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Di Gregorio E, Staelens M, Hosseinkhah N, Karimpoor M, Liburd J, Lim L, Shankar K, Tuszyński JA. Raman Spectroscopy Reveals Photobiomodulation-Induced α-Helix to β-Sheet Transition in Tubulins: Potential Implications for Alzheimer's and Other Neurodegenerative Diseases. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:1093. [PMID: 38998698 DOI: 10.3390/nano14131093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 07/14/2024]
Abstract
In small clinical studies, the application of transcranial photobiomodulation (PBM), which typically delivers low-intensity near-infrared (NIR) to treat the brain, has led to some remarkable results in the treatment of dementia and several neurodegenerative diseases. However, despite the extensive literature detailing the mechanisms of action underlying PBM outcomes, the specific mechanisms affecting neurodegenerative diseases are not entirely clear. While large clinical trials are warranted to validate these findings, evidence of the mechanisms can explain and thus provide credible support for PBM as a potential treatment for these diseases. Tubulin and its polymerized state of microtubules have been known to play important roles in the pathology of Alzheimer's and other neurodegenerative diseases. Thus, we investigated the effects of PBM on these cellular structures in the quest for insights into the underlying therapeutic mechanisms. In this study, we employed a Raman spectroscopic analysis of the amide I band of polymerized samples of tubulin exposed to pulsed low-intensity NIR radiation (810 nm, 10 Hz, 22.5 J/cm2 dose). Peaks in the Raman fingerprint region (300-1900 cm-1)-in particular, in the amide I band (1600-1700 cm-1)-were used to quantify the percentage of protein secondary structures. Under this band, hidden signals of C=O stretching, belonging to different structures, are superimposed, producing a complex signal as a result. An accurate decomposition of the amide I band is therefore required for the reliable analysis of the conformation of proteins, which we achieved through a straightforward method employing a Voigt profile. This approach was validated through secondary structure analyses of unexposed control samples, for which comparisons with other values available in the literature could be conducted. Subsequently, using this validated method, we present novel findings of statistically significant alterations in the secondary structures of polymerized NIR-exposed tubulin, characterized by a notable decrease in α-helix content and a concurrent increase in β-sheets compared to the control samples. This PBM-induced α-helix to β-sheet transition connects to reduced microtubule stability and the introduction of dynamism to allow for the remodeling and, consequently, refreshing of microtubule structures. This newly discovered mechanism could have implications for reducing the risks associated with brain aging, including neurodegenerative diseases like Alzheimer's disease, through the introduction of an intervention following this transition.
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Affiliation(s)
- Elisabetta Di Gregorio
- Department of Physics, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Mechanical and Aerospace Engineering (DIMEAS), Faculty of Biomedical Engineering, Polytechnic University of Turin, 10129 Turin, Italy
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Michael Staelens
- Department of Physics, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Instituto de Física Corpuscular, CSIC-Universitat de València, Carrer Catedràtic José Beltrán 2, 46980 Paterna, Spain
| | | | | | | | - Lew Lim
- Vielight Inc., Toronto, ON M4Y 2G8, Canada
| | - Karthik Shankar
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
| | - Jack A Tuszyński
- Department of Physics, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Mechanical and Aerospace Engineering (DIMEAS), Faculty of Biomedical Engineering, Polytechnic University of Turin, 10129 Turin, Italy
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland
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2
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McCullagh M, Zeczycki TN, Kariyawasam CS, Durie CL, Halkidis K, Fitzkee NC, Holt JM, Fenton AW. What is allosteric regulation? Exploring the exceptions that prove the rule! J Biol Chem 2024; 300:105672. [PMID: 38272229 PMCID: PMC10897898 DOI: 10.1016/j.jbc.2024.105672] [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: 06/21/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
"Allosteric" was first introduced to mean the other site (i.e., a site distinct from the active or orthosteric site), an adjective for "regulation" to imply a regulatory outcome resulting from ligand binding at another site. That original idea outlines a system with two ligand-binding events at two distinct locations on a macromolecule (originally a protein system), which defines a four-state energy cycle. An allosteric energy cycle provides a quantifiable allosteric coupling constant and focuses our attention on the unique properties of the four equilibrated protein complexes that constitute the energy cycle. Because many observed phenomena have been referenced as "allosteric regulation" in the literature, the goal of this work is to use literature examples to explore which systems are and are not consistent with the two-ligand thermodynamic energy cycle-based definition of allosteric regulation. We emphasize the need for consistent language so comparisons can be made among the ever-increasing number of allosteric systems. Building on the mutually exclusive natures of an energy cycle definition of allosteric regulation versus classic two-state models, we conclude our discussion by outlining how the often-proposed Rube-Goldberg-like mechanisms are likely inconsistent with an energy cycle definition of allosteric regulation.
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Affiliation(s)
- Martin McCullagh
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Tonya N Zeczycki
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, North Carolina, USA
| | - Chathuri S Kariyawasam
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Clarissa L Durie
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Konstantine Halkidis
- Department of Hematologic Malignancies and Cellular Therapeutics, The University of Kansas Medical Center, Kansas City, Kansas, USA; Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Jo M Holt
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.
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3
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Ye Q, Cairnie DR, Troya D, Kumar N, Yang X, Morris AJ. Photoinduced Dynamic Ligation in Metal-Organic Frameworks. J Am Chem Soc 2024; 146:101-105. [PMID: 38150536 PMCID: PMC10785796 DOI: 10.1021/jacs.3c12217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023]
Abstract
Metal organic frameworks (MOFs), a class of porous crystalline materials consisting of metal-based nodes and organic linkers, have emerged as a promising platform for photocatalysis due to their ultrahigh functional surface area, customizable topologies, and tunable energetics. While interesting photochemistry has been reported, the related photoinduced structural dynamics of MOFs remains unclear. The consensus is that the coordination bonds between MOF nodes and linkers are considered static during photoexcitation, while the open-metal sites on the nodes are taken as the key active sites for catalysis. In this work, through a complementary time-resolved visible and infrared (IR) spectroscopic investigation, along with computational studies, we report for the first time light-induced structural bond dissociation (COO-M) and reformation in an iron-oxo framework, MIL-101(Fe). The probed excited state displayed ligand-to-metal charge transfer (LMCT) characteristics and exhibited a ca. 30 μs lifetime. The incredibly long excited-state lifetime led us to probe potential structural rearrangements that facilitated charge separation in MIL-101(Fe). By probing the vibrational fingerprints of the carboxylate linker upon LMCT photoexcitation, we observed the reversible transition of the carboxylate-Fe bond from a bidentate bridging mode to a monodentate mode, indicating the partial dissociation of the carboxylate ligand. Importantly, the bidentate configuration is recovered on the same time scale of the excited state lifetimes as probed via visible transient absorption spectroscopy. The elucidated photoinduced configurational dynamics provides a foundation for an in-depth understanding of MOF-based photocatalytic mechanisms.
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Affiliation(s)
- Qingyu Ye
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Daniel R. Cairnie
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Diego Troya
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Naveen Kumar
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Xiaozhou Yang
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
| | - Amanda J. Morris
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
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4
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Poptic AL, Chen YP, Chang T, Chen YS, Moore CE, Zhang S. Site-Differentiated Mn IIFe II Complex Reproducing the Selective Assembly of Biological Heterobimetallic Mn/Fe Cofactors. J Am Chem Soc 2023; 145:3491-3498. [PMID: 36749207 DOI: 10.1021/jacs.2c11930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Class Ic ribonucleotide reductases (RNRIc) and R2-like ligand-binding oxidases (R2lox) are known to contain heterobimetallic MnIIFeII cofactors. How these enzymes assemble MnIIFeII cofactors has been a long-standing puzzle due to the weaker binding affinity of MnII versus FeII. In addition, the heterobimetallic selectivity of RNRIc and R2lox has yet to be reproduced with coordination complexes, leading to the hypothesis that RNRIc and R2lox overcome the thermodynamic preference for coordination of FeII over MnII with their carefully constructed three-dimensional protein structures. Herein, we report the selective formation of a heterobimetallic MnIIFeII complex accomplished in the absence of a protein scaffold. Treatment of the ligand Py4DMcT (L) with equimolar amounts of FeII and MnII along with two equivalents of acetate (OAc) affords [LMnIIFeII (OAc)2(OTf)]+ (MnIIFeII) in 80% yield, while the diiron complex [LFeIIFeII(OAc)2(OTf)]+ (FeIIFeII) is produced in only 8% yield. The formation of MnIIFeII is favored regardless of the order of addition of FeII and MnII sources. X-ray diffraction (XRD) of single crystals of MnIIFeII reveals an unsymmetrically coordinated carboxylate ligand─a primary coordination sphere feature shared by both RNRIc and R2lox that differentiates the two metal binding sites. Anomalous XRD studies confirm that MnIIFeII exhibits the same site selectivity as R2lox and RNRIc, with the FeII (d6) center preferentially occupying the distorted octahedral site. We conclude that the successful assembly of MnIIFeII originates from (1) Fe-deficient conditions, (2) site differentiation, and (3) the inability of ligand L to house a dimanganese complex.
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Affiliation(s)
- Anna L Poptic
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Ying-Pin Chen
- ChemMatCARS, University of Chicago, Argonne, Illinois 60439, United States
| | - Tieyan Chang
- ChemMatCARS, University of Chicago, Argonne, Illinois 60439, United States
| | - Yu-Sheng Chen
- ChemMatCARS, University of Chicago, Argonne, Illinois 60439, United States
| | - Curtis E Moore
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shiyu Zhang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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5
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Kisgeropoulos EC, Gan YJ, Greer SM, Hazel JM, Shafaat HS. Pulsed Multifrequency Electron Paramagnetic Resonance Spectroscopy Reveals Key Branch Points for One- vs Two-Electron Reactivity in Mn/Fe Proteins. J Am Chem Soc 2022; 144:11991-12006. [PMID: 35786920 DOI: 10.1021/jacs.1c13738] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Traditionally, the ferritin-like superfamily of proteins was thought to exclusively use a diiron active site in catalyzing a diverse array of oxygen-dependent reactions. In recent years, novel redox-active cofactors featuring heterobimetallic Mn/Fe active sites have been discovered in both the radical-generating R2 subunit of class Ic (R2c) ribonucleotide reductases (RNRs) and the related R2-like ligand-binding oxidases (R2lox). However, the protein-specific factors that differentiate the radical reactivity of R2c from the C-H activation reactions of R2lox remain unknown. In this work, multifrequency pulsed electron paramagnetic resonance (EPR) spectroscopy and ligand hyperfine techniques in conjunction with broken-symmetry density functional theory calculations are used to characterize the molecular and electronic structures of two EPR-active intermediates trapped during aerobic assembly of the R2lox Mn/Fe cofactor. A MnIII(μ-O)(μ-OH)FeIII species is identified as the first EPR-active species and represents a common state between the two classes of redox-active Mn/Fe proteins. The species downstream from the MnIII(μ-O)(μ-OH)FeIII state exhibits unique EPR properties, including unprecedented spectral breadth and isotope-dependent g-tensors, which are attributed to a weakly coupled, hydrogen-bonded MnIII(μ-OH)FeIII species. This final intermediate precedes formation of the MnIII/FeIII resting state and is suggested to be relevant to understanding the endogenous reactivity of R2lox.
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Affiliation(s)
- Effie C Kisgeropoulos
- The Ohio State Biochemistry Program, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
| | - Yunqiao J Gan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
| | - Samuel M Greer
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States.,Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Joseph M Hazel
- Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
| | - Hannah S Shafaat
- The Ohio State Biochemistry Program, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry, The Ohio State University, 100 W 18th Avenue, Columbus, Ohio 43210, United States
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6
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Paramagnetic resonance investigation of mono- and di-manganese-containing systems in biochemistry. Methods Enzymol 2022; 666:315-372. [DOI: 10.1016/bs.mie.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Zhou S, He P, Dhindwal S, Grum-Tokars VL, Li Y, Parker K, Modica JA, Bleher R, Dos Reis R, Zuchniarz J, Dravid VP, Voth GA, Roux B, Mrksich M. Synthesis, Characterization, and Simulation of Four-Armed Megamolecules. Biomacromolecules 2021; 22:2363-2372. [PMID: 33979120 DOI: 10.1021/acs.biomac.1c00118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper describes the synthesis, characterization, and modeling of a series of molecules having four protein domains attached to a central core. The molecules were assembled with the "megamolecule" strategy, wherein enzymes react with their covalent inhibitors that are substituted on a linker. Three linkers were synthesized, where each had four oligo(ethylene glycol)-based arms terminated in a para-nitrophenyl phosphonate group that is a covalent inhibitor for cutinase. This enzyme is a serine hydrolase and reacts efficiently with the phosphonate to give a new ester linkage at the Ser-120 residue in the active site of the enzyme. Negative-stain transmission electron microscopy (TEM) images confirmed the architecture of the four-armed megamolecules. These cutinase tetramers were also characterized by X-ray crystallography, which confirmed the active-site serine-phosphonate linkage by electron-density maps. Molecular dynamics simulations of the tetracutinase megamolecules using three different force field setups were performed and compared with the TEM observations. Using the Amberff99SB-disp + pH7 force field, the two-dimensional projection distances of the megamolecules were found to agree with the measured dimensions from TEM. The study described here, which combines high-resolution characterization with molecular dynamics simulations, will lead to a comprehensive understanding of the molecular structures and dynamics for this new class of molecules.
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Affiliation(s)
- Shengwang Zhou
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Peng He
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sonali Dhindwal
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Valerie L Grum-Tokars
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Chicago, Illinois 60611, United States
| | - Ying Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Kelly Parker
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Justin A Modica
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Reiner Bleher
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Roberto Dos Reis
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Joshua Zuchniarz
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Vinayak P Dravid
- Department of Materials Science, Northwestern University, Evanston, Illinois 60208, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
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8
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Kisgeropoulos EC, Griese JJ, Smith ZR, Branca RMM, Schneider CR, Högbom M, Shafaat HS. Key Structural Motifs Balance Metal Binding and Oxidative Reactivity in a Heterobimetallic Mn/Fe Protein. J Am Chem Soc 2020; 142:5338-5354. [PMID: 32062969 DOI: 10.1021/jacs.0c00333] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Heterobimetallic Mn/Fe proteins represent a new cofactor paradigm in bioinorganic chemistry and pose countless outstanding questions. The assembly of the active site defies common chemical convention by contradicting the Irving-Williams series, while the scope of reactivity remains unexplored. In this work, the assembly and C-H bond activation process in the Mn/Fe R2-like ligand-binding oxidase (R2lox) protein is investigated using a suite of biophysical techniques, including time-resolved optical spectroscopy, global kinetic modeling, X-ray crystallography, electron paramagnetic resonance spectroscopy, protein electrochemistry, and mass spectrometry. Selective metal binding is found to be under thermodynamic control, with the binding sites within the apo-protein exhibiting greater MnII affinity than FeII affinity. The comprehensive analysis of structure and reactivity of wild-type R2lox and targeted primary and secondary sphere mutants indicate that the efficiency of C-H bond activation directly correlates with the Mn/Fe cofactor reduction potentials and is inversely related to divalent metal binding affinity. These findings suggest the R2lox active site is precisely tuned for achieving both selective heterobimetallic binding and high levels of reactivity and offer a mechanism to examine the means by which proteins achieve appropriate metal incorporation.
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Affiliation(s)
| | - Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | | | - Rui M M Branca
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, SE-171 21 Solna, Sweden
| | | | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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9
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Mebs S, Srinivas V, Kositzki R, Griese JJ, Högbom M, Haumann M. Fate of oxygen species from O 2 activation at dimetal cofactors in an oxidase enzyme revealed by 57Fe nuclear resonance X-ray scattering and quantum chemistry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148060. [PMID: 31394094 DOI: 10.1016/j.bbabio.2019.148060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 10/26/2022]
Abstract
Oxygen (O2) activation is a central challenge in chemistry and catalyzed at prototypic dimetal cofactors in biological enzymes with diverse functions. Analysis of intermediates is required to elucidate the reaction paths of reductive O2 cleavage. An oxidase protein from the bacterium Geobacillus kaustophilus, R2lox, was used for aerobic in-vitro reconstitution with only 57Fe(II) or Mn(II) plus 57Fe(II) ions to yield [FeFe] or [MnFe] cofactors under various oxygen and solvent isotopic conditions including 16/18O and H/D exchange. 57Fe-specific X-ray scattering techniques were employed to collect nuclear forward scattering (NFS) and nuclear resonance vibrational spectroscopy (NRVS) data of the R2lox proteins. NFS revealed Fe/Mn(III)Fe(III) cofactor states and Mössbauer quadrupole splitting energies. Quantum chemical calculations of NRVS spectra assigned molecular structures, vibrational modes, and protonation patterns of the cofactors, featuring a terminal water (H2O) bound at iron or manganese in site 1 and a metal-bridging hydroxide (μOH-) ligand. A procedure for quantitation and correlation of experimental and computational NRVS difference signals due to isotope labeling was developed. This approach revealed that the protons of the ligands as well as the terminal water at the R2lox cofactors exchange with the bulk solvent whereas 18O from 18O2 cleavage is incorporated in the hydroxide bridge. In R2lox, the two water molecules from four-electron O2 reduction are released in a two-step reaction to the solvent. These results establish combined NRVS and QM/MM for tracking of iron-based oxygen activation in biological and chemical catalysts and clarify the reductive O2 cleavage route in an enzyme.
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Affiliation(s)
- Stefan Mebs
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16, 10691 Stockholm, Sweden
| | - Ramona Kositzki
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Julia J Griese
- Department of Cell and Molecular Biology, Structural Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16, 10691 Stockholm, Sweden
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
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10
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Griese JJ, Branca RMM, Srinivas V, Högbom M. Ether cross-link formation in the R2-like ligand-binding oxidase. J Biol Inorg Chem 2018; 23:879-886. [PMID: 29946980 PMCID: PMC6060897 DOI: 10.1007/s00775-018-1583-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/20/2018] [Indexed: 12/27/2022]
Abstract
R2-like ligand-binding oxidases contain a dinuclear metal cofactor which can consist either of two iron ions or one manganese and one iron ion, but the heterodinuclear Mn/Fe cofactor is the preferred assembly in the presence of MnII and FeII in vitro. We have previously shown that both types of cofactor are capable of catalyzing formation of a tyrosine–valine ether cross-link in the protein scaffold. Here we demonstrate that Mn/Fe centers catalyze cross-link formation more efficiently than Fe/Fe centers, indicating that the heterodinuclear cofactor is the biologically relevant one. We further explore the chemical potential of the Mn/Fe cofactor by introducing mutations at the cross-linking valine residue. We find that cross-link formation is possible also to the tertiary beta-carbon in an isoleucine, but not to the secondary beta-carbon or tertiary gamma-carbon in a leucine, nor to the primary beta-carbon of an alanine. These results illustrate that the reactivity of the cofactor is highly specific and directed.
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Affiliation(s)
- Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden. .,Department of Cell and Molecular Biology, Uppsala University, 751 24, Uppsala, Sweden.
| | - Rui M M Branca
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Box 1031, 171 21, Solna, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden.
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