1
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Abdullin D, Rauh Corro P, Hett T, Schiemann O. PDSFit: PDS data analysis in the presence of orientation selectivity, g-anisotropy, and exchange coupling. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:37-60. [PMID: 38130168 DOI: 10.1002/mrc.5415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
Pulsed dipolar electron paramagnetic resonance spectroscopy (PDS), encompassing techniques such as pulsed electron-electron double resonance (PELDOR or DEER) and relaxation-induced dipolar modulation enhancement (RIDME), is a valuable method in structural biology and materials science for obtaining nanometer-scale distance distributions between electron spin centers. An important aspect of PDS is the extraction of distance distributions from the measured time traces. Most software used for this PDS data analysis relies on simplifying assumptions, such as assuming isotropic g-factors of ~2 and neglecting orientation selectivity and exchange coupling. Here, the program PDSFit is introduced, which enables the analysis of PELDOR and RIDME time traces with or without orientation selectivity. It can be applied to spin systems consisting of up to two spin centers with anisotropic g-factors and to spin systems with exchange coupling. It employs a model-based fitting of the time traces using parametrized distance and angular distributions, and parametrized PDS background functions. The fitting procedure is followed by an error analysis for the optimized parameters of the distributions and backgrounds. Using five different experimental data sets published previously, the performance of PDSFit is tested and found to provide reliable solutions.
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Affiliation(s)
- Dinar Abdullin
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Pablo Rauh Corro
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Tobias Hett
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Olav Schiemann
- Clausius-Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
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2
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Harmer JR, Hakopian S, Niks D, Hille R, Bernhardt PV. Redox Characterization of the Complex Molybdenum Enzyme Formate Dehydrogenase from Cupriavidus necator. J Am Chem Soc 2023; 145:25850-25863. [PMID: 37967365 DOI: 10.1021/jacs.3c10199] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
The oxygen-tolerant and molybdenum-dependent formate dehydrogenase FdsDABG from Cupriavidus necator is capable of catalyzing both formate oxidation to CO2 and the reverse reaction (CO2 reduction to formate) at neutral pH, which are both reactions of great importance to energy production and carbon capture. FdsDABG is replete with redox cofactors comprising seven Fe/S clusters, flavin mononucleotide, and a molybdenum ion coordinated by two pyranopterin dithiolene ligands. The redox potentials of these centers are described herein and assigned to specific cofactors using combinations of potential-dependent continuous wave and pulse EPR spectroscopy and UV/visible spectroelectrochemistry on both the FdsDABG holoenzyme and the FdsBG subcomplex. These data represent the first redox characterization of a complex metal dependent formate dehydrogenase and provide an understanding of the highly efficient catalytic formate oxidation and CO2 reduction activity that are associated with the enzyme.
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Affiliation(s)
- Jeffrey R Harmer
- Centre for Advanced Imaging, University of Queensland, Brisbane 4072, Australia
| | - Sheron Hakopian
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Dimitri Niks
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Russ Hille
- Department of Biochemistry, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia
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3
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Hasanbasri Z, Moriglioni NA, Saxena S. Efficient sampling of molecular orientations for Cu(II)-based DEER on protein labels. Phys Chem Chem Phys 2023; 25:13275-13288. [PMID: 36939213 DOI: 10.1039/d3cp00404j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Combining rigid Cu(II) labels and pulsed-EPR techniques enables distance constraint measurements that are incisive probes of protein structure and dynamics. However, the labels can lead to a dipolar signal that is biased by the relative orientation of the two spins, which is typically unknown a priori in a bilabeled protein. This effect, dubbed orientational selectivity, becomes a bottleneck in measuring distances. This phenomenon also applies to other pulsed-EPR techniques that probe electron-nucleus interactions. In this work, we dissect orientational selectivity by generating an in silico sample of Cu(II)-labeled proteins to evaluate pulse excitation in the context of double electron-electron resonance (DEER) at Q-band frequencies. This approach enables the observation of the contribution of each protein orientation to the dipolar signal, which provides direct insights into optimizing acquisition schemes to mitigate orientational effects. Furthermore, we incorporate the excitation profile of realistic pulses to identify the excited spins. With this method, we show that rectangular pulses, despite their imperfect inversion capability, can sample similar spin orientations as other sophisticated pulses with the same bandwidth. Additionally, we reveal that the efficiency of exciting spin-pairs in DEER depends on the frequency offset of two pulses used in the experiment and the relative orientation of the two spins. Therefore, we systematically examine the frequency offset of the two pulses used in this double resonance experiment to determine the optimal frequency offset for optimal distance measurements. This procedure leads to a protocol where two measurements are sufficient to acquire orientational-independent DEER at Q-band. Notably, this procedure is feasible with any commercial pulsed-EPR spectrometer. Furthermore, we experimentally validate the computational results using DEER experiments on two different proteins. Finally, we show that increasing the amplitude of the rectangular pulse can increase the efficiency of DEER experiments by almost threefold. Overall, this work provides an attractive new approach for analyzing pulsed-EPR spectroscopy to obtain microscopic nuances that cannot be easily discerned from analytical or numerical calculations.
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Affiliation(s)
- Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | | | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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4
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Jozeliu̅naitė A, Neniškis A, Bertran A, Bowen AM, Di Valentin M, Raišys S, Baronas P, Kazlauskas K, Vilčiauskas L, Orentas E. Fullerene Complexation in a Hydrogen-Bonded Porphyrin Receptor via Induced-Fit: Cooperative Action of Tautomerization and C-H···π Interactions. J Am Chem Soc 2022; 145:455-464. [PMID: 36546690 PMCID: PMC9837862 DOI: 10.1021/jacs.2c10668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A supramolecular chiral hydrogen-bonded tetrameric aggregate possessing a large cavity and tetraarylporphyrin substituents was assembled using alternating 4H- and 2H-bonds between ureidopyrimidinone and isocytosine units, respectively. The aggregation mode was rationally shifted from social to narcissistic self-sorting by changing urea substituent size only. The H-bonded tetramer forms a strong complex with C60 guest, at the same time undergoing remarkable structural changes. Namely, the cavity adjusts to the guest via keto-to-enol tautomerization of the ureidopyrimidinone unit and as a result, porphyrin substituents move apart from each other in a scissor blade-like opening fashion. The rearrangement is accompanied by C-H···π interaction between the alkyl solubilizing groups and the nearby placed porphyrin π-systems. The latter interaction was found to be crucial for the guest complexation event, providing energetic compensation for otherwise costly tautomerization. We showed that only the systems possessing sufficiently long alkyl chains capable of interacting with a porphyrin ring are able to form a complex with C60. The structural rearrangement of the tetramer was quantitatively characterized by electron paramagnetic resonance pulsed dipolar spectroscopy measurements using photogenerated triplets of porphyrin and C60 as spin probes. Further exploring the C-H···π interaction as a decisive element for the C60 recognition, we investigated the guest-induced self-sorting phenomenon using scrambled tetramer assemblies composed of two types of monomers possessing alkyl chains of different lengths. The presence of the fullerene guest has enabled the selective scavenging of monomers capable of C-H···π interaction to form homo-tetrameric aggregates.
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Affiliation(s)
| | - Algirdas Neniškis
- Institute
of Chemistry, Vilnius University, LT-03225 Vilnius, Lithuania
| | - Arnau Bertran
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, OX1 3QR Oxford, United Kingdom
| | - Alice M. Bowen
- Department
of Chemistry, Photon Science Institute and The National EPR Research
Facility, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Marilena Di Valentin
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy,Centro
Interdipartimentale di Ricerca “Centro Studi di Economia e
Tecnica dell’energia Giorgio Levi Cases”, 35131 Padova, Italy
| | - Steponas Raišys
- Institute
of Photonics and Nanotechnology, Vilnius
University, Saulėtekio
av. 3, LT-10257 Vilnius, Lithuania
| | - Paulius Baronas
- Institute
of Photonics and Nanotechnology, Vilnius
University, Saulėtekio
av. 3, LT-10257 Vilnius, Lithuania
| | - Karolis Kazlauskas
- Institute
of Photonics and Nanotechnology, Vilnius
University, Saulėtekio
av. 3, LT-10257 Vilnius, Lithuania
| | - Linas Vilčiauskas
- Institute
of Chemistry, Vilnius University, LT-03225 Vilnius, Lithuania,Center
for Physical Sciences and Technology (FTMC), Saulėtekio al. 3, LT-10257 Vilnius, Lithuania
| | - Edvinas Orentas
- Institute
of Chemistry, Vilnius University, LT-03225 Vilnius, Lithuania,
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5
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Rogers CJ, Asthana D, Brookfield A, Chiesa A, Timco GA, Collison D, Natrajan LS, Carretta S, Winpenny REP, Bowen AM. Modelling Conformational Flexibility in a Spectrally Addressable Molecular Multi‐Qubit Model System. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ciarán J. Rogers
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Deepak Asthana
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
- Department of Chemistry Ashoka University Sonipat Haryana India
| | - Adam Brookfield
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Alessandro Chiesa
- Dipartimento di Scienze Matematiche Fisiche e Informatiche Università di Parma 43124 Parma Italy
- INFN–Sezione di Milano-Bicocca Gruppo Collegato di Parma I-43124 Parma Italy
- UdR Parma INSTM I-43124 Parma Italy
| | - Grigore A. Timco
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
| | - David Collison
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Louise S. Natrajan
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Stefano Carretta
- Dipartimento di Scienze Matematiche Fisiche e Informatiche Università di Parma 43124 Parma Italy
- INFN–Sezione di Milano-Bicocca Gruppo Collegato di Parma I-43124 Parma Italy
- UdR Parma INSTM I-43124 Parma Italy
| | - Richard E. P. Winpenny
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Alice M. Bowen
- National Research Facility for Electron Paramagnetic Resonance Spectroscopy Department of Chemistry and Photon Science Institute The University of Manchester Oxford Road Manchester M13 9PL UK
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6
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Rogers CJ, Asthana D, Brookfield A, Chiesa A, Timco GA, Collison D, Natrajan LS, Carretta S, Winpenny REP, Bowen AM. Modelling Conformational Flexibility in a Spectrally Addressable Molecular Multi-Qubit Model System. Angew Chem Int Ed Engl 2022; 61:e202207947. [PMID: 36222278 PMCID: PMC9828767 DOI: 10.1002/anie.202207947] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 11/11/2022]
Abstract
Dipolar coupled multi-spin systems have the potential to be used as molecular qubits. Herein we report the synthesis of a molecular multi-qubit model system with three individually addressable, weakly interacting, spin 1 / 2 ${{ 1/2 }}$ centres of differing g-values. We use pulsed Electron Paramagnetic Resonance (EPR) techniques to characterise and separately address the individual electron spin qubits; CuII , Cr7 Ni ring and a nitroxide, to determine the strength of the inter-qubit dipolar interaction. Orientation selective Relaxation-Induced Dipolar Modulation Enhancement (os-RIDME) detecting across the CuII spectrum revealed a strongly correlated CuII -Cr7 Ni ring relationship; detecting on the nitroxide resonance measured both the nitroxide and CuII or nitroxide and Cr7 Ni ring correlations, with switchability of the interaction based on differing relaxation dynamics, indicating a handle for implementing EPR-based quantum information processing (QIP) algorithms.
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Affiliation(s)
- Ciarán J. Rogers
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Deepak Asthana
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK,Department of ChemistryAshoka UniversitySonipatHaryanaIndia
| | - Adam Brookfield
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Alessandro Chiesa
- Dipartimento di Scienze Matematiche Fisiche e InformaticheUniversità di Parma43124ParmaItaly,INFN–Sezione di Milano-BicoccaGruppo Collegato di ParmaI-43124ParmaItaly,UdR ParmaINSTMI-43124ParmaItaly
| | - Grigore A. Timco
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - David Collison
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Louise S. Natrajan
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Stefano Carretta
- Dipartimento di Scienze Matematiche Fisiche e InformaticheUniversità di Parma43124ParmaItaly,INFN–Sezione di Milano-BicoccaGruppo Collegato di ParmaI-43124ParmaItaly,UdR ParmaINSTMI-43124ParmaItaly
| | - Richard E. P. Winpenny
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
| | - Alice M. Bowen
- National Research Facility for Electron Paramagnetic Resonance SpectroscopyDepartment of Chemistry and Photon Science InstituteThe University of ManchesterOxford RoadManchesterM13 9PLUK
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7
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Bertran A, Morbiato L, Aquilia S, Gabbatore L, De Zotti M, Timmel CR, Di Valentin M, Bowen AM. Erythrosin B as a New Photoswitchable Spin Label for Light-Induced Pulsed EPR Dipolar Spectroscopy. Molecules 2022; 27:molecules27217526. [PMID: 36364348 PMCID: PMC9657417 DOI: 10.3390/molecules27217526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 11/06/2022] Open
Abstract
We present a new photoswitchable spin label for light-induced pulsed electron paramagnetic resonance dipolar spectroscopy (LiPDS), the photoexcited triplet state of erythrosin B (EB), which is ideal for biological applications. With this label, we perform an in-depth study of the orientational effects in dipolar traces acquired using the refocused laser-induced magnetic dipole technique to obtain information on the distance and relative orientation between the EB and nitroxide labels in a rigid model peptide, in good agreement with density functional theory predictions. Additionally, we show that these orientational effects can be averaged to enable an orientation-independent analysis to determine the distance distribution. Furthermore, we demonstrate the feasibility of these experiments above liquid nitrogen temperatures, removing the need for expensive liquid helium or cryogen-free cryostats. The variety of choices in photoswitchable spin labels and the affordability of the experiments are critical for LiPDS to become a widespread methodology in structural biology.
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Affiliation(s)
- Arnau Bertran
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QR, UK
| | - Laura Morbiato
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Sara Aquilia
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Laura Gabbatore
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
- Centro Interdipartimentale di Ricerca “Centro Studi di Economia e Tecnica dell’Energia Giorgio Levi Cases”, University of Padova, 35131 Padova, Italy
| | - Christiane R. Timmel
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QR, UK
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy
- Centro Interdipartimentale di Ricerca “Centro Studi di Economia e Tecnica dell’Energia Giorgio Levi Cases”, University of Padova, 35131 Padova, Italy
- Correspondence: (M.D.V.); (A.M.B.)
| | - Alice M. Bowen
- The National Research Facility for Electron Paramagnetic Resonance, Department of Chemistry and Photon Science Institute, The University of Manchester, Manchester M13 9PL, UK
- Correspondence: (M.D.V.); (A.M.B.)
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8
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Hedison T, Iorgu AI, Calabrese D, Heyes DJ, Shanmugam M, Scrutton NS. Solution-State Inter-Copper Distribution of Redox Partner-Linked Copper Nitrite Reductases: A Pulsed Electron-Electron Double Resonance Spectroscopy Study. J Phys Chem Lett 2022; 13:6927-6934. [PMID: 35867774 PMCID: PMC9358711 DOI: 10.1021/acs.jpclett.2c01584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Copper nitrite reductases (CuNiRs) catalyze the reduction of nitrite to form nitric oxide. In recent years, new classes of redox partner linked CuNiRs have been isolated and characterized by crystallographic techniques. Solution-state biophysical studies have shed light on the complex catalytic mechanisms of these enzymes and implied that protein dynamics may play a role in CuNiR catalysis. To investigate the structural, dynamical, and functional relationship of these CuNiRs, we have used protein reverse engineering and pulsed electron-electron double resonance (PELDOR) spectroscopy to determine their solution-state inter-copper distributions. Data show the multidimensional conformational landscape of this family of enzymes and the role of tethering in catalysis. The importance of combining high-resolution crystallographic techniques and low-resolution solution-state approaches in determining the structures and mechanisms of metalloenzymes is emphasized by our approach.
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Affiliation(s)
- Tobias
M. Hedison
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- EPSRC/BBSRC
funded Future Biomanufacturing Research Hub, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Andreea I. Iorgu
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Donato Calabrese
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Derren J. Heyes
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Muralidharan Shanmugam
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology and Department of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- EPSRC/BBSRC
funded Future Biomanufacturing Research Hub, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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9
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Bogetti X, Hasanbasri Z, Hunter HR, Saxena S. An optimal acquisition scheme for Q-band EPR distance measurements using Cu 2+-based protein labels. Phys Chem Chem Phys 2022; 24:14727-14739. [PMID: 35574729 DOI: 10.1039/d2cp01032a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Recent advances in site-directed Cu2+ labeling of proteins and nucleic acids have added an attractive new methodology to measure the structure-function relationship in biomolecules. Despite the promise, accessing the higher sensitivity of Q-band Double Electron Electron Resonance (DEER) has been challenging for Cu2+ labels designed for proteins. Q-band DEER experiments on this label typically require many measurements at different magnetic fields, since the pulses can excite only a few orientations at a given magnetic field. Herein, we analyze such orientational effects through simulations and show that three DEER measurements, at strategically selected magnetic fields, are generally sufficient to acquire an orientational-averaged DEER time trace for this spin label at Q-band. The modeling results are experimentally verified on Cu2+ labeled human glutathione S-transferase (hGSTA1-1). The DEER distance distribution measured at the Q-band shows good agreement with the distance distribution sampled by molecular dynamics (MD) simulations and X-band experiments. The concordance of MD sampled distances and experimentally measured distances adds growing evidence that MD simulations can accurately predict distances for the Cu2+ labels, which remains a key bottleneck for the commonly used nitroxide label. In all, this minimal collection scheme reduces data collection time by as much as six-fold and is generally applicable to many octahedrally coordinated Cu2+ systems. Furthermore, the concepts presented here may be applied to other metals and pulsed EPR experiments.
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Affiliation(s)
- Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
| | - Zikri Hasanbasri
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
| | - Hannah R Hunter
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
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10
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Richardson KH, Seif-Eddine M, Sills A, Roessler MM. Controlling and exploiting intrinsic unpaired electrons in metalloproteins. Methods Enzymol 2022; 666:233-296. [PMID: 35465921 DOI: 10.1016/bs.mie.2022.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Electron paramagnetic resonance spectroscopy encompasses a versatile set of techniques that allow detailed insight into intrinsically occurring paramagnetic centers in metalloproteins and enzymes that undergo oxidation-reduction reactions. In this chapter, we discuss the process from isolating the protein to acquiring and analyzing pulse EPR spectra, adopting a practical perspective. We start with considerations when preparing the protein sample, explain techniques and procedures available for determining the reduction potential of the redox-active center of interest and provide details on methodologies to trap a given paramagnetic state for detailed pulse EPR studies, with an emphasis on biochemical and spectroscopic tools available when multiple EPR-active species are present. We elaborate on some of the most commonly used pulse EPR techniques and the choices the user has to make, considering advantages and disadvantages and how to avoid pitfalls. Examples are provided throughout.
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Affiliation(s)
| | - Maryam Seif-Eddine
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - Adam Sills
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - Maxie M Roessler
- Imperial College London, Molecular Sciences Research Hub, London, United Kingdom.
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11
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Bertran A, Barbon A, Bowen AM, Di Valentin M. Light-induced pulsed dipolar EPR spectroscopy for distance and orientation analysis. Methods Enzymol 2022; 666:171-231. [PMID: 35465920 DOI: 10.1016/bs.mie.2022.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Measuring distances in biology at the molecular level is of great importance for understanding the structure and function of proteins, nucleic acids and other biological molecules and their complexes. Pulsed Dipolar Spectroscopy (PDS) offers advantages with respect to other methods as it is uniquely sensitive and specific to electronic spin centers and allows measurements in near-native conditions, comprising the in-cell environment. PDS methods measure the electron spin-spin dipolar interaction, therefore they require the presence of at least two paramagnetic centers, which are often stable radicals. Recent developments have introduced transient triplet states, photo-activated by a laser pulse, as spin labels and probes, thereby establishing a new family of techniques-Light-induced PDS (LiPDS). In this chapter, an overview of these methods is provided, looking at the chromophores that can be used for LiPDS and some of the technical aspects of the experiments. A guide to the choice of technique that can yield the best results, depending on the type of system studied and the information required, is provided. Examples of previous LiPDS studies of model systems and proteins are given. Characterization data for the chromophores used in these studies is tabulated to help selection of appropriate triplet state probes in future studies.
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Affiliation(s)
- Arnau Bertran
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Antonio Barbon
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Alice M Bowen
- Centre for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom; EPSRC National Research Facility for Electron Paramagnetic Resonance Spectroscopy, Department of Chemistry and Photon Science Institute, The University of Manchester, Manchester, United Kingdom.
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12
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Casto J, Mandato A, Hofmann L, Yakobov I, Ghosh S, Ruthstein S, Saxena S. Cu(II)-based DNA Labeling Identifies the Structural Link Between Activation and Termination in a Metalloregulator. Chem Sci 2022; 13:1693-1697. [PMID: 35282619 PMCID: PMC8827015 DOI: 10.1039/d1sc06563g] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/16/2022] [Indexed: 11/25/2022] Open
Abstract
Understanding the structural and mechanistic details of protein-DNA interactions that lead to cellular defence against toxic metal ions in pathogenic bacteria can lead to new ways of combating their virulence. Herein, we examine the Copper Efflux Regulator (CueR) protein, a transcription factor which interacts with DNA to generate proteins that ameliorate excess free Cu(i). We exploit site directed Cu(ii) labeling to measure the conformational changes in DNA as a function of protein and Cu(i) concentration. Unexpectedly, the EPR data indicate that the protein can bend the DNA at high protein concentrations even in the Cu(i)-free state. On the other hand, the bent state of the DNA is accessed at a low protein concentration in the presence of Cu(i). Such bending enables the coordination of the DNA with RNA polymerase. Taken together, the results lead to a structural understanding of how transcription is activated in response to Cu(i) stress and how Cu(i)-free CueR can replace Cu(i)-bound CueR in the protein-DNA complex to terminate transcription. This work also highlights the utility of EPR to measure structural data under conditions that are difficult to access in order to shed light on protein function. Herein, we exploit site-directed Cu(ii)-labeling to measure the DNA conformations in each step of the transcription cycle of the Copper Efflux Regulator (CueR), in order to establish how transcription is activated and terminated.![]()
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Affiliation(s)
- Joshua Casto
- Department of Chemistry, University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Alysia Mandato
- Department of Chemistry, University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Lukas Hofmann
- Department of Chemistry, Faculty of Exact Sciences, The Institution of Nanotechnology and Advanced Materials, Bar-Ilan University Ramat-Gan 5290002 Israel
| | - Idan Yakobov
- Department of Chemistry, Faculty of Exact Sciences, The Institution of Nanotechnology and Advanced Materials, Bar-Ilan University Ramat-Gan 5290002 Israel
| | - Shreya Ghosh
- Department of Chemistry, University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
| | - Sharon Ruthstein
- Department of Chemistry, Faculty of Exact Sciences, The Institution of Nanotechnology and Advanced Materials, Bar-Ilan University Ramat-Gan 5290002 Israel
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh Pittsburgh Pennsylvania 15260 USA
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13
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Bowen AM, Bertran A, Henbest KB, Gobbo M, Timmel CR, Di Valentin M. Orientation-Selective and Frequency-Correlated Light-Induced Pulsed Dipolar Spectroscopy. J Phys Chem Lett 2021; 12:3819-3826. [PMID: 33856805 PMCID: PMC8154851 DOI: 10.1021/acs.jpclett.1c00595] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
We explore the potential of orientation-resolved pulsed dipolar spectroscopy (PDS) in light-induced versions of the experiment. The use of triplets as spin-active moieties for PDS offers an attractive tool for studying biochemical systems containing optically active cofactors. Cofactors are often rigidly bound within the protein structure, providing an accurate positional marker. The rigidity leads to orientation selection effects in PDS, which can be analyzed to give both distance and mutual orientation information. Herein we present a comprehensive analysis of the orientation selection of a full set of light-induced PDS experiments. We exploit the complementary information provided by the different light-induced techniques to yield atomic-level structural information. For the first time, we measure a 2D frequency-correlated laser-induced magnetic dipolar spectrum, and we are able to monitor the complete orientation dependence of the system in a single experiment. Alternatively, the summed spectrum enables an orientation-independent analysis to determine the distance distribution.
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Affiliation(s)
- Alice M. Bowen
- Department
of Chemistry, Photon Science Institute and The National EPR Research
Facility, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Arnau Bertran
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Kevin B. Henbest
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Marina Gobbo
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Christiane R. Timmel
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Marilena Di Valentin
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
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14
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Russell H, Stewart R, Prior C, Oganesyan VS, Gaule TG, Lovett JE. DEER and RIDME Measurements of the Nitroxide-Spin Labelled Copper-Bound Amine Oxidase Homodimer from Arthrobacter Globiformis. APPLIED MAGNETIC RESONANCE 2021; 52:995-1015. [PMID: 34720439 PMCID: PMC8550341 DOI: 10.1007/s00723-021-01321-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/23/2021] [Accepted: 03/10/2021] [Indexed: 06/13/2023]
Abstract
In the study of biological structures, pulse dipolar spectroscopy (PDS) is used to elucidate spin-spin distances at nanometre-scale by measuring dipole-dipole interactions between paramagnetic centres. The PDS methods of Double Electron Electron Resonance (DEER) and Relaxation Induced Dipolar Modulation Enhancement (RIDME) are employed, and their results compared, for the measurement of the dipolar coupling between nitroxide spin labels and copper-II (Cu(II)) paramagnetic centres within the copper amine oxidase from Arthrobacter globiformis (AGAO). The distance distribution results obtained indicate that two distinct distances can be measured, with the longer of these at c.a. 5 nm. Conditions for optimising the RIDME experiment such that it may outperform DEER for these long distances are discussed. Modelling methods are used to show that the distances obtained after data analysis are consistent with the structure of AGAO. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00723-021-01321-6.
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Affiliation(s)
- Hannah Russell
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, St Andrews, KY16 9SS UK
| | - Rachel Stewart
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, St Andrews, KY16 9SS UK
| | | | | | - Thembaninkosi G. Gaule
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Janet E. Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, St Andrews, KY16 9SS UK
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15
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Bertran A, Henbest KB, De Zotti M, Gobbo M, Timmel CR, Di Valentin M, Bowen AM. Light-Induced Triplet-Triplet Electron Resonance Spectroscopy. J Phys Chem Lett 2021; 12:80-85. [PMID: 33306382 PMCID: PMC8016185 DOI: 10.1021/acs.jpclett.0c02884] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
We present a new technique, light-induced triplet-triplet electron resonance spectroscopy (LITTER), which measures the dipolar interaction between two photoexcited triplet states, enabling both the distance and angular distributions between the two triplet moieties to be determined on a nanometer scale. This is demonstrated for a model bis-porphyrin peptide that renders dipolar traces with strong orientation selection effects. Using simulations and density functional theory calculations, we extract distance distributions and relative orientations of the porphyrin moieties, allowing the dominant conformation of the peptide in a frozen solution to be identified. LITTER removes the requirement of current light-induced electron spin resonance pulse dipolar spectroscopy techniques to have a permanent paramagnetic moiety, becoming more suitable for in-cell applications and facilitating access to distance determination in unmodified macromolecular systems containing photoexcitable moieties. LITTER also has the potential to enable direct comparison with Förster resonance energy transfer and combination with microscopy inside cells.
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Affiliation(s)
- Arnau Bertran
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Kevin B. Henbest
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Marta De Zotti
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Marina Gobbo
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Christiane R. Timmel
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Marilena Di Valentin
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Alice M. Bowen
- Centre
for Advanced Electron Spin Resonance and Inorganic Chemistry Laboratory,
Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
- Department
of Chemistry and Photon Science Institute, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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16
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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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17
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Ghosh S, Casto J, Bogetti X, Arora C, Wang J, Saxena S. Orientation and dynamics of Cu 2+ based DNA labels from force field parameterized MD elucidates the relationship between EPR distance constraints and DNA backbone distances. Phys Chem Chem Phys 2020; 22:26707-26719. [PMID: 33159779 PMCID: PMC10521111 DOI: 10.1039/d0cp05016d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Pulsed electron paramagnetic resonance (EPR) based distance measurements using the recently developed Cu2+-DPA label present a promising strategy for measuring DNA backbone distance constraints. Herein we develop force field parameters for Cu2+-DPA in order to understand the features of this label at an atomic level. We perform molecular dynamics (MD) simulations using the force field parameters of Cu2+-DPA on four different DNA duplexes. The distance between the Cu2+ centers, extracted from the 2 μs MD trajectories, agrees well with the experimental distance for all the duplexes. Further analyses of the trajectory provide insight into the orientation of the Cu2+-DPA inside the duplex that leads to such agreement with experiments. The MD results also illustrate the ability of the Cu2+-DPA to report on the DNA backbone distance constraints. Furthermore, measurement of fluctuations of individual residues showed that the flexibility of Cu2+-DPA in a DNA depends on the position of the label in the duplex, and a 2 μs MD simulation is not sufficient to fully capture the experimental distribution in some cases. Finally, the MD trajectories were utilized to understand the key aspects of the double electron electron resonance (DEER) results. The lack of orientational selectivity effects of the Cu2+-DPA at Q-band frequency is rationalized in terms of fluctuations in the Cu2+ coordination environment and rotameric fluctuations of the label linker. Overall, a combination of EPR and MD simulations based on the Cu2+-DPA labelling strategy can contribute towards understanding changes in DNA backbone conformations during protein-DNA interactions.
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Affiliation(s)
- Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, PA 15260, USA.
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18
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Lockyer SJ, Nawaz S, Brookfield A, Fielding AJ, Vitorica-Yrezabal IJ, Timco GA, Burton NA, Bowen AM, Winpenny REP, McInnes EJL. Conformational Flexibility of Hybrid [3]- and [4]-Rotaxanes. J Am Chem Soc 2020; 142:15941-15949. [PMID: 32820906 PMCID: PMC7605720 DOI: 10.1021/jacs.0c06547] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The synthesis, structures, and properties of [4]- and [3]-rotaxane complexes are reported where [2]-rotaxanes, formed from heterometallic {Cr7Ni} rings, are bound to a fluoride-centered {CrNi2} triangle. The compounds have been characterized by single-crystal X-ray diffraction and have the formulas [CrNi2(F)(O2CtBu)6]{(BH)[Cr7NiF8(O2CtBu)16]}3 (3) and [CrNi2(F)(O2CtBu)6(THF)]{(BH)[Cr7NiF8(O2CtBu)16]}2 (4), where B = py-CH2CH2NHCH2C6H4SCH3. The [4]-rotaxane 3 is an isosceles triangle of three [2]-rotaxanes bound to the central triangle while the [3]-rotaxane 4 contains only two [2]-rotaxanes bound to the central triangle. Studies of the behavior of 3 and 4 in solution by small-angle X-ray scattering and atomistic molecular dynamic simulations show that the structure of 3 is similar to that found in the crystal but that 4 has a different conformation to the crystal. Continuous wave and pulsed electron paramagnetic resonance spectroscopy was used to study the structures present and demonstrate that in frozen solutions (at 5 K) 4 forms more extended molecules than 3 and with a wider range of conformations.
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Affiliation(s)
- Selena J Lockyer
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Selina Nawaz
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Adam Brookfield
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Alistair J Fielding
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, U.K
| | - Inigo J Vitorica-Yrezabal
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Grigore A Timco
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Neil A Burton
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Alice M Bowen
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Richard E P Winpenny
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Eric J L McInnes
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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19
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Gamble Jarvi A, Sargun A, Bogetti X, Wang J, Achim C, Saxena S. Development of Cu 2+-Based Distance Methods and Force Field Parameters for the Determination of PNA Conformations and Dynamics by EPR and MD Simulations. J Phys Chem B 2020; 124:7544-7556. [PMID: 32790374 DOI: 10.1021/acs.jpcb.0c05509] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Peptide nucleic acids (PNAs) are a promising group of synthetic analogues of DNA and RNA that offer several distinct advantages over the naturally occurring nucleic acids for applications in biosensing, drug delivery, and nanoelectronics. Because of its structural differences from DNA/RNA, methods to analyze and assess the structure, conformations, and dynamics are needed. In this work, we develop synergistic techniques for the study of the PNA conformation. We use CuQ2, a Cu2+ complex with 8-hydroxyquinoline (HQ), as an alternative base pair and as a spin label in electron paramagnetic resonance (EPR) distance methods. We use molecular dynamics (MD) simulations with newly developed force field parameters for the spin labels to interpret the distance constraints determined by EPR. We complement these methods by UV-vis and circular dichroism measurements and assess the efficacy of the Cu2+ label on a PNA duplex whose backbone is based on aminoethylglycine and a duplex with a hydroxymethyl backbone modification. We show that the Cu2+ label functions efficiently within the standard PNA and the hydroxymethyl-modified PNA and that the MD parameters may be used to accurately reproduce our EPR findings. Through the combination of EPR and MD, we gain new insights into the PNA structure and conformations as well as into the mechanism of orientational selectivity in Cu2+ EPR at X-band. These results present for the first time a rigid Cu2+ spin label used for EPR distance measurements in PNA and the accompanying MD force fields for the spin label. Our studies also reveal that the spin labels have a low impact on the structure of the PNA duplexes. The combined MD and EPR approach represents an important new tool for the characterization of the PNA duplex structure and provides valuable information to aid in the rational application of PNA at large.
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Affiliation(s)
- Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Artur Sargun
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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20
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Potapov A. Application of spherical harmonics for DEER data analysis in systems with a conformational distribution. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 316:106769. [PMID: 32574865 DOI: 10.1016/j.jmr.2020.106769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Double electron-electron resonance (DEER) and other pulse electron paramagnetic resonance (EPR) techniques are valuable tools for determining distances between paramagnetic centres. DEER theory is well developed for a scenario where relative orientations of paramagnetic centres do not affect the DEER data. In particular, such theory enables a number of approaches for extracting distance distributions. However, in a more general case, when orientation selection effects become substantial, the analytical theory of DEER is less well developed, therefore quite commonly researchers rely on a comparison of some model-based simulations with experimental data. This work elaborates the theory of DEER with orientation selection effects, focusing on a scenario of a moderate conformational disorder, leading to an orientation distribution in a pair of paramagnetic centres. The analytical treatment based on expansions into spherical harmonics, provides important insights into the structure of DEER data. As follows from this treatment, DEER spectra with orientation selection can be represented as a linear combination of modified Pake pattern (MPP) components. The conformational disorder has a filtering effect on the weights of MPP components, specifically by significantly suppressing MPP components of higher degrees. The developed theory provides a pathway for model-based simulations of DEER data where orientation distribution is defined by analytical functions with parameters. The theory based on spherical harmonics expansions was also applied to develop an iterative processing algorithm based on Tikhonov regularization, which disentangles the distance and orientation information in a model-free manner. As an input, this procedure takes several DEER datasets measured at various positions of an EPR line, and outputs a distance distribution and orientation distribution information encoded in a set of coefficients related to the weights of MPP components. The model-based and model-free approaches based on the developed theory were validated for a nitroxide biradical and a spin-labelled protein.
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Affiliation(s)
- Alexey Potapov
- School of Physics and Astronomy, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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21
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Bogetti X, Ghosh S, Gamble Jarvi A, Wang J, Saxena S. Molecular Dynamics Simulations Based on Newly Developed Force Field Parameters for Cu 2+ Spin Labels Provide Insights into Double-Histidine-Based Double Electron-Electron Resonance. J Phys Chem B 2020; 124:2788-2797. [PMID: 32181671 DOI: 10.1021/acs.jpcb.0c00739] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Electron paramagnetic resonance (EPR) in combination with the recently developed double-histidine (dHis)-based Cu2+ spin labeling has provided valuable insights into protein structure and conformational dynamics. To relate sparse distance constraints measured by EPR to protein fluctuations in solution, modeling techniques are needed. In this work, we have developed force field parameters for Cu2+-nitrilotriacetic and Cu2+-iminodiacetic acid spin labels. We employed molecular dynamics (MD) simulations to capture the atomic-level details of dHis-labeled protein fluctuations. The interspin distances extracted from 200 ns MD trajectories show good agreement with the experimental results. The MD simulations also illustrate the dramatic rigidity of the Cu2+ labels compared to the standard nitroxide spin label. Further, the relative orientations between spin-labeled sites were measured to provide insight into the use of double electron-electron resonance (DEER) methods for such labels. The relative mean angles, as well as the standard deviations of the relative angles, agree well in general with the spectral simulations published previously. The fluctuations of relative orientations help rationalize why orientation selectivity effects are minimal at X-band frequencies, but observable at the Q-band for such labels. In summary, the results show that by combining the experimental results with MD simulations precise information about protein conformations as well as flexibility can be obtained.
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Affiliation(s)
- Xiaowei Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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22
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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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23
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Keller K, Ritsch I, Hintz H, Hülsmann M, Qi M, Breitgoff FD, Klose D, Polyhach Y, Yulikov M, Godt A, Jeschke G. Accessing distributions of exchange and dipolar couplings in stiff molecular rulers with Cu(ii) centres. Phys Chem Chem Phys 2020; 22:21707-21730. [DOI: 10.1039/d0cp03105d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel approaches to quantitatively analyse distributed exchange couplings are described and tested on experimental data sets for stiff synthetic molecules.
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24
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Reichenwallner J, Hauenschild T, Schmelzer CEH, Hülsmann M, Godt A, Hinderberger D. Fatty Acid Triangulation in Albumins Using a Landmark Spin Label. Isr J Chem 2019. [DOI: 10.1002/ijch.201900073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jörg Reichenwallner
- Institute of ChemistryMartin Luther University Halle-Wittenberg Von-Danckelmann-Platz 4 D-06120 Halle (Saale) Germany
| | - Till Hauenschild
- Institute of ChemistryMartin Luther University Halle-Wittenberg Von-Danckelmann-Platz 4 D-06120 Halle (Saale) Germany
| | - Christian E. H. Schmelzer
- Fraunhofer Institute for Microstructure of Materials and Systems IMWS Walter-Hülse-Straße 1 D-06120 Halle (Saale) Germany
- Institute of PharmacyMartin Luther University Halle-Wittenberg Wolfgang-Langenbeck-Straße 4 D-06120 Halle (Saale) Germany
| | - Miriam Hülsmann
- Faculty of Chemistry and Center for Molecular Materials (CM2)Bielefeld University Universitätsstraße 25 D-33615 Bielefeld Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2)Bielefeld University Universitätsstraße 25 D-33615 Bielefeld Germany
| | - Dariush Hinderberger
- Institute of ChemistryMartin Luther University Halle-Wittenberg Von-Danckelmann-Platz 4 D-06120 Halle (Saale) Germany
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25
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Breitgoff FD, Keller K, Qi M, Klose D, Yulikov M, Godt A, Jeschke G. UWB DEER and RIDME distance measurements in Cu(II)-Cu(II) spin pairs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 308:106560. [PMID: 31377151 DOI: 10.1016/j.jmr.2019.07.047] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
Distance determination by Electron Paramagnetic Resonance (EPR) based on measurements of the dipolar coupling are technically challenging for electron spin systems with broad spectra due to comparatively narrow microwave pulse excitation bandwidths. With Na4[{CuII(PyMTA)}-(stiff spacer)-{CuII(PyMTA)}] as a model compound, we compared DEER and RIDME measurements and investigated the use of frequency-swept pulses. We found very large improvements in sensitivity when substituting the monochromatic pump pulse by a frequency-swept one in DEER experiments with monochromatic observer pulses. This effect was especially strong in X band, where nearly the whole spectrum can be included in the experiment. The RIDME experiment is characterised by a trade-off in signal intensity and modulation depth. Optimal parameters are further influenced by varying steepness of the background decay. A simple 2-point optimization experiment was found to serve as good estimate to identify the mixing time of highest sensitivity. Using frequency-swept pulses in the observer sequences resulted in lower SNR in both the RIDME and the DEER experiment. Orientation selectivity was found to vary in both experiments with the detection position as well as with the settings of the pump pulse in DEER. In RIDME, orientation selection by relaxation anisotropy of the inverted spin appeared to be negligible as form factors remain relatively constant with varying mixing time. This reduces the overall observed orientation selection to the one given by the detection position. Field-averaged data from RIDME and DEER with a shaped pump pulse resulted in the same dipolar spectrum. We found that both methods have their advantages and disadvantages for given instrumental limitations and sample properties. Thus the choice of method depends on the situation at hand and we discuss which parameters should be considered for optimization.
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Affiliation(s)
- Frauke D Breitgoff
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland.
| | - Katharina Keller
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland.
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Daniel Klose
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland
| | - Maxim Yulikov
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
| | - Gunnar Jeschke
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland
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26
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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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27
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Bonucci A, Ouari O, Guigliarelli B, Belle V, Mileo E. In‐Cell EPR: Progress towards Structural Studies Inside Cells. Chembiochem 2019; 21:451-460. [DOI: 10.1002/cbic.201900291] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Alessio Bonucci
- Magnetic Resonance CenterCERMUniversity of Florence 50019 Sesto Fiorentino Italy
| | - Olivier Ouari
- Aix Marseille UnivCNRSICRInstitut de Chimie Radicalaire 13013 Marseille France
| | - Bruno Guigliarelli
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Valérie Belle
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
| | - Elisabetta Mileo
- Aix Marseille UnivCNRSBIPBioénergétique et Ingénierie des ProtéinesIMM 13009 Marseille France
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28
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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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29
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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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30
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Gamble Jarvi A, Ranguelova K, Ghosh S, Weber RT, Saxena S. On the Use of Q-Band Double Electron–Electron Resonance To Resolve the Relative Orientations of Two Double Histidine-Bound Cu2+ Ions in a Protein. J Phys Chem B 2018; 122:10669-10677. [DOI: 10.1021/acs.jpcb.8b07727] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Austin Gamble Jarvi
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kalina Ranguelova
- Bruker BioSpin, Inc., EPR Division, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ralph T. Weber
- Bruker BioSpin, Inc., EPR Division, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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31
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Gil-Ramírez G, Shah A, El Mkami H, Porfyrakis K, Briggs GAD, Morton JJL, Anderson HL, Lovett JE. Distance Measurement of a Noncovalently Bound Y@C82 Pair with Double Electron Electron Resonance Spectroscopy. J Am Chem Soc 2018; 140:7420-7424. [DOI: 10.1021/jacs.8b03889] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Guzmán Gil-Ramírez
- School of Chemistry, University of Lincoln, Joseph Banks Laboratories, Lincoln LN6 7DL, United Kingdom
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
| | - Anokhi Shah
- SUPA School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, United Kingdom
| | - Hassane El Mkami
- SUPA School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, United Kingdom
| | - Kyriakos Porfyrakis
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
| | - G. Andrew D. Briggs
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
| | - John J. L. Morton
- London Centre for Nanotechnology, UCL, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Harry L. Anderson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Janet E. Lovett
- SUPA School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, United Kingdom
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32
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Bowen AM, Johnson EOD, Mercuri F, Hoskins NJ, Qiao R, McCullagh JSO, Lovett JE, Bell SG, Zhou W, Timmel CR, Wong LL, Harmer JR. A Structural Model of a P450-Ferredoxin Complex from Orientation-Selective Double Electron-Electron Resonance Spectroscopy. J Am Chem Soc 2018; 140:2514-2527. [PMID: 29266939 DOI: 10.1021/jacs.7b11056] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cytochrome P450 (CYP) monooxygenases catalyze the oxidation of chemically inert carbon-hydrogen bonds in diverse endogenous and exogenous organic compounds by atmospheric oxygen. This C-H bond oxy-functionalization activity has huge potential in biotechnological applications. Class I CYPs receive the two electrons required for oxygen activation from NAD(P)H via a ferredoxin reductase and ferredoxin. The interaction of Class I CYPs with their cognate ferredoxin is specific. In order to reconstitute the activity of diverse CYPs, structural characterization of CYP-ferredoxin complexes is necessary, but little structural information is available. Here we report a structural model of such a complex (CYP199A2-HaPux) in frozen solution derived from distance and orientation restraints gathered by the EPR technique of orientation-selective double electron-electron resonance (os-DEER). The long-lived oscillations in the os-DEER spectra were well modeled by a single orientation of the CYP199A2-HaPux complex. The structure is different from the two known Class I CYP-Fdx structures: CYP11A1-Adx and CYP101A1-Pdx. At the protein interface, HaPux residues in the [Fe2S2] cluster-binding loop and the α3 helix and the C-terminus residue interact with CYP199A2 residues in the proximal loop and the C helix. These residue contacts are consistent with biochemical data on CYP199A2-ferredoxin binding and electron transfer. Electron-tunneling calculations indicate an efficient electron-transfer pathway from the [Fe2S2] cluster to the heme. This new structural model of a CYP-Fdx complex provides the basis for tailoring CYP enzymes for which the cognate ferredoxin is not known, to accept electrons from HaPux and display monooxygenase activity.
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Affiliation(s)
- Alice M Bowen
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Eachan O D Johnson
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Francesco Mercuri
- Consiglio Nazionale delle Ricerche (CNR), Istituto per lo Studio dei Materiali Nanostrutturati (ISMN) Via P. Gobetti 101, 40129 Bologna, Italy
| | - Nicola J Hoskins
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Ruihong Qiao
- College of Life Sciences, Nankai University , Tianjin 300071, China
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford , Mansfield Road, Oxford OX1 3TA, U.K
| | - Janet E Lovett
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Stephen G Bell
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Weihong Zhou
- College of Life Sciences, Nankai University , Tianjin 300071, China
| | - Christiane R Timmel
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Luet Lok Wong
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
| | - Jeffrey R Harmer
- Centre for Applied Electron Spin Resonance, Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QR, U.K
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33
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Fedin MV, Shevelev GY, Pyshnyi DV, Tormyshev VM, Jeschke G, Yulikov M, Bagryanskaya EG. Interaction of triarylmethyl radicals with DNA termini revealed by orientation-selective W-band double electron-electron resonance spectroscopy. Phys Chem Chem Phys 2018; 18:29549-29554. [PMID: 27748488 DOI: 10.1039/c6cp05904j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Spin labels selectively attached to biomolecules allow high-accuracy nanoscale distance measurements using pulsed electron paramagnetic resonance (EPR), in many cases providing the only access to the structure of complex biosystems. Triarylmethyl (TAM) radicals have recently emerged as a new class of spin labels expanding the applicability of the method to physiological temperatures. Along with other factors, the accuracy of the obtained distances crucially relies on the understanding of interactions between biomolecules and spin labels. In this work, we consider such crucial interactions and their impact on pulsed EPR distance measurements in TAM-labeled DNAs. Using orientation-selective high-frequency (94 GHz) double electron-electron resonance (DEER) we demonstrate strong specific interactions between DNA termini and TAM labels, leading to a significant restriction of their conformational mobility. An understanding of such interactions guides the way to select optimum TAM-labeling strategies, thus refining nanoscale EPR distance measurements in nucleic acids and their complexes under physiological conditions.
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Affiliation(s)
- Matvey V Fedin
- International Tomography Center SB RAS, Novosibirsk, 630090, Russia. and Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Georgiy Yu Shevelev
- Novosibirsk State University, Novosibirsk, 630090, Russia and Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Dmitrii V Pyshnyi
- Novosibirsk State University, Novosibirsk, 630090, Russia and Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Victor M Tormyshev
- Novosibirsk State University, Novosibirsk, 630090, Russia and N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, 630090, Russia.
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland.
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, 8093, Switzerland.
| | - Elena G Bagryanskaya
- Novosibirsk State University, Novosibirsk, 630090, Russia and N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, 630090, Russia.
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34
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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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35
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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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36
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Di Valentin M, Albertini M, Dal Farra MG, Zurlo E, Orian L, Polimeno A, Gobbo M, Carbonera D. Light-Induced Porphyrin-Based Spectroscopic Ruler for Nanometer Distance Measurements. Chemistry 2016; 22:17204-17214. [DOI: 10.1002/chem.201603666] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Marilena Di Valentin
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Marco Albertini
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Maria Giulia Dal Farra
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Enrico Zurlo
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
- Leiden Institute of Physics; Leiden University; Niels Bohrweg 2 2333 CA Leiden The Netherlands
| | - Laura Orian
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Antonino Polimeno
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Marina Gobbo
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
| | - Donatella Carbonera
- Dipartimento di Scienze Chimiche; Università di Padova; via Marzolo 1 35131 Padova Italy
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37
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Richert S, Cremers J, Anderson HL, Timmel CR. Exploring template-bound dinuclear copper porphyrin nanorings by EPR spectroscopy. Chem Sci 2016; 7:6952-6960. [PMID: 28451129 PMCID: PMC5363685 DOI: 10.1039/c6sc01810f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/24/2016] [Indexed: 11/25/2022] Open
Abstract
Electron paramagnetic resonance spectroscopy reveals the molecular geometry and metal–ligand interactions in template-bound ten-membered bis-copper porphyrin nanorings.
Electron paramagnetic resonance (EPR) spectroscopy has been used to study the molecular geometry as well as metal–ligand interactions in ten-membered porphyrin nanorings (c-P10Cu2) containing two copper and eight zinc centers. The presence of copper in the structures allows intramolecular interactions, including dipolar interactions between electron spins and hyperfine interactions to be quantified. Results obtained for c-P10Cu2 samples bound to two molecular templates with four or five binding sites, respectively, are compared to those obtained for a sample of the porphyrin ring in the absence of any templates. It is shown that the observed lower binding affinity of the nitrogen ligand to copper as compared to zinc has a strong impact on the geometries of the respective template-bound c-P10Cu2 structures. The interaction between the central copper atom and nitrogen ligands is weak, but pulsed EPR hyperfine techniques such as ENDOR and HYSCORE are very sensitive to this interaction. Upon binding of a nitrogen ligand to copper, the hyperfine couplings of the in-plane nitrogen atoms of the porphyrin core are reduced by about 3 MHz. In addition, the copper hyperfine couplings as well as the g-factors are altered, as detected by continuous wave EPR. DFT calculations of the hyperfine coupling tensors support the assignment of the measured couplings to the nuclei within the structure and reproduce the experimentally observed trends. Finally, Double Electron Electron Resonance (DEER) is used to measure the distances between the copper centers in a range between 2.5 and 5 nm, revealing the preferred geometries of the template-bound nanorings.
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Affiliation(s)
- Sabine Richert
- Centre for Advanced Electron Spin Resonance (CAESR) , University of Oxford , South Parks Road , Oxford , OX1 3QR , UK .
| | - Jonathan Cremers
- Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK
| | - Harry L Anderson
- Chemistry Research Laboratory , University of Oxford , Mansfield Road , Oxford , OX1 3TA , UK
| | - Christiane R Timmel
- Centre for Advanced Electron Spin Resonance (CAESR) , University of Oxford , South Parks Road , Oxford , OX1 3QR , UK .
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38
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Haugland MM, El-Sagheer AH, Porter RJ, Peña J, Brown T, Anderson EA, Lovett JE. 2'-Alkynylnucleotides: A Sequence- and Spin Label-Flexible Strategy for EPR Spectroscopy in DNA. J Am Chem Soc 2016; 138:9069-72. [PMID: 27409454 DOI: 10.1021/jacs.6b05421] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a powerful method to elucidate molecular structure through the measurement of distances between conformationally well-defined spin labels. Here we report a sequence-flexible approach to the synthesis of double spin-labeled DNA duplexes, where 2'-alkynylnucleosides are incorporated at terminal and internal positions on complementary strands. Post-DNA synthesis copper-catalyzed azide-alkyne cycloaddition (CuAAC) reactions with a variety of spin labels enable the use of double electron-electron resonance experiments to measure a number of distances on the duplex, affording a high level of detailed structural information.
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Affiliation(s)
- Marius M Haugland
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford, OX1 3TA, U.K
| | - Afaf H El-Sagheer
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford, OX1 3TA, U.K.,Chemistry Branch, Faculty of Petroleum and Mining Engineering, Suez University , Suez 43721, Egypt
| | - Rachel J Porter
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford, OX1 3TA, U.K
| | - Javier Peña
- Departamento de Química Orgánica, Universidad de Salamanca , Plaza de los Caídos 1-5, 37008 Salamanca, Spain
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford, OX1 3TA, U.K
| | - Edward A Anderson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Oxford, OX1 3TA, U.K
| | - Janet E Lovett
- SUPA, School of Physics and Astronomy, University of St Andrews , North Haugh, St Andrews, KY16 9SS, U.K
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39
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Jones CE, Berliner LJ. Nitroxide Spin-Labelling and Its Role in Elucidating Cuproprotein Structure and Function. Cell Biochem Biophys 2016; 75:195-202. [PMID: 27342129 DOI: 10.1007/s12013-016-0751-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/11/2016] [Indexed: 10/21/2022]
Abstract
Copper is one of the most abundant biological metals, and its chemical properties mean that organisms need sophisticated and multilayer mechanisms in place to maintain homoeostasis and avoid deleterious effects. Studying copper proteins requires multiple techniques, but electron paramagnetic resonance (EPR) plays a key role in understanding Cu(II) sites in proteins. When spin-labels such as aminoxyl radicals (commonly referred to as nitroxides) are introduced, then EPR becomes a powerful technique to monitor not only the coordination environment, but also to obtain structural information that is often not readily available from other techniques. This information can contribute to explaining how cuproproteins fold and misfold. The theory and practice of EPR can be daunting to the non-expert; therefore, in this mini review, we explore how nitroxide spin-labelling can be used to help the inorganic biochemist gain greater understanding of cuproprotein structure and function in vitro and how EPR imaging may help improve understanding of copper homoeostasis in vivo.
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Affiliation(s)
- Christopher E Jones
- The School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2759, Australia.
| | - Lawrence J Berliner
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80208-0183, USA
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40
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Meyer A, Schiemann O. PELDOR and RIDME Measurements on a High-Spin Manganese(II) Bisnitroxide Model Complex. J Phys Chem A 2016; 120:3463-72. [DOI: 10.1021/acs.jpca.6b00716] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Andreas Meyer
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstr. 12, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstr. 12, Bonn, Germany
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41
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Motion C, Lovett JE, Bell S, Cassidy SL, Cruickshank PAS, Bolton DR, Hunter RI, El Mkami H, Van Doorslaer S, Smith GM. DEER Sensitivity between Iron Centers and Nitroxides in Heme-Containing Proteins Improves Dramatically Using Broadband, High-Field EPR. J Phys Chem Lett 2016; 7:1411-5. [PMID: 27035368 PMCID: PMC4863198 DOI: 10.1021/acs.jpclett.6b00456] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/30/2016] [Indexed: 05/22/2023]
Abstract
This work demonstrates the feasibility of making sensitive nanometer distance measurements between Fe(III) heme centers and nitroxide spin labels in proteins using the double electron-electron resonance (DEER) pulsed EPR technique at 94 GHz. Techniques to measure accurately long distances in many classes of heme proteins using DEER are currently strongly limited by sensitivity. In this paper we demonstrate sensitivity gains of more than 30 times compared with previous lower frequency (X-band) DEER measurements on both human neuroglobin and sperm whale myoglobin. This is achieved by taking advantage of recent instrumental advances, employing wideband excitation techniques based on composite pulses and exploiting more favorable relaxation properties of low-spin Fe(III) in high magnetic fields. This gain in sensitivity potentially allows the DEER technique to be routinely used as a sensitive probe of structure and conformation in the large number of heme and many other metalloproteins.
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Affiliation(s)
- Claire
L. Motion
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Janet E. Lovett
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Stacey Bell
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Scott L. Cassidy
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Paul A. S. Cruickshank
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - David R. Bolton
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Robert I. Hunter
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | - Hassane El Mkami
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
| | | | - Graham M. Smith
- SUPA,
School of Physics & Astronomy, University
of St Andrews, North
Haugh, St. Andrews, Fife, KY16 9SS, United Kingdom
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42
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Stevens MA, McKay JE, Robinson JLS, El Mkami H, Smith GM, Norman DG. The use of the Rx spin label in orientation measurement on proteins, by EPR. Phys Chem Chem Phys 2016; 18:5799-806. [PMID: 26426572 PMCID: PMC4756314 DOI: 10.1039/c5cp04753f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/25/2015] [Indexed: 12/15/2022]
Abstract
The bipedal spin label Rx is more restricted in its conformation and dynamics than its monopodal counterpart R1. To systematically investigate the utility of the Rx label, we have attempted to comprehensively survey the attachment of Rx to protein secondary structures. We have examined the formation, structure and dynamics of the spin label in relation to the underlying protein in order to determine feasibility and optimum conditions for distance and orientation measurement by pulsed EPR. The labeled proteins have been studied using molecular dynamics, CW EPR, pulsed EPR distance measurement at X-band and orientation measurement at W-band. The utility of different modes and positions of attachment have been compared and contrasted.
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Affiliation(s)
- M A Stevens
- Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - J E McKay
- School of Physics and Astronomy, University of St Andrews, St. Andrews, KY16 9SS, UK
| | - J L S Robinson
- Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - H El Mkami
- School of Physics and Astronomy, University of St Andrews, St. Andrews, KY16 9SS, UK
| | - G M Smith
- School of Physics and Astronomy, University of St Andrews, St. Andrews, KY16 9SS, UK
| | - D G Norman
- Nucleic Acid Structure Research Group, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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43
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Collauto A, Feintuch A, Qi M, Godt A, Meade T, Goldfarb D. Gd(III) complexes as paramagnetic tags: Evaluation of the spin delocalization over the nuclei of the ligand. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 263:156-163. [PMID: 26802219 DOI: 10.1016/j.jmr.2015.12.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/28/2015] [Accepted: 12/30/2015] [Indexed: 05/15/2023]
Abstract
Complexes of the Gd(III) ion are currently being established as spin labels for distance determination in biomolecules by pulse dipolar spectroscopy. Because Gd(III) is an f ion, one expects electron spin density to be localized on the Gd(III) ion - an important feature for the mentioned application. Most of the complex ligands have nitrogens as Gd(III) coordinating atoms. Therefore, measurement of the (14)N hyperfine coupling gives access to information on the localization of the electron spin on the Gd(III) ion. We carried out W-band, 1D and 2D (14)N and (1)H ENDOR measurements on the Gd(III) complexes Gd-DOTA, Gd-538, Gd-595, and Gd-PyMTA that serve as spin labels for Gd-Gd distance measurements. The obtained (14)N spectra are particularly well resolved, revealing both the hyperfine and nuclear quadrupole splittings, which were assigned using 2D Mims ENDOR experiments. Additionally, the spectral contributions of the two different types of nitrogen atoms of Gd-PyMTA, the aliphatic N atom and the pyridine N atom, were distinguishable. The (14)N hyperfine interaction was found to have a very small isotropic hyperfine component of -0.25 to -0.37MHz. Furthermore, the anisotropic hyperfine interactions with the (14)N nuclei and with the non-exchangeable protons of the ligands are well described by the point-dipole approximation using distances derived from the crystal structures. We therefore conclude that the spin density is fully localized on the Gd(III) ion and that the spin density distribution over the nuclei of the ligands is rightfully ignored when analyzing distance measurements.
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Affiliation(s)
- A Collauto
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - A Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - M Qi
- University Bielefeld, Faculty of Chemistry and Center for Molecular Materials, D-33615 Bielefeld, Germany
| | - A Godt
- University Bielefeld, Faculty of Chemistry and Center for Molecular Materials, D-33615 Bielefeld, Germany
| | - T Meade
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - D Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel.
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44
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Bowen AM, Jones MW, Lovett JE, Gaule TG, McPherson MJ, Dilworth JR, Timmel CR, Harmer JR. Exploiting orientation-selective DEER: determining molecular structure in systems containing Cu(ii) centres. Phys Chem Chem Phys 2016; 18:5981-94. [DOI: 10.1039/c5cp06096f] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Analysis of orientation-selective DEER measurements using Cu(ii) centres in a series of molecules demonstrates its limits and capabilities in structure elucidation.
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Affiliation(s)
- Alice M. Bowen
- Centre for Advanced Electron Spin Resonance
- University of Oxford
- Oxford
- UK
- Institute of Physical and Theoretical Chemistry
| | - Michael W. Jones
- Centre for Advanced Electron Spin Resonance
- University of Oxford
- Oxford
- UK
| | - Janet E. Lovett
- Centre for Advanced Electron Spin Resonance
- University of Oxford
- Oxford
- UK
- SUPA
| | - Thembanikosi G. Gaule
- Astbury Centre for Structural Molecular Biology
- Institute of Molecular and Cellular Biology
- Faculty of Biological Sciences
- University of Leeds
- Leeds LS2 9JT
| | - Michael J. McPherson
- Astbury Centre for Structural Molecular Biology
- Institute of Molecular and Cellular Biology
- Faculty of Biological Sciences
- University of Leeds
- Leeds LS2 9JT
| | | | | | - Jeffrey R. Harmer
- Centre for Advanced Electron Spin Resonance
- University of Oxford
- Oxford
- UK
- Centre for Advanced Imaging
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45
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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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46
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Abdullin D, Duthie F, Meyer A, Müller ES, Hagelueken G, Schiemann O. Comparison of PELDOR and RIDME for Distance Measurements between Nitroxides and Low-Spin Fe(III) Ions. J Phys Chem B 2015; 119:13534-42. [DOI: 10.1021/acs.jpcb.5b02118] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Dinar Abdullin
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Fraser Duthie
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Andreas Meyer
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Elisa S. Müller
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Gregor Hagelueken
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and
Theoretical Chemistry, University of Bonn, Wegelerstrasse 12, 53115 Bonn, Germany
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47
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Prisner TF, Marko A, Sigurdsson ST. Conformational dynamics of nucleic acid molecules studied by PELDOR spectroscopy with rigid spin labels. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 252:187-98. [PMID: 25701439 DOI: 10.1016/j.jmr.2014.12.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/16/2014] [Accepted: 12/19/2014] [Indexed: 05/22/2023]
Abstract
Nucleic acid molecules can adopt a variety of structures and exhibit a large degree of conformational flexibility to fulfill their various functions in cells. Here we describe the use of Pulsed Electron-Electron Double Resonance (PELDOR or DEER) to investigate nucleic acid molecules where two cytosine analogs have been incorporated as spin probes. Because these new types of spin labels are rigid and incorporated into double stranded DNA and RNA molecules, there is no additional flexibility of the spin label itself present. Therefore the magnetic dipole-dipole interaction between both spin labels encodes for the distance as well as for the mutual orientation between the spin labels. All of this information can be extracted by multi-frequency/multi-field PELDOR experiments, which gives very precise and valuable information about the structure and conformational flexibility of the nucleic acid molecules. We describe in detail our procedure to obtain the conformational ensembles and show the accuracy and limitations with test examples and application to double-stranded DNA.
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Affiliation(s)
- T F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany.
| | - A Marko
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Germany
| | - S Th Sigurdsson
- Science Institute, University of Iceland, Reykjavik, Iceland
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48
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49
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Kaminker I, Bye M, Mendelman N, Gislason K, Sigurdsson ST, Goldfarb D. Distance measurements between manganese(ii) and nitroxide spin-labels by DEER determine a binding site of Mn2+ in the HP92 loop of ribosomal RNA. Phys Chem Chem Phys 2015; 17:15098-102. [DOI: 10.1039/c5cp01624j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
W-band (95 GHz) double electron–electron resonance (DEER) distance measurements between Mn2+ and nitroxide spin labels were used to determine the location of a Mn2+ binding site within an RNA molecule.
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Affiliation(s)
- Ilia Kaminker
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Morgan Bye
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Natanel Mendelman
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Kristmann Gislason
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Snorri Th. Sigurdsson
- University of Iceland
- Department of Chemistry
- Science Institute Dunhaga 3
- 107 Reykjavik
- Iceland
| | - Daniella Goldfarb
- University of Iceland
- Department of Chemistry
- Science Institute Dunhaga 3
- 107 Reykjavik
- Iceland
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50
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Abdullin D, Hagelueken G, Hunter RI, Smith GM, Schiemann O. Geometric model-based fitting algorithm for orientation-selective PELDOR data. Mol Phys 2014. [DOI: 10.1080/00268976.2014.960494] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | - Gregor Hagelueken
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | | | | | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
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