A simple double quantum coherence ESR sequence that minimizes nuclear modulations in Cu2+-ion based distance measurements

Journal of Magnetic Resonance

Volumn 257, Issue , 2015, Pages 45-50

  Ruthstein, Sharon ^a,b   Ji, Ming ^a   Shin, Byong Kyu ^a,c   Saxena, Sunil ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

^b BAR ILAN UNIVERSITY   (Israel)

^c Seoul National University   (South Korea)

Author keywords

Distance measurement; DQC; Electron electron dipolar interaction; Electron nuclear interaction; ESR spectroscopy

Indexed keywords

AMINO ACIDS; DISTANCE MEASUREMENT; ELECTRON SPIN RESONANCE SPECTROSCOPY; ELECTRONS; MODULATION; PEPTIDES;

DIPOLAR INTERACTION; DOUBLE QUANTUM COHERENCES; DOUBLE-QUANTUM COHERENCE ESR; ELECTRON-NUCLEAR INTERACTION; ESR SPECTROSCOPY; HISTIDINE RESIDUES; MAGNETIC DIPOLAR INTERACTIONS; MODIFIED PULSE SEQUENCES;

QUANTUM THEORY;

COPPER; HISTIDINE; NITRIC OXIDE; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; ELECTRON SPIN RESONANCE; FOURIER ANALYSIS; MOLECULAR GENETICS; PROCEDURES; PROTEIN CONFORMATION; QUANTUM THEORY; STATISTICAL ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; COPPER; DATA INTERPRETATION, STATISTICAL; ELECTRON SPIN RESONANCE SPECTROSCOPY; FOURIER ANALYSIS; HISTIDINE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NITRIC OXIDE; PROTEIN CONFORMATION; PROTEINS; QUANTUM THEORY;

EID: 84930942445     PISSN: 10907807     EISSN: 10960856     Source Type: Journal    
DOI: 10.1016/j.jmr.2015.05.005     Document Type: Article

References (46)

1. J.L. Kear, M.E. Blackburn, A.M. Veloro, B.M. Dunn, and G.E. Fanucci Subtype polymorphisms among HIV-1 protease variants confer altered flap conformations and flexibility J. Am. Chem. Soc. 131 2009 14650 14651
2. K.M. Stone, J.E. Townsend, J. Sarver, P.J. Sapienza, S. Saxena, and L. Jen-Jacobson Electron spin resonance shows common structural features for different classes of EcoRI-DNA complexes Angew. Chem. Int. Ed. 47 2008 10192 10194
3. O. Schiemann, N. Piton, Y. Mu, G. Stock, J.W. Engles, and T.F. Prisner A PELDOR-based nanometer distance ruler for oligonucleotides J. Am. Chem. Soc. 126 2004 5722 5729
4. O. Schiemann, P. Cekan, D. Margraf, T.F. Prisner, and S.T. Sigurdsson Relative orientation of rigid nitroxide by PELDOR: beyond distance measurements in nucleic acids Angew. Chem. Int. Ed. 48 2009 3292 3295
5. O. Scheimann, A. Weber, T. Edwards, T.F. Prisner, and S. Sigurdsson Nanometer distance measurements on RNA using PELDOR J. Am. Chem. Soc. 125 2003 3434 3435
6. N.-K. Kim, M.K. Bowman, and V.J. DeRose Precise mapping of RNA tertiary structure via nanometer distance measurements with double-electron electron resonance spectroscopy J. Am. Chem. Soc. 132 2010
7. S.-Y. Park, P.P. Borbat, G. Gonzalez-Bonet, J. Bhatnagar, A.M. Pollard, J.H. Freed, A.M. Bilwes, and B.R. Crane Reconstruction of the chemotaxis receptor-kinase assembly Nat. Struct. Mol. Biol. 13 2006 400 407
8. C. Altenbach, A.K. Kusnetzow, O.P. Ernst, K.P. Hofmann, and W.L. Hubbell High resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation Proc. Natl. Acad. Sci. USA 105 2008 7439 7444
9. P. Zou, M. Bortolus, and H.S. Mchaourab Conformational cycle of the ABC transporter MsbA in liposomes: detailed analysis using double electron electron resonance spectroscopy J. Mol. Biol. 393 2009 586 597
10. A.D. Milov, A.B. Ponomarev, and Y.D. Tsvetkov Electron-electron double resonance in electron spin echo: model biradical systems and the sensitized photolysis of declain Chem. Phys. Lett. 110 1984 67 72
11. A.D. Milov, and 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 1997 495 504
12. S. Saxena, and J.H. Freed Double quantum two-dimensional Fourier transform electron spin resonance. distance measurements Chem. Phys. Lett. 251 1996 102 110
13. S. Saxena, and J.H. Freed Theory of double quantum two-dimensional electron spin resonance with application to distance measurements J. Chem. Phys. 107 1997 1317 1340
14. P.P. Borbat, and J.H. Freed Measuring distances by pulsed dipolar ESR spectroscopy: spin-labeled histidine kinases Methods Enzymol. 423 2007 52 116
15. G. Jeschke, and Y. Polyhach Distance measurements on spin-labelled biomacro-molecules by pulsed electron paramagnetic resonance Phys. Chem. Chem. Phys. 9 2007 1895 1910
16. O. Scheimann, and T.F. Prisner Long-range distance determination in biomacromolecules by epr spectroscopy Quart. Rev. Biophys. 40 2007 1 53
17. G.E. Merz, P.P. Borbat, A.J. Pratt, E.D. Getzoff, J.H. Freed, and B.R. Crane Copper-based pulsed dipolar ESR spectroscopy as a probe of protein conformation linked to disease states Biophys. J. 107 2014 1669 1674
18. P.P. Borbat, and J.H. Freed Biol. Magn. Reson. 2000 Kluwer Academic/Plenum Publishers New York
19. P.P. Borbat, and J.H. Freed Pulse Dipolar Electron Spin Resonance. Distance Measurement in Structure and Bonding J. Harmer, C. Timmel, 2014 Springer Heidelberg, Germany, New York, USA 1 82
20. W.L. Hubbell, and C. Altenbach Investigation of structure and dynamics in membrane proteins using site-directed spin labeling Curr. Opin. Struct. Biol. 4 1994 566 573
21. W.L. Hubbell, A. Gross, R. Langen, and M.A. Lietzow Recent advances in site-directed spin labeling of proteins Curr. Opin. Struct. Biol. 8 1998 649 656
22. B.E. Bode, J. Plackmeyer, M. Bolte, T.F. Prisner, and O. Schiemann PELDOR on an exchange coupled nitroxide copper(II) spin pair J. Organometal. Chem. 694 2009 1172 1179
23. B.E. Bode, J. Plackmeyer, T.F. Prisner, and O. Schiemann PELDOR measurements on a nitroxide-labeled Cu(II) porhyrin: orientation selection, spin density distribution, and conformational flexibility J. Phys. Chem. A 112 2008 5064 5073
24. 3+ spin labeling J. Am. Chem. Soc. 132 2010 9040 9048
25. 3+ complexes as potential spin labels for high field pulsed EPR distance measurements J. Am. Chem. Soc. 129 2007 14138 14139
26. Z. Yang, J. Becker, and S. Saxena On Cu(II)-Cu(II) distance measurements using pulsed electron electron double resonance J. Magn. Reson. 188 2007 337 343
27. 2+ ions and ESR J. Phys. Chem. B 114 2010 6165 6174
28. M. Ji, S. Ruthstein, and S. Saxena Paramagnetic metal ions in pulsed ESR distance distribution measurements Acc. Chem. Res. 47 2013 688 695
29. J.S. Becker, and S. Saxena Double quantum coherence electron spin resonance on coupled Cu(II)-Cu(II) electron spins Chem. Phys. Lett. 414 2005 248 252
30. 2+ distance measurements in a protein-DNA complex by double-quantum coherence ESR J. Phys. Chem. B 117 2013 6227 6230
31. C. Elsasser, M. Brecht, and R. Bittl Pulsed electron-electron double resonance on multinuclear metal clusters: assignment of spin projection factors based on the dipolar interaction J. Am. Chem. Soc. 124 2002 12606 12611
32. C.W.M. Kay, H. El Mkami, R. Cammack, and R.W. Evans Pulsed ELDOR determination of the intramolecular distance between the metal binding sites in dicupric human serum transferrin and lactoferrin J. Am. Chem. Soc. 129 2007 4868-4689
33. I.M.C. van Amsterdam, M. Ubbink, G.W. Canters, and M. Huber Measurement of a Cu(II)-Cu(II) distance of 26 A by a pulsed EPR method Angew. Chem. Int. Ed. 42 2003 62 64
34. 3+ spin labeling J. Am. Chem. Soc. 136 2014 13458 13465
35. E. Matalon, T. Huber, G. Hagelueken, B. Graham, V. Frydman, A. Feintuch, G. Otting, and D. Goldfarb Gadolinium(III) spin labels for high-sensitivity distance measurements in transmembrane helices Angew. Chem. Int. Ed. 52 2013 11831 11834
36. 2+ tags J. Phys. Chem. Lett. 3 2012 157 160
37. J.H. van Wonderen, D.N. Kostrz, C. Dennison, and F. MacMillan Refined distances between paramagnetic centers of a multi-copper nitrite reductase determined by pulsed EPR (iDEER) spectroscopy Angew. Chem. Int. Ed. 52 2013 1990 1993
38. J. Abe, S. Ueki, T. Arata, S. Nakazawa, S. Yamauchi, and Y. Ohba Improved sensitivity by isotopic substitution in distance measurements based on double quantum coherence EPR Appl. Magn. Reson. 42 2012 473 485
39. A. Schweiger, and G. Jeschke Principles of Pulse Electron Paramagnetic Resonance 2001 Oxford University Press New York
40. J.H. Freed New technologies in electron spin resonance Annu. Rev. Phys. Chem. 51 2000 655 689
41. P.P. Borbat, and J.H. Freed Multiple quantum ESR and distance measurements Chem. Phys. Lett. 313 1999 145 154
42. M. Pannier, S. Viet, A. Godt, G. Jeschke, and H.W. Spiess Dead-time free measurement of dipole-dipole interactions between electron spins J. Magn. Reson. 142 2000 331 340
43. R.S. Magliozzo, L. Bubacco, J. McCracken, F. Jiang, M. Beltarmini, B. Salvato, and J. Peisach Cu(II) coordination in arthropod and mullusk green half-methemocyanins analyzed by electron spin-echo envelope modulation spectroscopy Biochemistry 34 1995 1513 1523
44. P.P. Borbat, J.H. Davis, S.E. Butcher, and J.H. Freed Measurement of large distances in biomolecules using double-quantum filtered refocused electron spin-echoes J. Am. Chem. Soc. 126 2004 7746 7747
45. P.P. Borbat, H.S. Mchaourab, and J.H. Freed Protein structure determination using long-distances constraints from double-quantum coherence ESR: study of T4 lysozyme J. Am. Chem. Soc. 124 2002 5304 5314
46. S.K. Misra, P.P. Borbat, and J.H. Freed Calculation of double-quantum-coherence two-dimensional spectra: distance measurements and orientational correlations Appl. Magn. Reson. 36 2009 237 258