1
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De Santis E, Alleva S, Minicozzi V, Morante S, Stellato F. Probing the Dynamic Landscape: From Static to Time-Resolved X-Ray Absorption Spectroscopy to Investigate Copper Redox Chemistry in Neurodegenerative Disorders. Chempluschem 2024; 89:e202300712. [PMID: 38526934 DOI: 10.1002/cplu.202300712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
Copper (Cu), with its ability to exist in various oxidation states, notably Cu(I) and Cu(II), plays a crucial role in diverse biological redox reactions. This includes its involvement in pathways associated with oxidative stress in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Transmissible Spongiform Encephalopathies. This paper offers an overview of X-ray Absorption Spectroscopy (XAS) studies designed to elucidate the interactions between Cu ions and proteins or peptides associated with these neurodegenerative diseases. The emphasis lies on XAS specificity, revealing the local coordination environment, and on its sensitivity to Cu oxidation states. Furthermore, the paper focuses on XAS applications targeting the characterization of intermediate reaction states and explores the opportunities arising from recent advancements in time-resolved XAS at ultrabright synchrotron and Free Electron Laser radiation sources.
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Affiliation(s)
- Emiliano De Santis
- Department of Chemistry-BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Stefania Alleva
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Velia Minicozzi
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Silvia Morante
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
| | - Francesco Stellato
- Department of Physics, University of Rome, Tor Vergata, Rome, 00133, Italy
- INFN, Rome, Tor Vergata, Rome, 00133, Italy
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2
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Munzone A, Pujol M, Tamhankar A, Joseph C, Mazurenko I, Réglier M, Jannuzzi SAV, Royant A, Sicoli G, DeBeer S, Orio M, Simaan AJ, Decroos C. Integrated Experimental and Theoretical Investigation of Copper Active Site Properties of a Lytic Polysaccharide Monooxygenase from Serratia marcescens. Inorg Chem 2024; 63:11063-11078. [PMID: 38814816 DOI: 10.1021/acs.inorgchem.4c00602] [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: 06/01/2024]
Abstract
In this paper, we employed a multidisciplinary approach, combining experimental techniques and density functional theory (DFT) calculations to elucidate key features of the copper coordination environment of the bacterial lytic polysaccharide monooxygenase (LPMO) from Serratia marcescens (SmAA10). The structure of the holo-enzyme was successfully obtained by X-ray crystallography. We then determined the copper(II) binding affinity using competing ligands and observed that the affinity of the histidine brace ligands for copper is significantly higher than previously described. UV-vis, advanced electron paramagnetic resonance (EPR), and X-ray absorption spectroscopy (XAS) techniques, including high-energy resolution fluorescence detected (HERFD) XAS, were further used to gain insight into the copper environment in both the Cu(II) and Cu(I) redox states. The experimental data were successfully rationalized by DFT models, offering valuable information on the electronic structure and coordination geometry of the copper center. Finally, the Cu(II)/Cu(I) redox potential was determined using two different methods at ca. 350 mV vs NHE and rationalized by DFT calculations. This integrated approach not only advances our knowledge of the active site properties of SmAA10 but also establishes a robust framework for future studies of similar enzymatic systems.
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Affiliation(s)
- Alessia Munzone
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Manon Pujol
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Ashish Tamhankar
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Chris Joseph
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | | | - Marius Réglier
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Sergio A V Jannuzzi
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Antoine Royant
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), Grenoble 38000, France
- European Synchrotron Radiation Facility, Grenoble 38043, France
| | - Giuseppe Sicoli
- LASIRE UMR CNRS 8516, Université de Lille, Villeneuve-d'Arcy 59655, France
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Maylis Orio
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - A Jalila Simaan
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
| | - Christophe Decroos
- Aix Marseille Univ, CNRS, Centrale Méditerranée, iSm2, Marseille 13013, France
- Department of Integrative Structural Biology, Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch 67400, France
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3
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Shelley KL, Garman EF. Identifying and avoiding radiation damage in macromolecular crystallography. Acta Crystallogr D Struct Biol 2024; 80:314-327. [PMID: 38700059 PMCID: PMC11066884 DOI: 10.1107/s2059798324003243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
Radiation damage remains one of the major impediments to accurate structure solution in macromolecular crystallography. The artefacts of radiation damage can manifest as structural changes that result in incorrect biological interpretations being drawn from a model, they can reduce the resolution to which data can be collected and they can even prevent structure solution entirely. In this article, we discuss how to identify and mitigate against the effects of radiation damage at each stage in the macromolecular crystal structure-solution pipeline.
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Affiliation(s)
- Kathryn L. Shelley
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
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4
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Wieduwilt EK, Lo Leggio L, Hedegård ED. A frontier-orbital view of the initial steps of lytic polysaccharide monooxygenase reactions. Dalton Trans 2024; 53:5796-5807. [PMID: 38445349 DOI: 10.1039/d3dt04275h] [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: 03/07/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes that oxidatively cleave the strong C-H bonds in recalcitrant polysaccharide substrates, thereby playing a crucial role in biomass degradation. Recently, LPMOs have also been shown to be important for several pathogens. It is well established that the Cu(II) resting state of LPMOs is inactive, and the electronic structure of the active site needs to be altered to transform the enzyme into an active form. Whether this transformation occurs due to substrate binding or due to a unique priming reduction has remained speculative. Starting from four different crystal structures of the LPMO LsAA9A with well-defined oxidation states, we use a frontier molecular orbital approach to elucidate the initial steps of the LPMO reaction. We give an explanation for the requirement of the unique priming reduction and analyse electronic structure changes upon substrate binding. We further investigate how the presence of the substrate could facilitate an electron transfer from the copper active site to an H2O2 co-substrate. Our findings could help to control experimental LPMO reactions.
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Affiliation(s)
- Erna Katharina Wieduwilt
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Erik Donovan Hedegård
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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5
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Hasan WANBW, Nezhad NG, Yaacob MA, Salleh AB, Rahman RNZRA, Leow TC. Shifting the pH profiles of Staphylococcus epidermidis lipase (SEL) and Staphylococcus hyicus lipase (SHL) through generating chimeric lipases by DNA shuffling strategy. World J Microbiol Biotechnol 2024; 40:106. [PMID: 38386107 DOI: 10.1007/s11274-024-03927-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Enzymes are often required to function in a particular reaction condition by the industrial procedure. In order to identify critical residues affecting the optimum pH of Staphylococcal lipases, chimeric lipases from homologous lipases were generated via a DNA shuffling strategy. Chimeric 1 included mutations of G166S, K212E, T243A, H271Y. Chimeric 2 consisted of substitutions of K212E, T243A, H271Y. Chimeric 3 contained substitutions of K212E, R359L. From the screening results, the pH profiles for chimeric 1 and 2 lipases were shifted from pH 7 to 6. While the pH of chimeric 3 was shifted to 8. It seems the mutation of K212E in chimeric 1 and 2 decreased the pH to 6 by changing the electrostatic potential surface. Furthermore, chimeric 3 showed 10 ˚C improvement in the optimum temperature due to the rigidification of the catalytic loop through the hydrophobic interaction network. Moreover, the substrate specificity of chimeric 1 and 2 was increased towards the longer carbon length chains due to the mutation of T243A adjacent to the lid region through increasing the flexibility of the lid. Current study illustrated that directed evolution successfully modified lipase properties including optimum pH, temperature and substrate specificity through mutations, especially near catalytic and lid regions.
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Affiliation(s)
- Wan Atiqah Najiah Binti Wan Hasan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Mohd Adilin Yaacob
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Abu Bakar Salleh
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abdul Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
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6
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Kumar A, Singh A, Sharma VK, Goel A, Kumar A. The upsurge of lytic polysaccharide monooxygenases in biomass deconstruction: characteristic functions and sustainable applications. FEBS J 2024. [PMID: 38291603 DOI: 10.1111/febs.17063] [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: 08/03/2023] [Revised: 12/19/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are one of the emerging classes of copper metalloenzymes that have received considerable attention due to their ability to boost the enzymatic conversion of intractable polysaccharides such as plant cell walls and chitin polymers. LPMOs catalyze the oxidative cleavage of β-1,4-glycosidic bonds using molecular O2 or H2 O2 in the presence of an external electron donor. LPMOs have been classified as an auxiliary active (AA) class of enzymes and, further based on substrate specificity, divided into eight families. Until now, multiple LPMOs from AA9 and AA10 families, mostly from microbial sources, have been investigated; the exact mechanism and structure-function are elusive to date, and recently discovered AA families of LPMOs are just scratched. This review highlights the origin and discovery of the enzyme, nomenclature, three-dimensional protein structure, substrate specificity, copper-dependent reaction mechanism, and different techniques used to determine the product formation through analytical and biochemical methods. Moreover, the diverse functions of proteins in various biological activities such as plant-pathogen/pest interactions, cell wall remodeling, antibiotic sensitivity of biofilms, and production of nanocellulose along with certain obstacles in deconstructing the complex polysaccharides have also been summarized, while highlighting the innovative and creative ways to overcome the limitations of LPMOs in hydrolyzing the biomass.
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Affiliation(s)
- Asheesh Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Aishwarya Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Vijay Kumar Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Akshita Goel
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Arun Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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7
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Garman EF, Weik M. Radiation damage to biological macromolecules∗. Curr Opin Struct Biol 2023; 82:102662. [PMID: 37573816 DOI: 10.1016/j.sbi.2023.102662] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/27/2023] [Accepted: 07/04/2023] [Indexed: 08/15/2023]
Abstract
In this review, we describe recent research developments into radiation damage effects in macromolecular X-ray crystallography observed at synchrotrons and X-ray free electron lasers. Radiation damage in small molecule X-ray crystallography, small angle X-ray scattering experiments, microelectron diffraction, and single particle cryo-electron microscopy is briefly covered.
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Affiliation(s)
- Elspeth F Garman
- Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK.
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
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8
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Hall K, Joseph C, Ayuso-Fernández I, Tamhankar A, Rieder L, Skaali R, Golten O, Neese F, Røhr ÅK, Jannuzzi SAV, DeBeer S, Eijsink VGH, Sørlie M. A Conserved Second Sphere Residue Tunes Copper Site Reactivity in Lytic Polysaccharide Monooxygenases. J Am Chem Soc 2023; 145:18888-18903. [PMID: 37584157 PMCID: PMC10472438 DOI: 10.1021/jacs.3c05342] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Indexed: 08/17/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are powerful monocopper enzymes that can activate strong C-H bonds through a mechanism that remains largely unknown. Herein, we investigated the role of a conserved glutamine/glutamate in the second coordination sphere. Mutation of the Gln in NcAA9C to Glu, Asp, or Asn showed that the nature and distance of the headgroup to the copper fine-tune LPMO functionality and copper reactivity. The presence of Glu or Asp close to the copper lowered the reduction potential and decreased the ratio between the reduction and reoxidation rates by up to 500-fold. All mutants showed increased enzyme inactivation, likely due to changes in the confinement of radical intermediates, and displayed changes in a protective hole-hopping pathway. Electron paramagnetic resonance (EPR) and X-ray absorption spectroscopic (XAS) studies gave virtually identical results for all NcAA9C variants, showing that the mutations do not directly perturb the Cu(II) ligand field. DFT calculations indicated that the higher experimental reoxidation rate observed for the Glu mutant could be reconciled if this residue is protonated. Further, for the glutamic acid form, we identified a Cu(III)-hydroxide species formed in a single step on the H2O2 splitting path. This is in contrast to the Cu(II)-hydroxide and hydroxyl intermediates, which are predicted for the WT and the unprotonated glutamate variant. These results show that this second sphere residue is a crucial determinant of the catalytic functioning of the copper-binding histidine brace and provide insights that may help in understanding LPMOs and LPMO-inspired synthetic catalysts.
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Affiliation(s)
- Kelsi
R. Hall
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Chris Joseph
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Iván Ayuso-Fernández
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Ashish Tamhankar
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Lukas Rieder
- Institute
for Molecular Biotechnology, Graz University
of Technology, 8010, Graz, Austria
| | - Rannei Skaali
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Ole Golten
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Åsmund K. Røhr
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Sergio A. V. Jannuzzi
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Vincent G. H. Eijsink
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
| | - Morten Sørlie
- Faculty
of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), 1432, Ås, Norway
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9
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Lim H, Brueggemeyer MT, Transue WJ, Meier KK, Jones SM, Kroll T, Sokaras D, Kelemen B, Hedman B, Hodgson KO, Solomon EI. Kβ X-ray Emission Spectroscopy of Cu(I)-Lytic Polysaccharide Monooxygenase: Direct Observation of the Frontier Molecular Orbital for H 2O 2 Activation. J Am Chem Soc 2023; 145:16015-16025. [PMID: 37441786 PMCID: PMC10557184 DOI: 10.1021/jacs.3c04048] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) catalyze the degradation of recalcitrant carbohydrate polysaccharide substrates. These enzymes are characterized by a mononuclear Cu(I) active site with a three-coordinate T-shaped "His-brace" configuration including the N-terminal histidine and its amine group as ligands. This study explicitly investigates the electronic structure of the d10 Cu(I) active site in a LPMO using Kβ X-ray emission spectroscopy (XES). The lack of inversion symmetry in the His-brace site enables the 3d/p mixing required for intensity in the Kβ valence-to-core (VtC) XES spectrum of Cu(I)-LPMO. These Kβ XES data are correlated to density functional theory (DFT) calculations to define the bonding, and in particular, the frontier molecular orbital (FMO) of the Cu(I) site. These experimentally validated DFT calculations are used to evaluate the reaction coordinate for homolytic cleavage of the H2O2 O-O bond and understand the contribution of this FMO to the low barrier of this reaction and how the geometric and electronic structure of the Cu(I)-LPMO site is activated for rapid reactivity with H2O2.
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Affiliation(s)
- Hyeongtaek Lim
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | | | - Wesley J Transue
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Katlyn K Meier
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen M Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Thomas Kroll
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Dimosthenis Sokaras
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Bradley Kelemen
- IFF Health and Biosciences, Palo Alto, California 94304, United States
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
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10
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Poore AT, Zuercher EC, Bury G, Whitesell C, Nguyen CC, Pushkar YN, Tian S. Revisit the E2 Domain of Amyloid Precursor Protein: Ferroxidase, Superoxide and Peroxynitrite Scavenging Activities. Inorg Chem 2023. [PMID: 37369063 DOI: 10.1021/acs.inorgchem.3c01336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Amyloid precursor protein (APP) is the biological precursor of β-amyloids, a known histopathological hallmark associated with Alzheimer's disease (AD). The function of APP is of great interest yet remains elusive. One of the extracellular domains of APP, the E2 domain, has been proposed to possess ferroxidase activity and affect neuronal iron homeostasis. However, contradicting evidence has been reported, and its precise role remains inconclusive. Here, we studied the Cu-binding site of the E2 domain using extended X-ray absorption fine structure (EXAFS), UV-vis, and electron paramagnetic resonance (EPR) and discovered that a new labile water ligand coordinates to the Cu(II) cofactor in addition to the four known histidines. We explored the proposed ferroxidase activity of the Cu(II)-E2 domain through reactions with ferrous iron and observed single-turnover ferrous oxidation activity with a rate up to 1.0 × 102 M-1 s-1. Cu(I)-E2 reacted with molecular oxygen at a rate of only 5.3 M-1 s-1, which would restrict any potential multiturnover ferroxidase activity to this slow rate and prevents observation of activity under multiturnover conditions. The positive electrostatic potential surface of the protein indicates possible reactivity with negatively charged small substrates such as superoxide radicals (O2•-) and peroxynitrite (ONOO-) that are major contributors to the oxidative stress prevalent in the extracellular environment. Our assays showed that Cu(I)-E2 can remove O2•- at a rate of 1.6 × 105 M-1 s-1, which is slower than the rates of native SODs. However, the reaction between Cu(I)-E2 and ONOO- achieved a rate of 1.1 × 105 M-1 s-1, comparable to native ONOO- scavenger peroxiredoxins (105-107 M-1 s-1). Therefore, the E2 domain of APP can serve as an enzymatic site that may function as a ferroxidase under substrate-limiting conditions, a supplemental O2•- scavenger, and an ONOO- remover in the vicinity of the cellular iron efflux channel and protect neuron cells from reactive oxygen species (ROS) and reactive nitrogen species (RNS) damage.
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Affiliation(s)
- Andrew T Poore
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| | - Eli C Zuercher
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| | - Gabriel Bury
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Caslyn Whitesell
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| | - Cuong C Nguyen
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
| | - Yulia N Pushkar
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Shiliang Tian
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47906, United States
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11
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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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Walton PH, Davies GJ, Diaz DE, Franco‐Cairo JP. The histidine brace: nature's copper alternative to haem? FEBS Lett 2023; 597:485-494. [PMID: 36660911 PMCID: PMC10952591 DOI: 10.1002/1873-3468.14579] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/21/2023]
Abstract
The copper histidine brace is a structural unit in metalloproteins (Proc Natl Acad Sci USA 2011, 108, 15079). It consists of a copper ion chelated by the NH2 and π-N atom of an N-terminal histidine, and the τ-N atom of a further histidine, in an overall T-shaped coordination geometry (Nat Catal 2018, 1, 571). Like haem-containing proteins, histidine-brace-containing proteins have peroxygenase and/or oxygenase activity, where the substrates are notable for resistance to oxidation, for example, lytic polysaccharide monooxygenases (LPMOs). Moreover, the histidine brace is an invariant unit around which different protein structures exert different activities. Given the similarities in the diversity of function of proteins that contain either the copper histidine brace or haem, the question arises as to whether the functions of histidine brace-containing proteins duplicate those containing haem groups.
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Tandrup T, Lo Leggio L, Meilleur F. Joint X-ray/neutron structure of Lentinus similis AA9_A at room temperature. Acta Crystallogr F Struct Biol Commun 2023; 79:1-7. [PMID: 36598350 PMCID: PMC9813973 DOI: 10.1107/s2053230x22011335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes which cleave polysaccharides oxidatively and are important in pathogen biology, carbon cycling and biotechnology. The Lentinus similis family AA9 isoform A (LsAA9_A) has been extensively studied as a model system because its activity towards smaller soluble saccharide substrates has allowed detailed structural characterization of its interaction with a variety of substrates by X-ray crystallography at high resolution. Here, the joint X-ray/neutron room-temperature crystallographic structure of carbohydrate-free LsAA9_A in the copper(II) resting state refined against X-ray and neutron data at 2.1 and 2.8 Å resolution, respectively, is presented. The results provide an experimental determination of the protonation states of the copper(II)-coordinating residues and second-shell residues in LsAA9_A, paving the way for future neutron crystallographic studies of LPMO-carbohydrate complexes.
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Affiliation(s)
- Tobias Tandrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, 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,Correspondence e-mail:
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Structural perturbations of substrate binding and oxidation state changes in a lytic polysaccharide monooxygenase. J Biol Inorg Chem 2022; 27:705-713. [PMID: 36208326 PMCID: PMC9653361 DOI: 10.1007/s00775-022-01966-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/20/2022] [Indexed: 01/06/2023]
Abstract
LPMOs are enzymes which catalyse the oxidation of a C-H bond within polysaccharides, leading to their oxidative cleavage. To achieve this, LPMOs employ highly reactive oxidising intermediates, the generation of which is likely coupled to substrate binding to the enzyme. The nature of this coupling is unknown. Here we report a statistical comparison for four three-dimensional structures of an AA9 LPMO crystallised in the same space group but in different oxidation and substrate-binding states, to determine which significant structural perturbations occur at the enzyme upon either oxidation state change or the binding of substrate. In a novel step, we determine the global random error associated with the positional coordinates of atoms using the method of moments to ascertain the statistical estimators of Gaussian distributions of pairwise RMS differences between individual atoms in different structures. The results show that a change in the oxidation state of the copper leads to no significant structural changes, and that binding of the substrate leads to a single change in the conformation of a tryptophan residue. This tryptophan has previously been identified as part of a charge transfer pathway between the active site and the external surface of the protein, and the structural change identified herein may be part of the substrate-enzyme coupling mechanism.
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