Spin pair geometry revealed by high-field DEER in the presence of conformational distributions

Polyhach Y, Godt A, Bauer C, Jeschke G (2007)

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Polyhach, Ye.; Godt, AdelheidUniBi; Bauer, C.; Jeschke, G.
Abstract / Bemerkung
Orientation selection on two nitroxide-labelled shape-persistent molecules is demonstrated by high-field pulsed electron-electron double resonance experiments at a frequency of 95 GHz with a commercial spectrometer. The experiments are performed with fixed observer and pump frequencies by variation of the magnetic field, so that the variation of both the dipolar frequencies and the modulation depths can be analyzed. By applying the deadtime-free four-pulse double electron-electron resonance (DEER) sequence, the lineshapes of the dipolar spectra are obtained. In the investigated linear biradical and equilateral triradical the nitroxide labels undergo restricted dynamics, so that their relative orientations are not fixed, but are correlated to some extent. In this situation, the general dependence of the dipolar spectra on the observer field can be satisfyingly modelled by simple geometrical models that involve only one rotational degree of freedom for the biradical and two rotational degrees of freedom for the triradical. A somewhat better agreement of the dipolar lineshapes for the biradical is obtained by simulations based on a molecular dynamics trajectory. For the triradical, small but significant deviations of the lineshape are observed with both models, indicating that the technique can reveal deficiencies in modelling of the conformational ensemble of a macromolecule. (c) 2006 Elsevier Inc. All rights reserved.
EPR; spin labeling; high-field EPR; ELDOR; orientation selection
Page URI


Polyhach Y, Godt A, Bauer C, Jeschke G. Spin pair geometry revealed by high-field DEER in the presence of conformational distributions. JOURNAL OF MAGNETIC RESONANCE. 2007;185(1):118-129.
Polyhach, Y., Godt, A., Bauer, C., & Jeschke, G. (2007). Spin pair geometry revealed by high-field DEER in the presence of conformational distributions. JOURNAL OF MAGNETIC RESONANCE, 185(1), 118-129. https://doi.org/10.1016/j.jmr.2006.11.012
Polyhach, Ye., Godt, Adelheid, Bauer, C., and Jeschke, G. 2007. “Spin pair geometry revealed by high-field DEER in the presence of conformational distributions”. JOURNAL OF MAGNETIC RESONANCE 185 (1): 118-129.
Polyhach, Y., Godt, A., Bauer, C., and Jeschke, G. (2007). Spin pair geometry revealed by high-field DEER in the presence of conformational distributions. JOURNAL OF MAGNETIC RESONANCE 185, 118-129.
Polyhach, Y., et al., 2007. Spin pair geometry revealed by high-field DEER in the presence of conformational distributions. JOURNAL OF MAGNETIC RESONANCE, 185(1), p 118-129.
Y. Polyhach, et al., “Spin pair geometry revealed by high-field DEER in the presence of conformational distributions”, JOURNAL OF MAGNETIC RESONANCE, vol. 185, 2007, pp. 118-129.
Polyhach, Y., Godt, A., Bauer, C., Jeschke, G.: Spin pair geometry revealed by high-field DEER in the presence of conformational distributions. JOURNAL OF MAGNETIC RESONANCE. 185, 118-129 (2007).
Polyhach, Ye., Godt, Adelheid, Bauer, C., and Jeschke, G. “Spin pair geometry revealed by high-field DEER in the presence of conformational distributions”. JOURNAL OF MAGNETIC RESONANCE 185.1 (2007): 118-129.

62 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Orientation selection in high-field RIDME and PELDOR experiments involving low-spin CoII ions.
Giannoulis A, Motion CL, Oranges M, Bühl M, Smith GM, Bode BE., Phys Chem Chem Phys 20(4), 2018
PMID: 29313041
The voltage-gated sodium channel pore exhibits conformational flexibility during slow inactivation.
Chatterjee S, Vyas R, Chalamalasetti SV, Sahu ID, Clatot J, Wan X, Lorigan GA, Deschênes I, Chakrapani S., J Gen Physiol 150(9), 2018
PMID: 30082431
Small neutral Gd(iii) tags for distance measurements in proteins by double electron-electron resonance experiments.
Mahawaththa MC, Lee MD, Giannoulis A, Adams LA, Feintuch A, Swarbrick JD, Graham B, Nitsche C, Goldfarb D, Otting G., Phys Chem Chem Phys 20(36), 2018
PMID: 30183028
Gd(III) complexes as paramagnetic tags: Evaluation of the spin delocalization over the nuclei of the ligand.
Collauto A, Feintuch A, Qi M, Godt A, Meade T, Goldfarb D., J Magn Reson 263(), 2016
PMID: 26802219
The use of the Rx spin label in orientation measurement on proteins, by EPR.
Stevens MA, McKay JE, Robinson JL, El Mkami H, Smith GM, Norman DG., Phys Chem Chem Phys 18(8), 2016
PMID: 26426572
A Bis-Manganese(II)-DOTA Complex for Pulsed Dipolar Spectroscopy.
Demay-Drouhard P, Ching HY, Akhmetzyanov D, Guillot R, Tabares LC, Bertrand HC, Policar C., Chemphyschem 17(13), 2016
PMID: 27017296
Overcoming artificial broadening in Gd(3+)-Gd(3+) distance distributions arising from dipolar pseudo-secular terms in DEER experiments.
Cohen MR, Frydman V, Milko P, Iron MA, Abdelkader EH, Lee MD, Swarbrick JD, Raitsimring A, Otting G, Graham B, Feintuch A, Goldfarb D., Phys Chem Chem Phys 18(18), 2016
PMID: 27102158
Separation of intra- and intermolecular contributions to the PELDOR signal.
Schöps P, Plackmeyer J, Marko A., J Magn Reson 269(), 2016
PMID: 27243966
EPR-correlated dipolar spectroscopy by Q-band chirp SIFTER.
Doll A, Jeschke G., Phys Chem Chem Phys 18(33), 2016
PMID: 27491304
Double quantum coherence ESR spectroscopy and quantum chemical calculations on a BDPA biradical.
Haeri HH, Spindler P, Plackmeyer J, Prisner T., Phys Chem Chem Phys 18(42), 2016
PMID: 27730235
Interaction of triarylmethyl radicals with DNA termini revealed by orientation-selective W-band double electron-electron resonance spectroscopy.
Fedin MV, Shevelev GY, Pyshnyi DV, Tormyshev VM, Jeschke G, Yulikov M, Bagryanskaya EG., Phys Chem Chem Phys 18(42), 2016
PMID: 27748488
Gd(III)-Gd(III) EPR distance measurements--the range of accessible distances and the impact of zero field splitting.
Dalaloyan A, Qi M, Ruthstein S, Vega S, Godt A, Feintuch A, Goldfarb D., Phys Chem Chem Phys 17(28), 2015
PMID: 26108866
Nanometric distance measurements between Mn(ii)DOTA centers.
Vincent Ching HY, Demay-Drouhard P, Bertrand HC, Policar C, Tabares LC, Un S., Phys Chem Chem Phys 17(36), 2015
PMID: 26287752
A chimeric prokaryotic pentameric ligand-gated channel reveals distinct pathways of activation.
Schmandt N, Velisetty P, Chalamalasetti SV, Stein RA, Bonner R, Talley L, Parker MD, Mchaourab HS, Yee VC, Lodowski DT, Chakrapani S., J Gen Physiol 146(4), 2015
PMID: 26415570
Conformational dynamics of ligand-dependent alternating access in LeuT.
Kazmier K, Sharma S, Quick M, Islam SM, Roux B, Weinstein H, Javitch JA, McHaourab HS., Nat Struct Mol Biol 21(5), 2014
PMID: 24747939
Gd3+ spin labeling for distance measurements by pulse EPR spectroscopy.
Goldfarb D., Phys Chem Chem Phys 16(21), 2014
PMID: 24429839
An algorithm to analyze PELDOR data of rigid spin label pairs.
Marko A, Prisner TF., Phys Chem Chem Phys 15(2), 2013
PMID: 23183777
Orientation selection in distance measurements between nitroxide spin labels at 94 GHz EPR with variable dual frequency irradiation.
Tkach I, Pornsuwan S, Höbartner C, Wachowius F, Sigurdsson ST, Baranova TY, Diederichsen U, Sicoli G, Bennati M., Phys Chem Chem Phys 15(10), 2013
PMID: 23381580
Orthogonal spin labeling and Gd(III)-nitroxide distance measurements on bacteriophage T4-lysozyme.
Garbuio L, Bordignon E, Brooks EK, Hubbell WL, Jeschke G, Yulikov M., J Phys Chem B 117(11), 2013
PMID: 23442004
Monomeric TonB and the Ton box are required for the formation of a high-affinity transporter-TonB complex.
Freed DM, Lukasik SM, Sikora A, Mokdad A, Cafiso DS., Biochemistry 52(15), 2013
PMID: 23517233
Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme.
Islam SM, Stein RA, McHaourab HS, Roux B., J Phys Chem B 117(17), 2013
PMID: 23510103
High-field EPR on membrane proteins - crossing the gap to NMR.
Möbius K, Lubitz W, Savitsky A., Prog Nucl Magn Reson Spectrosc 75(), 2013
PMID: 24160760
DEER distance measurements on proteins.
Jeschke G., Annu Rev Phys Chem 63(), 2012
PMID: 22404592
Spectroscopic selection of distance measurements in a protein dimer with mixed nitroxide and Gd3+ spin labels.
Kaminker I, Yagi H, Huber T, Feintuch A, Otting G, Goldfarb D., Phys Chem Chem Phys 14(13), 2012
PMID: 22362220
The global analysis of DEER data.
Brandon S, Beth AH, Hustedt EJ., J Magn Reson 218(), 2012
PMID: 22578560
Distance measurements in Au nanoparticles functionalized with nitroxide radicals and Gd(3+)-DTPA chelate complexes.
Yulikov M, Lueders P, Warsi MF, Chechik V, Jeschke G., Phys Chem Chem Phys 14(30), 2012
PMID: 22743649
High sensitivity and versatility of the DEER experiment on nitroxide radical pairs at Q-band frequencies.
Polyhach Y, Bordignon E, Tschaggelar R, Gandra S, Godt A, Jeschke G., Phys Chem Chem Phys 14(30), 2012
PMID: 22751953
The world as viewed by and with unpaired electrons.
Eaton SS, Eaton GR., J Magn Reson 223(), 2012
PMID: 22975244
A synthetic two-spin quantum bit: g-engineered exchange-coupled biradical designed for controlled-NOT gate operations.
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., Angew Chem Int Ed Engl 51(39), 2012
PMID: 22936609
Simultaneous acquisition of pulse EPR orientation selective spectra.
Kaminker I, Florent M, Epel B, Goldfarb D., J Magn Reson 208(1), 2011
PMID: 21075028
Pulsed dipolar spectroscopy distance measurements in biomacromolecules labeled with Gd(III) markers.
Song Y, Meade TJ, Astashkin AV, Klein EL, Enemark JH, Raitsimring A., J Magn Reson 210(1), 2011
PMID: 21388847
W-Band pulse EPR distance measurements in peptides using Gd(3+)-dipicolinic acid derivatives as spin labels.
Gordon-Grossman M, Kaminker I, Gofman Y, Shai Y, Goldfarb D., Phys Chem Chem Phys 13(22), 2011
PMID: 21552622
PELDOR analysis of enzyme-induced structural changes in damaged DNA duplexes.
Kuznetsov NA, Milov AD, Isaev NP, Vorobjev YN, Koval VV, Dzuba SA, Fedorova OS, Tsvetkov YD., Mol Biosyst 7(9), 2011
PMID: 21731955
Monomeric and dimeric conformation of the vinculin tail five-helix bundle in solution studied by EPR spectroscopy.
Abé C, Dietrich F, Gajula P, Benz M, Vogel KP, van Gastel M, Illenberger S, Ziegler WH, Steinhoff HJ., Biophys J 101(7), 2011
PMID: 21961604
Distance and dynamics determination by W-band DEER and W-band ST-EPR.
Song L, Larion M, Chamoun J, Bonora M, Fajer PG., Eur Biophys J 39(4), 2010
PMID: 20012080
Polar tagging in the synthesis of monodisperse oligo(p-phenyleneethynylene)s and an update on the synthesis of oligoPPEs.
Sahoo D, Thiele S, Schulte M, Ramezanian N, Godt A., Beilstein J Org Chem 6(), 2010
PMID: 20625532
Distribution of guest molecules in Pluronic micelles studied by double electron electron spin resonance and small angle X-ray scattering.
Ruthstein S, Raitsimring AM, Bitton R, Frydman V, Godt A, Goldfarb D., Phys Chem Chem Phys 11(1), 2009
PMID: 19081918
Relative orientation of rigid nitroxides by PELDOR: beyond distance measurements in nucleic acids.
Schiemann O, Cekan P, Margraf D, Prisner TF, Sigurdsson ST., Angew Chem Int Ed Engl 48(18), 2009
PMID: 19322852
Molecular orientation studies by pulsed electron-electron double resonance experiments.
Marko A, Margraf D, Yu H, Mu Y, Stock G, Prisner T., J Chem Phys 130(6), 2009
PMID: 19222262
Ferro- and antiferromagnetic exchange coupling constants in PELDOR spectra.
Margraf D, Cekan P, Prisner TF, Sigurdsson ST, Schiemann O., Phys Chem Chem Phys 11(31), 2009
PMID: 19639144
Structural information from orientationally selective DEER spectroscopy.
Lovett JE, Bowen AM, Timmel CR, Jones MW, Dilworth JR, Caprotti D, Bell SG, Wong LL, Harmer J., Phys Chem Chem Phys 11(31), 2009
PMID: 19639159
A kilowatt pulsed 94 GHz electron paramagnetic resonance spectrometer with high concentration sensitivity, high instantaneous bandwidth, and low dead time.
Cruickshank PA, Bolton DR, Robertson DA, Hunter RI, Wylde RJ, Smith GM., Rev Sci Instrum 80(10), 2009
PMID: 19895049
High-field EPR.
Savitsky A, Möbius K., Photosynth Res 102(2-3), 2009
PMID: 19468856
Structure of the tyrosyl biradical in mouse R2 ribonucleotide reductase from high-field PELDOR.
Denysenkov VP, Biglino D, Lubitz W, Prisner TF, Bennati M., Angew Chem Int Ed Engl 47(7), 2008
PMID: 18172843
High-frequency dynamic nuclear polarization using biradicals: a multifrequency EPR lineshape analysis.
Hu KN, Song C, Yu HH, Swager TM, Griffin RG., J Chem Phys 128(5), 2008
PMID: 18266419
HYSCORE and DEER with an upgraded 95GHz pulse EPR spectrometer.
Goldfarb D, Lipkin Y, Potapov A, Gorodetsky Y, Epel B, Raitsimring AM, Radoul M, Kaminker I., J Magn Reson 194(1), 2008
PMID: 18571956
Long-range distance determinations in biomacromolecules by EPR spectroscopy.
Schiemann O, Prisner TF., Q Rev Biophys 40(1), 2007
PMID: 17565764
On Cu(II)-Cu(II) distance measurements using pulsed electron electron double resonance.
Yang Z, Becker J, Saxena S., J Magn Reson 188(2), 2007
PMID: 17825593

42 References

Daten bereitgestellt von Europe PubMed Central.

Schweiger, 2001
Investigation of structure and dynamics in membrane proteins using site-directed spin labeling
Hubbell, Curr. Opin. Struct. Biol. 4(), 1994
Recent advances in site-directed spin labeling of proteins.
Hubbell WL, Gross A, Langen R, Lietzow MA., Curr. Opin. Struct. Biol. 8(5), 1998
PMID: 9818271
Identifying conformational changes with site-directed spin labeling.
Hubbell WL, Cafiso DS, Altenbach C., Nat. Struct. Biol. 7(9), 2000
PMID: 10966640
Combining high-field EPR with site-directed spin labeling reveals unique information on proteins in action.
Mobius K, Savitsky A, Wegener C, Plato M, Fuchs M, Schnegg A, Dubinskii AA, Grishin YA, Grigor'ev IA, Kuhn M, Duche D, Zimmermann H, Steinhoff HJ., Magn Reson Chem 43 Spec no.(), 2005
PMID: 16235212
Accessibility and dynamics of nitroxide side chains in T4 lysozyme measured by saturation recovery EPR.
Pyka J, Ilnicki J, Altenbach C, Hubbell WL, Froncisz W., Biophys. J. 89(3), 2005
PMID: 15994892
Conformational dynamics of loop 262-274 in G- and F-actin.
Shvetsov A, Stamm JD, Phillips M, Warshaviak D, Altenbach C, Rubenstein PA, Hideg K, Hubbell WL, Reisler E., Biochemistry 45(20), 2006
PMID: 16700564
Application of ELDOR in electron spin echo for paramagnetic center space distributions in solids
Milov, Fiz. Tverd. Tela (Leningrad) 23(), 1981
Electron–electron double-resonance in electron spin echo: model biradical systems and the sensitized photolysis of decalin
Milov, Chem. Phys. Lett. 110(), 1984
Dead-time free measurement of dipole-dipole interactions between electron spins.
Pannier M, Veit S, Godt A, Jeschke G, Spiess HW., J. Magn. Reson. 142(2), 2000
PMID: 10648151
Double quantum two-dimensional Fourier transform electron spin resonance: distance measurements
Saxena, Chem. Phys. Lett. 251(), 1996
Multiple-quantum ESR and distance measurements
Borbat, Chem. Phys. Lett. 313(), 1999
Comparison of electron paramagnetic resonance methods to determine distances between spin labels on human carbonic anhydrase II.
Persson M, Harbridge JR, Hammarstrom P, Mitri R, Martensson LG, Carlsson U, Eaton GR, Eaton SS., Biophys. J. 80(6), 2001
PMID: 11371461
Solution structure of the cytoplasmic domain of erythrocyte membrane band 3 determined by site-directed spin labeling.
Zhou Z, DeSensi SC, Stein RA, Brandon S, Dixit M, McArdle EJ, Warren EM, Kroh HK, Song L, Cobb CE, Hustedt EJ, Beth AH., Biochemistry 44(46), 2005
PMID: 16285715
Localization of the N-terminal domain in light-harvesting chlorophyll a/b protein by EPR measurements.
Jeschke G, Bender A, Schweikardt T, Panek G, Decker H, Paulsen H., J. Biol. Chem. 280(19), 2005
PMID: 15755729
Assessing oligomerization of membrane proteins by four-pulse DEER: pH-dependent dimerization of NhaA Na+/H+ antiporter of E. coli.
Hilger D, Jung H, Padan E, Wegener C, Vogel KP, Steinhoff HJ, Jeschke G., Biophys. J. 89(2), 2005
PMID: 15894644
A PELDOR-based nanometer distance ruler for oligonucleotides.
Schiemann O, Piton N, Mu Y, Stock G, Engels JW, Prisner TF., J. Am. Chem. Soc. 126(18), 2004
PMID: 15125665
Self-assembling properties of membrane-peptides studied by Peldor and cw-ESR spectroscopies
Milov, J. Am. Chem. Soc. 122(), 2000
Determination of ion cluster size and cluster-to-cluster distances in ionomers by four-pulse double electron–electron resonance spectroscopy
Pannier, Macromolecules 33(), 2000
Determination of the nanostructure of polymer materials by electron paramagnetic resonance spectroscopy
Jeschke, Macromol. Rapid Comm. 23(), 2002
Co-conformational distribution of nanosized [2]catenanes determined by pulse EPR measurements
Jeschke, Chem. Phys. Chem 4(), 2003
Electrostatic site attachment of divalent counterions to rodlike ruthenium(II) coordination polymers characterized by EPR spectroscopy.
Hinderberger D, Schmelz O, Rehahn M, Jeschke G., Angew. Chem. Int. Ed. Engl. 43(35), 2004
PMID: 15317002
Pulsed electron double resonance (PELDOR) and its applications in free-radicals research
Milov, Appl. Magn. Reson. 15(), 1998
The effect of microwave pulse duration on the distance distribution function between spin labels obtained by PELDOR data analysis
Milov, Appl. Magn. Reson. 26(), 2004
Distance measurements in the nanometer range by pulse EPR
Jeschke, Chem. Phys. Chem 3(), 2002
Data analysis procedures for pulse ELDOR measurements of broad distance distributions
Jeschke, Appl. Magn. Reson. 26(), 2004
Sensitivity enhancement in pulse EPR distance measurements.
Jeschke G, Bender A, Paulsen H, Zimmermann H, Godt A., J. Magn. Reson. 169(1), 2004
PMID: 15183350
Isotope selection in distance measurements between nitroxides.
Jeschke G, Zimmermann H, Godt A., J. Magn. Reson. 180(1), 2006
PMID: 16495097

The determination of pair distance distributions by pulsed ESR using Tikhonov regularization.
Chiang YW, Borbat PP, Freed JH., J. Magn. Reson. 172(2), 2005
PMID: 15649755
Double electron–electron resonance spin-echo modulation: spectroscopic measurement of electron spin-pair separations in orientationally disordered solids
Larsen, J. Chem. Phys. 98(), 1993
Weakly coupled radical pairs in solids: ELDOR in ESE structure studies
Maryasov, Appl. Magn. Reson. 14(), 1998
High-frequency 180GHz PELDOR
Denysenkov, Appl. Magn. Reson. 29(), 2005
EPR probes with well-defined, long distances between two or three unpaired electrons
Godt A, Franzen C, Veit S, Enkelmann V V, Pannier M, Jeschke G., J. Org. Chem. 65(22), 2000
PMID: 11076617
Distance Measurements in Solid-State NMR and EPR Spectroscopy
Jeschke, Lect. Notes Phys. 684(), 2006

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

PMID: 17188008
PubMed | Europe PMC

Suchen in

Google Scholar