1
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Wilson CB, Qi M, Han S, Sherwin MS. Gadolinium Spin Decoherence Mechanisms at High Magnetic Fields. J Phys Chem Lett 2023; 14:10578-10584. [PMID: 37976425 PMCID: PMC10694812 DOI: 10.1021/acs.jpclett.3c01847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023]
Abstract
Favorable relaxation processes, high-field spectral properties, and biological compatibility have made spin-7/2 Gd3+-based spin labels an increasingly popular choice for protein structure studies using high-field electron paramagnetic resonance. However, high-field relaxation and decoherence in ensembles of half-integer high-spin systems, such as Gd3+, remain poorly understood. We report spin-lattice (T1) and phase memory (TM) relaxation times at 8.6 T (240 GHz), and we present the first comprehensive model of high-field, high-spin decoherence accounting for both the electron spin concentration and temperature. The model includes four principal mechanisms driving decoherence: energy-conserving electron spin flip-flops, direct "T1" spin-lattice relaxation-driven electron spin flip processes, indirect T1-driven flips of nearby electron spins, and nuclear spin flip-flops. Mechanistic insight into decoherence can inform the design of experiments making use of Gd3+ as spin probes or relaxivity agents and can be used to measure local average interspin distances as long as 17 nm.
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Affiliation(s)
- C. Blake Wilson
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Mian Qi
- Faculty
of Chemistry and Center for Molecular Materials, Bielefeld University, 33615 Bielefeld, Germany
| | - Songi Han
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, Santa Barbara, California 93106, United States
- Department
of Chemical Engineering, University of California,
Santa Barbara, Santa
Barbara, California 93106, United States
- Institute
for Terahertz Science and Technology, University
of California, Santa Barbara, Santa
Barbara, California 93106, United States
| | - Mark S. Sherwin
- Institute
for Terahertz Science and Technology, University
of California, Santa Barbara, Santa
Barbara, California 93106, United States
- Department
of Physics, University of California, Santa
Barbara, Santa Barbara, California 93106, United States
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2
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Seal M, Feintuch A, Goldfarb D. The effect of spin-lattice relaxation on DEER background decay. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 345:107327. [PMID: 36410061 DOI: 10.1016/j.jmr.2022.107327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
The common approach to background removal in double electron-electron resonance (DEER) measurements on frozen solutions with a three-dimensional homogeneous distribution of doubly labeled biomolecules is to fit the background to an exponential decay function. Excluded volume effects or distribution in a dimension lower than three, such as proteins in a membrane, can lead to a stretched exponential decay. In this work, we show that in cases of spin labels with short spin-lattice relaxation time, up to an order of magnitude longer than the DEER trace length, relevant for metal-based spin labels, spin flips that take place during the DEER evolution time affect the background decay shape. This was demonstrated using a series of temperature-dependent DEER measurements on frozen solutions of a nitroxide radical, a Gd(III) complex, Cu(II) ions, and a bis-Gd(III) model complex. As expected, the background decay was exponential for the nitroxide, whereas deviations were noted for Gd(III) and Cu(II). Based on the theoretical approach of Keller et al. (Phys. Chem. Chem. Phys. 21 (2019) 8228-8245), which addresses the effect of spin-lattice relaxation-induced spin flips during the evolution time, we show that the background decay can be fitted to an exponent including a linear and quadratic term in t, which is the position of the pump pulse. Analysis of the data in terms of the probability of spontaneous spin flips induced by spin-lattice relaxation showed that this approach worked well for the high temperature range studied for Gd(III) and Cu(II). At the low temperature range, the spin flips that occured during the DEER evolution time for Gd(III) exceeded the measured spin-lattice relaxation rate and include contributions from spin flips due to another mechanisms, most likely nuclear spin diffusion.
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Affiliation(s)
- Manas Seal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Akiva Feintuch
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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3
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Scherer A, Yao X, Qi M, Wiedmaier M, Godt A, Drescher M. Increasing the Modulation Depth of Gd III-Based Pulsed Dipolar EPR Spectroscopy (PDS) with Porphyrin-Gd III Laser-Induced Magnetic Dipole Spectroscopy. J Phys Chem Lett 2022; 13:10958-10964. [PMID: 36399541 PMCID: PMC9720741 DOI: 10.1021/acs.jpclett.2c02138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Distance determination with pulsed EPR has become an important technique for the structural investigation of biomacromolecules, with double electron-electron resonance spectroscopy (DEER) as the most important method. GdIII-based spin labels are one of the most frequently used spin labels for DEER owing to their stability against reduction, high magnetic moment, and absence of orientation selection. A disadvantage of GdIII-GdIII DEER is the low modulation depth due to the broad EPR spectrum of GdIII. Here, we introduce laser-induced magnetic dipole spectroscopy (LaserIMD) with a spin pair consisting of GdIII(PymiMTA) and a photoexcited porphyrin as an alternative technique. We show that the excited state of the porphyrin is not disturbed by the presence of the GdIII complex and that herewith modulation depths of almost 40% are possible. This is significantly higher than the value of 7.2% that was achieved with GdIII-GdIII DEER.
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Affiliation(s)
- Andreas Scherer
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Xuemei Yao
- Faculty
of Chemistry and Center of Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Mian Qi
- Faculty
of Chemistry and Center of Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Max Wiedmaier
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Adelheid Godt
- Faculty
of Chemistry and Center of Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Malte Drescher
- Department
of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
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4
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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5
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Keeley J, Choudhury T, Galazzo L, Bordignon E, Feintuch A, Goldfarb D, Russell H, Taylor MJ, Lovett JE, Eggeling A, Fábregas Ibáñez L, Keller K, Yulikov M, Jeschke G, Kuprov I. Neural networks in pulsed dipolar spectroscopy: A practical guide. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 338:107186. [PMID: 35344921 DOI: 10.1016/j.jmr.2022.107186] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
This is a methodological guide to the use of deep neural networks in the processing of pulsed dipolar spectroscopy (PDS) data encountered in structural biology, organic photovoltaics, photosynthesis research, and other domains featuring long-lived radical pairs and paramagnetic metal ions. PDS uses distance dependence of magnetic dipolar interactions; measuring a single well-defined distance is straightforward, but extracting distance distributions is a hard and mathematically ill-posed problem requiring careful regularisation and background fitting. Neural networks do this exceptionally well, but their "robust black box" reputation hides the complexity of their design and training - particularly when the training dataset is effectively infinite. The objective of this paper is to give insight into training against simulated databases, to discuss network architecture choices, to describe options for handling DEER (double electron-electron resonance) and RIDME (relaxation-induced dipolar modulation enhancement) experiments, and to provide a practical data processing flowchart.
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Affiliation(s)
- Jake Keeley
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Tajwar Choudhury
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Geneva, Switzerland
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Geneva, Switzerland
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Hannah Russell
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, United Kingdom
| | - Michael J Taylor
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, United Kingdom
| | - Janet E Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, United Kingdom
| | - Andrea Eggeling
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology in Zurich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Luis Fábregas Ibáñez
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology in Zurich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Katharina Keller
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology in Zurich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Maxim Yulikov
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology in Zurich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology in Zurich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom.
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6
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Abstract
Different types of spin labels are currently available for structural studies of biomolecules both in vitro and in cells using Electron Paramagnetic Resonance (EPR) and pulse dipolar spectroscopy (PDS). Each type of label has its own advantages and disadvantages, that will be addressed in this chapter. The spectroscopically distinct properties of the labels have fostered new applications of PDS aimed to simultaneously extract multiple inter-label distances on the same sample. In fact, combining different labels and choosing the optimal strategy to address their inter-label distances can increase the information content per sample, and this is pivotal to better characterize complex multi-component biomolecular systems. In this review, we provide a brief background of the spectroscopic properties of the four most common orthogonal spin labels for PDS measurements and focus on the various methods at disposal to extract homo- and hetero-label distances in proteins. We also devote a section to possible artifacts arising from channel crosstalk and provide few examples of applications in structural biology.
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7
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Giannoulis A, Ben-Ishay Y, Goldfarb D. Characteristics of Gd(III) spin labels for the study of protein conformations. Methods Enzymol 2021; 651:235-290. [PMID: 33888206 DOI: 10.1016/bs.mie.2021.01.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gd(III) complexes are currently established as spin labels for structural studies of biomolecules using pulse dipolar electron paramagnetic resonance (PD-EPR) techniques. This has been achieved by the availability of medium- and high-field spectrometers, understanding the spin physics underlying the spectroscopic properties of high spin Gd(III) (S=7/2) pairs and their dipolar interaction, the design of well-defined model compounds and optimization of measurement techniques. In addition, a variety of Gd(III) chelates and labeling schemes have allowed a broad scope of applications. In this review, we provide a brief background of the spectroscopic properties of Gd(III) pertinent for effective PD-EPR measurements and focus on the various labels available to date. We report on their use in PD-EPR applications and highlight their pros and cons for particular applications. We also devote a section to recent in-cell structural studies of proteins using Gd(III), which is an exciting new direction for Gd(III) spin labeling.
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Affiliation(s)
- Angeliki Giannoulis
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Yasmin Ben-Ishay
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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8
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Tkach I, Diederichsen U, Bennati M. Studies of transmembrane peptides by pulse dipolar spectroscopy with semi-rigid TOPP spin labels. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:143-157. [PMID: 33640998 PMCID: PMC8071797 DOI: 10.1007/s00249-021-01508-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 12/01/2022]
Abstract
Electron paramagnetic resonance (EPR)-based pulsed dipolar spectroscopy measures the dipolar interaction between paramagnetic centers that are separated by distances in the range of about 1.5-10 nm. Its application to transmembrane (TM) peptides in combination with modern spin labelling techniques provides a valuable tool to study peptide-to-lipid interactions at a molecular level, which permits access to key parameters characterizing the structural adaptation of model peptides incorporated in natural membranes. In this mini-review, we summarize our approach for distance and orientation measurements in lipid environment using novel semi-rigid TOPP [4-(3,3,5,5-tetramethyl-2,6-dioxo-4-oxylpiperazin-1-yl)-L-phenylglycine] labels specifically designed for incorporation in TM peptides. TOPP labels can report single peak distance distributions with sub-angstrom resolution, thus offering new capabilities for a variety of TM peptide investigations, such as monitoring of various helix conformations or measuring of tilt angles in membranes.
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Affiliation(s)
- Igor Tkach
- Max Planck Institute for Biophysical Chemistry, RG Electron-Spin Resonance Spectroscopy, 37077, Göttingen, Germany.
| | - Ulf Diederichsen
- Department of Organic and Biomolecular Chemistry, University of Göttingen, 37077, Göttingen, Germany
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, RG Electron-Spin Resonance Spectroscopy, 37077, Göttingen, Germany
- Department of Organic and Biomolecular Chemistry, University of Göttingen, 37077, Göttingen, Germany
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9
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EL Mkami H, Hunter R, Cruickshank P, Taylor M, Lovett J, Feintuch A, Qi M, Godt A, Smith G. High-sensitivity Gd 3+-Gd 3+ EPR distance measurements that eliminate artefacts seen at short distances. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:301-313. [PMID: 37904818 PMCID: PMC10500690 DOI: 10.5194/mr-1-301-2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/18/2020] [Indexed: 11/01/2023]
Abstract
Gadolinium complexes are attracting increasing attention as spin labels for EPR dipolar distance measurements in biomolecules and particularly for in-cell measurements. It has been shown that flip-flop transitions within the central transition of the high-spin Gd3 + ion can introduce artefacts in dipolar distance measurements, particularly when measuring distances less than 3 nm. Previous work has shown some reduction of these artefacts through increasing the frequency separation between the two frequencies required for the double electron-electron resonance (DEER) experiment. Here we use a high-power (1 kW), wideband, non-resonant system operating at 94 GHz to evaluate DEER measurement protocols using two stiff Gd(III) rulers, consisting of two b i s -Gd3 + -PyMTA complexes, with separations of 2.1 nm and 6.0 nm, respectively. We show that by avoiding the - 1 2 → 1 2 central transition completely, and placing both the pump and the observer pulses on either side of the central transition, we can now observe apparently artefact-free spectra and narrow distance distributions, even for a Gd-Gd distance of 2.1 nm. Importantly we still maintain excellent signal-to-noise ratio and relatively high modulation depths. These results have implications for in-cell EPR measurements at naturally occurring biomolecule concentrations.
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Affiliation(s)
- Hassane EL Mkami
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Robert I. Hunter
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Paul A. S. Cruickshank
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Michael J. Taylor
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Janet E. Lovett
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science,
Rehovot, Israel
| | - Mian Qi
- Faculty of Chemistry and Center of Molecular Materials (CM2),
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld,
Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center of Molecular Materials (CM2),
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld,
Germany
| | - Graham M. Smith
- SUPA, School of Physics and Astronomy, University of St Andrews, St
Andrews, KY16 9SS, UK
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10
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Yardeni EH, Bahrenberg T, Stein RA, Mishra S, Zomot E, Graham B, Tuck KL, Huber T, Bibi E, Mchaourab HS, Goldfarb D. Probing the solution structure of the E. coli multidrug transporter MdfA using DEER distance measurements with nitroxide and Gd(III) spin labels. Sci Rep 2019; 9:12528. [PMID: 31467343 PMCID: PMC6715713 DOI: 10.1038/s41598-019-48694-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/08/2019] [Indexed: 11/09/2022] Open
Abstract
Methodological and technological advances in EPR spectroscopy have enabled novel insight into the structural and dynamic aspects of integral membrane proteins. In addition to an extensive toolkit of EPR methods, multiple spin labels have been developed and utilized, among them Gd(III)-chelates which offer high sensitivity at high magnetic fields. Here, we applied a dual labeling approach, employing nitroxide and Gd(III) spin labels, in conjunction with Q-band and W-band double electron-electron resonance (DEER) measurements to characterize the solution structure of the detergent-solubilized multidrug transporter MdfA from E. coli. Our results identify highly flexible regions of MdfA, which may play an important role in its functional dynamics. Comparison of distance distribution of spin label pairs on the periplasm with those calculated using inward- and outward-facing crystal structures of MdfA, show that in detergent micelles, the protein adopts a predominantly outward-facing conformation, although more closed than the crystal structure. The cytoplasmic pairs suggest a small preference to the outward-facing crystal structure, with a somewhat more open conformation than the crystal structure. Parallel DEER measurements with the two types of labels led to similar distance distributions, demonstrating the feasibility of using W-band spectroscopy with a Gd(III) label for investigation of the structural dynamics of membrane proteins.
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Affiliation(s)
- Eliane H Yardeni
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, 76100, Israel
| | - Thorsten Bahrenberg
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Elia Zomot
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, 76100, Israel
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Kellie L Tuck
- School of Chemistry, Monash University, Wellington Road, Clayton, Victoria, Australia
| | - Thomas Huber
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Eitan Bibi
- Department of Biomolecular Sciences, Weizmann Institute of Science Rehovot, Rehovot, 76100, Israel.
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel.
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11
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Azarkh M, Bieber A, Qi M, Fischer JW, Yulikov M, Godt A, Drescher M. Gd(III)-Gd(III) Relaxation-Induced Dipolar Modulation Enhancement for In-Cell Electron Paramagnetic Resonance Distance Determination. J Phys Chem Lett 2019; 10:1477-1481. [PMID: 30864799 PMCID: PMC6625747 DOI: 10.1021/acs.jpclett.9b00340] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/13/2019] [Indexed: 05/26/2023]
Abstract
In-cell distance determination by electron paramagnetic resonance (EPR) spectroscopy reveals essential structural information about biomacromolecules under native conditions. We demonstrate that the pulsed EPR technique RIDME (relaxation induced dipolar modulation enhancement) can be utilized for such distance determination. The performance of in-cell RIDME has been assessed at Q-band using stiff molecular rulers labeled with Gd(III)-PyMTA and microinjected into Xenopus laevis oocytes. The overtone coefficients are determined to be the same for protonated aqueous solutions and inside cells. As compared to in-cell DEER (double electron-electron resonance, also abbreviated as PELDOR), in-cell RIDME features approximately 5 times larger modulation depth and does not show artificial broadening in the distance distributions due to the effect of pseudosecular terms.
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Affiliation(s)
- Mykhailo Azarkh
- Department
of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Anna Bieber
- Department
of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Mian Qi
- Faculty
of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Jörg W.
A. Fischer
- Department
of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Maxim Yulikov
- Laboratory
of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Adelheid Godt
- Faculty
of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Malte Drescher
- Department
of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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12
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Shah A, Roux A, Starck M, Mosely JA, Stevens M, Norman DG, Hunter RI, El Mkami H, Smith GM, Parker D, Lovett JE. A Gadolinium Spin Label with Both a Narrow Central Transition and Short Tether for Use in Double Electron Electron Resonance Distance Measurements. Inorg Chem 2019; 58:3015-3025. [DOI: 10.1021/acs.inorgchem.8b02892] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Anokhi Shah
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
- BSRC, University of St Andrews, St Andrews KY16 9ST, U.K
| | - Amandine Roux
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Matthieu Starck
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Jackie A. Mosely
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Michael Stevens
- College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - David G. Norman
- College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Robert I. Hunter
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - Hassane El Mkami
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - Graham M. Smith
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
| | - David Parker
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Janet E. Lovett
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, U.K
- BSRC, University of St Andrews, St Andrews KY16 9ST, U.K
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13
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Giannoulis A, Yang Y, Gong YJ, Tan X, Feintuch A, Carmieli R, Bahrenberg T, Liu Y, Su XC, Goldfarb D. DEER distance measurements on trityl/trityl and Gd(iii)/trityl labelled proteins. Phys Chem Chem Phys 2019; 21:10217-10227. [DOI: 10.1039/c8cp07249c] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Trityl–trityl and trityl–Gd(iii) DEER distance measurements in proteins are performed using a new trityl spin label affording thioether–protein conjugation.
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Affiliation(s)
- Angeliki Giannoulis
- Department of Chemical and Biological Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yin Yang
- Department of Chemical and Biological Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering
- Nankai University
- Tianjin 300071
- China
| | - Xiaoli Tan
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics
- School of Pharmacy
- Tianjin Medical University
- Tianjin 300070
- China
| | - Akiva Feintuch
- Department of Chemical and Biological Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Raanan Carmieli
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Thorsten Bahrenberg
- Department of Chemical and Biological Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics
- School of Pharmacy
- Tianjin Medical University
- Tianjin 300070
- China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering
- Nankai University
- Tianjin 300071
- China
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
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14
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Worswick SG, Spencer JA, Jeschke G, Kuprov I. Deep neural network processing of DEER data. SCIENCE ADVANCES 2018; 4:eaat5218. [PMID: 30151430 PMCID: PMC6108566 DOI: 10.1126/sciadv.aat5218] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/20/2018] [Indexed: 05/24/2023]
Abstract
The established model-free methods for the processing of two-electron dipolar spectroscopy data [DEER (double electron-electron resonance), PELDOR (pulsed electron double resonance), DQ-EPR (double-quantum electron paramagnetic resonance), RIDME (relaxation-induced dipolar modulation enhancement), etc.] use regularized fitting. In this communication, we describe an attempt to process DEER data using artificial neural networks trained on large databases of simulated data. Accuracy and reliability of neural network outputs from real experimental data were found to be unexpectedly high. The networks are also able to reject exchange interactions and to return a measure of uncertainty in the resulting distance distributions. This paper describes the design of the training databases, discusses the training process, and rationalizes the observed performance. Neural networks produced in this work are incorporated as options into Spinach and DeerAnalysis packages.
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Affiliation(s)
- Steven G. Worswick
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - James A. Spencer
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology in Zurich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
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15
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Clayton JA, Keller K, Qi M, Wegner J, Koch V, Hintz H, Godt A, Han S, Jeschke G, Sherwin MS, Yulikov M. Quantitative analysis of zero-field splitting parameter distributions in Gd(iii) complexes. Phys Chem Chem Phys 2018; 20:10470-10492. [PMID: 29617015 DOI: 10.1039/c7cp08507a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The magnetic properties of paramagnetic species with spin S > 1/2 are parameterized by the familiar g tensor as well as "zero-field splitting" (ZFS) terms that break the degeneracy between spin states even in the absence of a magnetic field. In this work, we determine the mean values and distributions of the ZFS parameters D and E for six Gd(iii) complexes (S = 7/2) and critically discuss the accuracy of such determination. EPR spectra of the Gd(iii) complexes were recorded in glassy frozen solutions at 10 K or below at Q-band (∼34 GHz), W-band (∼94 GHz) and G-band (240 GHz) frequencies, and simulated with two widely used models for the form of the distributions of the ZFS parameters D and E. We find that the form of the distribution of the ZFS parameter D is bimodal, consisting roughly of two Gaussians centered at D and -D with unequal amplitudes. The extracted values of D (σD) for the six complexes are, in MHz: Gd-NO3Pic, 485 ± 20 (155 ± 37); Gd-DOTA/Gd-maleimide-DOTA, -714 ± 43 (328 ± 99); iodo-(Gd-PyMTA)/MOMethynyl-(Gd-PyMTA), 1213 ± 60 (418 ± 141); Gd-TAHA, 1361 ± 69 (457 ± 178); iodo-Gd-PCTA-[12], 1861 ± 135 (467 ± 292); and Gd-PyDTTA, 1830 ± 105 (390 ± 242). The sign of D was adjusted based on the Gaussian component with larger amplitude. We relate the extracted P(D) distributions to the structure of the individual Gd(iii) complexes by fitting them to a model that superposes the contribution to the D tensor from each coordinating atom of the ligand. Using this model, we predict D, σD, and E values for several additional Gd(iii) complexes that were not measured in this work. The results of this paper may be useful as benchmarks for the verification of quantum chemical calculations of ZFS parameters, and point the way to designing Gd(iii) complexes for particular applications and estimating their magnetic properties a priori.
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Affiliation(s)
- Jessica A Clayton
- University of California, Santa Barbara, Department of Physics, Santa Barbara, CA, USA.
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16
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Prokopiou G, Lee MD, Collauto A, Abdelkader EH, Bahrenberg T, Feintuch A, Ramirez-Cohen M, Clayton J, Swarbrick JD, Graham B, Otting G, Goldfarb D. Small Gd(III) Tags for Gd(III)–Gd(III) Distance Measurements in Proteins by EPR Spectroscopy. Inorg Chem 2018; 57:5048-5059. [DOI: 10.1021/acs.inorgchem.8b00133] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Georgia Prokopiou
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Alberto Collauto
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elwy H. Abdelkader
- Research School of Chemistry, Australian National University, Canberra, ACT 2601,Australia
| | - Thorsten Bahrenberg
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marie Ramirez-Cohen
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jessica Clayton
- Department of Physics, University of California, Santa Barbara, California 93106-9530, United States
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601,Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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17
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Mahawaththa MC, Lee MD, Giannoulis A, Adams LA, Feintuch A, Swarbrick JD, Graham B, Nitsche C, Goldfarb D, Otting G. Small neutral Gd(iii) tags for distance measurements in proteins by double electron–electron resonance experiments. Phys Chem Chem Phys 2018; 20:23535-23545. [DOI: 10.1039/c8cp03532f] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small Gd(iii) tags based on DO3A deliver narrow and readily predictable distances by double electron–electron resonance (DEER) measurements.
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Affiliation(s)
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Angeliki Giannoulis
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Luke A. Adams
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Akiva Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - Christoph Nitsche
- Research School of Chemistry
- The Australian National University
- Canberra
- Australia
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 76100
- Israel
| | - Gottfried Otting
- Research School of Chemistry
- The Australian National University
- Canberra
- Australia
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18
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Manukovsky N, Feintuch A, Kuprov I, Goldfarb D. Time domain simulation of Gd3+–Gd3+ distance measurements by EPR. J Chem Phys 2017; 147:044201. [DOI: 10.1063/1.4994084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nurit Manukovsky
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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19
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Clayton JA, Qi M, Godt A, Goldfarb D, Han S, Sherwin MS. Gd 3+-Gd 3+ distances exceeding 3 nm determined by very high frequency continuous wave electron paramagnetic resonance. Phys Chem Chem Phys 2017; 19:5127-5136. [PMID: 28139788 PMCID: PMC5394103 DOI: 10.1039/c6cp07119h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance spectroscopy in combination with site-directed spin labeling is a very powerful tool for elucidating the structure and organization of biomolecules. Gd3+ complexes have recently emerged as a new class of spin labels for distance determination by pulsed EPR spectroscopy at Q- and W-band. We present CW EPR measurements at 240 GHz (8.6 Tesla) on a series of Gd-rulers of the type Gd-PyMTA-spacer-Gd-PyMTA, with Gd-Gd distances ranging from 1.2 nm to 4.3 nm. CW EPR measurements of these Gd-rulers show that significant dipolar broadening of the central |-1/2〉 → |1/2〉 transition occurs at 30 K for Gd-Gd distances up to ∼3.4 nm with Gd-PyMTA as the spin label. This represents a significant extension for distances accessible by CW EPR, as nitroxide-based spin labels at X-band frequencies can typically only access distances up to ∼2 nm. We show that this broadening persists at biologically relevant temperatures above 200 K, and that this method is further extendable up to room temperature by immobilizing the sample in glassy trehalose. We show that the peak-to-peak broadening of the central transition follows the expected 1/r3 dependence for the electron-electron dipolar interaction, from cryogenic temperatures up to room temperature. A simple procedure for simulating the dependence of the lineshape on interspin distance is presented, in which the broadening of the central transition is modeled as an S = 1/2 spin whose CW EPR lineshape is broadened through electron-electron dipolar interactions with a neighboring S = 7/2 spin.
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Affiliation(s)
- Jessica A Clayton
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, USA. and Institute for Terahertz Science and Technology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Bielefeld, Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Bielefeld, Germany
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Songi Han
- Institute for Terahertz Science and Technology, University of California, Santa Barbara, Santa Barbara, CA, USA and Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA, USA and Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Mark S Sherwin
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, USA. and Institute for Terahertz Science and Technology, University of California, Santa Barbara, Santa Barbara, CA, USA
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20
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Keller K, Mertens V, Qi M, Nalepa AI, Godt A, Savitsky A, Jeschke G, Yulikov M. Computing distance distributions from dipolar evolution data with overtones: RIDME spectroscopy with Gd(iii)-based spin labels. Phys Chem Chem Phys 2017; 19:17856-17876. [DOI: 10.1039/c7cp01524k] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extraction of distance distributions between high-spin paramagnetic centers from relaxation induced dipolar modulation enhancement (RIDME) data is affected by the presence of overtones of dipolar frequencies.
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Affiliation(s)
- Katharina Keller
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Valerie Mertens
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Anna I. Nalepa
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Anton Savitsky
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
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21
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Doll A, Qi M, Godt A, Jeschke G. CIDME: Short distances measured with long chirp pulses. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 273:73-82. [PMID: 27788378 DOI: 10.1016/j.jmr.2016.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/10/2016] [Accepted: 10/14/2016] [Indexed: 06/06/2023]
Abstract
Frequency-swept pulses have recently been introduced as pump pulses into double electron-electron resonance (DEER) experiments. A limitation of this approach is that the pump pulses need to be short in comparison to dipolar evolution periods. The "chirp-induced dipolar modulation enhancement" (CIDME) pulse sequence introduced in this work circumvents this limitation by means of longitudinal storage during the application of one single or two consecutive pump pulses. The resulting six-pulse sequence is closely related to the five-pulse "relaxation-induced dipolar modulation enhancement" (RIDME) pulse sequence: While dipolar modulation in RIDME is due to stochastic spin flips during longitudinal storage, modulation in CIDME is due to the pump pulse during longitudinal storage. Experimentally, CIDME is examined for Gd-Gd and nitroxide-nitroxide distance determination using a high-power Q-band spectrometer. Since longitudinal storage results in a 50% signal loss, comparisons between DEER using short chirp pump pulses of 64ns duration and CIDME using longer pump pulses are in favor of DEER. While the lower sensitivity restrains the applicability of CIDME for routine distance determination on high-power spectrometers, this result is not to be generalized to spectrometers having lower power and to specialized "non-routine" applications or different types of spin labels. In particular, the advantage of prolonged CIDME pump pulses is demonstrated for experiments at large frequency offset between the pumped and observed spins. At a frequency separation of 1GHz, where broadening due to dipolar pseudo-secular contributions becomes largely suppressed, a Gd-Gd modulation depth larger than 10% is achieved. Moreover, a CIDME experiment at deliberately reduced power underlines the potential of the new technique for spectrometers with lower power, as often encountered at higher microwave frequencies. With longitudinal storage times T below 10μs, however, CIDME appears rather susceptible to artifacts. For nitroxide-nitroxide experiments, these currently inhibit a faithful data analysis. To facilitate further developments, the artifacts are characterized experimentally. In addition, effects that are specific to the high spin of S=7/2 Gd-centers are examined. Herein, population transfer within the observer spin's multiplet due to the pump pulse as well as excitation of dipolar harmonics are discussed.
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Affiliation(s)
- Andrin Doll
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials, Bielefeld University, Unversitätsstraße 25, 33615 Bielefeld, Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials, Bielefeld University, Unversitätsstraße 25, 33615 Bielefeld, Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland.
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22
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Akhmetzyanov D, Ching HYV, Denysenkov V, Demay-Drouhard P, Bertrand HC, Tabares LC, Policar C, Prisner TF, Un S. RIDME spectroscopy on high-spin Mn2+ centers. Phys Chem Chem Phys 2016; 18:30857-30866. [DOI: 10.1039/c6cp05239h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A bis-MnDOTA complex was investigated by EPR dipolar spectroscopy. RIDME experiment revealed higher modulation depth compared to PELDOR and featured harmonics of the dipolar coupling frequency.
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Affiliation(s)
- D. Akhmetzyanov
- Goethe-University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
| | - H. Y. V. Ching
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology, Université Paris-Saclay
- CEA
- CNRS UMR 9198
| | - V. Denysenkov
- Goethe-University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
| | - P. Demay-Drouhard
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - H. C. Bertrand
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - L. C. Tabares
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology, Université Paris-Saclay
- CEA
- CNRS UMR 9198
| | - C. Policar
- Département de Chimie
- Ecole Normale Supérieure
- PSL Research University
- UPMC Univ Paris 06
- CNRS
| | - T. F. Prisner
- Goethe-University Frankfurt am Main
- Institute of Physical and Theoretical Chemistry and Center for Biomolecular Magnetic Resonance
- 60438 Frankfurt am Main
- Germany
| | - S. Un
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology, Université Paris-Saclay
- CEA
- CNRS UMR 9198
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23
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Collauto A, Frydman V, Lee MD, Abdelkader EH, Feintuch A, Swarbrick JD, Graham B, Otting G, Goldfarb D. RIDME distance measurements using Gd(iii) tags with a narrow central transition. Phys Chem Chem Phys 2016; 18:19037-49. [DOI: 10.1039/c6cp03299k] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Methods based on pulse electron paramagnetic resonance allow measurement of the electron–electron dipolar coupling between two high-spin labels.
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Affiliation(s)
- A. Collauto
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - V. Frydman
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - M. D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - E. H. Abdelkader
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - A. Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - J. D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - B. Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - G. Otting
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - D. Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
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