1
|
Bui S, Gil-Guerrero S, van der Linden P, Carpentier P, Ceccarelli M, Jambrina PG, Steiner RA. Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the α/β-hydrolase fold. Chem Sci 2023; 14:10547-10560. [PMID: 37799987 PMCID: PMC10548524 DOI: 10.1039/d3sc03044j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/31/2023] [Indexed: 10/07/2023] Open
Abstract
Protein fold adaptation to novel enzymatic reactions is a fundamental evolutionary process. Cofactor-independent oxygenases degrading N-heteroaromatic substrates belong to the α/β-hydrolase (ABH) fold superfamily that typically does not catalyze oxygenation reactions. Here, we have integrated crystallographic analyses under normoxic and hyperoxic conditions with molecular dynamics and quantum mechanical calculations to investigate its prototypic 1-H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase (HOD) member. O2 localization to the "oxyanion hole", where catalysis occurs, is an unfavorable event and the direct competition between dioxygen and water for this site is modulated by the "nucleophilic elbow" residue. A hydrophobic pocket that overlaps with the organic substrate binding site can act as a proximal dioxygen reservoir. Freeze-trap pressurization allowed the structure of the ternary complex with a substrate analogue and O2 bound at the oxyanion hole to be determined. Theoretical calculations reveal that O2 orientation is coupled to the charge of the bound organic ligand. When 1-H-3-hydroxy-4-oxoquinaldine is uncharged, O2 binds with its molecular axis along the ligand's C2-C4 direction in full agreement with the crystal structure. Substrate activation triggered by deprotonation of its 3-OH group by the His-Asp dyad, rotates O2 by approximately 60°. This geometry maximizes the charge transfer between the substrate and O2, thus weakening the double bond of the latter. Electron density transfer to the O2(π*) orbital promotes the formation of the peroxide intermediate via intersystem crossing that is rate-determining. Our work provides a detailed picture of how evolution has repurposed the ABH-fold architecture and its simple catalytic machinery to accomplish metal-independent oxygenation.
Collapse
Affiliation(s)
- Soi Bui
- Randall Centre for Cell and Molecular Biophysics, King's College London London SE1 1UL UK
| | - Sara Gil-Guerrero
- Departamento de Química Física, University of Salamanca Salamanca 37008 Spain
| | - Peter van der Linden
- European Synchrotron Radiation Facility (ESRF), Partnership for Soft Condensed Matter (PSCM) 71 Avenue des Martyrs Grenoble 38000 France
| | - Philippe Carpentier
- European Synchrotron Radiation Facility (ESRF) 71 Avenue des Martyrs 38043 Grenoble France
- Université Grenoble Alpes, CNRS, CEA, Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM) UMR 5249 17 Avenue des Martyrs 38054 Grenoble France
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari Monserrato 09042 Italy
- IOM-CNR Unità di Cagliari, Cittadella Universitaria Monserrato 09042 Italy
| | - Pablo G Jambrina
- Departamento de Química Física, University of Salamanca Salamanca 37008 Spain
| | - Roberto A Steiner
- Randall Centre for Cell and Molecular Biophysics, King's College London London SE1 1UL UK
- Department of Biomedical Sciences, University of Padova Italy
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Ortega P, Gil-Guerrero S, González-Sánchez L, Sanz-Sanz C, Jambrina PG. Spin-Forbidden Addition of Molecular Oxygen to Stable Enol Intermediates-Decarboxylation of 2-Methyl-1-tetralone-2-carboxylic Acid. Int J Mol Sci 2023; 24:ijms24087424. [PMID: 37108586 PMCID: PMC10138960 DOI: 10.3390/ijms24087424] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The deprotonation of an organic substrate is a common preactivation step for the enzymatic cofactorless addition of O2 to this substrate, as it promotes charge-transfer between the two partners, inducing intersystem crossing between the triplet and singlet states involved in the process. Nevertheless, the spin-forbidden addition of O2 to uncharged ligands has also been observed in the laboratory, and the detailed mechanism of how the system circumvents the spin-forbiddenness of the reaction is still unknown. One of these examples is the cofactorless peroxidation of 2-methyl-3,4-dihydro-1-naphthol, which will be studied computationally using single and multi-reference electronic structure calculations. Our results show that the preferred mechanism is that in which O2 picks a proton from the substrate in the triplet state, and subsequently hops to the singlet state in which the product is stable. For this reaction, the formation of the radical pair is associated with a higher barrier than that associated with the intersystem crossing, even though the absence of the negative charge leads to relatively small values of the spin-orbit coupling.
Collapse
Affiliation(s)
- Pablo Ortega
- Departamento de Química-Física, Universidad de Salamanca, 37008 Salamanca, Spain
| | - Sara Gil-Guerrero
- Departamento de Química-Física, Universidad de Salamanca, 37008 Salamanca, Spain
- CICECO-Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
| | | | - Cristina Sanz-Sanz
- Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Pablo G Jambrina
- Departamento de Química-Física, Universidad de Salamanca, 37008 Salamanca, Spain
| |
Collapse
|
4
|
Li X, Li X, Zhang QY, Lv P, Jia Y, Wei D. Cofactor-free ActVA-Orf6 monooxygenase catalysis via proton-coupled electron transfer: A QM/MM study. Org Biomol Chem 2022; 20:5525-5534. [DOI: 10.1039/d2ob00848c] [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
Uncovering the comprehensive catalytic mechanism for the activation of triplet O2 through metal-free and cofactor-free oxidases and oxygenases remains one of the most challenging questions in the area of enzymatic...
Collapse
|
5
|
Klauda JB. Virtual Issue on Docking. J Phys Chem B 2021; 125:5455-5457. [PMID: 34078077 DOI: 10.1021/acs.jpcb.1c03303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland
| |
Collapse
|
6
|
Ortega P, Gil-Guerrero S, Veselinova A, Zanchet A, González-Sánchez L, Jambrina PG, Sanz-Sanz C. Multi- and single-reference methods for the analysis of multi-state peroxidation of enolates. J Chem Phys 2021; 154:144303. [PMID: 33858147 DOI: 10.1063/5.0046906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In spite of being spin-forbidden, some enzymes are capable of catalyzing the incorporation of O2(Σg-3) to organic substrates without needing any cofactor. It has been established that the process followed by these enzymes starts with the deprotonation of the substrate forming an enolate. In a second stage, the peroxidation of the enolate formation occurs, a process in which the system changes its spin multiplicity from a triplet state to a singlet state. In this article, we study the addition of O2 to enolates using state-of-the-art multi-reference and single-reference methods. Our results confirm that intersystem crossing is promoted by stabilization of the singlet state along the reaction path. When multi-reference methods are used, large active spaces are required, and in this situation, semistochastic heat-bath configuration interaction emerges as a powerful method to study these multi-configurational systems and is in good agreement with PNO-LCCSD(T) when the system is well-represented by a single-configuration.
Collapse
Affiliation(s)
- P Ortega
- Departamento de Química-Física, University of Salamanca, Salamanca 37008, Spain
| | - S Gil-Guerrero
- Departamento de Química-Física, University of Salamanca, Salamanca 37008, Spain
| | - A Veselinova
- Departamento de Química-Física, University of Salamanca, Salamanca 37008, Spain
| | - A Zanchet
- Instituto de Física Fundamental (CSIC), Madrid 28006, Spain
| | - L González-Sánchez
- Departamento de Química-Física, University of Salamanca, Salamanca 37008, Spain
| | - P G Jambrina
- Departamento de Química-Física, University of Salamanca, Salamanca 37008, Spain
| | - C Sanz-Sanz
- Departamento de Química Física Aplicada. Universidad Autónoma de Madrid, Madrid 28049, Spain
| |
Collapse
|
7
|
Ortega P, Zanchet A, Sanz-Sanz C, Gómez-Carrasco S, González-Sánchez L, Jambrina PG. DpgC-Catalyzed Peroxidation of 3,5-Dihydroxyphenylacetyl-CoA (DPA-CoA): Insights into the Spin-Forbidden Transition and Charge Transfer Mechanisms*. Chemistry 2020; 27:1700-1712. [PMID: 32975323 DOI: 10.1002/chem.202002993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Indexed: 11/06/2022]
Abstract
Despite being a very strong oxidizing agent, most organic molecules are not oxidized in the presence of O2 at room temperature because O2 is a diradical whereas most organic molecules are closed-shell. Oxidation then requires a change in the spin state of the system, which is forbidden according to non-relativistic quantum theory. To overcome this limitation, oxygenases usually rely on metal or redox cofactors to catalyze the incorporation of, at least, one oxygen atom into an organic substrate. However, some oxygenases do not require any cofactor, and the detailed mechanism followed by these enzymes remains elusive. To fill this gap, here the mechanism for the enzymatic cofactor-independent oxidation of 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) is studied by combining multireference calculations on a model system with QM/MM calculations. Our results reveal that intersystem crossing takes place without requiring the previous protonation of molecular oxygen. The characterization of the electronic states reveals that electron transfer is concomitant with the triplet-singlet transition. The enzyme plays a passive role in promoting the intersystem crossing, although spontaneous reorganization of the water wire connecting the active site with the bulk presets the substrate for subsequent chemical transformations. The results show that the stabilization of the singlet radical-pair between dioxygen and enolate is enough to promote spin-forbidden reaction without the need for neither metal cofactors nor basic residues in the active site.
Collapse
Affiliation(s)
- Pablo Ortega
- Departamento de Química Física, University of Salamanca, Salamanca, 37008, Spain
| | - Alexandre Zanchet
- Departamento de Química Física, University of Salamanca, Salamanca, 37008, Spain.,Instituto de Física Fundamental (CSIC), Madrid, 28006, Spain
| | - Cristina Sanz-Sanz
- Departamento de Química Física Aplicada, University Autónoma de Madrid, Madrid, 28049, Spain
| | | | | | - Pablo G Jambrina
- Departamento de Química Física, University of Salamanca, Salamanca, 37008, Spain
| |
Collapse
|
8
|
Bioengineering of Cytochrome P450 OleT JE: How Does Substrate Positioning Affect the Product Distributions? Molecules 2020; 25:molecules25112675. [PMID: 32526971 PMCID: PMC7321372 DOI: 10.3390/molecules25112675] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/29/2020] [Accepted: 06/04/2020] [Indexed: 02/04/2023] Open
Abstract
The cytochromes P450 are versatile enzymes found in all forms of life. Most P450s use dioxygen on a heme center to activate substrates, but one class of P450s utilizes hydrogen peroxide instead. Within the class of P450 peroxygenases, the P450 OleTJE isozyme binds fatty acid substrates and converts them into a range of products through the α-hydroxylation, β-hydroxylation and decarboxylation of the substrate. The latter produces hydrocarbon products and hence can be used as biofuels. The origin of these product distributions is unclear, and, as such, we decided to investigate substrate positioning in the active site and find out what the effect is on the chemoselectivity of the reaction. In this work we present a detailed computational study on the wild-type and engineered structures of P450 OleTJE using a combination of density functional theory and quantum mechanics/molecular mechanics methods. We initially explore the wild-type structure with a variety of methods and models and show that various substrate activation transition states are close in energy and hence small perturbations as through the protein may affect product distributions. We then engineered the protein by generating an in silico model of the double mutant Asn242Arg/Arg245Asn that moves the position of an active site Arg residue in the substrate-binding pocket that is known to form a salt-bridge with the substrate. The substrate activation by the iron(IV)-oxo heme cation radical species (Compound I) was again studied using quantum mechanics/molecular mechanics (QM/MM) methods. Dramatic differences in reactivity patterns, barrier heights and structure are seen, which shows the importance of correct substrate positioning in the protein and the effect of the second-coordination sphere on the selectivity and activity of enzymes.
Collapse
|
9
|
Ellis ES, MacHale LT, Szilagyi RK, DuBois JL. How Chemical Environment Activates Anthralin and Molecular Oxygen for Direct Reaction. J Org Chem 2020; 85:1315-1321. [PMID: 31830417 DOI: 10.1021/acs.joc.9b03133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The role of the chemical environment in promoting anthralin/O2 reactions was discovered using neat solvents to model the amino acids of a cofactor-independent oxygenase. Experimental and computational results highlight the importance of the substrate-enolate, which is accessed via energetically small, escalating steps in which the ground-state keto-isomer is tautomerized to an enol and then ionized by solvent. The resulting ion-pair is poised for spontaneous electron transfer to O2. Similar activation may be exploited in biological/nonbiological oxidations involving O2.
Collapse
Affiliation(s)
- Emerald S Ellis
- Department of Chemistry and Biochemistry , Montana State University , P.O. Box 173400, Bozeman , Montana 59717 , United States
| | - Luke T MacHale
- Department of Chemistry and Biochemistry , Montana State University , P.O. Box 173400, Bozeman , Montana 59717 , United States
| | - Robert K Szilagyi
- Department of Chemistry and Biochemistry , Montana State University , P.O. Box 173400, Bozeman , Montana 59717 , United States
| | - Jennifer L DuBois
- Department of Chemistry and Biochemistry , Montana State University , P.O. Box 173400, Bozeman , Montana 59717 , United States
| |
Collapse
|
10
|
Li H, Zhu W, Liu Y. Mechanism of Uncoupled Carbocyclization and Epimerization Catalyzed by Two Non-Heme Iron/α-Ketoglutarate Dependent Enzymes. J Chem Inf Model 2019; 59:5086-5098. [PMID: 31790238 DOI: 10.1021/acs.jcim.9b00837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The non-heme iron/α-ketoglutarate dependent enzymes SnoK and SnoN from Streptomyces nogalater are involved in the biosynthesis of anthracycline nogalamycin. Although they have similar active sites, SnoK is responsible for carbocyclization whereas SnoN solely catalyzes the hydroxyl epimerization. Herein, we performed docking, molecular simulations, and a series of combined quantum mechanics and molecular mechanics (QM/MM) calculations to illuminate the mechanisms of two enzymes. The catalytic reactions of two enzymes occur on the quintet state surface. For SnoK, the whole reaction includes two separated hydrogen-abstraction steps and one radical addition, and the latter step is calculated to be rate limiting with an energy barrier of 21.7 kcal/mol. Residue D106 is confirmed to participate in the construction of the hydrogen bond network, which plays a crucial role in positioning the bulky substrate in a specific orientation. Moreover, it is found that SnoN is only responsible for the hydrogen abstraction of the intermediate, and no residue was suggested to be suitable for donating a hydrogen atom to the substrate radical, which further confirms the suggestion based on experiments that either a cellular reductant or another enzyme protein could donate a hydrogen atom to the substrate. Our docking results coincide with the previous structural study that the different roles of two enzymes are achieved by minor changes in the alignment of the substrates in front of the reactive ferryl-oxo species. This work highlights the reaction mechanisms catalyzed by SnoK and SnoN, which is helpful for engineering the enzymes for the biosynthesis of anthracycline nogalamycin.
Collapse
Affiliation(s)
- Hong Li
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , Shandong 250100 , China
| | - Wenyou Zhu
- College of Chemistry and Chemical Engineering , Xuzhou Institute of Technology , Xuzhou , Jiangsu 221111 , China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , Shandong 250100 , China
| |
Collapse
|