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Li Z, Bhowmik S, Sagresti L, Brancato G, Smith M, Benson DE, Li P, Merz KM. Simulating Metal-Imidazole Complexes. J Chem Theory Comput 2024; 20:6706-6716. [PMID: 39081207 PMCID: PMC11325557 DOI: 10.1021/acs.jctc.4c00581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
One commonly observed binding motif in metalloproteins involves the interaction between a metal ion and histidine's imidazole side chains. Although previous imidazole-M(II) parameters established the flexibility and reliability of the 12-6-4 Lennard-Jones (LJ)-type nonbonded model by simply tuning the ligating atom's polarizability, they have not been applied to multiple-imidazole complexes. To fill this gap, we systematically simulate multiple-imidazole complexes (ranging from one to six) for five metal ions (Co(II), Cu(II), Mn(II), Ni(II), and Zn(II)) which commonly appear in metalloproteins. Using extensive (40 ns per PMF window) sampling to assemble free energy association profiles (using OPC water and standard HID imidazole charge models from AMBER) and comparing the equilibrium distances to DFT calculations, a new set of parameters was developed to focus on energetic and geometric features of multiple-imidazole complexes. The obtained free energy profiles agree with the experimental binding free energy and DFT calculated distances. To validate our model, we show that we can close the thermodynamic cycle for metal-imidazole complexes with up to six imidazole molecules in the first solvation shell. Given the success in closing the thermodynamic cycles, we then used the same extended sampling method for six other metal ions (Ag(I), Ca(II), Cd(II), Cu(I), Fe(II), and Mg(II)) to obtain new parameters. Since these new parameters can reproduce the one-imidazole geometry and energy accurately, we hypothesize that they will reasonably predict the binding free energy of higher-level coordination numbers. Hence, we did not extend the analysis of these ions up to six imidazole complexes. Overall, the results shed light on metal-protein interactions by emphasizing the importance of ligand-ligand interaction and metal-π-stacking within metalloproteins.
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Affiliation(s)
- Zhen Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Subhamoy Bhowmik
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Luca Sagresti
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- CSGI, Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- CSGI, Istituto Nazionale di Fisica Nucleare (INFN) Sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Madelyn Smith
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - David E Benson
- Department of Chemistry & Biochemistry, Calvin University, Grand Rapids, Michigan 49546, United States
| | - Pengfei Li
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Kenneth M Merz
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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2
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Ren P, Zhang T, Jain N, Ching HYV, Jaworski A, Barcaro G, Monti S, Silvestre-Albero J, Celorrio V, Chouhan L, Rokicińska A, Debroye E, Kuśtrowski P, Van Doorslaer S, Van Aert S, Bals S, Das S. An Atomically Dispersed Mn-Photocatalyst for Generating Hydrogen Peroxide from Seawater via the Water Oxidation Reaction (WOR). J Am Chem Soc 2023. [PMID: 37487055 DOI: 10.1021/jacs.3c03785] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
In this work, we have fabricated an aryl amino-substituted graphitic carbon nitride (g-C3N4) catalyst with atomically dispersed Mn capable of generating hydrogen peroxide (H2O2) directly from seawater. This new catalyst exhibited excellent reactivity, obtaining up to 2230 μM H2O2 in 7 h from alkaline water and up to 1800 μM from seawater under identical conditions. More importantly, the catalyst was quickly recovered for subsequent reuse without appreciable loss in performance. Interestingly, unlike the usual two-electron oxygen reduction reaction pathway, the generation of H2O2 was through a less common two-electron water oxidation reaction (WOR) process in which both the direct and indirect WOR processes occurred; namely, photoinduced h+ directly oxidized H2O to H2O2 via a one-step 2e- WOR, and photoinduced h+ first oxidized a hydroxide (OH-) ion to generate a hydroxy radical (•OH), and H2O2 was formed indirectly by the combination of two •OH. We have characterized the material, at the catalytic sites, at the atomic level using electron paramagnetic resonance, X-ray absorption near edge structure, extended X-ray absorption fine structure, high-resolution transmission electron microscopy, X-ray photoelectron spectroscopy, magic-angle spinning solid-state NMR spectroscopy, and multiscale molecular modeling, combining classical reactive molecular dynamics simulations and quantum chemistry calculations.
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Affiliation(s)
- Peng Ren
- Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium
| | - Tong Zhang
- Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium
| | - Noopur Jain
- EMAT and NANOlab Center of Excellence, Department of Physics, University of Antwerp, Antwerp 2020, Belgium
| | - H Y Vincent Ching
- Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium
| | - Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 10691, Sweden
| | - Giovanni Barcaro
- CNR-IPCF, Institute for Chemical and Physical Processes, Area della Ricerca, Pisa I-56124, Italy
| | - Susanna Monti
- CNR-ICCOM, Institute of Chemistry of Organometallic Compounds, Area della Ricerca, Pisa I-56124, Italy
| | | | - Veronica Celorrio
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, U.K
| | - Lata Chouhan
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
| | - Anna Rokicińska
- Department of Chemical Technology, Jagiellonian University, Krakow 30-387, Poland
| | - Elke Debroye
- Department of Chemistry, KU Leuven, Leuven 3001, Belgium
| | - Piotr Kuśtrowski
- Department of Chemical Technology, Jagiellonian University, Krakow 30-387, Poland
| | | | - Sandra Van Aert
- EMAT and NANOlab Center of Excellence, Department of Physics, University of Antwerp, Antwerp 2020, Belgium
| | - Sara Bals
- EMAT and NANOlab Center of Excellence, Department of Physics, University of Antwerp, Antwerp 2020, Belgium
| | - Shoubhik Das
- Department of Chemistry, University of Antwerp, Antwerp 2020, Belgium
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Zand Z, Mousazade Y, Arevalo RL, Bagheri R, Mohammadi MR, Bikas R, Chernev P, Aleshkevych P, Vandichel M, Song Z, Dau H, Najafpour MM. Role of decomposition products in the oxidation of cyclohexene using a manganese(III) complex. Commun Chem 2023; 6:94. [PMID: 37198430 DOI: 10.1038/s42004-023-00881-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Metal complexes are extensively explored as catalysts for oxidation reactions; molecular-based mechanisms are usually proposed for such reactions. However, the roles of the decomposition products of these materials in the catalytic process have yet to be considered for these reactions. Herein, the cyclohexene oxidation in the presence of manganese(III) 5,10,15,20-tetra(4-pyridyl)-21H,23H-porphine chloride tetrakis(methochloride) (1) in a heterogeneous system via loading the complex on an SBA-15 substrate is performed as a study case. A molecular-based mechanism is usually suggested for such a metal complex. Herein, 1 was selected and investigated under the oxidation reaction by iodosylbenzene or (diacetoxyiodo)benzene (PhI(OAc)2). In addition to 1, at least one of the decomposition products of 1 formed during the oxidation reaction could be considered a candidate to catalyze the reaction. First-principles calculations show that Mn dissolution is energetically feasible in the presence of iodosylbenzene and trace amounts of water.
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Affiliation(s)
- Zahra Zand
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
| | - Younes Mousazade
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
| | - Ryan Lacdao Arevalo
- Department of Chemical Sciences and Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Robabeh Bagheri
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, 315201, Ningbo, China
| | | | - Rahman Bikas
- Department of Chemistry, Faculty of Science, Imam Khomeini International University, 34148-96818, Qazvin, Iran
| | - Petko Chernev
- Fachbereich Physik, Freie Universit-t Berlin, Arnimallee 14, 14195, Berlin, Germany
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, Uppsala, 751 20, Sweden
| | - Pavlo Aleshkevych
- Institute of Physics, Polish Academy of Sciences (PAN), Al. Lotnikow 32/46, PL-02-668, Warsaw, Poland
| | - Matthias Vandichel
- Department of Chemical Sciences and Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Zhenlun Song
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, 315201, Ningbo, China
| | - Holger Dau
- Fachbereich Physik, Freie Universit-t Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Mohammad Mahdi Najafpour
- Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran.
- Center of Climate Change and Global Warming, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran.
- Research Center for Basic Sciences & Modern Technologies (RBST), Institute for Advanced Studies in Basic Sciences (IASBS), 45137-66731, Zanjan, Iran.
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Dynamic Polyphosphate Metabolism Coordinating with Manganese Ions Defends against Oxidative Stress in the Extreme Bacterium Deinococcus radiodurans. Appl Environ Microbiol 2021; 87:AEM.02785-20. [PMID: 33452031 DOI: 10.1128/aem.02785-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/08/2021] [Indexed: 02/05/2023] Open
Abstract
Deinococcus radiodurans is an extreme bacterium with unparalleled resistance to oxidative stresses. Accumulation of intracellular Mn2+ complexing with small metabolites is the key contributor to the tolerance of D. radiodurans against oxidative stress. However, the intracellular reservoir of Mn ions and homeostatic regulation of the Mn complex in D. radiodurans remain unclear. We identified an evolutionarily ancient and negatively charged phosphate polymer (polyphosphate [PolyP]) in D. radiodurans We investigated PolyP metabolism in the response of D. radiodurans to oxidative stress. The genes dr1939, encoding polyphosphatase kinase (PPKDr; the subscript "Dr" refers to D. radiodurans), and dra0185, encoding exopolyphosphatase (PPXDr), were identified. PPXDr is a novel exopolyphosphatase with a cofactor preference to Mn2+, which enhances the dimerization and activity of PPXDr to allow the effective cleavage of PolyP-Mn. PPKDr and PPXDr exhibited different dynamic expression profiles under oxidative stress. First, ppkDr was upregulated leading to the accumulation of PolyP, which chelated large amounts of intracellular Mn ions. Subsequently, the expression level of ppkDr decreased while ppxDr was substantially upregulated and effectively hydrolyzed inactive PolyP-Mn to release phosphate (Pi) and Mn2+, which could form into Mn-Pi complexes to scavenge O2 - and protect proteins from oxidative damage. Hence, dynamic cellular PolyP metabolites complexed with free Mn ions highlight a defense strategy of D. radiodurans in response to oxidative stress.IMPORTANCE The Mn-phosphate complex (Mn-Pi) plays a key role in the cellular resistance of radioresistant bacteria. The evolutionarily ancient polyphosphate polymers (polyphosphate [PolyP]) could effectively chelate Mn2+ and donate phosphates. However, the intracellular reservoir of Mn ions and homeostatic regulation of the Mn-Pi complex remain unclear. Here, we investigated the relationship of PolyP metabolites and Mn2+ homeostasis and how they function to defend against oxidative stress in the radioresistant bacterium Deinococcus radiodurans We found that PPXDr (the subscript "Dr" refers to D. radiodurans) is a novel exopolyphosphatase with a cofactor preference for Mn2+, mediating PolyP-Mn degradation into Pi and Mn ions. The formed Mn-Pi complexes effectively protect proteins. The dynamic PolyP metabolism coordinating with Mn ions is a defense strategy of D. radiodurans in response to oxidative stress. The findings not only provide new insights into the resistance mechanism of the extreme bacterium D. radiodurans but also broaden our understanding of the functions of PolyP metabolism in organisms.
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Demay-Drouhard P, Ching HYV, Decroos C, Guillot R, Li Y, Tabares LC, Policar C, Bertrand HC, Un S. Understanding the g-tensors of perchlorotriphenylmethyl and Finland-type trityl radicals. Phys Chem Chem Phys 2020; 22:20792-20800. [PMID: 32909565 DOI: 10.1039/d0cp03626a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The 285 GHz EPR spectra of perchlorotriphenylmethyl and tetrathiatriarylmethyl radicals in frozen solution have been accurately measured. The relationship between their molecular structures and their g-tensors has been investigated with the aid of DFT calculations, revealing that the degree of spin density delocalization away from the central methylene carbon is an important determining factor of the g-anisotropy. In particular, the small amount of spin densities on the Cl or S heteroatoms at the 2 and 6 positions with respect to the central carbon have the strongest influence. Furthermore, the amount of spin densities on these heteroatoms and thus the anisotropy can be modulated by the protonation (esterification) state of the carboxylate groups at the 4 position. These results provide unique insights into the g-anisotropy of persistent trityl radicals and how it can be tuned.
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Affiliation(s)
- Paul Demay-Drouhard
- Laboratoire des Biomolécules, LBM, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - H Y Vincent Ching
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Christophe Decroos
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, Université Paris-Sud, CNRS UMR 8182, Université Paris-Saclay, 91405 Orsay, France
| | - Yun Li
- Laboratoire de Chimie des Processus Biologiques, CNRS UMR 8229, Collège de France, PSL University, Sorbonne Université, 11 Place Marcelin Berthelot, 75231 Paris Cedex 05, France
| | - Leandro C Tabares
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Clotilde Policar
- Laboratoire des Biomolécules, LBM, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Helene C Bertrand
- Laboratoire des Biomolécules, LBM, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Sun Un
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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6
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Hadley RC, Gagnon DM, Ozarowski A, Britt RD, Nolan EM. Murine Calprotectin Coordinates Mn(II) at a Hexahistidine Site with Ca(II)-Dependent Affinity. Inorg Chem 2019; 58:13578-13590. [PMID: 31145609 DOI: 10.1021/acs.inorgchem.9b00763] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Manganese is an essential metal ion that bacterial pathogens need to acquire from the vertebrate host during infection. In the mammalian nutritional immunity strategy to combat bacterial infection, the host restricts bacterial access to Mn(II) by sequestering this metal nutrient using the protein calprotectin (CP). The role of murine calprotectin (mCP) in Mn(II) sequestration has been demonstrated in vivo, but the molecular basis of this function has not been evaluated. Herein, biochemical assays and electron paramagnetic resonance (EPR) spectroscopy are employed to characterize the Mn(II) binding properties of mCP. We report that mCP has one high-affinity Mn(II) binding site. This site is a His6 site composed of His17 and His27 of mS100A8 and His92, His97, His105, and His107 of mS100A9. Similar to the human ortholog (hCP), Ca(II) binding to the EF-hand domains of mCP enhances the Mn(II) affinity of the protein; however, this effect requires ≈10-fold more Ca(II) than was previously observed for hCP. Mn(II) coordination to the His6 site also promotes self-association of two mCP heterodimers to form a heterotetramer. Low-temperature X-band EPR spectroscopy revealed a nearly octahedral Mn(II) coordination sphere for the Mn(II)-His6 site characterized by the zero-field splitting parameters D = 525 MHz and E/D = 0.3. Further electron-nuclear double resonance studies with globally 15N-labeled mCP provided hyperfine couplings from the coordinating ε-nitrogen atoms of the His ligands (aiso = 4.3 MHz) as well as the distal δ-nitrogen atoms (aiso = 0.25 MHz). Mn(II) competition assays between mCP and two bacterial Mn(II) solute-binding proteins, staphylococcal MntC and streptococcal PsaA, showed that mCP outcompetes both proteins for Mn(II) under conditions of excess Ca(II). In total, this work provides the first coordination chemistry study of mCP and reveals striking similarities in the Mn(II) coordination sphere as well as notable differences in the Ca(II) sensitivity and oligomerization behavior between hCP and mCP.
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Affiliation(s)
- Rose C Hadley
- Department of Chemistry , Massachusetts Institute of Technology (MIT) , Cambridge , Massachusetts 02139 , United States
| | - Derek M Gagnon
- Department of Chemistry , University of California, Davis , Davis , California 95616 , United States
| | - Andrew Ozarowski
- National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - R David Britt
- Department of Chemistry , University of California, Davis , Davis , California 95616 , United States
| | - Elizabeth M Nolan
- Department of Chemistry , Massachusetts Institute of Technology (MIT) , Cambridge , Massachusetts 02139 , United States
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7
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Banerjee A, Tolla AS, Stjepanovic S, Sevilla MD, Goodsell JL, Angerhofer A, Brennessel WW, Loloee R, Chavez FA. Structural, Spectroscopic, Electrochemical, and Magnetic Properties for Manganese(II) Triazamacrocyclic Complexes. Inorganica Chim Acta 2019; 486:546-555. [PMID: 33981118 PMCID: PMC8112617 DOI: 10.1016/j.ica.2018.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report the synthesis of [Mn(tacud)2](OTf)2 (1) (tacud = 1,4,8-triazacycloundecane), [Mn(tacd)2](OTf)2 (2) (tacd = 1,4,7-triazacyclodecane), and [Mn(tacn)2](OTf)2 (3) (tacn = 1,4,7-triazacyclononane). Electrochemical measurements on the MnIII/II redox couple show that complex 1 has the largest anodic potential of the set (E 1/2 = 1.16 V vs NHE, ΔE p = 106 mV) compared to 2 (E 1/2 = 0.95 V, ΔE p = 108 mV) and 3 (E 1/2 = 0.93 V, ΔE p = 96 mV). This is due to the fact that 1 has the fewest 5-membered chelate rings and thus is least stabilized. Magnetic studies of 1-3 revealed that all complexes remain high spin throughout the temperature range investigated (2 - 300 K). X-band EPR investigations in methanol glass indicated that the manganese(II) centers for 2 and 3 resided in a more distorted octahedral geometric configuration compared to 1. To ease spectral interpretation and extract ZFS parameters, we performed high-frequency high-field EPR (HFEPR) at frequencies above 200 GHz and a field of 7.5 T. Simulation of the spectral data yielded g = 2.0013 and D = -0.031 cm-1 for 1, g = 2.0008, D = -0.0824 cm-1, |E/D| = 0.12 for 2, and g = 2.00028, D = -0.0884 cm-1 for 3. These results are consistent with 3 possessing the most distorted geometry. Calculations (PBE0/6-31G(d)) were performed on 1-3. Results show that 1 has the largest HOMO-LUMO gap energy (6.37 eV) compared to 2 (6.12 eV) and 3 (6.26 eV). Complex 1 also has the lowest HOMO energies indicating higher stability.
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Affiliation(s)
- Atanu Banerjee
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
| | - Azam S Tolla
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
| | | | - Michael D Sevilla
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
| | - Justin L Goodsell
- Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA
| | | | | | - Reza Loloee
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824-1322, USA
| | - Ferman A Chavez
- Department of Chemistry, Oakland University, Rochester, MI 48309-4477, USA
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8
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Litvinov A, Feintuch A, Un S, Goldfarb D. Triple resonance EPR spectroscopy determines the Mn 2+ coordination to ATP. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 294:143-152. [PMID: 30053753 PMCID: PMC6230374 DOI: 10.1016/j.jmr.2018.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/18/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
Mn2+ often serves as a paramagnetic substitute to Mg2+, providing means for exploring the close environment of Mg2+ in many biological systems where it serves as an essential co-factor. This applies to proteins with ATPase activity, where the ATP hydrolysis requires the binding of Mg2+-ATP to the ATPase active site. In this context, it is important to distinguish between the Mn2+ coordination mode with free ATP in solution as compared to the protein bound case. In this work, we explore the Mn2+ complexes with ATP, the non-hydrolysable ATP analog, AMPPNP, and ADP free in solution. Using W-band 31P electron-nuclear double resonance (ENDOR) we obtained information about the coordination to the phosphates, whereas from electron-electron double resonance (ELDOR) - detected NMR (EDNMR) we determined the coordination to an adenosine nitrogen. The coordination to these ligands has been reported earlier, but whether the nitrogen and phosphate coordination is within the same nucleotide molecules or different ones is still under debate. By applying the correlation technique, THYCOS (triple hyperfine correlation spectroscopy), and measuring 15N-31P correlations we establish that in Mn-ATP in solution both phosphates and a nitrogen are coordinated to the Mn2+ ion. We also carried out DFT calculations to substantiate this finding. In addition, we expanded the understanding of the THYCOS experiment by comparing it to 2D-EDNMR for 55Mn-31P correlation experiments and through simulations of THYCOS and 2D-EDNMR spectra with 15N-31P correlations.
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Affiliation(s)
- Aleksei Litvinov
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Israel
| | - Akiva Feintuch
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Israel
| | - Sun Un
- Department of Biochemistry, Biophysics and Structural Biology, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS UMR 9198, CEA-Saclay, Gif-sur-Yvette F-91198, France
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Israel.
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Barwinska-Sendra A, Baslé A, Waldron KJ, Un S. A charge polarization model for the metal-specific activity of superoxide dismutases. Phys Chem Chem Phys 2018; 20:2363-2372. [PMID: 29308487 PMCID: PMC5901066 DOI: 10.1039/c7cp06829h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The pathogenicity of Staphylococcus aureus is enhanced by having two superoxide dismutases (SODs): a Mn-specific SOD and another that can use either Mn or Fe. Using 94 GHz electron-nuclear double resonance (ENDOR) and electron double resonance detected (ELDOR)-NMR we show that, despite their different metal-specificities, their structural and electronic similarities extend down to their active-site 1H- and 14N-Mn(ii) hyperfine interactions. However these interactions, and hence the positions of these nuclei, are different in the inactive Mn-reconstituted Escherichia coli Fe-specific SOD. Density functional theory modelling attributes this to a different angular position of the E. coli H171 ligand. This likely disrupts the Mn-H171-E170' triad causing a shift in charge and in metal redox potential, leading to the loss of activity. This is supported by the correlated differences in the Mn(ii) zero-field interactions of the three SOD types and suggests that the triad is important for determining metal specific activity.
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Affiliation(s)
- Anna Barwinska-Sendra
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Kevin J Waldron
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
| | - Sun Un
- Department of Biochemistry, Biophysics and Structural Biology, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS UMR 9198, CEA-Saclay, Gif-sur-Yvette, F-91198, France.
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10
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Collauto A, Mishra S, Litvinov A, Mchaourab HS, Goldfarb D. Direct Spectroscopic Detection of ATP Turnover Reveals Mechanistic Divergence of ABC Exporters. Structure 2017; 25:1264-1274.e3. [PMID: 28712805 DOI: 10.1016/j.str.2017.06.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 04/05/2017] [Accepted: 06/15/2017] [Indexed: 12/27/2022]
Abstract
We have applied high-field (W-band) pulse electron-nuclear double resonance (ENDOR) and electron-electron double resonance (ELDOR)-detected nuclear magnetic resonance (EDNMR) to characterize the coordination sphere of the Mn2+ co-factor in the nucleotide binding sites (NBSs) of ABC transporters. MsbA and BmrCD are two efflux transporters hypothesized to represent divergent catalytic mechanisms. Our results reveal distinct coordination of Mn2+ to ATP and transporter residues in the consensus and degenerate NBSs of BmrCD. In contrast, the coordination of Mn2+ at the two NBSs of MsbA is similar, which provides a mechanistic rationale for its higher rate constant of ATP hydrolysis relative to BmrCD. Direct detection of vanadate ion, trapped in a high-energy post-hydrolysis intermediate, further supports the notion of asymmetric hydrolysis by the two NBSs of BmrCD. The integrated spectroscopic approach presented here, which link energy input to conformational dynamics, can be applied to a variety of systems powered by ATP turnover.
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Affiliation(s)
- Alberto Collauto
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Aleksei Litvinov
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel.
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11
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Cox N, Nalepa A, Lubitz W, Savitsky A. ELDOR-detected NMR: A general and robust method for electron-nuclear hyperfine spectroscopy? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 280:63-78. [PMID: 28579103 DOI: 10.1016/j.jmr.2017.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 06/07/2023]
Abstract
ELDOR-detected NMR (EDNMR) performed at higher magnetic fields is becoming an increasingly popular alternative to conventional ENDOR for the characterization of electron-nuclear hyperfine interactions owing to its enhanced sensitivity. However there are two key problems that limit its widespread adoption, with factors controlling: (i) lineshape distortions and; (ii) overall spectral resolution, still largely understood only at a qualitative level. Indeed highly anisotropic (dipolar) coupled species are particularly problematic in the EDNMR experiment. Nor is it clear as to whether line intensities measured in EDNMR can provide quantitative information. Here we describe how all these problems can be overcome for a nitroxide radical as model system. We introduce a simulation procedure/protocol for the simulation of EDNMR line-shapes collected over a range of high turning angle (HTA) pulse lengths. It is shown that spectral line-shapes can be robustly reproduced and that the intensities of spectral lines and the spin nutation behavior can be quantitatively assessed. This broadens the scope of the EDNMR experiment as a generally applicable, quantitative double resonance method.
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Affiliation(s)
- Nicholas Cox
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany; Research School of Chemistry, The Australian National University, Canberra, Australia.
| | - Anna Nalepa
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Anton Savitsky
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany.
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12
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Ramirez Cohen M, Mendelman N, Radoul M, Wilson TD, Savelieff MG, Zimmermann H, Kaminker I, Feintuch A, Lu Y, Goldfarb D. Thiolate Spin Population of Type I Copper in Azurin Derived from 33S Hyperfine Coupling. Inorg Chem 2017; 56:6163-6174. [DOI: 10.1021/acs.inorgchem.7b00167] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Marie Ramirez Cohen
- Department of Chemical
Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Netanel Mendelman
- Department of Chemical
Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marina Radoul
- Department of Chemical
Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tiffany D. Wilson
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Masha G. Savelieff
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Herbert Zimmermann
- Abteilung Biophysik, Max Planck-Institut für Medizinische Forschung, Heidelberg 69120, Germany
| | - Ilia Kaminker
- Department of Chemical
Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Akiva Feintuch
- Department of Chemical
Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yi Lu
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Daniella Goldfarb
- Department of Chemical
Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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13
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Yang Y, Gong YJ, Litvinov A, Liu HK, Yang F, Su XC, Goldfarb D. Generic tags for Mn(ii) and Gd(iii) spin labels for distance measurements in proteins. Phys Chem Chem Phys 2017; 19:26944-26956. [DOI: 10.1039/c7cp04311b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The coordination mode of the metal ion in the spin label affects the distance distribution determined by DEER distance measurements.
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Affiliation(s)
- Yin Yang
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Aleksei Litvinov
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Hong-Kai Liu
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
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14
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Ching HYV, Mascali FC, Bertrand HC, Bruch EM, Demay-Drouhard P, Rasia RM, Policar C, Tabares LC, Un S. The Use of Mn(II) Bound to His-tags as Genetically Encodable Spin-Label for Nanometric Distance Determination in Proteins. J Phys Chem Lett 2016; 7:1072-1076. [PMID: 26938795 DOI: 10.1021/acs.jpclett.6b00362] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A genetically encodable paramagnetic spin-label capable of self-assembly from naturally available components would offer a means for studying the in-cell structure and interactions of a protein by electron paramagnetic resonance (EPR). Here, we demonstrate pulse electron-electron double resonance (DEER) measurements on spin-labels consisting of Mn(II) ions coordinated to a sequence of histidines, so-called His-tags, that are ubiquitously added by genetic engineering to facilitate protein purification. Although the affinity of His-tags for Mn(II) was low (800 μM), Mn(II)-bound His-tags yielded readily detectable DEER time traces even at concentrations expected in cells. We were able to determine accurately the distance between two His-tag Mn(II) spin-labels at the ends of a rigid helical polyproline peptide of known structure, as well as at the ends of a completely cell-synthesized 3-helix bundle. This approach not only greatly simplifies the labeling procedure but also represents a first step towards using self-assembling metal spin-labels for in-cell distance measurements.
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Affiliation(s)
- H Y Vincent Ching
- Institute for Integrative Biology of the Cell (I2BC), Department of Biochemistry, Biophysics and Structural Biology, Université Paris-Saclay, CEA, CNRS UMR 9198 , F-91191 Gif-sur-Yvette, France
| | - Florencia C Mascali
- Instituto de Biología Molecular y Celular de Rosario; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , 2000 Rosario, Argentina
| | - Hélène C Bertrand
- Ecole Normale Supérieure-PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 7203 LBM , F-75005 Paris, France
- CNRS, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
| | - Eduardo M Bruch
- Institute for Integrative Biology of the Cell (I2BC), Department of Biochemistry, Biophysics and Structural Biology, Université Paris-Saclay, CEA, CNRS UMR 9198 , F-91191 Gif-sur-Yvette, France
| | - Paul Demay-Drouhard
- Ecole Normale Supérieure-PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 7203 LBM , F-75005 Paris, France
- CNRS, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
| | - Rodolfo M Rasia
- Instituto de Biología Molecular y Celular de Rosario; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario , 2000 Rosario, Argentina
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 7203 LBM , F-75005 Paris, France
- CNRS, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7203, Laboratoire des Biomolécules, F-75005 Paris, France
| | - Leandro C Tabares
- Institute for Integrative Biology of the Cell (I2BC), Department of Biochemistry, Biophysics and Structural Biology, Université Paris-Saclay, CEA, CNRS UMR 9198 , F-91191 Gif-sur-Yvette, France
| | - Sun Un
- Institute for Integrative Biology of the Cell (I2BC), Department of Biochemistry, Biophysics and Structural Biology, Université Paris-Saclay, CEA, CNRS UMR 9198 , F-91191 Gif-sur-Yvette, France
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15
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Kim MC, Lee SY. Peroxidase-like oxidative activity of a manganese-coordinated histidyl bolaamphiphile self-assembly. NANOSCALE 2015; 7:17063-70. [PMID: 26419275 DOI: 10.1039/c5nr04893a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A peroxidase-like catalyst was constructed through the self-assembly of histidyl bolaamphiphiles coordinated to Mn(2+) ions. The prepared catalyst exhibited oxidation activity for the organic substrate o-phenylenediamine (OPD) in the presence of hydrogen peroxide (H2O2). The histidyl bolaamphiphiles of bis(N-alpha-amido-histidine)-1,7-heptane dicarboxylates self-assembled to make spherical structures in an aqueous solution. Subsequent association of Mn(2+) ions with the histidyl imidazoles in the self-assembly produced catalytic active sites. The optimal Mn(2+) ion concentration was determined and coordination of the Mn(2+) ion with multiple histidine imidazoles was investigated using spectroscopy analysis. The activation energy of the produced catalysts was 55.0 kJ mol(-1), which was comparable to other peroxidase-mimetic catalysts. A detailed kinetics study revealed that the prepared catalyst followed a ping-pong mechanism and that the turnover reaction was promoted by increasing the substrate concentration. Finally, application of the prepared catalyst for glucose detection was demonstrated through cascade enzyme catalysis. This study demonstrated a facile way to prepare an enzyme-mimetic catalyst through the self-assembly of an amphiphilic molecule containing amino acid segments.
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Affiliation(s)
- Min-Chul Kim
- Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea.
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16
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Xie Q, Li Z, Yang L, Lv J, Jobe TO, Wang Q. A Newly Identified Passive Hyperaccumulator Eucalyptus grandis × E. urophylla under Manganese Stress. PLoS One 2015; 10:e0136606. [PMID: 26327118 PMCID: PMC4556624 DOI: 10.1371/journal.pone.0136606] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/06/2015] [Indexed: 12/12/2022] Open
Abstract
Manganese (Mn) is an essential micronutrient needed for plant growth and development, but can be toxic to plants in excess amounts. However, some plant species have detoxification mechanisms that allow them to accumulate Mn to levels that are normally toxic, a phenomenon known as hyperaccumulation. These species are excellent candidates for developing a cost-effective remediation strategy for Mn-polluted soils. In this study, we identified a new passive Mn-hyperaccumulator Eucalyptus grandis × E. urophylla during a field survey in southern China in July 2010. This hybrid can accumulate as much as 13,549 mg/kg DW Mn in its leaves. Our results from Scanning Electron Microscope (SEM) X-ray microanalysis indicate that Mn is distributed in the entire leaf and stem cross-section, especially in photosynthetic palisade, spongy mesophyll tissue, and stem xylem vessels. Results from size-exclusion chromatography coupled with ICP-MS (Inductively coupled plasma mass spectrometry) lead us to speculate that Mn associates with relatively high molecular weight proteins and low molecular weight organic acids, including tartaric acid, to avoid Mn toxicity. Our results provide experimental evidence that both proteins and organic acids play important roles in Mn detoxification in Eucalyptus grandis × E. urophylla. The key characteristics of Eucalyptus grandis × E. urophylla are an increased Mn translocation facilitated by transpiration through the xylem to the leaves and further distribution throughout the leaf tissues. Moreover, the Mn-speciation profile obtained for the first time in different cellular organelles of Eucalyptus grandis × E. urophylla suggested that different organelles have differential accumulating abilities and unique mechanisms for Mn-detoxification.
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Affiliation(s)
- Qingqing Xie
- Department of Chemistry, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhenji Li
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Limin Yang
- Department of Chemistry, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jing Lv
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Timothy O. Jobe
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, United States of America
| | - Qiuquan Wang
- Department of Chemistry, the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China
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17
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Bruch EM, Warner MT, Thomine S, Tabares LC, Un S. Pulse Electron Double Resonance Detected Multinuclear NMR Spectra of Distant and Low Sensitivity Nuclei and Its Application to the Structure of Mn(II) Centers in Organisms. J Phys Chem B 2015; 119:13515-23. [PMID: 25730710 DOI: 10.1021/acs.jpcb.5b01624] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The ability to characterize the structure of metal centers beyond their primary ligands is important to understanding their chemistry. High-magnetic-field pulsed electron double resonance detected NMR (ELDOR-NMR) is shown to be a very sensitive approach to measuring the multinuclear NMR spectra of the nuclei surrounding Mn(II) ions. Resolved spectra of intact organisms with resonances arising from (55)Mn, (31)P, (1)H, (39)K, (35)Cl, (23)Na, and (14)N nuclei surrounding Mn(2+) centers were obtained. Naturally abundant cellular (13)C could be routinely measured as well. The amplitudes of the (14)N and (2)H ELDOR-NMR spectra were found to be linearly dependent on the number of nuclei in the ligand sphere. The evolution of the Mn(II) ELDOR-NMR spectra as a function of excitation time was found to be best described by a saturation phenomenon rather than a coherently driven process. Mn(II) ELDOR-NMR revealed details about not only the immediate ligands to the Mn(II) ions but also more distant nuclei, providing a view of their extended structures. This will be important for understanding the speciation and chemistry of the manganese complexes as well as other metals found in organisms.
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Affiliation(s)
- Eduardo M Bruch
- Service de Bioénergétique, Biologie Structurale et Mécanismes (CNRS UMR-8221), Institut de Biologie et de Technologies de Saclay, CEA-Saclay , F-91191 Gif-sur-Yvette, France
| | - Melissa T Warner
- Service de Bioénergétique, Biologie Structurale et Mécanismes (CNRS UMR-8221), Institut de Biologie et de Technologies de Saclay, CEA-Saclay , F-91191 Gif-sur-Yvette, France.,Department of Biology, Tufts University , Medford, Massachusetts 02155, United States
| | - Sébastien Thomine
- Institute for Integrative Biology of the Cell (I2BC), Saclay Plant Sciences, Université Paris-Saclay, CEA, CNRS, Université Paris-Sud , Gif-sur-Yvette, F-91198 France
| | - Leandro C Tabares
- Service de Bioénergétique, Biologie Structurale et Mécanismes (CNRS UMR-8221), Institut de Biologie et de Technologies de Saclay, CEA-Saclay , F-91191 Gif-sur-Yvette, France
| | - Sun Un
- Service de Bioénergétique, Biologie Structurale et Mécanismes (CNRS UMR-8221), Institut de Biologie et de Technologies de Saclay, CEA-Saclay , F-91191 Gif-sur-Yvette, France
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18
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Gagnon DM, Brophy MB, Bowman SEJ, Stich TA, Drennan CL, Britt RD, Nolan EM. Manganese binding properties of human calprotectin under conditions of high and low calcium: X-ray crystallographic and advanced electron paramagnetic resonance spectroscopic analysis. J Am Chem Soc 2015; 137:3004-16. [PMID: 25597447 DOI: 10.1021/ja512204s] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The antimicrobial protein calprotectin (CP), a hetero-oligomer of the S100 family members S100A8 and S100A9, is the only identified mammalian Mn(II)-sequestering protein. Human CP uses Ca(II) ions to tune its Mn(II) affinity at a biologically unprecedented hexahistidine site that forms at the S100A8/S100A9 interface, and the molecular basis for this phenomenon requires elucidation. Herein, we investigate the remarkable Mn(II) coordination chemistry of human CP using X-ray crystallography as well as continuous-wave (CW) and pulse electron paramagnetic resonance (EPR) spectroscopies. An X-ray crystallographic structure of Mn(II)-CP containing one Mn(II), two Ca(II), and two Na(I) ions per CP heterodimer is reported. The CW EPR spectrum of Ca(II)- and Mn(II)-bound CP prepared with a 10:0.9:1 Ca(II):Mn(II):CP ratio is characterized by an unusually low zero-field splitting of 485 MHz (E/D = 0.30) for the S = 5/2 Mn(II) ion, consistent with the high symmetry of the His6 binding site observed crystallographically. Results from electron spin-echo envelope modulation and electron-nuclear double resonance experiments reveal that the six Mn(II)-coordinating histidine residues of Ca(II)- and Mn(II)-bound CP are spectroscopically equivalent. The observed (15)N (I = 1/2) hyperfine couplings (A) arise from two distinct classes of nitrogen atoms: the coordinating ε-nitrogen of the imidazole ring of each histidine ligand (A = [3.45, 3.71, 5.91] MHz) and the distal δ-nitrogen (A = [0.11, 0.18, 0.42] MHz). In the absence of Ca(II), the binding affinity of CP for Mn(II) drops by two to three orders of magnitude and coincides with Mn(II) binding at the His6 site as well as other sites. This study demonstrates the role of Ca(II) in enabling high-affinity and specific binding of Mn(II) to the His6 site of human calprotectin.
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Affiliation(s)
- Derek M Gagnon
- Department of Chemistry, University of California , Davis, California 95616, United States
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19
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Vincent Ching HY, Demay-Drouhard P, Bertrand HC, Policar C, Tabares LC, Un S. Nanometric distance measurements between Mn(ii)DOTA centers. Phys Chem Chem Phys 2015; 17:23368-77. [DOI: 10.1039/c5cp03487f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The distance between two Mn(ii)DOTA complexes attached to the ends of polyproline helices of varying lengths was measured by 94 GHz PELDOR spectroscopy with good accuracy demonstrating their effectiveness as spin-labels.
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Affiliation(s)
- H. Y. Vincent Ching
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
| | - Paul Demay-Drouhard
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Hélène C. Bertrand
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Leandro C. Tabares
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
| | - Sun Un
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
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20
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Cox N, Nalepa A, Pandelia ME, Lubitz W, Savitsky A. Pulse Double-Resonance EPR Techniques for the Study of Metallobiomolecules. Methods Enzymol 2015; 563:211-49. [DOI: 10.1016/bs.mie.2015.08.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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21
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Bruch EM, Thomine S, Tabares LC, Un S. Variations in Mn(II) speciation among organisms: what makes D. radiodurans different. Metallomics 2014; 7:136-44. [PMID: 25407388 DOI: 10.1039/c4mt00265b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The manganese(II) speciation in intact cells of D. radiodurans, E. coli, S. cerevisiae and Arabidopsis thaliana seeds was measured using high-field electron paramagnetic resonance techniques. The majority of the Mn(II) ions in these organisms were six-coordinate, bound predominately by water, phosphates and nitrogen-based molecules. The relative distribution of the different phosphates in bacteria and S. cerevisiae was the same and dominated by monophosphate monoesters. Mn(II) was also found bound to the phosphate backbone of nucleic acids in these organisms. Phosphate ligation in Arabidopsis seeds was dominated by phytate. The extent of nitrogen ligation in the four organisms was also determined. On average, the Mn(II) in D. radiodurans had the most nitrogen ligands followed by E. coli. This was attributed to higher concentrations of Mn(II) bound to proteins in these species. Although constitutively expressed in all four organisms, MnSOD was only detected in D. radiodurans. As previously reported, D. radiodurans also accumulates a second abundant Mn containing protein species. The high concentration of proteinaceous Mn(II) is a unique feature of D. radiodurans.
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Affiliation(s)
- E M Bruch
- Service de Bioénergétique, Biologie Structurale et Mécanismes (CNRS UMR-8221), Institut de Biologie et de Technologies de Saclay, CEA-Saclay, F-91191 Gif-sur-Yvette, France.
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22
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Vícha J, Straka M, Munzarová ML, Marek R. Mechanism of Spin–Orbit Effects on the Ligand NMR Chemical Shift in Transition-Metal Complexes: Linking NMR to EPR. J Chem Theory Comput 2014; 10:1489-99. [DOI: 10.1021/ct400726y] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Jan Vícha
- CEITEC
- Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
| | - Michal Straka
- CEITEC
- Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
- Institute of Organic Chemistry and Biochemistry of the ASCR, Flemingovo nám. 2, CZ-16610 Praha, Czech Republic
| | - Markéta L. Munzarová
- CEITEC
- Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, CZ-62500 Brno, Czech Republic
| | - Radek Marek
- CEITEC
- Central European Institute of Technology, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
- National
Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk University, Kamenice
5, CZ-62500 Brno, Czech Republic
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23
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Kaminker I, Wilson TD, Savelieff MG, Hovav Y, Zimmermann H, Lu Y, Goldfarb D. Correlating nuclear frequencies by two-dimensional ELDOR-detected NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 240:77-89. [PMID: 24530956 DOI: 10.1016/j.jmr.2013.12.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 12/26/2013] [Accepted: 12/27/2013] [Indexed: 06/03/2023]
Abstract
ELDOR (Electron Double Resonance)-detected NMR (EDNMR) is a pulse EPR experiment that is used to measure the transition frequencies of nuclear spins coupled to electron spins. These frequencies are further used to determine hyperfine and quadrupolar couplings, which are signatures of the electronic and spatial structures of paramagnetic centers. In recent years, EDNMR has been shown to be particularly useful at high fields/high frequencies, such as W-band (∼95 GHz, ∼3.5 T), for low γ quadrupolar nuclei. Although at high fields the nuclear Larmor frequencies are usually well resolved, the limited resolution of EDNMR still remains a major concern. In this work we introduce a two dimensional, triple resonance, correlation experiment based on the EDNMR pulse sequence, which we term 2D-EDNMR. This experiment allows circumventing the resolution limitation by spreading the signals in two dimensions and the observed correlations help in the assignment of the signals. First we demonstrate the utility of the 2D-EDNMR experiment on a nitroxide spin label, where we observe correlations between (14)N nuclear frequencies. Negative cross-peaks appear between lines belonging to different MS electron spin manifolds. We resolved two independent correlation patterns for nuclear frequencies arising from the EPR transitions corresponding to the (14)N mI=0 and mI=-1 nuclear spin states, which severely overlap in the one dimensional EDNMR spectrum. The observed correlations could be accounted for by considering changes in the populations of energy levels that S=1/2, I=1 spin systems undergo during the pulse sequence. In addition to these negative cross-peaks, positive cross-peaks appear as well. We present a theoretical model based on the Liouville equation and use it to calculate the time evolution of populations of the various energy levels during the 2D-EDNMR experiment and generated simulated 2D-EDMR spectra. These calculations show that the positive cross-peaks appear due to off resonance effects and/or nuclear relaxation effects. These results suggest that the 2D-EDNMR experiment can be also useful for relaxation pathway studies. Finally we present preliminary results demonstrating that 2D-EDNMR can resolve overlapping (33)S and (14)N signals of type 1 Cu(II) center in (33)S enriched Azurin.
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Affiliation(s)
- Ilia Kaminker
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Tiffany D Wilson
- Department of Chemistry, University of Illinois, Urbana, IL, United States
| | - Masha G Savelieff
- Department of Chemistry, University of Illinois, Urbana, IL, United States
| | - Yonatan Hovav
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Herbert Zimmermann
- Abteilung Biophysik, Max-Planck-Institut für Medizinische Forschung, Heidelberg, Germany
| | - Yi Lu
- Department of Chemistry, University of Illinois, Urbana, IL, United States
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel.
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