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Abstract
Many applications of lanthanides exploit their electron spin relaxation properties. Double electron-electron measurements of distances are possible because of the relatively long relaxation times of Gd3+. Relaxation enhancement measurements of distance are possible because of the much shorter relaxation times of other lanthanides. Magnetic resonance imaging contrast agents use the long relaxation time of the S-state Gd3+ ion, and NMR shift reagents use the fast relaxation of selected other lanthanides. Other than Gd3+ and the isoelectronic Eu2+ ion, spin relaxation of the lanthanides is so fast that their EPR spectra can be observed only in the liquid helium temperature range. In this chapter the EPR properties of each of the lanthanides is briefly summarized, with an emphasis on electron spin relaxation.
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Affiliation(s)
- Joseph E McPeak
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, United States
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, United States
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, United States.
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2
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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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3
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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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4
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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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5
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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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6
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Gigli L, Andrałojć W, Dalaloyan A, Parigi G, Ravera E, Goldfarb D, Luchinat C. Assessing protein conformational landscapes: integration of DEER data in Maximum Occurrence analysis. Phys Chem Chem Phys 2018; 20:27429-27438. [PMID: 30357188 DOI: 10.1039/c8cp06195e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The properties of the conformational landscape of a biomolecule are of capital importance to understand its function. It is widely accepted that a statistical ensemble is far more representative than a single structure, especially for proteins with disordered regions. While experimental data provide the most important handle on the conformational variability that the system is experiencing, they usually report on either time or ensemble averages. Since the available conformations largely outnumber the (independent) available experimental data, the latter can be equally well reproduced by a variety of ensembles. We have proposed the Maximum Occurrence (MaxOcc) approach to provide an upper bound of the statistical weight of each conformation. This method is expected to converge towards the true statistical weights by increasing the number of independent experimental datasets. In this paper we explore the ability of DEER (Double Electron Electron Resonance) data, which report on the distance distribution between two spin labels attached to a biomolecule, to restrain the MaxOcc values and its complementarity to previously introduced experimental techniques such as NMR and Small-Angle X-ray Scattering. We here present the case of Ca2+ bound calmodulin (CaM) as a test case and show that DEER data impose a sizeable reduction of the conformational space described by high MaxOcc conformations.
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Affiliation(s)
- Lucia Gigli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.
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7
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Ghosh S, Lawless MJ, Rule GS, Saxena S. The Cu 2+-nitrilotriacetic acid complex improves loading of α-helical double histidine site for precise distance measurements by pulsed ESR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 286:163-171. [PMID: 29272745 DOI: 10.1016/j.jmr.2017.12.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 05/09/2023]
Abstract
Site-directed spin labeling using two strategically placed natural histidine residues allows for the rigid attachment of paramagnetic Cu2+. This double histidine (dHis) motif enables extremely precise, narrow distance distributions resolved by Cu2+-based pulsed ESR. Furthermore, the distance measurements are easily relatable to the protein backbone-structure. The Cu2+ ion has, till now, been introduced as a complex with the chelating agent iminodiacetic acid (IDA) to prevent unspecific binding. Recently, this method was found to have two limiting concerns that include poor selectivity towards α-helices and incomplete Cu2+-IDA complexation. Herein, we introduce an alternative method of dHis-Cu2+ loading using the nitrilotriacetic acid (NTA)-Cu2+ complex. We find that the Cu2+-NTA complex shows a four-fold increase in selectivity toward α-helical dHis sites. Furthermore, we show that 100% Cu2+-NTA complexation is achievable, enabling precise dHis loading and resulting in no free Cu2+ in solution. We analyze the optimum dHis loading conditions using both continuous wave and pulsed ESR. We implement these findings to show increased sensitivity of the Double Electron-Electron Resonance (DEER) experiment in two different protein systems. The DEER signal is increased within the immunoglobulin binding domain of protein G (called GB1). We measure distances between a dHis site on an α-helix and dHis site either on a mid-strand or a non-hydrogen bonded edge-strand β-sheet. Finally, the DEER signal is increased twofold within two α-helix dHis sites in the enzymatic dimer glutathione S-transferase exemplifying the enhanced α-helical selectivity of Cu2+-NTA.
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Affiliation(s)
- Shreya Ghosh
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Matthew J Lawless
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Gordon S Rule
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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8
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Wu Z, Feintuch A, Collauto A, Adams LA, Aurelio L, Graham B, Otting G, Goldfarb D. Selective Distance Measurements Using Triple Spin Labeling with Gd 3+, Mn 2+, and a Nitroxide. J Phys Chem Lett 2017; 8:5277-5282. [PMID: 28990781 DOI: 10.1021/acs.jpclett.7b01739] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Distance measurements by pulse electron paramagnetic resonance techniques, such as double electron-electron resonance (DEER, also called PELDOR), have become an established tool to explore structural properties of biomacromolecules and their assemblies. In such measurements a pair of spin labels provides a single distance constraint. Here we show that by employing three different types of spin labels that differ in their spectroscopic and spin dynamics properties it is possible to extract three independent distances from a single sample. We demonstrate this using the Antennapedia homeodomain orthogonally labeled with Gd3+ and Mn2+ tags in complex with its cognate DNA binding site labeled with a nitroxide.
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Affiliation(s)
- Zuyan Wu
- Research School of Chemistry, Australian National University , Canberra ACT 2601, Australia
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Alberto Collauto
- Department of Chemical Physics, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Luke A Adams
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Luigi Aurelio
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University , Parkville VIC 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University , Canberra ACT 2601, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science , Rehovot 76100, Israel
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9
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Bahrenberg T, Rosenski Y, Carmieli R, Zibzener K, Qi M, Frydman V, Godt A, Goldfarb D, Feintuch A. Improved sensitivity for W-band Gd(III)-Gd(III) and nitroxide-nitroxide DEER measurements with shaped pulses. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 283:1-13. [PMID: 28834777 DOI: 10.1016/j.jmr.2017.08.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 06/07/2023]
Abstract
Chirp and shaped pulses have been recently shown to be highly advantageous for improving sensitivity in DEER (double electron-electron resonance, also called PELDOR) measurements due to their large excitation bandwidth. The implementation of such pulses for pulse EPR has become feasible due to the availability of arbitrary waveform generators (AWG) with high sampling rates to support pulse shaping for pulses with tens of nanoseconds duration. Here we present a setup for obtaining chirp pulses on our home-built W-band (95GHz) spectrometer and demonstrate its performance on Gd(III)-Gd(III) and nitroxide-nitroxide DEER measurements. We carried out an extensive optimization procedure on two model systems, Gd(III)-PyMTA-spacer-Gd(III)-PyMTA (Gd-PyMTA ruler; zero-field splitting parameter (ZFS) D∼1150MHz) as well as nitroxide-spacer-nitroxide (nitroxide ruler) to evaluate the applicability of shaped pulses to Gd(III) complexes and nitroxides, which are two important classes of spin labels used in modern DEER/EPR experiments. We applied our findings to ubiquitin, doubly labeled with Gd-DOTA-monoamide (D∼550MHz) asa model for a system with a small ZFS. Our experiments were focused on the questions (i) what are the best conditions for positioning of the detection frequency, (ii) which pump pulse parameters (bandwidth, positioning in the spectrum, length) yield the best signal-to-noise ratio (SNR) improvements when compared to classical DEER, and (iii) how do the sample's spectral parameters influence the experiment. For the nitroxide ruler, we report an improvement of up to 1.9 in total SNR, while for the Gd-PyMTA ruler the improvement was 3.1-3.4 and for Gd-DOTA-monoamide labeled ubiquitin it was a factor of 1.8. Whereas for the Gd-PyMTA ruler the two setups pump on maximum and observe on maximum gave about the same improvement, for Gd-DOTA-monoamide a significant difference was found. In general the choice of the best set of parameters depends on the D parameter of the Gd(III) complex.
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Affiliation(s)
- Thorsten Bahrenberg
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Yael Rosenski
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Raanan Carmieli
- Department of Chemical Research Support, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Koby Zibzener
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, 33615 Bielefeld, Germany
| | - Veronica Frydman
- Department of Chemical Research Support, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, 33615 Bielefeld, Germany
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, 76100 Rehovot, Israel.
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10
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Yang Y, Gong YJ, Litvinov A, Liu HK, Yang F, Su XC, Goldfarb D. Generic tags for Mn(ii) and Gd(iii) spin labels for distance measurements in proteins. Phys Chem Chem Phys 2017; 19:26944-26956. [DOI: 10.1039/c7cp04311b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The coordination mode of the metal ion in the spin label affects the distance distribution determined by DEER distance measurements.
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Affiliation(s)
- Yin Yang
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Aleksei Litvinov
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Hong-Kai Liu
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin)
- College of Chemistry
- Nankai University
- Tianjin 300071
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
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11
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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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12
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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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13
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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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14
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Cohen MR, Frydman V, Milko P, Iron MA, Abdelkader EH, Lee MD, Swarbrick JD, Raitsimring A, Otting G, Graham B, Feintuch A, Goldfarb D. Overcoming artificial broadening in Gd3+–Gd3+ distance distributions arising from dipolar pseudo-secular terms in DEER experiments. Phys Chem Chem Phys 2016; 18:12847-59. [DOI: 10.1039/c6cp00829a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Double electron–electron resonance (DEER) is used to probe structure of Gd3+-tagged biomolecules by determining Gd3+–Gd3+ distances.
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Affiliation(s)
- Marie Ramirez Cohen
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Veronica Frydman
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Petr Milko
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Mark A. Iron
- Department of Chemical Research Support
- Weizmann Institute of Science
- Rehovot 7610001
- Israel
| | - Elwy H. Abdelkader
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | | | - Gottfried Otting
- Research School of Chemistry
- Australian National University
- Canberra
- Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences
- Monash University
- Parkville
- Australia
| | - 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
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15
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Doll A, Qi M, Wili N, Pribitzer S, Godt A, Jeschke G. Gd(III)-Gd(III) distance measurements with chirp pump pulses. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 259:153-62. [PMID: 26340436 DOI: 10.1016/j.jmr.2015.08.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/13/2015] [Accepted: 08/14/2015] [Indexed: 05/15/2023]
Abstract
The broad EPR spectrum of Gd(III) spin labels restricts the dipolar modulation depth in distance measurements between Gd(III) pairs to a few percent. To overcome this limitation, frequency-swept chirp pulses are utilized as pump pulses in the DEER experiment. Using a model system with 3.4 nm Gd-Gd distance, application of one single chirp pump pulse at Q-band frequencies leads to modulation depths beyond 10%. However, the larger modulation depth is counteracted by a reduction of the absolute echo intensity due to the pump pulse. As supported by spin dynamics simulations, this effect is primarily driven by signal loss to double-quantum coherence and specific to the Gd(III) high spin state of S=7/2. In order to balance modulation depth and echo intensity for optimum sensitivity, a simple experimental procedure is proposed. An additional improvement by 25% in DEER sensitivity is achieved with two consecutive chirp pump pulses. These pulses pump the Gd(III) spectrum symmetrically around the observation position, therefore mutually compensating for dynamical Bloch-Siegert phase shifts at the observer spins. The improved sensitivity of the DEER data with modulation depths on the order of 20% is due to mitigation of the echo reduction effects by the consecutive pump pulses. In particular, the second pump pulse does not lead to additional signal loss if perfect inversion is assumed. Moreover, the compensation of the dynamical Bloch-Siegert phase prevents signal loss due to spatial dependence of the dynamical phase, which is caused by inhomogeneities in the driving field. The new methodology is combined with pre-polarization techniques to measure long distances up to 8.6 nm, where signal intensity and modulation depth become attenuated by long dipolar evolution windows. In addition, the influence of the zero-field splitting parameters on the echo intensity is studied with simulations. Herein, larger sensitivity is anticipated for Gd(III) complexes with zero-field splitting that is smaller than for the employed Gd-PyMTA complex.
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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
| | - Nino Wili
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Stephan Pribitzer
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - 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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16
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Vincent Ching HY, Demay-Drouhard P, Bertrand HC, Policar C, Tabares LC, Un S. Nanometric distance measurements between Mn(ii)DOTA centers. Phys Chem Chem Phys 2015; 17:23368-77. [DOI: 10.1039/c5cp03487f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The distance between two Mn(ii)DOTA complexes attached to the ends of polyproline helices of varying lengths was measured by 94 GHz PELDOR spectroscopy with good accuracy demonstrating their effectiveness as spin-labels.
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Affiliation(s)
- H. Y. Vincent Ching
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
| | - Paul Demay-Drouhard
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Hélène C. Bertrand
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Clotilde Policar
- Ecole Normale Supérieure-PSL Research University
- Départment de Chimie
- Sorbonne Universités – UPMC Univ Paris 06
- CNRS UMR 7203 LBM
- F-75005 Paris
| | - Leandro C. Tabares
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
| | - Sun Un
- Institute for Integrative Biology of the Cell (I2BC)
- Department of Biochemistry
- Biophysics and Structural Biology
- Université Paris-Saclay
- CEA
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17
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Dalaloyan A, Qi M, Ruthstein S, Vega S, Godt A, Feintuch A, Goldfarb D. Gd(iii)–Gd(iii) EPR distance measurements – the range of accessible distances and the impact of zero field splitting. Phys Chem Chem Phys 2015; 17:18464-76. [DOI: 10.1039/c5cp02602d] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gd rulers were designed in the 2–8 nm range for in-depth evaluation of Gd(iii) complexes as spin labels for EPR distance measurements.
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Affiliation(s)
- Arina Dalaloyan
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Mian Qi
- Bielefeld University
- Faculty of Chemistry and Center for Molecular Materials
- D-33615 Bielefeld
- Germany
| | - Sharon Ruthstein
- Department of Chemistry
- Faculty of Exact Sciences
- Bar-Ilan University
- Ramat Gan
- Israel
| | - Shimon Vega
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Adelheid Godt
- Bielefeld University
- Faculty of Chemistry and Center for Molecular Materials
- D-33615 Bielefeld
- Germany
| | - Akiva Feintuch
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
| | - Daniella Goldfarb
- Department of Chemical Physics
- Weizmann Institute of Science
- Rehovot
- Israel
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18
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Feintuch A, Otting G, Goldfarb D. Gd3+ Spin Labeling for Measuring Distances in Biomacromolecules. Methods Enzymol 2015; 563:415-57. [DOI: 10.1016/bs.mie.2015.07.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Doll A, Qi M, Pribitzer S, Wili N, Yulikov M, Godt A, Jeschke G. Sensitivity enhancement by population transfer in Gd(iii) spin labels. Phys Chem Chem Phys 2015; 17:7334-44. [DOI: 10.1039/c4cp05893c] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Frequency-swept chirp pulses with bandwidths > 1 GHz rearrange electron spin populations in the S = 7/2 spin of Gd(iii) ions for better sensitivity, as demonstrated with distance measurements between Gd(iii) ions.
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Affiliation(s)
- Andrin Doll
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials
- Bielefeld University
- 33615 Bielefeld
- Germany
| | | | - Nino Wili
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry
- ETH Zurich
- 8093 Zurich
- Switzerland
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20
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Raitsimring A, Dalaloyan A, Collauto A, Feintuch A, Meade T, Goldfarb D. Zero field splitting fluctuations induced phase relaxation of Gd3+ in frozen solutions at cryogenic temperatures. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 248:71-80. [PMID: 25442776 PMCID: PMC4495766 DOI: 10.1016/j.jmr.2014.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 09/14/2014] [Accepted: 09/16/2014] [Indexed: 05/18/2023]
Abstract
Distance measurements using double electron-electron resonance (DEER) and Gd(3+) chelates for spin labels (GdSL) have been shown to be an attractive alternative to nitroxide spin labels at W-band (95GHz). The maximal distance that can be accessed by DEER measurements and the sensitivity of such measurements strongly depends on the phase relaxation of Gd(3+) chelates in frozen, glassy solutions. In this work, we explore the phase relaxation of Gd(3+)-DOTA as a representative of GdSL in temperature and concentration ranges typically used for W-band DEER measurements. We observed that in addition to the usual mechanisms of phase relaxation known for nitroxide based spin labels, GdSL are subjected to an additional phase relaxation mechanism that features an increase in the relaxation rate from the center to the periphery of the EPR spectrum. Since the EPR spectrum of GdSL is the sum of subspectra of the individual EPR transitions, we attribute this field dependence to transition dependent phase relaxation. Using simulations of the EPR spectra and its decomposition into the individual transition subspectra, we isolated the phase relaxation of each transition and found that its rate increases with |ms|. We suggest that this mechanism is due to transient zero field splitting (tZFS), where its magnitude and correlation time are scaled down and distributed as compared with similar situations in liquids. This tZFS induced phase relaxation mechanism becomes dominant (or at least significant) when all other well-known phase relaxation mechanisms, such as spectral diffusion caused by nuclear spin diffusion, instantaneous and electron spin spectral diffusion, are significantly suppressed by matrix deuteration and low concentration, and when the temperature is sufficiently low to disable spin lattice interaction as a source of phase relaxation.
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Affiliation(s)
| | - A Dalaloyan
- Weizmann Institute of Science, Rehovot, Israel
| | - A Collauto
- Weizmann Institute of Science, Rehovot, Israel
| | - A Feintuch
- Weizmann Institute of Science, Rehovot, Israel
| | - T Meade
- Northwestern University, Evanston, IL 60208, USA
| | - D Goldfarb
- Weizmann Institute of Science, Rehovot, Israel.
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21
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Edwards D, Huber T, Hussain S, Stone K, Kinnebrew M, Kaminker I, Matalon E, Sherwin M, Goldfarb D, Han S. Determining the Oligomeric Structure of Proteorhodopsin by Gd3+-Based Pulsed Dipolar Spectroscopy of Multiple Distances. Structure 2014; 22:1677-86. [DOI: 10.1016/j.str.2014.09.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/15/2014] [Accepted: 09/04/2014] [Indexed: 12/30/2022]
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22
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Martorana A, Bellapadrona G, Feintuch A, Di Gregorio E, Aime S, Goldfarb D. Probing protein conformation in cells by EPR distance measurements using Gd3+ spin labeling. J Am Chem Soc 2014; 136:13458-65. [PMID: 25163412 DOI: 10.1021/ja5079392] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein structure investigations are usually carried out in vitro under conditions far from their native environment in the cell. Differences between in-cell and in vitro structures of proteins can be generated by crowding effects, local pH changes, specific and nonspecific protein and ligand binding events, and chemical modifications. Double electron-electron resonance (DEER), in conjunction with site-directed spin-labeling, has emerged in the past decade as a powerful technique for exploring protein conformations in frozen solutions. The major challenges facing the application of this methodology to in-cell measurements are the instabilities of the standard nitroxide spin labels in the cell environment and the limited sensitivity at conventional X-band frequencies. We present a new approach for in-cell DEER distance measurement in human cells, based on the use of: (i) reduction resistant Gd(3+) chelates as spin labels, (ii) high frequency (94.9 GHz) for sensitivity enhancement, and (iii) hypo-osmotic shock for efficient delivery of the labeled protein into the cell. The proof of concept is demonstrated on doubly labeled ubiquitin in HeLa cells.
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Affiliation(s)
- Andrea Martorana
- Department of Chemical Physics and ‡Department of Materials and Interfaces, Weizmann Institute of Science , Rehovot, Israel 7610001
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23
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Goldfarb D. Gd3+ spin labeling for distance measurements by pulse EPR spectroscopy. Phys Chem Chem Phys 2014; 16:9685-99. [DOI: 10.1039/c3cp53822b] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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