental Medicine, University of Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (A.D.V.); (E.N.)
| | - Eleonora Nicolai
- Department of Experimental Medicine, University of Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (A.D.V.); (E.N.)
| | - Sabine Stehling
- Institute of Biochemistry, Charite—University Medicine Berlin, Corporate member of Free University Berlin, Humboldt University Berlin and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany;
| | - José M. Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; (A.C.); (J.M.L.); (À.G.-L.)
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Àngels González-Lafont
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; (A.C.); (J.M.L.); (À.G.-L.)
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Hartmut Kuhn
- Institute of Biochemistry, Charite—University Medicine Berlin, Corporate member of Free University Berlin, Humboldt University Berlin and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany;
- Correspondence: ; Tel.: +49-30-450-528040
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7
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Soler J, González-Lafont À, Lluch JM. A protocol to obtain multidimensional quantum tunneling corrections derived from QM(DFT)/MM calculations for an enzyme reaction. Phys Chem Chem Phys 2020; 22:27385-27393. [DOI: 10.1039/d0cp05265e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The multidimensional small-curvature tunneling (SCT) method with Electrostatic Embedding calculations is a compromise between an accessible computational cost and the attainment of an accurate enough estimation of tunneling for an enzyme reaction.
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Affiliation(s)
- Jordi Soler
- Departament de Química Universitat Autònoma de Barcelona
- Bellaterra
- Spain
| | - Àngels González-Lafont
- Departament de Química Universitat Autònoma de Barcelona
- Bellaterra
- Spain
- Institut de Biotecnologia i de Biomedicina (IBB)
- Universitat Autònoma de Barcelona
| | - José M. Lluch
- Departament de Química Universitat Autònoma de Barcelona
- Bellaterra
- Spain
- Institut de Biotecnologia i de Biomedicina (IBB)
- Universitat Autònoma de Barcelona
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8
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Ivanov I, Golovanov AB, Ferretti C, Canyelles-Niño M, Heydeck D, Stehling S, Lluch JM, González-Lafont À, Kühn H. Mutations of Triad Determinants Changes the Substrate Alignment at the Catalytic Center of Human ALOX5. ACS Chem Biol 2019; 14:2768-2782. [PMID: 31664810 DOI: 10.1021/acschembio.9b00674] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
For the specificity of ALOX15 orthologs of different mammals, the geometry of the amino acids Phe353, Ile418, Met419, and Ile593 ("triad determinants") is important, and mutagenesis of these residues altered the reaction specificity of these enzymes. Here we expressed wild-type human ALOX5 and its F359W/A424I/N425M/A603I mutant in Sf9 insect cells and characterized the catalytic differences of the two enzyme variants. We found that wild-type ALOX5 converted arachidonic acid mainly to 5(S)-hydroperoxyeicosatetraenoic acid (HpETE). In contrast, 15(S)- and 8(S)-H(p)ETE were formed by the mutant enzyme. In addition to arachidonic acid, wild-type ALOX5 accepted eicosapentaenoic acid (EPA) as substrate, but C18 fatty acids were not oxygenated. The quadruple mutant also accepted linoleic acid and α- and γ-linolenic acid as substrate. Structural analysis of the oxygenation products and kinetic studies with stereospecifically labeled 11(S)- and 11(R)-deutero-linoleic acid suggested alternative ways of substrate orientation at the active site. In silico docking studies, molecular dynamics simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations confirmed this hypothesis. These data indicate that "triad determinant" mutagenesis alters the catalytic properties of ALOX5 abolishing its leukotriene synthase activity but improving its biosynthetic capacity for pro-resolving lipoxins.
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Affiliation(s)
- Igor Ivanov
- Lomonosov Institute of Fine Chemical Technologies, MIREA - Russian Technological University, Vernadskogo pr. 86, 119571 Moscow, Russia
| | - Alexey B. Golovanov
- Lomonosov Institute of Fine Chemical Technologies, MIREA - Russian Technological University, Vernadskogo pr. 86, 119571 Moscow, Russia
| | | | | | - Dagmar Heydeck
- Institute of Biochemistry, Charite - University Medicine Berlin, Corporate member of Free University Berlin, Humboldt University Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
| | - Sabine Stehling
- Institute of Biochemistry, Charite - University Medicine Berlin, Corporate member of Free University Berlin, Humboldt University Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
| | | | | | - Hartmut Kühn
- Institute of Biochemistry, Charite - University Medicine Berlin, Corporate member of Free University Berlin, Humboldt University Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
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9
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Cebrián-Prats A, González-Lafont À, Lluch JM. Understanding the Molecular Details of the Mechanism That Governs the Oxidation of Arachidonic Acid Catalyzed by Aspirin-Acetylated Cyclooxygenase-2. ACS Catal 2019. [DOI: 10.1021/acscatal.9b04223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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10
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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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Kuhn H, Humeniuk L, Kozlov N, Roigas S, Adel S, Heydeck D. The evolutionary hypothesis of reaction specificity of mammalian ALOX15 orthologs. Prog Lipid Res 2018; 72:55-74. [PMID: 30237084 DOI: 10.1016/j.plipres.2018.09.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/04/2018] [Accepted: 09/13/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Hartmut Kuhn
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Charitéplatz 1, CCO- Building, Virchowweg 6, D-10117 Berlin, Germany.
| | - Lia Humeniuk
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Charitéplatz 1, CCO- Building, Virchowweg 6, D-10117 Berlin, Germany
| | - Nikita Kozlov
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Charitéplatz 1, CCO- Building, Virchowweg 6, D-10117 Berlin, Germany
| | - Sophie Roigas
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Charitéplatz 1, CCO- Building, Virchowweg 6, D-10117 Berlin, Germany
| | - Susan Adel
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Internal Medicine, Division of Hepathology and Gastroenterology, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Dagmar Heydeck
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Biochemistry, Charitéplatz 1, CCO- Building, Virchowweg 6, D-10117 Berlin, Germany
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