51
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Garbuio L, Bordignon E, Brooks EK, Hubbell WL, Jeschke G, Yulikov M. Orthogonal spin labeling and Gd(III)-nitroxide distance measurements on bacteriophage T4-lysozyme. J Phys Chem B 2013; 117:3145-53. [PMID: 23442004 DOI: 10.1021/jp401806g] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the first example of chemoselective site-specific spin labeling of a monomeric protein with two spectroscopically orthogonal spin labels: a gadolinium(III) chelate complex and a nitroxide radical. A detailed analysis of the performance of two commercially available Gd(III) ligands in the Gd(III)-nitroxide pulse double electron-electron resonance (DEER or PELDOR) experiment is reported. A modification of the flip angle of the pump pulse in the Gd(III)-nitroxide DEER experiment is proposed to optimize sensitivity.
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Affiliation(s)
- Luca Garbuio
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
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52
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Tkach I, Pornsuwan S, Höbartner C, Wachowius F, Sigurdsson ST, Baranova TY, Diederichsen U, Sicoli G, Bennati M. Orientation selection in distance measurements between nitroxide spin labels at 94 GHz EPR with variable dual frequency irradiation. Phys Chem Chem Phys 2013; 15:3433-7. [PMID: 23381580 DOI: 10.1039/c3cp44415e] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pulsed electron-electron double resonance (PELDOR, also known as DEER) has become a method of choice to measure distances in biomolecules. In this work we show how the performance of the method can be improved at high EPR frequencies (94 GHz) using variable dual frequency irradiation in a dual mode cavity in order to obtain enhanced resolution toward orientation selection. Dipolar evolution traces of a representative RNA duplex and an α-helical peptide were analysed in terms of possible bi-radical structures by considering the inherent ambiguity of symmetry-related solutions.
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Affiliation(s)
- Igor Tkach
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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53
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Kaminker I, Tkach I, Manukovsky N, Huber T, Yagi H, Otting G, Bennati M, Goldfarb D. W-band orientation selective DEER measurements on a Gd3+/nitroxide mixed-labeled protein dimer with a dual mode cavity. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 227:66-71. [PMID: 23314001 DOI: 10.1016/j.jmr.2012.11.028] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 11/29/2012] [Accepted: 11/29/2012] [Indexed: 06/01/2023]
Abstract
Double electron-electron resonance (DEER) at W-band (95 GHz) was applied to measure the distance between a pair of nitroxide and Gd(3+) chelate spin labels, about 6 nm apart, in a homodimer of the protein ERp29. While high-field DEER measurements on systems with such mixed labels can be highly attractive in terms of sensitivity and the potential to access long distances, a major difficulty arises from the large frequency spacing (about 700 MHz) between the narrow, intense signal of the Gd(3+) central transition and the nitroxide signal. This is particularly problematic when using standard single-mode cavities. Here we show that a novel dual-mode cavity that matches this large frequency separation dramatically increases the sensitivity of DEER measurements, allowing evolution times as long as 12 μs in a protein. This opens the possibility of accessing distances of 8 nm and longer. In addition, orientation selection can be resolved and analyzed, thus providing additional structural information. In the case of W-band DEER on a Gd(3+)-nitroxide pair, only two angles and their distributions have to be determined, which is a much simpler problem to solve than the five angles and their distributions associated with two nitroxide spin labels.
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Affiliation(s)
- Ilia Kaminker
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
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54
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Orientation-Selective DEER Using Rigid Spin Labels, Cofactors, Metals, and Clusters. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2013. [DOI: 10.1007/430_2013_115] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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55
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Marko A, Prisner TF. An algorithm to analyze PELDOR data of rigid spin label pairs. Phys Chem Chem Phys 2013. [DOI: 10.1039/c2cp42942j] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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56
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Lovett JE, Lovett BW, Harmer J. DEER-Stitch: combining three- and four-pulse DEER measurements for high sensitivity, deadtime free data. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:98-106. [PMID: 22975240 DOI: 10.1016/j.jmr.2012.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 07/20/2012] [Accepted: 08/13/2012] [Indexed: 06/01/2023]
Abstract
Over approximately the last 15 years the electron paramagnetic resonance (EPR) technique of double electron electron resonance (DEER) has attracted considerable attention since it allows for the precise measurement of the dipole-dipole coupling between radicals and thus can lead to distance information between pairs of radicals separated by up to ca. 8 nm. The "deadtime free" 4-pulse DEER sequence is widely used but can suffer from poor sensitivity if the electron spin-echo decays too quickly to allow collection of a sufficiently long time trace. In this paper we present a method which takes advantage of the much greater sensitivity that the 3-pulse sequence offers over the 4-pulse sequence since the measured electron spin-echo intensity (for equal sequence lengths) is greater. By combining 3- and 4-pulse DEER time traces using a method coined DEER-Stitch (DEERS) accurate dipole-dipole coupling measurements can be made which combine the sensitivity of the 3-pulse DEER sequence with the deadtime free advantage of the 4-pulse DEER sequence. To develop the DEER-Stitch method three systems were measured: a semi-rigid bis-nitroxide labeled nanowire, the bis-nitroxide labeled protein CD55 with a distance between labels of almost 8 nm and a dimeric copper amine oxidase from Arthrobacter globiformis (AGAO).
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Affiliation(s)
- J E Lovett
- EaStCHEM School of Chemistry, Joseph Black Building, The King's Buildings, Edinburgh EH9 3JJ, UK.
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57
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Eaton SS, Eaton GR. The world as viewed by and with unpaired electrons. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:151-63. [PMID: 22975244 PMCID: PMC3496796 DOI: 10.1016/j.jmr.2012.07.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 06/01/2023]
Abstract
Recent advances in electron paramagnetic resonance (EPR) include capabilities for applications to areas as diverse as archeology, beer shelf life, biological structure, dosimetry, in vivo imaging, molecular magnets, and quantum computing. Enabling technologies include multifrequency continuous wave, pulsed, and rapid scan EPR. Interpretation is enhanced by increasingly powerful computational models.
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Affiliation(s)
- Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208, USA
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58
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Edwards DT, Takahashi S, Sherwin MS, Han S. Distance measurements across randomly distributed nitroxide probes from the temperature dependence of the electron spin phase memory time at 240 GHz. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 223:198-206. [PMID: 22975249 DOI: 10.1016/j.jmr.2012.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/27/2012] [Accepted: 07/05/2012] [Indexed: 06/01/2023]
Abstract
At 8.5 T, the polarization of an ensemble of electron spins is essentially 100% at 2 K, and decreases to 30% at 20 K. The strong temperature dependence of the electron spin polarization between 2 and 20 K leads to the phenomenon of spin bath quenching: temporal fluctuations of the dipolar magnetic fields associated with the energy-conserving spin "flip-flop" process are quenched as the temperature of the spin bath is lowered to the point of nearly complete spin polarization. This work uses pulsed electron paramagnetic resonance (EPR) at 240 GHz to investigate the effects of spin bath quenching on the phase memory times (T(M)) of randomly-distributed ensembles of nitroxide molecules below 20 K at 8.5 T. For a given electron spin concentration, a characteristic, dipolar flip-flop rate (W) is extracted by fitting the temperature dependence of T(M) to a simple model of decoherence driven by the spin flip-flop process. In frozen solutions of 4-Amino-TEMPO, a stable nitroxide radical in a deuterated water-glass, a calibration is used to quantify average spin-spin distances as large as r=6.6 nm from the dipolar flip-flop rate. For longer distances, nuclear spin fluctuations, which are not frozen out, begin to dominate over the electron spin flip-flop processes, placing an effective ceiling on this method for nitroxide molecules. For a bulk solution with a three-dimensional distribution of nitroxide molecules at concentration n, we find W∝n∝1/r(3), which is consistent with magnetic dipolar spin interactions. Alternatively, we observe W∝n(32) for nitroxides tethered to a quasi two-dimensional surface of large (Ø∼200 nm), unilamellar, lipid vesicles, demonstrating that the quantification of spin bath quenching can also be used to discern the geometry of molecular assembly or organization.
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Affiliation(s)
- Devin T Edwards
- Department of Physics, University of California, Santa Barbara, CA 93106, United States
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59
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Nakazawa S, Nishida S, Ise T, Yoshino T, Mori N, Rahimi RD, Sato K, Morita Y, Toyota K, Shiomi D, Kitagawa M, Hara H, Carl P, Höfer P, Takui T. A Synthetic Two-Spin Quantum Bit:g-Engineered Exchange-Coupled Biradical Designed for Controlled-NOT Gate Operations. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204489] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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60
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Nakazawa S, Nishida S, Ise T, Yoshino T, Mori N, Rahimi RD, Sato K, Morita Y, Toyota K, Shiomi D, Kitagawa M, Hara H, Carl P, Höfer P, Takui T. A Synthetic Two-Spin Quantum Bit:g-Engineered Exchange-Coupled Biradical Designed for Controlled-NOT Gate Operations. Angew Chem Int Ed Engl 2012; 51:9860-4. [DOI: 10.1002/anie.201204489] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Revised: 08/06/2012] [Indexed: 12/20/2022]
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61
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Brandon S, Beth AH, Hustedt EJ. The global analysis of DEER data. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 218:93-104. [PMID: 22578560 PMCID: PMC3608411 DOI: 10.1016/j.jmr.2012.03.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 03/10/2012] [Accepted: 03/12/2012] [Indexed: 05/11/2023]
Abstract
Double Electron-Electron Resonance (DEER) has emerged as a powerful technique for measuring long range distances and distance distributions between paramagnetic centers in biomolecules. This information can then be used to characterize functionally relevant structural and dynamic properties of biological molecules and their macromolecular assemblies. Approaches have been developed for analyzing experimental data from standard four-pulse DEER experiments to extract distance distributions. However, these methods typically use an a priori baseline correction to account for background signals. In the current work an approach is described for direct fitting of the DEER signal using a model for the distance distribution which permits a rigorous error analysis of the fitting parameters. Moreover, this approach does not require a priori background correction of the experimental data and can take into account excluded volume effects on the background signal when necessary. The global analysis of multiple DEER data sets is also demonstrated. Global analysis has the potential to provide new capabilities for extracting distance distributions and additional structural parameters in a wide range of studies.
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Affiliation(s)
| | | | - Eric J. Hustedt
- Corresponding author. Address: 735B Light Hall, Vanderbilt University, Nashville, TN 37232, United States. (E.J. Hustedt)
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62
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Wunnicke D, Ding P, Seela F, Steinhoff HJ. Site-directed spin labeling of DNA reveals mismatch-induced nanometer distance changes between flanking nucleotides. J Phys Chem B 2012; 116:4118-23. [PMID: 22424032 DOI: 10.1021/jp212421c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multiple forms of DNA damages such as base modifications, double-strand breaks, and mispairings are related to inheritable diseases, cancer, and aging. Here, the structural changes of duplex DNA upon incorporation of mismatched base pairs are examined by EPR spectroscopy. Two ethynyl-7-deaza-2'-deoxyadenosine residues separated by two nucleotides were incorporated in DNA and functionalized with 4-azido-2,2,6,6-tetramethyl-piperidine-1-oxyl (4-azido TEMPO) by the click reaction. Mismatches such as dT·dT or dA·dA mispairs were positioned between these two spin labels in DNA duplexes. Pulse EPR experiments reveal that the mismatch-induced local conformational changes are transmitted to the flanking nucleotides and that the impact of this mismatch depends on the nearest neighbor environment.
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Affiliation(s)
- Dorith Wunnicke
- Department of Physics, University Osnabrück, Barbarastraße 7, 49076 Osnabrück, Germany
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63
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Abé C, Klose D, Dietrich F, Ziegler WH, Polyhach Y, Jeschke G, Steinhoff HJ. Orientation selective DEER measurements on vinculin tail at X-band frequencies reveal spin label orientations. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 216:53-61. [PMID: 22285633 DOI: 10.1016/j.jmr.2011.12.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 12/29/2011] [Accepted: 12/30/2011] [Indexed: 05/22/2023]
Abstract
Double electron electron resonance (DEER) spectroscopy has been established as a valuable method to determine distances between spin labels bound to protein molecules. Caused by selective excitation of molecular orientations DEER primary data also depend on the mutual orientation of the spin labels. For a doubly spin labeled variant of the cytoskeletal protein vinculin tail strong orientation selection can be observed already at X-band frequencies, which allows us to reduce the problem to the relative orientation of two molecular axes and the spin-spin axis parameterized by three angles. A full grid search of parameter space reveals that the DEER experiment introduces parameter-space symmetry higher than the symmetry of the spin Hamiltonian. Thus, the number of equivalent parameter sets is twice as large as expected and the relative orientation of the two spin labels is ambiguous. Except for this inherent ambiguity the most probable relative orientation of the two spin labels can be determined with good confidence and moderate uncertainty by global fitting of a set of five DEER experiments at different offsets between pump and observer frequency. The experiment provides restraints on the angles between the z axis of the nitroxide molecular frame and the spin-spin vector and on the dihedral between the two z axes. When using the same type of label at both sites, assignment of the angle restraints is ambiguous and the sign of the dihedral restraint is also ambiguous.
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Affiliation(s)
- Christoph Abé
- University of Osnabrück, Department of Physics, Barbarastr. 7, 49076 Osnabrück, Germany
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64
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Reginsson GW, Hunter RI, Cruickshank PAS, Bolton DR, Sigurdsson ST, Smith GM, Schiemann O. W-band PELDOR with 1 kW microwave power: molecular geometry, flexibility and exchange coupling. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2012; 216:175-182. [PMID: 22386646 DOI: 10.1016/j.jmr.2012.01.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 01/09/2012] [Accepted: 01/29/2012] [Indexed: 05/31/2023]
Abstract
A technique that is increasingly being used to determine the structure and conformational flexibility of biomacromolecules is Pulsed Electron-Electron Double Resonance (PELDOR or DEER), an Electron Paramagnetic Resonance (EPR) based technique. At X-band frequencies (9.5 GHz), PELDOR is capable of precisely measuring distances in the range of 1.5-8 nm between paramagnetic centres but the orientation selectivity is weak. In contrast, working at higher frequencies increases the orientation selection but usually at the expense of decreased microwave power and PELDOR modulation depth. Here it is shown that a home-built high-power pulsed W-band EPR spectrometer (HiPER) with a large instantaneous bandwidth enables one to achieve PELDOR data with a high degree of orientation selectivity and large modulation depths. We demonstrate a measurement methodology that gives a set of PELDOR time traces that yield highly constrained data sets. Simulating the resulting time traces provides a deeper insight into the conformational flexibility and exchange coupling of three bisnitroxide model systems. These measurements provide strong evidence that W-band PELDOR may prove to be an accurate and quantitative tool in assessing the relative orientations of nitroxide spin labels and to correlate those orientations to the underlying biological structure and dynamics.
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Affiliation(s)
- Gunnar W Reginsson
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
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65
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Abstract
Distance distributions between paramagnetic centers in the range of 1.8 to 6 nm in membrane proteins and up to 10 nm in deuterated soluble proteins can be measured by the DEER technique. The number of paramagnetic centers and their relative orientation can be characterized. DEER does not require crystallization and is not limited with respect to the size of the protein or protein complex. Diamagnetic proteins are accessible by site-directed spin labeling. To characterize structure or structural changes, experimental protocols were optimized and techniques for artifact suppression were introduced. Data analysis programs were developed, and it was realized that interpretation of the distance distributions must take into account the conformational distribution of spin labels. First methods have appeared for deriving structural models from a small number of distance constraints. The present scope and limitations of the technique are illustrated.
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Affiliation(s)
- Gunnar Jeschke
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, Switzerland.
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66
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Abé C, Dietrich F, Gajula P, Benz M, Vogel KP, van Gastel M, Illenberger S, Ziegler WH, Steinhoff HJ. Monomeric and dimeric conformation of the vinculin tail five-helix bundle in solution studied by EPR spectroscopy. Biophys J 2012; 101:1772-80. [PMID: 21961604 DOI: 10.1016/j.bpj.2011.08.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 08/03/2011] [Accepted: 08/31/2011] [Indexed: 11/28/2022] Open
Abstract
The cytoskeletal adaptor protein vinculin plays an important role in the control of cell adhesion and migration, linking the actin cytoskeleton to adhesion receptor complexes in cell adhesion sites. The conformation of the vinculin tail dimer, which is crucial for protein function, was analyzed using site-directed spin labeling in electron paramagnetic resonance spectroscopy. Interspin distances for a set of six singly and four doubly spin-labeled mutants of the tail domain of vinculin were determined and used as constraints for modeling of the vinculin tail dimer. A comparison of the results obtained by molecular dynamic simulations and a rotamer library approach reveals that the crystal structure of the vinculin tail monomer is essentially preserved in aqueous solution. The orientation of monomers within the dimer observed previously by x-ray crystallography agrees with the solution electron paramagnetic resonance data. Furthermore, the distance between positions 1033 is shown to increase by >3 nm upon interaction of the vinculin tail domain with F-actin.
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Affiliation(s)
- Christoph Abé
- Department of Physics, University of Osnabrück, Osnabrück, Germany
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67
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Metal-Based Spin Labeling for Distance Determination. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2012. [DOI: 10.1007/430_2011_63] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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68
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Kaminker I, Yagi H, Huber T, Feintuch A, Otting G, Goldfarb D. Spectroscopic selection of distance measurements in a protein dimer with mixed nitroxide and Gd3+ spin labels. Phys Chem Chem Phys 2012; 14:4355-8. [DOI: 10.1039/c2cp40219j] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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69
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Polyhach Y, Bordignon E, Tschaggelar R, Gandra S, Godt A, Jeschke G. High sensitivity and versatility of the DEER experiment on nitroxide radical pairs at Q-band frequencies. Phys Chem Chem Phys 2012; 14:10762-73. [DOI: 10.1039/c2cp41520h] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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70
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Yulikov M, Lueders P, Farooq Warsi M, Chechik V, Jeschke G. Distance measurements in Au nanoparticles functionalized with nitroxide radicals and Gd3+–DTPA chelate complexes. Phys Chem Chem Phys 2012; 14:10732-46. [DOI: 10.1039/c2cp40282c] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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71
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Spiess HW. Addendum to the paper "Dead-time free measurement of dipole-dipole interactions between electron spins" by M. Pannier, S. Veit, A. Godt, G. Jeschke, and H.W. Spiess [J. Magn. Reson. 142 (2000) 331-340]. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 213:326-328. [PMID: 21890390 DOI: 10.1016/j.jmr.2011.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The development of four-pulse DEER as described, which has been published in the Journal of Magnetic Resonance more than 10 years ago. The corresponding paper is an example where a slight advance, such as adding a refocusing pulse, which in retrospect looks so simple, can have a remarkable impact on an entire field of science. In our case it offered a simple way to exact measurements of distances between defined species in the nanometer range. The current applications are mainly in determining structures of proteins and nucleic acids.
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72
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Savitsky A, Dubinskii AA, Zimmermann H, Lubitz W, Möbius K. High-Field Dipolar Electron Paramagnetic Resonance (EPR) Spectroscopy of Nitroxide Biradicals for Determining Three-Dimensional Structures of Biomacromolecules in Disordered Solids. J Phys Chem B 2011; 115:11950-63. [DOI: 10.1021/jp206841v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anton Savitsky
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany
| | | | - Herbert Zimmermann
- Max-Planck-Institut für Medizinische Forschung, Abt. Biophysik, 69120 Heidelberg, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany
| | - Klaus Möbius
- Max-Planck-Institut für Bioanorganische Chemie, 45470 Mülheim an der Ruhr, Germany
- Department of Physics, Free University Berlin, 14195 Berlin, Germany
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73
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Junk MJN, Spiess HW, Hinderberger D. Characterization of the solution structure of human serum albumin loaded with a metal porphyrin and fatty acids. Biophys J 2011; 100:2293-301. [PMID: 21539799 DOI: 10.1016/j.bpj.2011.03.050] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 03/21/2011] [Accepted: 03/25/2011] [Indexed: 10/18/2022] Open
Abstract
The structure of human serum albumin loaded with a metal porphyrin and fatty acids in solution is characterized by orientation-selective double electron-electron resonance (DEER) spectroscopy. Human serum albumin, spin-labeled fatty acids, and Cu(II) protoporphyrin IX-a hemin analog-form a fully self-assembled system that allows obtaining distances and mutual orientations between the paramagnetic guest molecules. We report a simplified analysis for the orientation-selective DEER data which can be applied when the orientation selection of one spin in the spin pair dominates the orientation selection of the other spin. The dipolar spectra reveal a dominant distance of 3.85 nm and a dominant orientation of the spin-spin vectors between Cu(II) protoporphyrin IX and 16-doxyl stearic acid, the electron paramagnetic resonance reporter group of the latter being located near the entry points to the fatty acid binding sites. This observation is in contrast to crystallographic data that suggest an asymmetric distribution of the entry points in the protein and hence the occurrence of various distances. In conjunction with the findings of a recent DEER study, the obtained data are indicative of a symmetric distribution of the binding site entries on the protein's surface. The overall anisotropic shape of the protein is reflected by one spin-spin vector orientation dominating the DEER data.
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74
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Yagi H, Banerjee D, Graham B, Huber T, Goldfarb D, Otting G. Gadolinium tagging for high-precision measurements of 6 nm distances in protein assemblies by EPR. J Am Chem Soc 2011; 133:10418-21. [PMID: 21661728 DOI: 10.1021/ja204415w] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Double electron-electron resonance (DEER) distance measurements of a protein complex tagged with two Gd(3+) chelates developed for rigid positioning of the metal ion are shown to deliver outstandingly accurate distance measurements in the 6 nm range. The accuracy was assessed by comparison with modeled distance distributions based on the three-dimensional molecular structures of the protein and the tag and further comparison with paramagnetic NMR data. The close agreement between the predicted and experimentally measured distances opens new possibilities for investigating the structure of biomolecular assemblies. As an example, we show that the dimer interface of rat ERp29 in solution is the same as that determined previously for human ERp29 in the single crystal.
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Affiliation(s)
- Hiromasa Yagi
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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75
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Song Y, Meade TJ, Astashkin A, Klein E, Enemark J, Raitsimring A. Pulsed dipolar spectroscopy distance measurements in biomacromolecules labeled with Gd(III) markers. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 210:59-68. [PMID: 21388847 PMCID: PMC3081411 DOI: 10.1016/j.jmr.2011.02.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 02/03/2011] [Accepted: 02/08/2011] [Indexed: 05/11/2023]
Abstract
This work demonstrates the feasibility of using Gd(III) tags for long-range Double Electron Electron Resonance (DEER) distance measurements in biomacromolecules. Double-stranded 14- base pair Gd(III)-DNA conjugates were synthesized and investigated at K(a) band. For the longest Gd(III) tag the average distance and average deviation between Gd(III) ions determined from the DEER time domains was about 59±12Å. This result demonstrates that DEER measurements with Gd(III) tags can be routinely carried out for distances of at least 60Å, and analysis indicates that distance measurements up to 100Å are possible. Compared with commonly used nitroxide labels, Gd(III)-based labels will be most beneficial for the detection of distance variations in large biomacromolecules, with an emphasis on large scale changes in shape or distance. Tracking the folding/unfolding and domain interactions of proteins and the conformational changes in DNA are examples of such applications.
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Affiliation(s)
- Y. Song
- Departments of Chemistry; Molecular Biosciences; Neurobiology & Physiology; and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - T. J. Meade
- Departments of Chemistry; Molecular Biosciences; Neurobiology & Physiology; and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - A.V. Astashkin
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
| | - E.L. Klein
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
| | - J.H. Enemark
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
| | - A. Raitsimring
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
- Corresponding Author: Arnold Raitsimring, Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA.
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76
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Pulsed electron-electron double resonance: beyond nanometre distance measurements on biomacromolecules. Biochem J 2011; 434:353-63. [PMID: 21348855 DOI: 10.1042/bj20101871] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PELDOR (or DEER; pulsed electron-electron double resonance) is an EPR (electron paramagnetic resonance) method that measures via the dipolar electron-electron coupling distances in the nanometre range, currently 1.5-8 nm, with high precision and reliability. Depending on the quality of the data, the error can be as small as 0.1 nm. Beyond mere mean distances, PELDOR yields distance distributions, which provide access to conformational distributions and dynamics. It can also be used to count the number of monomers in a complex and allows determination of the orientations of spin centres with respect to each other. If, in addition to the dipolar through-space coupling, a through-bond exchange coupling mechanism contributes to the overall coupling both mechanisms can be separated and quantified. Over the last 10 years PELDOR has emerged as a powerful new biophysical method without size restriction to the biomolecule to be studied, and has been applied to a large variety of nucleic acids as well as proteins and protein complexes in solution or within membranes. Small nitroxide spin labels, paramagnetic metal ions, amino acid radicals or intrinsic clusters and cofactor radicals have been used as spin centres.
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77
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Tkach I, Sicoli G, Höbartner C, Bennati M. A dual-mode microwave resonator for double electron-electron spin resonance spectroscopy at W-band microwave frequencies. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 209:341-6. [PMID: 21333570 DOI: 10.1016/j.jmr.2011.01.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/10/2011] [Accepted: 01/11/2011] [Indexed: 05/21/2023]
Abstract
We present a dual-mode resonator operating at/near 94 GHz (W-band) microwave frequencies and supporting two microwave modes with the same field polarization at the sample position. Numerical analysis shows that the frequencies of both modes as well as their frequency separation can be tuned in a broad range up to GHz. The resonator was constructed to perform pulsed ELDOR experiments with a variable separation of "pump" and "detection" frequencies up to Δν=350 MHz. To examine its performance, test ESE/PELDOR experiments were performed on a representative biradical system.
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Affiliation(s)
- Igor Tkach
- Max Planck Institute for Biophysical Chemistry, Research Group Electron Paramagnetic Resonance, Göttingen, Germany.
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78
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Jeschke G. Interpretation of Dipolar EPR Data in Terms of Protein Structure. STRUCTURAL INFORMATION FROM SPIN-LABELS AND INTRINSIC PARAMAGNETIC CENTRES IN THE BIOSCIENCES 2011. [DOI: 10.1007/430_2011_61] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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79
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Kuznetsov NA, Milov AD, Isaev NP, Vorobjev YN, Koval VV, Dzuba SA, Fedorova OS, Tsvetkov YD. PELDOR analysis of enzyme-induced structural changes in damaged DNA duplexes. MOLECULAR BIOSYSTEMS 2011; 7:2670-80. [DOI: 10.1039/c1mb05189j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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80
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Kaminker I, Florent M, Epel B, Goldfarb D. Simultaneous acquisition of pulse EPR orientation selective spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 208:95-102. [PMID: 21075028 DOI: 10.1016/j.jmr.2010.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 10/14/2010] [Accepted: 10/14/2010] [Indexed: 05/30/2023]
Abstract
High resolution pulse EPR methods are usually applied to resolve weak magnetic electron-nuclear or electron-electron interactions that are otherwise unresolved in the EPR spectrum. Complete information regarding different magnetic interactions, namely, principal components and orientation of principal axis system with respect to the molecular frame, can be derived from orientation selective pulsed EPR measurements that are performed at different magnetic field positions within the inhomogeneously broadened EPR spectrum. These experiments are usually carried out consecutively, namely a particular field position is chosen, data are accumulated until the signal to noise ratio is satisfactory, and then the next field position is chosen and data are accumulated. Here we present a new approach for data acquisition of pulsed EPR experiments referred to as parallel acquisition. It is applicable when the spectral width is much broader than the excitation bandwidth of the applied pulse sequence and it is particularly useful for orientation selective pulse EPR experiments. In this approach several pulse EPR measurements are performed within the waiting (repetition) time between consecutive pulse sequences during which spin lattice relaxation takes place. This is achieved by rapidly changing the main magnetic field, B(0), to different values within the EPR spectrum, performing the same experiment on the otherwise idle spins. This scheme represents an efficient utilization of the spectrometer and provides the same spectral information in a shorter time. This approach is demonstrated on W-band orientation selective electron-nuclear double resonance (ENDOR), electron spin echo envelope modulation (ESEEM), electron-electron double resonance (ELDOR)--detected NMR and double electron-electron resonance (DEER) measurements on frozen solutions of nitroxides. We show that a factors of 3-6 reduction in total acquisition time can be obtained, depending on the experiment applied.
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Affiliation(s)
- Ilia Kaminker
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel
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81
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Gordon-Grossman M, Kaminker I, Gofman Y, Shai Y, Goldfarb D. W-Band pulse EPR distance measurements in peptides using Gd3+–dipicolinic acid derivatives as spin labels. Phys Chem Chem Phys 2011; 13:10771-80. [DOI: 10.1039/c1cp00011j] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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82
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Margraf D, Bode BE, Marko A, Schiemann O, Prisner TF. Conformational flexibility of nitroxide biradicals determined by X-band PELDOR experiments. Mol Phys 2010. [DOI: 10.1080/00268970701724982] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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83
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Potapov A, Song Y, Meade TJ, Goldfarb D, Astashkin A, Raitsimring A. Distance measurements in model bis-Gd(III) complexes with flexible "bridge". Emulation of biological molecules having flexible structure with Gd(III) labels attached. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 205:38-49. [PMID: 20418132 PMCID: PMC2885582 DOI: 10.1016/j.jmr.2010.03.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Revised: 03/30/2010] [Accepted: 03/30/2010] [Indexed: 05/18/2023]
Abstract
In this work, we continue to explore Gd(III) as a possible spin label for high-field Double Electron-Electron Resonance (DEER) based distance measurements in biological molecules with flexible geometry. For this purpose, a bis-Gd(III) complex with a flexible "bridge" was used as a model. The distances in the model were expected to be distributed in the range of 5-26 A, allowing us to probe the shortest limits of accessible distances which were found to be as small as 13 A. The upper distance limit for these labels was also evaluated and was found to be about 60 A. Various pulse duration setups can result in apparent differences in the distribution function derived from DEER kinetics due to short distance limit variations. The advantages, such as the ability to perform measurements at cryogenic temperatures and high repetition rates simultaneously, the use of very short pumping and observation pulses without mutual interference, the lack of orientational selectivity, as well as the shortcomings, such as the limited mw operational frequency range and intrinsically smaller amplitude of oscillation related to dipolar interaction as compared with nitroxide spin labels are discussed. Most probably the use of nitroxide and Gd-based labels for distance measurements will be complementary depending on the particulars of the problem and the availability of instrumentation.
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Affiliation(s)
- A. Potapov
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Y. Song
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - T. J. Meade
- Department of Chemistry; Department of Biochemistry, Cell Biology, and Molecular Biology; Neurobiology & Physiology; Department of Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - D. Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - A.V. Astashkin
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA
| | - A. Raitsimring
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA
- Corresponding author: Dr. A. Raitsimring, University of Arizona, Department of Chemistry, 1306 E. University Blvd, Tucson, AZ 85721. ; tel (520)621-9968; fax (520)621-8407
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84
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Potapov A, Yagi H, Huber T, Jergic S, Dixon NE, Otting G, Goldfarb D. Nanometer-Scale Distance Measurements in Proteins Using Gd3+ Spin Labeling. J Am Chem Soc 2010; 132:9040-8. [DOI: 10.1021/ja1015662] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexey Potapov
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Hiromasa Yagi
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Thomas Huber
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Slobodan Jergic
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Nicholas E. Dixon
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Gottfried Otting
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel, Research School of Chemistry, The Australian National University, Canberra ACT 0200, Australia, and School of Chemistry, University of Wollongong, NSW 2522, Australia
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85
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Sahoo D, Thiele S, Schulte M, Ramezanian N, Godt A. Polar tagging in the synthesis of monodisperse oligo(p-phenyleneethynylene)s and an update on the synthesis of oligoPPEs. Beilstein J Org Chem 2010; 6:57. [PMID: 20625532 PMCID: PMC2900939 DOI: 10.3762/bjoc.6.57] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 04/22/2010] [Indexed: 11/23/2022] Open
Abstract
One important access to monodisperse (functionalized) oligoPPEs is based on the orthogonality of the alkyne protecting groups triisopropylsilyl and hydroxymethyl (HOM) and on the polar tagging with the hydroxymethyl moiety for an easy chromatographic separation of the products. This paper provides an update of this synthetic route. For the deprotection of HOM protected alkynes, γ-MnO₂ proved to be better than (highly) activated MnO₂. The use of HOM as an alkyne protecting group is accompanied by carbometalation as a side reaction in the alkynyl-aryl coupling. The extent of carbometalation can be distinctly reduced through substitution of HOM for 1-hydroxyethyl. The strategy of polar tagging is extended by embedding ether linkages within the solubilising side chains. With building blocks such as 1,4-diiodo-2,5-bis(6-methoxyhexyl) less steps are needed to assemble oligoPPEs with functional end groups and the isolation of pure compounds becomes simple. For the preparation of 1,4-dialkyl-2,5-diiodobenzene a better procedure is presented together with the finding that 1,4-dialkyl-2,3-diiodobenzene, a constitutional isomer of 1,4-dialkyl-2,5-diiodobenzene, is one of the byproducts.
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Affiliation(s)
- Dhananjaya Sahoo
- Bielefeld University, Faculty of Chemistry, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Susanne Thiele
- Bielefeld University, Faculty of Chemistry, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Miriam Schulte
- Bielefeld University, Faculty of Chemistry, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Navid Ramezanian
- Bielefeld University, Faculty of Chemistry, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Adelheid Godt
- Bielefeld University, Faculty of Chemistry, Universitätsstr. 25, D-33615 Bielefeld, Germany
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86
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Abstract
The present review deals with the preparation and the properties of star-shaped conjugated compounds. Three, four or six conjugated arms are attached to cross-conjugated cores, which consist of single atoms (B, C+, N), benzene or azine rings or polycyclic ring systems, as for example triphenylene or tristriazolotriazine. Many of these shape-persistent [n]star compounds tend to π-stacking and self-organization, and exhibit interesting properties in materials science: Linear and non-linear optics, electrical conductivity, electroluminescence, formation of liquid crystalline phases, etc.
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87
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Yang Z, Kise D, Saxena S. An Approach towards the Measurement of Nanometer Range Distances Based on Cu2+ Ions and ESR. J Phys Chem B 2010; 114:6165-74. [DOI: 10.1021/jp911637s] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhongyu Yang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Drew Kise
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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88
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Endeward B, Butterwick JA, MacKinnon R, Prisner TF. Pulsed electron-electron double-resonance determination of spin-label distances and orientations on the tetrameric potassium ion channel KcsA. J Am Chem Soc 2010; 131:15246-50. [PMID: 19919160 DOI: 10.1021/ja904808n] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pulsed electron-electron double-resonance (PELDOR) measurements are presented from the potassium ion channel KcsA both solubilized in detergent and reconstituted in lipids. Site-directed spin-labeling using (1-oxyl-2,2,5,5-tetramethyl-3-pyrrolin-3-yl)methyl methanethiosulfonate was performed with a R64C mutant of the protein. The orientations of the spin-labels in the tetramer were determined by PELDOR experiments performed at two magnetic field strengths (0.3 T/X-band and 1.2 T/Q-band) and variable probe frequency. Quantitative simulation of the PELDOR data supports a strongly restricted nitroxide, oriented at an angle of 65 degrees relative to the central channel axis. In general, poorer quality PELDOR data were obtained from membrane-reconstituted preparations compared to soluble proteins or detergent-solubilized samples. One reason for this is the reduced transverse spin relaxation time T(2) of nitroxides due to crowding of tetramers within the membrane that occurs even at low protein to lipid ratios. This reduced T(2) can be overcome by reconstituting mixtures of unlabeled and labeled proteins, yielding high-quality PELDOR data. Identical PELDOR oscillation frequencies and their dependencies on the probe frequency were observed in the detergent and membrane-reconstituted preparations, indicating that the position and orientation of the spin-labels are the same in both environments.
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Affiliation(s)
- Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, Frankfurt am Main, Germany
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89
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Marko A, Margraf D, Cekan P, Sigurdsson ST, Schiemann O, Prisner TF. Analytical method to determine the orientation of rigid spin labels in DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:021911. [PMID: 20365599 DOI: 10.1103/physreve.81.021911] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Indexed: 05/29/2023]
Abstract
We demonstrate the ability of pulsed electron double resonance (PELDOR) experiments to determine the orientation of spin labels in biological macromolecules. Thus, the distance information usually obtained from PELDOR data can be complemented by the mutual orientation of macromolecular domains. A method to determine the angle beta between the spin label normal and the interspin axis is proposed and analyzed mathematically. The obtained analytical expression allows extraction of angles beta without a fitting procedure if these angles are equal for both nitroxide of biradical. The method was applied to the experimental data gathered on ten spin-labeled DNA samples. The angles estimated from the PELDOR data are in excellent agreement with literature values.
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Affiliation(s)
- Andriy Marko
- Institute of Physical and Theoretical Chemistry, J. W. Goethe University, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany.
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90
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Distance and dynamics determination by W-band DEER and W-band ST-EPR. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:711-9. [PMID: 20012080 DOI: 10.1007/s00249-009-0565-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/30/2009] [Accepted: 11/12/2009] [Indexed: 10/20/2022]
Abstract
To explore high-field EPR in biological applications we have compared measurements of dynamics with X-band (9 GHz) and W-band (94 GHz) saturation transfer EPR (ST-EPR) and distance determination by X and W-band DEER. A fourfold increase of sensitivity was observed for W-band ST-EPR compared with X-band. The distance measurements at both fields showed very good agreement in both the average distances and in the distance distributions. Multifrequency EPR thus provides an additional experimental dimension to facilitate extraction of distance populations. However, the expected orientational selectivity of W-band DEER to determine the relative orientation of spins has not been realized, most likely because of the large orientational disorder of spin labels on the protein surface.
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91
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Milikisyants S, Scarpelli F, Finiguerra MG, Ubbink M, Huber M. A pulsed EPR method to determine distances between paramagnetic centers with strong spectral anisotropy and radicals: the dead-time free RIDME sequence. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 201:48-56. [PMID: 19758831 DOI: 10.1016/j.jmr.2009.08.008] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 07/15/2009] [Accepted: 08/07/2009] [Indexed: 05/09/2023]
Abstract
Methods to determine distances between paramagnetic metal centers and radicals are scarce. This is unfortunate because paramagnetic metal centers are frequent in biological systems and so far have not been employed much as distance markers. Successful pulse sequences that directly target the dipolar interactions cannot be applied to paramagnetic metal centers with fast relaxation rates and large g-anisotropy, if no echos can be detected and the excitation bandwidth is not sufficient to cover a sufficiently large part of the spectrum. The RIDME method Kulik et al. (2002) [20] circumvents this problem by making use of the T(1)-induced spin-flip of the transition-metal ion. Designed to measure distance between such a fast relaxing metal center and a radical, it suffers from a dead time problem. We show that this is severe because the anisotropy of the metal center broadens the dipolar curves, which therefore, only can be analyzed if the full curve is known. Here, we introduce five-pulse RIDME (5p-RIDME) that is intrinsically dead-time free. Proper functioning of the sequence is demonstrated on a nitroxide biradical. The distance between a low-spin Fe(III) center and a spin label in spin-labeled cytochrome f shows the complete dipolar trace of a transition-metal ion center and a spin label, yielding the distance expected from the structure.
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Affiliation(s)
- Sergey Milikisyants
- Department of Molecular Physics, Huygens Laboratory, Leiden University, 2300 RA Leiden, The Netherlands
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92
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Savitsky A, Möbius K. High-field EPR. PHOTOSYNTHESIS RESEARCH 2009; 102:311-333. [PMID: 19468856 DOI: 10.1007/s11120-009-9432-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 04/29/2009] [Indexed: 05/27/2023]
Abstract
Among the numerous spectroscopic techniques utilized in photosynthesis research, high-field/high-frequency EPR and its pulse extensions ESE, ENDOR, ESEEM, and PELDOR play an important role in the endeavor to understand, on the basis of structure and dynamics data, dominant factors that control specificity and efficiency of light-induced electron- and proton-transfer processes in primary photosynthesis. Short-lived transient intermediates of the photocycle can be characterized by high-field EPR techniques, and detailed structural information can be obtained even from disordered sample preparations. The chapter describes how multifrequency high-field EPR methodology, in conjunction with mutation strategies for site-specific isotope or spin labeling and with the support of modern quantum-chemical computation methods for data interpretation, is capable of providing new insights into the photosynthetic transfer processes. The information obtained is complementary to that of protein crystallography, solid-state NMR and laser spectroscopy.
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Affiliation(s)
- Anton Savitsky
- Department of Physics, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
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93
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Cruickshank PAS, Bolton DR, Robertson DA, Hunter RI, Wylde RJ, Smith GM. A kilowatt pulsed 94 GHz electron paramagnetic resonance spectrometer with high concentration sensitivity, high instantaneous bandwidth, and low dead time. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2009; 80:103102. [PMID: 19895049 DOI: 10.1063/1.3239402] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We describe a quasioptical 94 GHz kW pulsed electron paramagnetic resonance spectrometer featuring pi/2 pulses as short as 5 ns and an instantaneous bandwidth of 1 GHz in nonresonant sample holders operating in induction mode and at low temperatures. Low power pulses can be as short as 200 ps and kilowatt pulses as short as 1.5 ns with timing resolution of a few hundred picoseconds. Phase and frequency can be changed on nanosecond time scales and complex high power pulse sequences can be run at repetition rates up to 80 kHz with low dead time. We demonstrate that the combination of high power pulses at high frequencies and nonresonant cavities can offer excellent concentration sensitivity for orientation selective pulsed electron double resonance (double electron-electron resonance), where we demonstrate measurements at 1 microM concentration levels.
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Affiliation(s)
- Paul A S Cruickshank
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, United Kingdom
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94
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Schiemann O, Cekan P, Margraf D, Prisner T, Sigurdsson S. Relative Orientation of Rigid Nitroxides by PELDOR: Beyond Distance Measurements in Nucleic Acids. Angew Chem Int Ed Engl 2009; 48:3292-5. [DOI: 10.1002/anie.200805152] [Citation(s) in RCA: 168] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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95
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Schiemann O, Cekan P, Margraf D, Prisner T, Sigurdsson S. Relative Orientation of Rigid Nitroxides by PELDOR: Beyond Distance Measurements in Nucleic Acids. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805152] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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96
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Bode BE, Plackmeyer J, Bolte M, Prisner TF, Schiemann O. PELDOR on an exchange coupled nitroxide copper(II) spin pair. J Organomet Chem 2009. [DOI: 10.1016/j.jorganchem.2008.11.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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97
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Marko A, Margraf D, Yu H, Mu Y, Stock G, Prisner T. Molecular orientation studies by pulsed electron-electron double resonance experiments. J Chem Phys 2009; 130:064102. [DOI: 10.1063/1.3073040] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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98
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Lovett JE, Bowen AM, Timmel CR, Jones MW, Dilworth JR, Caprotti D, Bell SG, Wong LL, Harmer J. Structural information from orientationally selective DEER spectroscopy. Phys Chem Chem Phys 2009; 11:6840-8. [DOI: 10.1039/b907010a] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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99
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Ruthstein S, Raitsimring AM, Bitton R, Frydman V, Godt A, Goldfarb D. Distribution of guest molecules in Pluronic micelles studied by double electron electron spin resonance and small angle X-ray scattering. Phys Chem Chem Phys 2009; 11:148-60. [DOI: 10.1039/b812475b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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100
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Margraf D, Cekan P, Prisner TF, Sigurdsson ST, Schiemann O. Ferro- and antiferromagnetic exchange coupling constants in PELDOR spectra. Phys Chem Chem Phys 2009; 11:6708-14. [DOI: 10.1039/b905524j] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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