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Hashemi Haeri H, Schneegans N, Eisenschmidt-Bönn D, Brandt W, Wittstock U, Hinderberger D. Characterization of the active site in the thiocyanate-forming protein from Thlaspi arvense (TaTFP) using EPR spectroscopy. Biol Chem 2024; 405:105-118. [PMID: 37586381 DOI: 10.1515/hsz-2023-0187] [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: 04/16/2023] [Accepted: 07/19/2023] [Indexed: 08/18/2023]
Abstract
Glucosinolates are plant thioglucosides, which act as chemical defenses. Upon tissue damage, their myrosinase-catalyzed hydrolysis yields aglucones that rearrange to toxic isothiocyanates. Specifier proteins such as thiocyanate-forming protein from Thlaspi arvense (TaTFP) are non-heme iron proteins, which capture the aglucone to form alternative products, e.g. nitriles or thiocyanates. To resolve the electronic state of the bound iron cofactor in TaTFP, we applied continuous wave electron paramagnetic resonance (CW EPR) spectroscopy at X-and Q-band frequencies (∼9.4 and ∼34 GHz). We found characteristic features of high spin and low spin states of a d 5 electronic configuration and local rhombic symmetry during catalysis. We monitored the oxidation states of bound iron during conversion of allylglucosinolate by myrosinase and TaTFP in presence and absence of supplemented Fe2+. Without added Fe2+, most high spin features of bound Fe3+ were preserved, while different g'-values of the low spin part indicated slight rearrangements in the coordination sphere and/or structural geometry. We also examined involvement of the redox pair Fe3+/Fe2 in samples with supplemented Fe2+. The absence of any EPR signal related to Fe3+ or Fe2+ using an iron-binding deficient TaTFP variant allowed us to conclude that recorded EPR signals originated from the bound iron cofactor.
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Affiliation(s)
- Haleh Hashemi Haeri
- Martin Luther University Halle-Wittenberg, Institute of Chemistry, Von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany
| | - Nicola Schneegans
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, D-38106 Braunschweig, Germany
| | - Daniela Eisenschmidt-Bönn
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
| | - Wolfgang Brandt
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
| | - Ute Wittstock
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, D-38106 Braunschweig, Germany
| | - Dariush Hinderberger
- Martin Luther University Halle-Wittenberg, Institute of Chemistry, Von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany
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2
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Wiechers H, Kehl A, Hiller M, Eltzner B, Huckemann SF, Meyer A, Tkach I, Bennati M, Pokern Y. Bayesian optimization to estimate hyperfine couplings from 19F ENDOR spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 353:107491. [PMID: 37301045 DOI: 10.1016/j.jmr.2023.107491] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/19/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023]
Abstract
ENDOR spectroscopy is a fundamental method to detect nuclear spins in the vicinity of paramagnetic centers and their mutual hyperfine interaction. Recently, site-selective introduction of 19F as nuclear labels has been proposed as a tool for ENDOR-based distance determination in biomolecules, complementing pulsed dipolar spectroscopy in the range of angstrom to nanometer. Nevertheless, one main challenge of ENDOR still consists of its spectral analysis, which is aggravated by a large parameter space and broad resonances from hyperfine interactions. Additionally, at high EPR frequencies and fields (⩾94 GHz/3.4 Tesla), chemical shift anisotropy might contribute to broadening and asymmetry in the spectra. Here, we use two nitroxide-fluorine model systems to examine a statistical approach to finding the best parameter fit to experimental 263 GHz 19F ENDOR spectra. We propose Bayesian optimization for a rapid, global parameter search with little prior knowledge, followed by a refinement by more standard gradient-based fitting procedures. Indeed, the latter suffer from finding local rather than global minima of a suitably defined loss function. Using a new and accelerated simulation procedure, results for the semi-rigid nitroxide-fluorine two and three spin systems lead to physically reasonable solutions, if minima of similar loss can be distinguished by DFT predictions. The approach also delivers the stochastic error of the obtained parameter estimates. Future developments and perspectives are discussed.
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Affiliation(s)
- H Wiechers
- Felix-Bernstein-Institute for Mathematical Statistics in the Biosciences, Georgia-Augusta-University, Goldschmidtstr. 7, D-37077 Göttingen, Germany
| | - A Kehl
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - M Hiller
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - B Eltzner
- Research Group Computational Biomolecular Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - S F Huckemann
- Felix-Bernstein-Institute for Mathematical Statistics in the Biosciences, Georgia-Augusta-University, Goldschmidtstr. 7, D-37077 Göttingen, Germany
| | - A Meyer
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany; Institute of Physical Chemistry, Georgia-Augusta-University, Tammanstr. 6, D-37077 Göttingen, Germany
| | - I Tkach
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - M Bennati
- Research Group EPR Spectroscopy, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany; Institute of Physical Chemistry, Georgia-Augusta-University, Tammanstr. 6, D-37077 Göttingen, Germany.
| | - Y Pokern
- Department of Statistical Science, University College London, WC1E 6BT, United Kingdom.
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3
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Van Brempt N, Sgammato R, Beirinckx Q, Hammerschmid D, Sobott F, Dewilde S, Moens L, Herrebout W, Johannessen C, Van Doorslaer S. The effect of pH and nitrite on the haem pocket of GLB-33, a globin-coupled neuronal transmembrane receptor of Caenorhabditis elegans. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140913. [PMID: 37004900 DOI: 10.1016/j.bbapap.2023.140913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023]
Abstract
Out of the 34 globins in Caenorhabditis elegans, GLB-33 is a putative globin-coupled transmembrane receptor with a yet unknown function. The globin domain (GD) contains a particularly hydrophobic haem pocket, that rapidly oxidizes to a low-spin hydroxide-ligated haem state at physiological pH. Moreover, the GD has one of the fastest nitrite reductase activity ever reported for globins. Here, we use a combination of electronic circular dichroism, resonance Raman and electron paramagnetic resonance (EPR) spectroscopy with mass spectrometry to study the pH dependence of the ferric form of the recombinantly over-expressed GD in the presence and absence of nitrite. The competitive binding of nitrite and hydroxide is examined as well as nitrite-induced haem modifications at acidic pH. Comparison of the spectroscopic results with data from other haem proteins allows to deduce the important effect of Arg at position E10 in stabilization of exogenous ligands. Furthermore, continuous-wave and pulsed EPR indicate that ligation of nitrite occurs in a nitrito mode at pH 5.0 and above. At pH 4.0, an additional formation of a nitro-bound haem form is observed along with fast formation of a nitri-globin.
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Affiliation(s)
- Niels Van Brempt
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Roberta Sgammato
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | - Quinten Beirinckx
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | | | - Frank Sobott
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
| | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Luc Moens
- Department of Biomedical Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Wouter Herrebout
- Department of Chemistry, University of Antwerp, 2610 Antwerp, Belgium
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4
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Pang Z, Jain S, Yang C, Kong X, Tan KO. A unified description for polarization-transfer mechanisms in magnetic resonance in static solids: Cross polarization and DNP. J Chem Phys 2022; 156:244109. [DOI: 10.1063/5.0092265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Polarization transfers are crucial building blocks in magnetic resonance experiments, i.e., they can be used to polarize insensitive nuclei and correlate nuclear spins in multidimensional nuclear magnetic resonance (NMR) spectroscopy. The polarization can be transferred either across different nuclear spin species or from electron spins to the relatively low-polarized nuclear spins. The former route occurring in solid-state NMR can be performed via cross polarization (CP), while the latter route is known as dynamic nuclear polarization (DNP). Despite having different operating conditions, we opinionate that both mechanisms are theoretically similar processes in ideal conditions, i.e., the electron is merely another spin-1/2 particle with a much higher gyromagnetic ratio. Here, we show that the CP and DNP processes can be described using a unified theory based on average Hamiltonian theory combined with fictitious operators. The intuitive and unified approach has allowed new insights into the cross-effect DNP mechanism, leading to better design of DNP polarizing agents and extending the applications beyond just hyperpolarization. We explore the possibility of exploiting theoretically predicted DNP transients for electron–nucleus distance measurements—such as routine dipolar-recoupling experiments in solid-state NMR.
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Affiliation(s)
- Zhenfeng Pang
- Department of Chemistry, Zhejiang University, 310027 Hangzhou, China
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Sheetal Jain
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Chen Yang
- Amazon Robotics, 300 Riverpark Drive, North Reading, Massachusetts 01864, USA
| | - Xueqian Kong
- Department of Chemistry, Zhejiang University, 310027 Hangzhou, China
| | - Kong Ooi Tan
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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5
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Gorka M, Charles P, Kalendra V, Baldansuren A, Lakshmi KV, Golbeck JH. A dimeric chlorophyll electron acceptor differentiates type I from type II photosynthetic reaction centers. iScience 2021; 24:102719. [PMID: 34278250 PMCID: PMC8267441 DOI: 10.1016/j.isci.2021.102719] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 01/09/2023] Open
Abstract
This research addresses one of the most compelling issues in the field of photosynthesis, namely, the role of the accessory chlorophyll molecules in primary charge separation. Using a combination of empirical and computational methods, we demonstrate that the primary acceptor of photosystem (PS) I is a dimer of accessory and secondary chlorophyll molecules, Chl2A and Chl3A, with an asymmetric electron charge density distribution. The incorporation of highly coupled donors and acceptors in PS I allows for extensive delocalization that prolongs the lifetime of the charge-separated state, providing for high quantum efficiency. The discovery of this motif has widespread implications ranging from the evolution of naturally occurring reaction centers to the development of a new generation of highly efficient artificial photosynthetic systems. Video abstract
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Affiliation(s)
- Michael Gorka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Philip Charles
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Vidmantas Kalendra
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Amgalanbaatar Baldansuren
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - K V Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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6
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Gorka M, Gruszecki E, Charles P, Kalendra V, Lakshmi KV, Golbeck JH. Two-dimensional HYSCORE spectroscopy reveals a histidine imidazole as the axial ligand to Chl 3A in the M688H PsaA genetic variant of Photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148424. [PMID: 33785317 DOI: 10.1016/j.bbabio.2021.148424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/28/2021] [Accepted: 03/24/2021] [Indexed: 12/17/2022]
Abstract
Recent studies on Photosystem I (PS I) have shown that the six core chlorophyll a molecules are highly coupled, allowing for efficient creation and stabilization of the charge-separated state. One area of particular interest is the identity and function of the primary acceptor, A0, as the factors that influence its ultrafast processes and redox properties are not yet fully elucidated. It was recently shown that A0 exists as a dimer of the closely-spaced Chl2/Chl3 molecules wherein the reduced A0- state has an asymmetric distribution of electron spin density that favors Chl3. Previous experimental work in which this ligand was changed to a hard base (histidine, M688HPsaA) revealed severely impacted electron transfer processes at both the A0 and A1 acceptors; molecular dynamics simulations further suggested two distinct conformations of PS I in which the His residue coordinates and forms a hydrogen bond to the A0 and A1 cofactors, respectively. In this study, we have applied 2D HYSCORE spectroscopy in conjunction with molecular dynamics simulations and density functional theory calculations to the study of the M688HPsaA variant. Analysis of the hyperfine parameters demonstrates that the His imidazole serves as the axial ligand to the central Mg2+ ion in Chl3A in the M688HPsaA variant. Although the change in ligand identity does not alter delocalization of electron density over the Chl2/Chl3 dimer, a small shift in the asymmetry of delocalization, coupled with the electron withdrawing properties of the ligand, most likely accounts for the inhibition of forward electron transfer in the His-ligated conformation.
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Affiliation(s)
- Michael Gorka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA 16802, USA
| | - Elijah Gruszecki
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Philip Charles
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Vidmantas Kalendra
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - K V Lakshmi
- Department of Chemistry and Chemical Biology and The Baruch '60 Center for Biochemical Solar Energy Research, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, PA 16802, USA; Department of Chemistry, The Pennsylvania State University, State College, PA 16802, USA.
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7
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Charles P, Kalendra V, He Z, Khatami MH, Golbeck JH, van der Est A, Lakshmi KV, Bryant DA. Two-dimensional 67Zn HYSCORE spectroscopy reveals that a Zn-bacteriochlorophyll aP′ dimer is the primary donor (P840) in the type-1 reaction centers of Chloracidobacterium thermophilum. Phys Chem Chem Phys 2020; 22:6457-6467. [DOI: 10.1039/c9cp06556c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Using pulsed EPR spectroscopy and isotopic labeling we demonstrate that reaction centers of Chloracidobacterium thermophilum have an unusual primary donor that is a dimer of Zn-bacteriochlorophyll aP′ molecules.
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Affiliation(s)
- Philip Charles
- Departments of Chemistry and Physics and The Baruch ’60 Center for Biochemical Solar Energy Research
- Rensselaer Polytechnic Institute
- Troy
- USA
| | - Vidmantas Kalendra
- Departments of Chemistry and Physics and The Baruch ’60 Center for Biochemical Solar Energy Research
- Rensselaer Polytechnic Institute
- Troy
- USA
| | - Zhihui He
- Department of Biochemistry and Molecular Biology
- The Pennsylvania State University
- State College
- USA
| | | | - John H. Golbeck
- Department of Biochemistry and Molecular Biology
- The Pennsylvania State University
- State College
- USA
- Department of Chemistry
| | | | - K. V. Lakshmi
- Departments of Chemistry and Physics and The Baruch ’60 Center for Biochemical Solar Energy Research
- Rensselaer Polytechnic Institute
- Troy
- USA
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology
- The Pennsylvania State University
- State College
- USA
- Department of Chemistry and Biochemistry
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8
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Ivanov MY, Fedin MV. Nanoscale heterogeneities in ionic liquids: insights from EPR of spin probes. MENDELEEV COMMUNICATIONS 2018. [DOI: 10.1016/j.mencom.2018.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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9
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Continuous Wave and Pulse EPR Characterization of Open-Shell Ti3+ Ions Generated in Hybrid SiO2–TiO2 Monoliths. Top Catal 2018. [DOI: 10.1007/s11244-018-1037-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Wu X, Clavaguera C, Lagardère L, Piquemal JP, de la Lande A. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms. J Chem Theory Comput 2018; 14:2705-2720. [PMID: 29630819 DOI: 10.1021/acs.jctc.7b01128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H2O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.
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Affiliation(s)
- Xiaojing Wu
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Carine Clavaguera
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Louis Lagardère
- Sorbonne Université, CNRS , Institut Parisien de Chimie Physique et Théorique (IP2CT) , 4 Place Jussieu , F-75005 , Paris , France.,Sorbonne Université , Institut des Sciences du Calcul et des Données (ISCD) , 4 place Jussieu , F-75005 , Paris , France
| | - Jean-Philip Piquemal
- Sorbonne Université, CNRS , Laboratoire de Chimie Théorique (LCT) , 4 Place Jussieu , F-75005 , Paris , France.,Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States.,Institut Universitaire de France , 75005 , Paris , France
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
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11
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Van Doorslaer S, Cuypers B. Electron paramagnetic resonance of globin proteins – a successful match between spectroscopic development and protein research. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1392629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Bert Cuypers
- Department of Physics, University of Antwerp, Antwerp, Belgium
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