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Torbjörnsson M, Hagemann MM, Ryde U, Hedegård ED. Histidine oxidation in lytic polysaccharide monooxygenase. J Biol Inorg Chem 2023; 28:317-328. [PMID: 36828975 PMCID: PMC10036459 DOI: 10.1007/s00775-023-01993-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/10/2023] [Indexed: 02/26/2023]
Abstract
The lytic polysaccharide monooxygenases (LPMOs) comprise a super-family of copper enzymes that boost the depolymerisation of polysaccharides by oxidatively disrupting the glycosidic bonds connecting the sugar units. Industrial use of LPMOs for cellulose depolymerisation has already begun but is still far from reaching its full potential. One issue is that the LPMOs self-oxidise and thereby deactivate. The mechanism of this self-oxidation is unknown, but histidine residues coordinating to the copper atom are the most susceptible. An unusual methyl modification of the NE2 atom in one of the coordinating histidine residues has been proposed to have a protective role. Furthermore, substrate binding is also known to reduce oxidative damage. We here for the first time investigate the mechanism of histidine oxidation with combined quantum and molecular mechanical (QM/MM) calculations, with outset in intermediates previously shown to form from a reaction with peroxide and a reduced LPMO. We show that an intermediate with a [Cu-O]+ moiety is sufficiently potent to oxidise the nearest C-H bond on both histidine residues, but methylation of the NE2 atom of His-1 increases the reaction barrier of this reaction. The substrate further increases the activation barrier. We also investigate a [Cu-OH]2+ intermediate with a deprotonated tyrosine radical. This intermediate was previously proposed to have a protective role, and we also find it to have higher barriers than the corresponding a [Cu-O]+ intermediate.
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Affiliation(s)
- Magne Torbjörnsson
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Marlisa M Hagemann
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden.
| | - Erik Donovan Hedegård
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden.
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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2
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Hagemann MM, Hedegård ED. Molecular Mechanism of Substrate Oxidation in Lytic Polysaccharide Monooxygenases: Insight from Theoretical Investigations. Chemistry 2023; 29:e202202379. [PMID: 36207279 PMCID: PMC10107554 DOI: 10.1002/chem.202202379] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 12/12/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes that today comprise a large enzyme superfamily, grouped into the distinct members AA9-AA17 (with AA12 exempted). The LPMOs have the potential to facilitate the upcycling of biomass waste products by boosting the breakdown of cellulose and other recalcitrant polysaccharides. The cellulose biopolymer is the main component of biomass waste and thus comprises a large, unexploited resource. The LPMOs work through a catalytic, oxidative reaction whose mechanism is still controversial. For instance, the nature of the intermediate performing the oxidative reaction is an open question, and the same holds for the employed co-substrate. Here we review theoretical investigations addressing these questions. The applied theoretical methods are usually based on quantum mechanics (QM), often combined with molecular mechanics (QM/MM). We discuss advantages and disadvantages of the employed theoretical methods and comment on the interplay between theoretical and experimental results.
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Affiliation(s)
- Marlisa M Hagemann
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Erik D Hedegård
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
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Zlobin A, Belyaeva J, Golovin A. Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms. J Chem Inf Model 2023; 63:546-560. [PMID: 36633836 DOI: 10.1021/acs.jcim.2c01071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) simulations fuel discoveries in many fields of science including computational biochemistry and enzymology. Development of more convenient tools leads to an increase in the number of works in which mechanical insights into enzymes' mode of operation are obtained. Most commonly, these tools feature hydrogen-capping (link atom) approach to provide coupling between QM and MM subsystems across a covalent bond. Extensive studies were conducted to provide a solid foundation for the correctness of such an approach when a bond to a nonpolar MM atom is considered. However, not every task may be accomplished this way. Certain scenarios of using QM/MM in computational enzymology encourage or even necessitate the incorporation of backbone atoms into the QM region. Two out of three backbone atoms are polar, and in QM/MM with electrostatic embedding, a neighboring link atom will be hyperpolarized. Several schemes to mitigate this effect were previously proposed alongside a rigorous assessment of quantitative effects on model systems. However, it was not clear whether they may translate into qualitatively different results and how link atom hyperpolarization may manifest itself in a real-life enzymological scenario. Here, we show that the consequences of such an artifact may be severe and may completely overturn the conclusions drawn from the simulations. Our case advocates for the use of charge redistribution schemes whenever intra-backbone QM/MM boundaries are considered. Moreover, we addressed how different boundary types and charge redistribution schemes influence backbone dynamics. We showed that the results are heavily dependent on which boundary MM terms are retained, with charge alteration being of secondary importance. In the worst case, only three intra-backbone boundaries may be used with relative confidence in the adequacy of resulting simulations, irrespective of the hyperpolarization mitigation scheme. Thus, advances in the field are certainly needed to fuel new discoveries. As of now, we believe that issues raised in this work might encourage authors in the field to report what boundaries, boundary MM terms, and charge redistribution schemes they are using, so their results may be correctly interpreted.
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Affiliation(s)
- Alexander Zlobin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Julia Belyaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Andrey Golovin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
- Sirius University of Science and Technology, 354340 Sochi, Russia
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Tandrup T, Muderspach SJ, Banerjee S, Santoni G, Ipsen JØ, Hernández-Rollán C, Nørholm MHH, Johansen KS, Meilleur F, Lo Leggio L. Changes in active-site geometry on X-ray photoreduction of a lytic polysaccharide monooxygenase active-site copper and saccharide binding. IUCRJ 2022; 9:666-681. [PMID: 36071795 PMCID: PMC9438499 DOI: 10.1107/s2052252522007175] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
The recently discovered lytic polysaccharide monooxygenases (LPMOs) are Cu-containing enzymes capable of degrading polysaccharide substrates oxidatively. The generally accepted first step in the LPMO reaction is the reduction of the active-site metal ion from Cu2+ to Cu+. Here we have used a systematic diffraction data collection method to monitor structural changes in two AA9 LPMOs, one from Lentinus similis (LsAA9_A) and one from Thermoascus auranti-acus (TaAA9_A), as the active-site Cu is photoreduced in the X-ray beam. For LsAA9_A, the protein produced in two different recombinant systems was crystallized to probe the effect of post-translational modifications and different crystallization conditions on the active site and metal photoreduction. We can recommend that crystallographic studies of AA9 LPMOs wishing to address the Cu2+ form use a total X-ray dose below 3 × 104 Gy, while the Cu+ form can be attained using 1 × 106 Gy. In all cases, we observe the transition from a hexa-coordinated Cu site with two solvent-facing ligands to a T-shaped geometry with no exogenous ligands, and a clear increase of the θ2 parameter and a decrease of the θ3 parameter by averages of 9.2° and 8.4°, respectively, but also a slight increase in θT. Thus, the θ2 and θ3 parameters are helpful diagnostics for the oxidation state of the metal in a His-brace protein. On binding of cello-oligosaccharides to LsAA9_A, regardless of the production source, the θT parameter increases, making the Cu site less planar, while the active-site Tyr-Cu distance decreases reproducibly for the Cu2+ form. Thus, the θT increase found on copper reduction may bring LsAA9_A closer to an oligosaccharide-bound state and contribute to the observed higher affinity of reduced LsAA9_A for cellulosic substrates.
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Affiliation(s)
- Tobias Tandrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK, Copenhagen, Denmark
| | - Sebastian J. Muderspach
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK, Copenhagen, Denmark
| | - Sanchari Banerjee
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK, Copenhagen, Denmark
| | - Gianluca Santoni
- ESRF, Structural Biology Group, 71 avenue des Martyrs, 38027 Grenoble cedex, France
| | - Johan Ø. Ipsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958-DK, Frederiksberg, Denmark
| | - Cristina Hernández-Rollán
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800-DK, Kgs. Lyngby, Denmark
| | - Morten H. H. Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800-DK, Kgs. Lyngby, Denmark
| | - Katja S. Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1958-DK, Frederiksberg, Denmark
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Campus Box 7622, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100-DK, Copenhagen, Denmark
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Da Silva WDB, Dias RP, Da Silva JCS. Refining details of the structural and electronic properties of the Cu B site in pMMO enzyme through sequential molecular dynamics/CPKS-EPR calculations. Phys Chem Chem Phys 2022; 24:16611-16621. [PMID: 35730560 DOI: 10.1039/d2cp01217k] [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
This work investigated the structural and electronic properties of the copper mononuclear site of the PmoB part of the pMMO enzyme at the molecular level. We propose that the CuB catalytic site in the soluble portion of pMMO at room temperature and under physiological conditions is a mononuclear copper complex in a distorted octahedral arrangement with the residues His33, His137, and His139 on the equatorial base and two water molecules on the axial axis. Our view was based on the molecular dynamics results and DFT calculations of the electronic paramagnetic resonance parameters and comparisons with experimental EPR data. This new proposed model for the CuB site brings additional support concerning the recent experimental evidence, which pointed out that a saturated coordination sphere of the copper ion in the CuB center is an essential factor that makes it less efficient than the CuC site in the methane oxidation. Therefore, according to the CuB site model proposed here, an additional step involving a displacement of at least one water molecule of the copper coordination sphere by the O2 molecule prior to its activation must be necessary. This scenario is less likely to occur in the CuC center once this one is buried in the alpha-helices, which are part of the pMMO structure bound to the membrane wall, and consequently located in a less solvent-exposed region. In addition, we also present a simple and efficient sequential S-MD/CPKS protocol to compute EPR parameters that can, in principle, be expanded for the study of other copper-containing proteins.
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Affiliation(s)
- William Daniel B Da Silva
- LQCBio: Laboratório de Química Computacional e Modelagem de Biomoléculas, Instituto de Química e Biotecnologia, IQB, Universidade Federal de Alagoas, Campus A. C. Simões, 57072-900, Maceió, AL, Brazil.
| | - Roberta P Dias
- GIMMM: Grupo Interdisciplinar de Modelagem Molecular e Simulação de Materiais, Núcleo Interdisciplinar de Ciências Exatas e da Natureza - NICEN, Campus do Agreste, Universidade Federal de Pernambuco, 55002-970, Caruaru, PE, Brazil
| | - Júlio C S Da Silva
- LQCBio: Laboratório de Química Computacional e Modelagem de Biomoléculas, Instituto de Química e Biotecnologia, IQB, Universidade Federal de Alagoas, Campus A. C. Simões, 57072-900, Maceió, AL, Brazil.
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Gómez-Piñeiro R, Drosou M, Bertaina S, Decroos C, Simaan AJ, Pantazis DA, Orio M. Decoding the Ambiguous Electron Paramagnetic Resonance Signals in the Lytic Polysaccharide Monooxygenase from Photorhabdus luminescens. Inorg Chem 2022; 61:8022-8035. [PMID: 35549254 PMCID: PMC9131454 DOI: 10.1021/acs.inorgchem.2c00766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Indexed: 11/29/2022]
Abstract
Understanding the structure and function of lytic polysaccharide monooxygenases (LPMOs), copper enzymes that degrade recalcitrant polysaccharides, requires the reliable atomistic interpretation of electron paramagnetic resonance (EPR) data on the Cu(II) active site. Among various LPMO families, the chitin-active PlAA10 shows an intriguing phenomenology with distinct EPR signals, a major rhombic and a minor axial signal. Here, we combine experimental and computational investigations to uncover the structural identity of these signals. X-band EPR spectra recorded at different pH values demonstrate pH-dependent population inversion: the major rhombic signal at pH 6.5 becomes minor at pH 8.5, where the axial signal dominates. This suggests that a protonation change is involved in the interconversion. Precise structural interpretations are pursued with quantum chemical calculations. Given that accurate calculations of Cu g-tensors remain challenging for quantum chemistry, we first address this problem via a thorough calibration study. This enables us to define a density functional that achieves accurate and reliable prediction of g-tensors, giving confidence in our evaluation of PlAA10 LPMO models. Large models were considered that include all parts of the protein matrix surrounding the Cu site, along with the characteristic second-sphere features of PlAA10. The results uniquely identify the rhombic signal with a five-coordinate Cu ion bearing two water molecules in addition to three N-donor ligands. The axial signal is attributed to a four-coordinate Cu ion where only one of the waters remains bound, as hydroxy. Alternatives that involve decoordination of the histidine brace amino group are unlikely based on energetics and spectroscopy. These results provide a reliable spectroscopy-consistent view on the plasticity of the resting state in PlAA10 LPMO as a foundation for further elucidating structure-property relationships and the formation of catalytically competent species. Our strategy is generally applicable to the study of EPR parameters of mononuclear copper-containing metalloenzymes.
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Affiliation(s)
| | - Maria Drosou
- Inorganic
Chemistry Laboratory, National and Kapodistrian
University of Athens, Panepistimiopolis, Zografou 15771, Greece
| | - Sylvain Bertaina
- Aix-Marseille
Université, CNRS, IM2NP UMR 7334, Marseille 13397, France
| | - Christophe Decroos
- Aix
Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille 13397, France
| | - A. Jalila Simaan
- Aix
Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille 13397, France
| | - Dimitrios A. Pantazis
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an
der Ruhr 45470, Germany
| | - Maylis Orio
- Aix
Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille 13397, France
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EPR Spectroscopy of Cu(II) Complexes: Prediction of g-Tensors Using Double-Hybrid Density Functional Theory. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8040036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Computational electron paramagnetic resonance (EPR) spectroscopy is an important field of applied quantum chemistry that contributes greatly to connecting spectroscopic observations with the fundamental description of electronic structure for open-shell molecules. However, not all EPR parameters can be predicted accurately and reliably for all chemical systems. Among transition metal ions, Cu(II) centers in inorganic chemistry and biology, and their associated EPR properties such as hyperfine coupling and g-tensors, pose exceptional difficulties for all levels of quantum chemistry. In the present work, we approach the problem of Cu(II) g-tensor calculations using double-hybrid density functional theory (DHDFT). Using a reference set of 18 structurally and spectroscopically characterized Cu(II) complexes, we evaluate a wide range of modern double-hybrid density functionals (DHDFs) that have not been applied previously to this problem. Our results suggest that the current generation of DHDFs consistently and systematically outperform other computational approaches. The B2GP-PLYP and PBE0-DH functionals are singled out as the best DHDFs on average for the prediction of Cu(II) g-tensors. The performance of the different functionals is discussed and suggestions are made for practical applications and future methodological developments.
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Lindley PJ, Parkin A, Davies GJ, Walton PH. Mapping the protonation states of the histidine brace in an AA10 lytic polysaccharide monooxygenase using CW-EPR spectroscopy and DFT calculations. Faraday Discuss 2022; 234:336-348. [PMID: 35171174 DOI: 10.1039/d1fd00068c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The active site of the polysaccharide-degrading lytic polysaccharide monooxygenase (LPMO) enzyme features a single copper ion coordinated by a histidine brace. The primary coordination sphere of the copper contains several ligating atoms which are bonded to ionisable protons (e.g. OH2, NH2), the pKas of which are unknown. Using a combination of CW-EPR X-band spectroscopy over a range of pH values and DFT calculations, we show that the active site of a chitin-active AA10 LPMO can exist in three different protonation states (pKa1 = 8.7, pKa2 ∼ 11.5), representing the ionisation of the coordinating groups. The middle pH species (fully formed at pH ∼ 10.5) is proposed to be Cu(II)(His)2(OH)2 (N2O2 coordination) with a decoordinated R-NH3+ group at the amino terminus. This species also sees a rotation of the SOMO equatorial plane from the canonical histidine brace plane, whereby the nominal Cu d(x2 - y2)-orbital has rotated some 45° along the His-Cu(II)-His axis, driven by the elongation and decoordination of the amino group. The highest pH species (>12) is proposed to exist as a Cu(II)-azanide, in which the NH2 of the amino terminus has been deprotonated. The high pH means that this species is unlikely to be biologically relevant in the catalytic cycle of AA10 LPMOs.
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Affiliation(s)
- Peter J Lindley
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Alison Parkin
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Paul H Walton
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
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Zou J, Chen Y, Feng W. Mechanism of DOPA radical generation and transfer in metal-free class Ie ribonucleotide reductase based on density functional theory. Comput Struct Biotechnol J 2022; 20:1111-1131. [PMID: 35317236 PMCID: PMC8902622 DOI: 10.1016/j.csbj.2022.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 11/12/2022] Open
Abstract
The mechanism of DOPA radical generation, transfer and regeneration is revealed. The superoxide O2•− should be protonated to HO2• prior to oxidizing Tyr126 to DOPA radical. The protonation of Asp88 is the prerequisite for the DOPA radical generation and radical transfer. Lys213 is a key residue for the transfer of the DOPA radical.
Quantum mechanical/molecular mechanical (QM/MM) calculations were carried out to investigate the mechanisms of the generation, transfer, and regeneration of the DOPA radical for metal-free class Ie ribonucleotide reductase. The crystal structure of MfR2 (Nature, 2018, 563, 416–420) was adopted for the calculations. The QM/MM calculations have revealed several key points that are vital for understanding the mechanisms. The superoxide O2•− provided by the flavoprotein NrdI cannot directly oxidize the residue Tyr126 to the DOPA radical. It should be protonated to HO2•. The calculation results suggest that the covalent modification of Tyr126 and the DOPA radical generation can be carried out with no involvement of metal cofactors. This addresses the concerns of the articles (Nature, 2018, 563, 416–420; PNAS, 2018, 115, 10022–10027). Another concern from the articles is that how the DOPA radical is transferred from the radical trap. The DFT calculations have demonstrated that Lys213 is a key residue for the radical transfer from the DOPA radical. The ε-amino group of Lys213 is used not only as a bridge for the electron transfer but also as a proton donor. It can provide a proton to DOPA126 via a water molecule, and thus the radical transfer from DOPA126 to Trp52 is facilitated. It has also been revealed that the protonation of Asp88 is the prerequisite for the DOPA radical generation and the radical transfer in class Ie. Once the radical is quenched, it can be regenerated via the oxidations by superoxide O2•− and hydroperoxyl radical HO2•.
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