1
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Rudolph M, Tampé R, Joseph B. Time-Resolved Mn 2+ -NO and NO-NO Distance Measurements Reveal That Catalytic Asymmetry Regulates Alternating Access in an ABC Transporter. Angew Chem Int Ed Engl 2023; 62:e202307091. [PMID: 37459565 DOI: 10.1002/anie.202307091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
ATP-binding cassette (ABC) transporters shuttle diverse substrates across biological membranes. Transport is often achieved through a transition between an inward-facing (IF) and an outward-facing (OF) conformation of the transmembrane domains (TMDs). Asymmetric nucleotide-binding sites (NBSs) are present among several ABC subfamilies and their functional role remains elusive. Here we addressed this question using concomitant NO-NO, Mn2+ -NO, and Mn2+ -Mn2+ pulsed electron-electron double-resonance spectroscopy of TmrAB in a time-resolved manner. This type-IV ABC transporter undergoes a reversible transition in the presence of ATP with a significantly faster forward transition. The impaired degenerate NBS stably binds Mn2+ -ATP, and Mn2+ is preferentially released at the active consensus NBS. ATP hydrolysis at the consensus NBS considerably accelerates the reverse transition. Both NBSs fully open during each conformational cycle and the degenerate NBS may regulate the kinetics of this process.
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Affiliation(s)
- Michael Rudolph
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Benesh Joseph
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
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2
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A Low-Spin CoII/Nitroxide Complex for Distance Measurements at Q-Band Frequencies. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8040043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pulse dipolar electron paramagnetic resonance spectroscopy (PDS) is continuously furthering the understanding of chemical and biological assemblies through distance measurements in the nanometer range. New paramagnets and pulse sequences can provide structural insights not accessible through other techniques. In the pursuit of alternative spin centers for PDS, we synthesized a low-spin CoII complex bearing a nitroxide (NO) moiety, where both the CoII and NO have an electron spin S of 1/2. We measured CoII-NO distances with the well-established double electron–electron resonance (DEER aka PELDOR) experiment, as well as with the five- and six-pulse relaxation-induced dipolar modulation enhancement (RIDME) spectroscopies at Q-band frequencies (34 GHz). We first identified challenges related to the stability of the complex in solution via DEER and X-ray crystallography and showed that even in cases where complex disproportionation is unavoidable, CoII-NO PDS measurements are feasible and give good signal-to-noise (SNR) ratios. Specifically, DEER and five-pulse RIDME exhibited an SNR of ~100, and while the six-pulse RIDME exhibited compromised SNR, it helped us minimize unwanted signals from the RIDME traces. Last, we demonstrated RIDME at a 10 μM sample concentration. Our results demonstrate paramagnetic CoII to be a feasible spin center in medium magnetic fields with opportunities for PDS studies involving CoII ions.
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3
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Abdullin D, Schiemann O. Localization of metal ions in biomolecules by means of pulsed dipolar EPR spectroscopy. Dalton Trans 2021; 50:808-815. [PMID: 33416053 DOI: 10.1039/d0dt03596c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal ions are important for the folding, structure, and function of biomolecules. Thus, knowing where their binding sites are located in proteins or oligonucleotides is a critical objective. X-ray crystallography and nuclear magnetic resonance are powerful methods in this respect, but both have their limitations. Here, a complementary method is highlighted in which paramagnetic metal ions are localized by means of trilateration using a combination of site-directed spin labeling and pulsed dipolar electron paramagnetic resonance spectroscopy. The working principle, the requirements, and the limitations of the method are critically discussed. Several applications of the method are outlined and compared with each other.
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Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany.
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4
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Teucher M, Qi M, Cati N, Hintz H, Godt A, Bordignon E. Strategies to identify and suppress crosstalk signals in double electron-electron resonance (DEER) experiments with gadolinium III and nitroxide spin-labeled compounds. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:285-299. [PMID: 37904822 PMCID: PMC10500692 DOI: 10.5194/mr-1-285-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/31/2020] [Indexed: 11/01/2023]
Abstract
Double electron-electron resonance (DEER) spectroscopy applied to orthogonally spin-labeled biomolecular complexes simplifies the assignment of intra- and intermolecular distances, thereby increasing the information content per sample. In fact, various spin labels can be addressed independently in DEER experiments due to spectroscopically nonoverlapping central transitions, distinct relaxation times, and/or transition moments; hence, they are referred to as spectroscopically orthogonal. Molecular complexes which are, for example, orthogonally spin-labeled with nitroxide (NO) and gadolinium (Gd) labels give access to three distinct DEER channels that are optimized to selectively probe NO-NO, NO-Gd, and Gd-Gd distances. Nevertheless, it has been previously recognized that crosstalk signals between individual DEER channels can occur, for example, when a Gd-Gd distance appears in a DEER channel optimized to detect NO-Gd distances. This is caused by residual spectral overlap between NO and Gd spins which, therefore, cannot be considered as perfectly orthogonal. Here, we present a systematic study on how to identify and suppress crosstalk signals that can appear in DEER experiments using mixtures of NO-NO, NO-Gd, and Gd-Gd molecular rulers characterized by distinct, nonoverlapping distance distributions. This study will help to correctly assign the distance peaks in homo- and heterocomplexes of biomolecules carrying not perfectly orthogonal spin labels.
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Affiliation(s)
- Markus Teucher
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Ninive Cati
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Henrik Hintz
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
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5
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EL Mkami H, Hunter R, Cruickshank P, Taylor M, Lovett J, Feintuch A, Qi M, Godt A, Smith G. High-sensitivity Gd 3+-Gd 3+ EPR distance measurements that eliminate artefacts seen at short distances. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:301-313. [PMID: 37904818 PMCID: PMC10500690 DOI: 10.5194/mr-1-301-2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/18/2020] [Indexed: 11/01/2023]
Abstract
Gadolinium complexes are attracting increasing attention as spin labels for EPR dipolar distance measurements in biomolecules and particularly for in-cell measurements. It has been shown that flip-flop transitions within the central transition of the high-spin Gd3 + ion can introduce artefacts in dipolar distance measurements, particularly when measuring distances less than 3 nm. Previous work has shown some reduction of these artefacts through increasing the frequency separation between the two frequencies required for the double electron-electron resonance (DEER) experiment. Here we use a high-power (1 kW), wideband, non-resonant system operating at 94 GHz to evaluate DEER measurement protocols using two stiff Gd(III) rulers, consisting of two b i s -Gd3 + -PyMTA complexes, with separations of 2.1 nm and 6.0 nm, respectively. We show that by avoiding the - 1 2 → 1 2 central transition completely, and placing both the pump and the observer pulses on either side of the central transition, we can now observe apparently artefact-free spectra and narrow distance distributions, even for a Gd-Gd distance of 2.1 nm. Importantly we still maintain excellent signal-to-noise ratio and relatively high modulation depths. These results have implications for in-cell EPR measurements at naturally occurring biomolecule concentrations.
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Affiliation(s)
- Hassane EL Mkami
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Robert I. Hunter
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Paul A. S. Cruickshank
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Michael J. Taylor
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Janet E. Lovett
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science,
Rehovot, Israel
| | - Mian Qi
- Faculty of Chemistry and Center of Molecular Materials (CM2),
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld,
Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center of Molecular Materials (CM2),
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld,
Germany
| | - Graham M. Smith
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
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6
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Schmidt T, Clore GM. Tm filtering by 1H-methyl labeling in a deuterated protein for pulsed double electron-electron resonance EPR. Chem Commun (Camb) 2020; 56:10890-10893. [PMID: 32940289 PMCID: PMC7498720 DOI: 10.1039/d0cc04369a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modulating the phase-memory relaxation time (Tm) of a spin label by introducing 1H-methyl groups in a perdeuterated protein background is used in DEER experiments to assign interactions in multimodal P(r) distributions. Proof of principle is demonstrated using Protein A where one nitroxide label occupies two distinct regions of conformational space. The presence of a single protonated methyl group in close proximity (4-8 Å) to only one of the two nitroxide rotamer ensembles results in a selective and substantial decrease in Tm, manifested by differential decay of the peak intensities in the bimodal P(r) distance distribution as a function of the total dipolar evolution time. This form of Tm filtering will facilitate DEER structural analysis of biomolecular systems with three spin labels, including complexes involving multimeric proteins.
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Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
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7
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Abdullin D, Schiemann O. Pulsed Dipolar EPR Spectroscopy and Metal Ions: Methodology and Biological Applications. Chempluschem 2020; 85:353-372. [DOI: 10.1002/cplu.201900705] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/16/2020] [Indexed: 01/18/2023]
Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
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8
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Sameach H, Ruthstein S. EPR Distance Measurements as a Tool to Characterize Protein‐DNA Interactions. Isr J Chem 2019. [DOI: 10.1002/ijch.201900091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hila Sameach
- The Department of Chemistry, Faculty of Exact SciencesBar Ilan University Ramat Gan Israel 5290002
| | - Sharon Ruthstein
- The Department of Chemistry, Faculty of Exact SciencesBar Ilan University Ramat Gan Israel 5290002
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9
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Abdullin D, Brehm P, Fleck N, Spicher S, Grimme S, Schiemann O. Pulsed EPR Dipolar Spectroscopy on Spin Pairs with one Highly Anisotropic Spin Center: The Low-Spin Fe III Case. Chemistry 2019; 25:14388-14398. [PMID: 31386227 PMCID: PMC6900076 DOI: 10.1002/chem.201902908] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/05/2019] [Indexed: 02/01/2023]
Abstract
Pulsed electron paramagnetic resonance (EPR) dipolar spectroscopy (PDS) offers several methods for measuring dipolar coupling constants and thus the distance between electron spin centers. Up to now, PDS measurements have been mostly applied to spin centers whose g-anisotropies are moderate and therefore have a negligible effect on the dipolar coupling constants. In contrast, spin centers with large g-anisotropy yield dipolar coupling constants that depend on the g-values. In this case, the usual methods of extracting distances from the raw PDS data cannot be applied. Here, the effect of the g-anisotropy on PDS data is studied in detail on the example of the low-spin Fe3+ ion. First, this effect is described theoretically, using the work of Bedilo and Maryasov (Appl. Magn. Reson. 2006, 30, 683-702) as a basis. Then, two known Fe3+ /nitroxide compounds and one new Fe3+ /trityl compound were synthesized and PDS measurements were carried out on them using a method called relaxation induced dipolar modulation enhancement (RIDME). Based on the theoretical results, a RIDME data analysis procedure was developed, which facilitated the extraction of the inter-spin distance and the orientation of the inter-spin vector relative to the Fe3+ g-tensor frame from the RIDME data. The accuracy of the determined distances and orientations was confirmed by comparison with MD simulations. This method can thus be applied to the highly relevant class of metalloproteins with, for example, low-spin Fe3+ ions.
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Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Philipp Brehm
- Institute of Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
- Current address: Institute of Inorganic ChemistryUniversity of Bonn53115BonnGermany
| | - Nico Fleck
- Institute of Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Sebastian Spicher
- Mulliken Center for Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryUniversity of Bonn53115BonnGermany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of Bonn53115BonnGermany
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10
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Abdullin D, Matsuoka H, Yulikov M, Fleck N, Klein C, Spicher S, Hagelueken G, Grimme S, Lützen A, Schiemann O. Pulsed EPR Dipolar Spectroscopy under the Breakdown of the High-Field Approximation: The High-Spin Iron(III) Case. Chemistry 2019; 25:8820-8828. [PMID: 31017706 DOI: 10.1002/chem.201900977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Indexed: 12/11/2022]
Abstract
Pulsed EPR dipolar spectroscopy (PDS) offers several methods for measuring dipolar coupling and thus the distance between electron-spin centers. To date, PDS measurements to metal centers were limited to ions that adhere to the high-field approximation. Here, the PDS methodology is extended to cases where the high-field approximation breaks down on the example of the high-spin Fe3+ /nitroxide spin-pair. First, the theory developed by Maryasov et al. (Appl. Magn. Reson. 2006, 30, 683-702) was adapted to derive equations for the dipolar coupling constant, which revealed that the dipolar spectrum does not only depend on the length and orientation of the interspin distance vector with respect to the applied magnetic field but also on its orientation to the effective g-tensor of the Fe3+ ion. Then, it is shown on a model system and a heme protein that a PDS method called relaxation-induced dipolar modulation enhancement (RIDME) is well-suited to measuring such spectra and that the experimentally obtained dipolar spectra are in full agreement with the derived equations. Finally, a RIDME data analysis procedure was developed, which facilitates the determination of distance and angular distributions from the RIDME data. Thus, this study enables the application of PDS to for example, the highly relevant class of high-spin Fe3+ heme proteins.
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Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Hideto Matsuoka
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany.,Current address: Graduate School of Science, Osaka City University, Osaka, Japan
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Nico Fleck
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Christoph Klein
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany.,Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany
| | - Sebastian Spicher
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Arne Lützen
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
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11
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Abdullin D, Fleck N, Klein C, Brehm P, Spicher S, Lützen A, Grimme S, Schiemann O. Synthesis of μ
2
‐Oxo‐Bridged Iron(III) Tetraphenylporphyrin–Spacer–Nitroxide Dimers and their Structural and Dynamics Characterization by using EPR and MD Simulations. Chemistry 2019; 25:2586-2596. [DOI: 10.1002/chem.201805016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/13/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Nico Fleck
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Christoph Klein
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
- Kekulé Institute of Organic Chemistry and Biochemistry Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Philipp Brehm
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
| | - Sebastian Spicher
- Mulliken Center for Theoretical ChemistryUniversity of Bonn Beringstr. 4 53115 Bonn Germany
| | - Arne Lützen
- Kekulé Institute of Organic Chemistry and Biochemistry Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryUniversity of Bonn Beringstr. 4 53115 Bonn Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical ChemistryUniversity of Bonn Wegelerstr. 12 53115 Bonn Germany
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12
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Sameach H, Ghosh S, Gevorkyan‐Airapetov L, Saxena S, Ruthstein S. EPR Spectroscopy Detects Various Active State Conformations of the Transcriptional Regulator CueR. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201810656] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hila Sameach
- Department of Chemistry Faculty of Exact Sciences Bar-Ilan University Ramat-Gan 5290002 Israel
| | - Shreya Ghosh
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | | | - Sunil Saxena
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Sharon Ruthstein
- Department of Chemistry Faculty of Exact Sciences Bar-Ilan University Ramat-Gan 5290002 Israel
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13
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Sameach H, Ghosh S, Gevorkyan-Airapetov L, Saxena S, Ruthstein S. EPR Spectroscopy Detects Various Active State Conformations of the Transcriptional Regulator CueR. Angew Chem Int Ed Engl 2019; 58:3053-3056. [PMID: 30566257 DOI: 10.1002/anie.201810656] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/29/2018] [Indexed: 01/14/2023]
Abstract
The interactions between proteins and their specific DNA sequences are the basis of many cellular processes. Hence, developing methods to build an atomic level picture of these interactions helps improve our understanding of key cellular mechanisms. CueR is an Escherichia coli copper-sensing transcription regulator. The inhibition of copper-sensing transcription regulators can kill pathogens, without harming the host. Several spectroscopic studies and crystallographic data have suggested that changes in the conformation of both the DNA and the protein control transcription. However, due to the inadequate resolution of these methods, the exact number of active conformations of CueR has not been determined. Resolving the structure of CueR in its active state is highly important for the development of specific inhibitors. Herein, the potential of double-histidine (dHis)-based CuII spin labeling for the identification of various conformational states of CueR during transcription is shown.
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Affiliation(s)
- Hila Sameach
- Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Lada Gevorkyan-Airapetov
- Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Sharon Ruthstein
- Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
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14
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Ritsch I, Hintz H, Jeschke G, Godt A, Yulikov M. Improving the accuracy of Cu(ii)–nitroxide RIDME in the presence of orientation correlation in water-soluble Cu(ii)–nitroxide rulers. Phys Chem Chem Phys 2019; 21:9810-9830. [DOI: 10.1039/c8cp06573j] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Detailed analysis of artefacts in the Cu(ii)–nitroxide RIDME experiments, related to orientation averaging, echo-crossing, ESEEM and background-correction is presented.
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Affiliation(s)
- Irina Ritsch
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Henrik Hintz
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
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15
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Keller K, Qi M, Gmeiner C, Ritsch I, Godt A, Jeschke G, Savitsky A, Yulikov M. Intermolecular background decay in RIDME experiments. Phys Chem Chem Phys 2019; 21:8228-8245. [DOI: 10.1039/c8cp07815g] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Theoretical and experimental studies of the RIDME background reveal electron and nuclear spectral diffusion contributions.
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Affiliation(s)
- Katharina Keller
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Christoph Gmeiner
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Irina Ritsch
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Anton Savitsky
- Physics Department
- Technical University Dortmund
- Dortmund
- Germany
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
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16
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Merz GE, Borbat PP, Muok AR, Srivastava M, Bunck DN, Freed JH, Crane BR. Site-Specific Incorporation of a Cu 2+ Spin Label into Proteins for Measuring Distances by Pulsed Dipolar Electron Spin Resonance Spectroscopy. J Phys Chem B 2018; 122:9443-9451. [PMID: 30222354 DOI: 10.1021/acs.jpcb.8b05619] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pulsed dipolar electron spin resonance spectroscopy (PDS) is a powerful tool for measuring distances in solution-state macromolecules. Paramagnetic metal ions, such as Cu2+, are used as spin probes because they can report on metalloprotein features and can be spectroscopically distinguished from traditional nitroxide (NO)-based labels. Here, we demonstrate site-specific incorporation of Cu2+ into non-metalloproteins through the use of a genetically encodable non-natural amino acid, 3-pyrazolyltyrosine (PyTyr). We first incorporate PyTyr in cyan fluorescent protein to measure Cu2+-to-NO distances and examine the effects of solvent conditions on Cu2+ binding and protein aggregation. We then apply the method to characterize the complex formed by the histidine kinase CheA and its target response regulator CheY. The X-ray structure of CheY-PyTyr confirms Cu labeling at PyTyr but also reveals a secondary Cu site. Cu2+-to-NO and Cu2+-to-Cu2+ PDS measurements of CheY-PyTyr with nitroxide-labeled CheA provide new insights into the conformational landscape of the phosphotransfer complex and have implications for kinase regulation.
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Affiliation(s)
- Gregory E Merz
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Alise R Muok
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Madhur Srivastava
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - David N Bunck
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
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17
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Kuzhelev AA, Krumkacheva OA, Shevelev GY, Yulikov M, Fedin MV, Bagryanskaya EG. Room-temperature distance measurements using RIDME and the orthogonal spin labels trityl/nitroxide. Phys Chem Chem Phys 2018; 20:10224-10230. [PMID: 29594278 DOI: 10.1039/c8cp01093e] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance (EPR) based nanometer distance measurements at ambient temperatures are of particular interest for structural biology applications. The nitroxide spin labels commonly used in EPR reveal relatively short transverse relaxation under these conditions, which limits their use for detecting static dipolar interactions. At the same time, the longitudinal relaxation of nitroxide spin labels is still long enough to allow using them as 'pumped' species in the relaxation induced dipolar modulation enhancement (RIDME) experiment where the detection is carried out on the slower relaxing triarylmethyl (TAM) spin labels. In the present study, we report the first demonstration of room-temperature RIDME distance measurements in nucleic acids using TAM as the slow-relaxing detected species and traditional nitroxide as the fast-relaxing partner spin. Two types of immobilizers, glassy trehalose and the modified silica gel Nucleosil, were used for immobilization of the spin-labeled biomolecules. The room-temperature RIDME-based distance distributions are in good agreement with those measured at 80 K by other techniques. Room-temperature RIDME on the spin pairs trityl/nitroxide may become a useful method for the structural characterization of biomacromolecules and biomolecular complexes at near physiological temperatures.
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Affiliation(s)
- Andrey A Kuzhelev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia.
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18
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Giannoulis A, Motion CL, Oranges M, Bühl M, Smith GM, Bode BE. Orientation selection in high-field RIDME and PELDOR experiments involving low-spin CoII ions. Phys Chem Chem Phys 2018; 20:2151-2154. [DOI: 10.1039/c7cp07248a] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Orientation selective pulse dipolar electron paramagnetic resonance unravels relative geometries of spin centres from RIDME and PELDOR data.
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Affiliation(s)
- Angeliki Giannoulis
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews
- UK
- Biomedical Sciences Research Complex, University of St Andrews
- UK
| | | | - Maria Oranges
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews
- UK
- Biomedical Sciences Research Complex, University of St Andrews
- UK
| | - Michael Bühl
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews
- UK
| | - Graham M. Smith
- SUPA, School of Physics & Astronomy, University of St Andrews
- UK
| | - Bela E. Bode
- EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews
- UK
- Biomedical Sciences Research Complex, University of St Andrews
- UK
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19
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Engelhard DM, Meyer A, Berndhäuser A, Schiemann O, Clever GH. Di-copper(ii) DNA G-quadruplexes as EPR distance rulers. Chem Commun (Camb) 2018; 54:7455-7458. [DOI: 10.1039/c8cc04053b] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Paramagnetic Cu(ii) complexes, immobilized via four-point-attachment to both ends of G-quadruplexes, serve as EPR-based distance rulers for studying DNA structure.
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Affiliation(s)
- David M. Engelhard
- Depart. of Chemistry and Chemical Biology
- TU Dortmund University
- Dortmund
- Germany
| | - Andreas Meyer
- Institute for Physical and Theoretical Chemistry
- Wegelerstr. 12
- Rheinische Friedrich-Wilhelms-Universität Bonn
- Bonn
- Germany
| | - Andreas Berndhäuser
- Institute for Physical and Theoretical Chemistry
- Wegelerstr. 12
- Rheinische Friedrich-Wilhelms-Universität Bonn
- Bonn
- Germany
| | - Olav Schiemann
- Institute for Physical and Theoretical Chemistry
- Wegelerstr. 12
- Rheinische Friedrich-Wilhelms-Universität Bonn
- Bonn
- Germany
| | - Guido H. Clever
- Depart. of Chemistry and Chemical Biology
- TU Dortmund University
- Dortmund
- Germany
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20
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Meyer A, Jassoy JJ, Spicher S, Berndhäuser A, Schiemann O. Performance of PELDOR, RIDME, SIFTER, and DQC in measuring distances in trityl based bi- and triradicals: exchange coupling, pseudosecular coupling and multi-spin effects. Phys Chem Chem Phys 2018; 20:13858-13869. [DOI: 10.1039/c8cp01276h] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The performance of pulsed EPR methods for distance measurements is evaluated on three different trityl model systems.
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Affiliation(s)
- Andreas Meyer
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Jean Jacques Jassoy
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Sebastian Spicher
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Andreas Berndhäuser
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
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21
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Wu Z, Feintuch A, Collauto A, Adams LA, Aurelio L, Graham B, Otting G, Goldfarb D. Selective Distance Measurements Using Triple Spin Labeling with Gd 3+, Mn 2+, and a Nitroxide. J Phys Chem Lett 2017; 8:5277-5282. [PMID: 28990781 DOI: 10.1021/acs.jpclett.7b01739] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Distance measurements by pulse electron paramagnetic resonance techniques, such as double electron-electron resonance (DEER, also called PELDOR), have become an established tool to explore structural properties of biomacromolecules and their assemblies. In such measurements a pair of spin labels provides a single distance constraint. Here we show that by employing three different types of spin labels that differ in their spectroscopic and spin dynamics properties it is possible to extract three independent distances from a single sample. We demonstrate this using the Antennapedia homeodomain orthogonally labeled with Gd3+ and Mn2+ tags in complex with its cognate DNA binding site labeled with a nitroxide.
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Affiliation(s)
- Zuyan Wu
- Research School of Chemistry, Australian National University , Canberra ACT 2601, Australia
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Alberto Collauto
- Department of Chemical Physics, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Luke A Adams
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Luigi Aurelio
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University , Canberra ACT 2601, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science , Rehovot 76100, Israel
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22
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Gmeiner C, Klose D, Mileo E, Belle V, Marque SRA, Dorn G, Allain FHT, Guigliarelli B, Jeschke G, Yulikov M. Orthogonal Tyrosine and Cysteine Site-Directed Spin Labeling for Dipolar Pulse EPR Spectroscopy on Proteins. J Phys Chem Lett 2017; 8:4852-4857. [PMID: 28933855 DOI: 10.1021/acs.jpclett.7b02220] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Site-directed spin labeling of native tyrosine residues in isolated domains of the protein PTBP1, using a Mannich-type reaction, was combined with conventional spin labeling of cysteine residues. Double electron-electron resonance (DEER) EPR measurements were performed for both the nitroxide-nitroxide and Gd(III)-nitroxide label combinations within the same protein molecule. For the prediction of distance distributions from a structure model, rotamer libraries were generated for the two linker forms of the tyrosine-reactive isoindoline-based nitroxide radical Nox. Only moderate differences exist between the spatial spin distributions for the two linker forms of Nox. This strongly simplifies DEER data analysis, in particular, if only mean distances need to be predicted.
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Affiliation(s)
- Christoph Gmeiner
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
| | - Daniel Klose
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
| | - Elisabetta Mileo
- Aix Marseille Univ , CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Valérie Belle
- Aix Marseille Univ , CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Sylvain R A Marque
- Aix Marseille Univ , CNRS, ICR, Institut de Chimie Radicalaire, Marseille 13397, France
- N. N. Vorozhtsov Novosibirsk Insititute of Organic Chemistry , 630090 Novosibirsk, Russia
| | - Georg Dorn
- Institute of Molecular Biology and Biophysics, ETH Zurich , Zurich 8093, Switzerland
| | - Frédéric H T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich , Zurich 8093, Switzerland
| | - Bruno Guigliarelli
- Aix Marseille Univ , CNRS, BIP, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille 13402, France
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich , Zurich 8093, Switzerland
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23
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Giannoulis A, Oranges M, Bode BE. Monitoring Complex Formation by Relaxation-Induced Pulse Electron Paramagnetic Resonance Distance Measurements. Chemphyschem 2017; 18:2318-2321. [PMID: 28672084 PMCID: PMC5601224 DOI: 10.1002/cphc.201700666] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Indexed: 12/14/2022]
Abstract
Biomolecular complexes are often multimers fueling the demand for methods that allow unraveling their composition and geometric arrangement. Pulse electron paramagnetic resonance (EPR) spectroscopy is increasingly applied for retrieving geometric information on the nanometer scale. The emerging RIDME (relaxation‐induced dipolar modulation enhancement) technique offers improved sensitivity in distance experiments involving metal centers (e.g. on metalloproteins or proteins labelled with metal ions). Here, a mixture of a spin labelled ligand with increasing amounts of paramagnetic CuII ions allowed accurate quantification of ligand‐metal binding in the model complex formed. The distance measurement was highly accurate and critical aspects for identifying multimerization could be identified. The potential to quantify binding in addition to the high‐precision distance measurement will further increase the scope of EPR applications.
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Affiliation(s)
- Angeliki Giannoulis
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and, EaStCHEM School of Chemistry, University of St AndrewsNorth Haugh, St Andrews, KY16 9ST, UK
| | - Maria Oranges
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and, EaStCHEM School of Chemistry, University of St AndrewsNorth Haugh, St Andrews, KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and, EaStCHEM School of Chemistry, University of St AndrewsNorth Haugh, St Andrews, KY16 9ST, UK
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24
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Boulon M, Fernandez A, Moreno Pineda E, Chilton NF, Timco G, Fielding AJ, Winpenny REP. Measuring Spin⋅⋅⋅Spin Interactions between Heterospins in a Hybrid [2]Rotaxane. Angew Chem Int Ed Engl 2017; 56:3876-3879. [PMID: 28276620 PMCID: PMC5434811 DOI: 10.1002/anie.201612249] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Indexed: 12/29/2022]
Abstract
Use of molecular electron spins as qubits for quantum computing will depend on the ability to produce molecules with weak but measurable interactions between the qubits. Here we demonstrate use of pulsed EPR spectroscopy to measure the interaction between two inequivalent spins in a hybrid rotaxane molecule.
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Affiliation(s)
- Marie‐Emmanuelle Boulon
- The School of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Antonio Fernandez
- The School of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Eufemio Moreno Pineda
- The School of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Nicholas F. Chilton
- The School of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Grigore Timco
- The School of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Alistair J. Fielding
- The School of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Richard E. P. Winpenny
- The School of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
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25
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Boulon ME, Fernandez A, Moreno Pineda E, Chilton NF, Timco G, Fielding AJ, Winpenny REP. Measuring Spin⋅⋅⋅Spin Interactions between Heterospins in a Hybrid [2]Rotaxane. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612249] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Marie-Emmanuelle Boulon
- The School of Chemistry and Photon Science Institute; The University of Manchester; Oxford Road Manchester M13 9PL UK
| | - Antonio Fernandez
- The School of Chemistry and Photon Science Institute; The University of Manchester; Oxford Road Manchester M13 9PL UK
| | - Eufemio Moreno Pineda
- The School of Chemistry and Photon Science Institute; The University of Manchester; Oxford Road Manchester M13 9PL UK
| | - Nicholas F. Chilton
- The School of Chemistry and Photon Science Institute; The University of Manchester; Oxford Road Manchester M13 9PL UK
| | - Grigore Timco
- The School of Chemistry and Photon Science Institute; The University of Manchester; Oxford Road Manchester M13 9PL UK
| | - Alistair J. Fielding
- The School of Chemistry and Photon Science Institute; The University of Manchester; Oxford Road Manchester M13 9PL UK
| | - Richard E. P. Winpenny
- The School of Chemistry and Photon Science Institute; The University of Manchester; Oxford Road Manchester M13 9PL UK
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26
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Keller K, Mertens V, Qi M, Nalepa AI, Godt A, Savitsky A, Jeschke G, Yulikov M. Computing distance distributions from dipolar evolution data with overtones: RIDME spectroscopy with Gd(iii)-based spin labels. Phys Chem Chem Phys 2017; 19:17856-17876. [DOI: 10.1039/c7cp01524k] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extraction of distance distributions between high-spin paramagnetic centers from relaxation induced dipolar modulation enhancement (RIDME) data is affected by the presence of overtones of dipolar frequencies.
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Affiliation(s)
- Katharina Keller
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Valerie Mertens
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Anna I. Nalepa
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Anton Savitsky
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
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27
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Keller K, Doll A, Qi M, Godt A, Jeschke G, Yulikov M. Averaging of nuclear modulation artefacts in RIDME experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 272:108-113. [PMID: 27684788 DOI: 10.1016/j.jmr.2016.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/16/2016] [Accepted: 09/21/2016] [Indexed: 05/15/2023]
Abstract
The presence of artefacts due to Electron Spin Echo Envelope Modulation (ESEEM) complicates the analysis of dipolar evolution data in Relaxation Induced Dipolar Modulation Enhancement (RIDME) experiments. Here we demonstrate that averaging over the two delay times in the refocused RIDME experiment allows for nearly quantitative removal of the ESEEM artefacts, resulting in potentially much better performance than the so far used methods. The analytical equations are presented and analyzed for the case of electron and nuclear spins S=1/2,I=1/2. The presented analysis is also relevant for Double Electron Electron Resonance (DEER) and Chirp-Induced Dipolar Modulation Enhancement (CIDME) techniques. The applicability of the ESEEM averaging approach is demonstrated on a Gd(III)-Gd(III) rigid ruler compound in deuterated frozen solution at Q band (35GHz).
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Affiliation(s)
- Katharina Keller
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Andrin Doll
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland.
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28
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Akhmetzyanov D, Ching HYV, Denysenkov V, Demay-Drouhard P, Bertrand HC, Tabares LC, Policar C, Prisner TF, Un S. RIDME spectroscopy on high-spin Mn2+ centers. Phys Chem Chem Phys 2016; 18:30857-30866. [DOI: 10.1039/c6cp05239h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A bis-MnDOTA complex was investigated by EPR dipolar spectroscopy. RIDME experiment revealed higher modulation depth compared to PELDOR and featured harmonics of the dipolar coupling frequency.
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Affiliation(s)
- D. Akhmetzyanov
- Goethe-University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
| | - H. Y. V. Ching
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology, Université Paris-Saclay
- CEA
- CNRS UMR 9198
| | - V. Denysenkov
- Goethe-University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
| | - P. Demay-Drouhard
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - H. C. Bertrand
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - L. C. Tabares
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology, Université Paris-Saclay
- CEA
- CNRS UMR 9198
| | - C. Policar
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - T. F. Prisner
- Goethe-University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
| | - S. Un
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology, Université Paris-Saclay
- CEA
- CNRS UMR 9198
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29
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Collauto A, Frydman V, Lee MD, Abdelkader EH, Feintuch A, Swarbrick JD, Graham B, Otting G, Goldfarb D. RIDME distance measurements using Gd(iii) tags with a narrow central transition. Phys Chem Chem Phys 2016; 18:19037-49. [DOI: 10.1039/c6cp03299k] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Methods based on pulse electron paramagnetic resonance allow measurement of the electron–electron dipolar coupling between two high-spin labels.
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Affiliation(s)
- A. Collauto
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - V. Frydman
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - M. D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - E. H. Abdelkader
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - A. Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - J. D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - B. Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - G. Otting
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - D. Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
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30
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Keller K, Zalibera M, Qi M, Koch V, Wegner J, Hintz H, Godt A, Jeschke G, Savitsky A, Yulikov M. EPR characterization of Mn(ii) complexes for distance determination with pulsed dipolar spectroscopy. Phys Chem Chem Phys 2016; 18:25120-25135. [DOI: 10.1039/c6cp04884f] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
EPR properties of four Mn(ii) complexes and Tikhonov regularization-based analysis of RIDME data containing dipolar overtones are presented.
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Affiliation(s)
- Katharina Keller
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Michal Zalibera
- Max Planck Institut for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
- Institute of Physical Chemistry and Chemical Physics
- Slovak University of Technology in Bratislava
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Vanessa Koch
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Julia Wegner
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Henrik Hintz
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Anton Savitsky
- Max Planck Institut for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Bioscience
- ETH Zurich
- 8093 Zurich
- Switzerland
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