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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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Kim W, Chen TY, Cha L, Zhou G, Xing K, Canty NK, Zhang Y, Chang WC. Elucidation of divergent desaturation pathways in the formation of vinyl isonitrile and isocyanoacrylate. Nat Commun 2022; 13:5343. [PMID: 36097268 PMCID: PMC9467999 DOI: 10.1038/s41467-022-32870-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/19/2022] [Indexed: 11/10/2022] Open
Abstract
Two different types of desaturations are employed by iron- and 2-oxoglutarate-dependent (Fe/2OG) enzymes to construct vinyl isonitrile and isocyanoacrylate moieties found in isonitrile-containing natural products. A substrate-bound protein structure reveals a plausible strategy to affect desaturation and hints at substrate promiscuity of these enzymes. Analogs are synthesized and used as mechanistic probes to validate structural observations. Instead of proceeding through hydroxylated intermediate as previously proposed, a plausible carbocation species is utilized to trigger C=C bond installation. These Fe/2OG enzymes can also accommodate analogs with opposite chirality and different functional groups including isonitrile-(D)-tyrosine, N-formyl tyrosine, and phloretic acid, while maintaining the reaction selectivity. While canonical oxygen-rebound pathway has been utilized by several Fe/2OG enzymes, insights into the desaturation process remain to be elucidated. Here, the authors suggest that a carbocation might be deployed to enable chemically divergent desaturations through decarboxylation and deprotonation.
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Parkinson EI, Lakkis HG, Alwali AA, Metcalf MEM, Modi R, Metcalf WW. An Unusual Oxidative Rearrangement Catalyzed by a Divergent Member of the 2-Oxoglutarate-Dependent Dioxygenase Superfamily during Biosynthesis of Dehydrofosmidomycin. Angew Chem Int Ed Engl 2022; 61:e202206173. [PMID: 35588368 PMCID: PMC9296572 DOI: 10.1002/anie.202206173] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Indexed: 12/20/2022]
Abstract
The biosynthesis of the natural product dehydrofosmidomycin involves an unusual transformation in which 2-(trimethylamino)ethylphosphonate is rearranged, desaturated and demethylated by the enzyme DfmD, a divergent member of the 2-oxoglutarate-dependent dioxygenase superfamily. Although other members of this enzyme family catalyze superficially similar transformations, the combination of all three reactions in a single enzyme has not previously been observed. By characterizing the products of in vitro reactions with labeled and unlabeled substrates, we show that DfmD performs this transformation in two steps, with the first involving desaturation of the substrate to form 2-(trimethylamino)vinylphosphonate, and the second involving rearrangement and demethylation to form methyldehydrofosmidomycin. These data reveal significant differences from the desaturation and rearrangement reactions catalyzed by other family members.
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Affiliation(s)
- Elizabeth I. Parkinson
- Institute for Genomic BiologyUniversity of Illinois at Urbana-Champaign1206 W. Gregory Dr.UrbanaIL 61801USA
- Department of ChemistryPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
- Department of Medicinal Chemistry and Molecular PharmacologyPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
| | - Hani G. Lakkis
- Department of ChemistryPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
| | - Amir A. Alwali
- Department of ChemistryPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
| | - Mary Elizabeth M. Metcalf
- Institute for Genomic BiologyUniversity of Illinois at Urbana-Champaign1206 W. Gregory Dr.UrbanaIL 61801USA
- Department of MicrobiologyUniversity of Illinois at Urbana-Champaign, B103C&LSL601 S. GoodwinUrbanaIL 61801USA
| | - Ramya Modi
- Department of ChemistryPurdue UniversityHerbert C. Brown Laboratory of Chemistry, Room 4103E560 Oval Drive, Box 59West LafayetteIN 47907USA
| | - William W. Metcalf
- Institute for Genomic BiologyUniversity of Illinois at Urbana-Champaign1206 W. Gregory Dr.UrbanaIL 61801USA
- Department of MicrobiologyUniversity of Illinois at Urbana-Champaign, B103C&LSL601 S. GoodwinUrbanaIL 61801USA
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Liu Y, Liu Y. Computational Study of Aromatic Hydroxylation Catalyzed by the Iron-Dependent Hydroxylase PqqB Involved in the Biosynthesis of Redox Cofactor Pyrroloquinoline Quinone. Inorg Chem 2022; 61:5943-5956. [PMID: 35362953 DOI: 10.1021/acs.inorgchem.2c00419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PqqB from Methylobacterium extorquens is a unique nonheme iron-dependent hydroxylase involved in the biosynthesis of redox cofactor pyrroloquinoline quinone (PQQ). A series of recent experiments have demonstrated that PqqB catalyzes the stepwise insertions of two oxygen atoms into the tyrosine ring of the diamino acid substrate, generating the quinone moiety of PQQ; however, the reaction details have not been elucidated yet. In this paper, on the basis of the crystal structures, the enzyme-substrate complex models were constructed, and the catalytic mechanism of PqqB was explored by performing a series of combined QM/MM calculations. Our results confirmed that the first hydroxylation is performed by the highly reactive FeIV-oxo species and follows the typical H-abstraction/hydroxyl rebound mechanism, which is similar to the common aliphatic hydroxylation catalyzed by the α-KG enzymes. Nevertheless, the second hydroxylation is achieved by the Fe-O2 species, and the reactant complex can be described as an intermediate radical-FeII-superoxide, that is, the dioxygen is activated by accepting an electron from the bidentate coordination intermediate. Since both the dioxygen and intermediate are activated by electron transfer, the distal oxygen of superoxide can directly attack the carbonyl carbon of substrate to form an alkylperoxo intermediate, then the O-O heterolysis occurs to afford the epoxide intermediate, which finally evolves into the product by rearrangement. It is the bidentate coordination of catechol moiety to iron that leads to the one-electron oxidation of the substrate by the dioxygen, which significantly activates the substrate and promotes the superoxide radical attack. During the catalysis, Asp90 and His240 in the second sphere play an important role by acting as acid-base catalysts to mediate the proton transfer and manipulate the suitable orientation of superoxide. These findings may provide useful information for understanding the unique reaction mechanism of PqqB that employs both the FeIV-oxo and FeII-superoxide to carry out the aromatic hydroxylation.
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Affiliation(s)
- Yaru Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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Wojdyla Z, Borowski T. Properties of the Reactants and Their Interactions within and with the Enzyme Binding Cavity Determine Reaction Selectivities. The Case of Fe(II)/2-Oxoglutarate Dependent Enzymes. Chemistry 2022; 28:e202104106. [PMID: 34986268 DOI: 10.1002/chem.202104106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 12/12/2022]
Abstract
Fe(II)/2-oxoglutarate dependent dioxygenases (ODDs) share a double stranded beta helix (DSBH) fold and utilise a common reactive intermediate, ferryl species, to catalyse oxidative transformations of substrates. Despite the structural similarities, ODDs accept a variety of substrates and facilitate a wide range of reactions, that is hydroxylations, desaturations, (oxa)cyclisations and ring rearrangements. In this review we present and discuss the factors contributing to the observed (regio)selectivities of ODDs. They span from inherent properties of the reactants, that is, substrate molecule and iron cofactor, to the interactions between the substrate and the enzyme's binding cavity; the latter can counterbalance the effect of the former. Based on results of both experimental and computational studies dedicated to ODDs, we also line out the properties of the reactants which promote reaction outcomes other than the "default" hydroxylation. It turns out that the reaction selectivity depends on a delicate balance of interactions between the components of the investigated system.
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Affiliation(s)
- Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
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