Abstract
The feasibility of one-dimensional two-pulse correlation spectroscopy (COSY) Electron Paramagnetic Resonance (EPR) sequence for distance measurements in biological systems using nitroxide biradicals is investigated numerically at Ku-band. It is found that the COSY sequences can be exploited to measure distances between the two nitroxides in the range \(17.3 \AA \lesssim r \lesssim 47.0 \AA (0.5 \mathrm{MHz}\le d\le 10 \mathrm{MHz})\), where \(d=\frac{2}{3}D\), with \(D\) being the dipolar-coupling constant. Taking into account the dead time after the second pulse, it is found that the modulation depth can only be measured for \(0.5 \mathrm{MHz}\le d \le 7.0\) MHz. However, for \(d>7.0 \mathrm{MHz}\), for which a significant part of the initial signal is lost in the dead time, the Fourier transform of the observable part of the signal after the dead time as a function of \({t}_{1}-{t}_{d}\), where \({t}_{1}\) is the time of the echo after the second pulse and \({t}_{d}\) is the dead time, still provides undistorted Pake doublets centered at \(\pm d\). It is shown here numerically that the amplitudes of the Pake doublets of the COSY signal are the most intense, one-to-two orders of magnitude larger, as compared to those of the four-, five-, six- pulse double quantum coherence (DQC), two-pulse double quantum (DQ), and five-pulse DQM (double quantum modulation) sequences. Another advantage of the COSY technique is that it provides a measurement of \({T}_{2}^{S}\), the spin–spin relaxation time over the \(p=\pm 1\) coherence pathways.
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References
S. Saxena, J.H. Freed, Theory of double quantum two-dimensional electron spin resonance with application to distance measurements. J. Chem. Phys 107, 1317 (1997)
S.K. Misra, P.P. Borbat, J.H. Freed, Calculation of double-quantum-coherence two-dimensional spectra: distance measurements and orientational correlations. Appl. Magn. Reson. 36, 237 (2009)
P.P. Borbat, J.H. Freed, Double-Quantum ESR and Distance Measurements. Distance Measurements in Biological Systems by EPR (Springer, Boston, 2002), pp. 383–459
P.P. Borbat, J.H. Freed, Pros and cons of pulse dipolar ESR: DQC and DEER. EPR Newslett. 17, 2–3 (2007)
A.M. Raitsimring, K.M. Salikhov, Electron spin echo method as used to analyze the spatial distribution of paramagnetic centers. Bull. Magn. Reson. 7(4), 184–217 (1985)
A.D. Milov, K.M. Salikhov, M.D. Shirov, Application of the double resonance method to electron spin echo in a study of the spatial distribution of paramagnetic centers in solids. Sov. Phys. Solid State 23, 565–569 (1981)
K.M. Salikhov, S.A. Dzuba, A.M. Raitsimring, The theory of electron spin-echo signal decay resulting from dipole-dipole interactions between paramagnetic centers in solids. J. Magn. Reson. 42(2), 255–276 (1969)
A.D. Milov, K.M. Salikhov, Y.D. Tsvetkov, Phase relaxation of hydrogen atoms stabilized in an amorphous matrix. Phys. Solid State 15(4), 802–806 (1973)
A.D. Milov, Y.D. Tsvetkov, F. Formaggio, M. Crisma, C. Toniolo, J. Raap, Self-assembling properties of membrane-modifying peptides studied by PELDOR and CW-ESR spectroscopies. J. Am. Chem. Soc 122(16), 3843–3848 (2000)
A.D. Milov, Y.D. Tsvetkov, F. Formaggio, M. Crisma, C. Toniolo, J. Raap, The secondary structure of a membrane-modifying peptide in a supramolecular assembly studied by PELDOR and CW-ESR spectroscopies. J. Am. Chem. Soc 123(16), 3784–3789 (2001)
A.D. Milov, Y.D. Tsvetkov, F. Formaggio, S. Oancea, C. Toniolo, J. Raap, Aggregation of spin labeled trichogin GA IV dimers: Distance distribution between spin labels in frozen solutions by PELDOR data. J. Phys. Chem. B 107(49), 13719–13727 (2003)
A.D. Milov, B.D. Naumov, Y.D. Tsvetkov, The effect of microwave pulse duration on the distance distribution function between spin labels obtained by PELDOR data analysis. Appl. Magn. Reson. 26(4), 587 (2004)
B. Joseph, A. Sikora, E. Bordignon, G. Jeschke, D.S. Cafiso, T.F. Prisner, Distance measurement on an endogenous membrane transporter in E. coli cells and native membranes using EPR spectroscopy. Angew. Chem. 127(21), 6294–6297 (2015)
O. Krumkacheva, E. Bagryanskaya, EPR-based distance measurements at ambient temperature. J. Magn. Reson. 280, 117–126 (2017)
P. Widder, J. Schuck, D. Summerer, M. Drescher, Combining site-directed spin labeling in vivo and in-cell EPR distance determination. Phys. Chem. Chem. Phys. 22(9), 4875–4879 (2020)
G. Jeschke, The contribution of modern EPR to structural biology. Emerg. Top. Life Sci. 2(1), 9–18 (2018)
J.J. Jassoy, A. Berndhäuser, F. Duthie, S.P. Kühn, G. Hagelueken, O. Schiemann, Versatile trityl spin labels for nanometer distance measurements on biomolecules in vitro and within cells. Angew. Chem. 129(1), 183–187 (2017)
Y. Yang, F. Yang, Y.J. Gong, J.L. Chen, D. Goldfarb, X.C. Su, A reactive, rigid GdIII labeling tag for in-cell EPR distance measurements in proteins. Angew. Chem. Int. 56(11), 2914–2918 (2017)
M.J. Lawless, A. Shimshi, T.F. Cunningham, M.N. Kinde, P. Tang, S. Saxena, Analysis of nitroxide-based distance measurements in cell extracts and in cells by pulsed ESR spectroscopy. Chem. Phys. Chem. 18(12), 1653–1660 (2017)
Y. Yang, B.B. Pan, X. Tan, F. Yang, Y. Liu, X.C. Su, D. Goldfarb, In-cell Trityl–Trityl distance measurements on proteins. J. Phys. Chem. Lett. 11(3), 1141–1147 (2020)
A.D. Milov, Y.D. Tsvetkov, Double electron-electron resonance in electron spin echo: conformations of spin-labeled poly-4-vinilpyridine in glassy solutions. Appl. Magn. Reson 12(4), 495–504 (1997)
P.G. Fajer, L. Brown, L. Song, Practical Pulsed Dipolar ESR (DEER). ESR Spectroscopy in Membrane Biophysics (Springer, Boston, 2007), pp. 95–128
D. Abdullin, F. Duthie, A. Meyer, E.S. Müller, G. Hagelueken, O. Schiemann, Comparison of PELDOR and RIDME for distance measurements between nitroxides and low-spin Fe (III) ions. J. Phys. Chem. B 119(43), 13534–13542 (2015). https://doi.org/10.1021/acs.jpcb.5b02118
N. Stein, L. Mainali, J.S. Hyde, W.K. Subczynski, Appl. Magn. Reson. 50(7), 903–918 (2019)
S. Pfenninger, W.E. Antholine, M.E. Barr, J.S. Hyde, P.M. Kroneck, W.G. Zumft, Biophys. J. 69(6), 2761–2769 (1995)
S.K. Misra, H.R. Salahi, Relaxation in pulsed EPR: thermal fluctuation of spin-hamiltonian parameters of an electron-nuclear spin-coupled system in a malonic acid single crystal in a strong harmonic-oscillator restoring potential. Appl. Magn. Reson. 52, 247–261 (2021)
G. Jeschke, A. Koch, U. Jonas, A. Godt, Direct conversion of EPR dipolar time evolution data to distance distributions. J. Magn. Reson. 155(1), 72–82 (2002)
K. Halbmair, J. Wegner, U. Diederichsen, M. Bennati, Pulse EPR measurements of intramolecular distances in a topp-labeled transmembrane peptide in lipids. Biophys. J. 111(11), 2345–2348 (2016)
J.E. Lovett, B.W. Lovett, J. Harmer, DEER-Stitch: Combining three-and four-pulse DEER measurements for high sensitivity, deadtime free data. J. Magn. Reson. 223, 98–106 (2012)
J.M. Franck, R.P. Barnes, T.J. Keller, T. Kaufmann, S. Han, Active cancellation–a means to zero dead-time pulse EPR. J. Magn. Reson. 261, 199–204 (2015)
D.J. Schneider, J.H. Freed, in Spin Labeling: Theory and Application. ed. by L.J. Berliner (Academic, New York, 1976). (Chap. 2)
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Misra, S.K., Salahi, H.R. Two-Pulse EPR COSY (Correlation Spectroscopy) Sequence: Feasibility for Distance Measurements in Biological Systems. Appl Magn Reson 53, 343–370 (2022). https://doi.org/10.1007/s00723-021-01447-7
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DOI: https://doi.org/10.1007/s00723-021-01447-7