Measuring distances in proteins by saturation-recovery epr

Nature Protocols

Volumn 2, Issue 7, 2007, Pages 1770-1781

  Hirsh, Donald J ^a   Brudvig, Gary W ^b  

^a The College of New Jersey   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FREE RADICAL; PROTEIN; TYROSINE;

ARTICLE; CHEMISTRY; ELECTROMAGNETIC FIELD; ELECTRON SPIN RESONANCE; INSTRUMENTATION; ISOLATION AND PURIFICATION; METHODOLOGY; MICROWAVE RADIATION; PHOTOSYSTEM II; QUANTUM THEORY; REPRODUCIBILITY;

ELECTROMAGNETIC FIELDS; ELECTRON SPIN RESONANCE SPECTROSCOPY; FREE RADICALS; MICROWAVES; PHOTOSYSTEM II PROTEIN COMPLEX; PROTEINS; QUANTUM THEORY; REPRODUCIBILITY OF RESULTS; TYROSINE;

EID: 34548567870     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2007.255     Document Type: Article

References (48)

1. Lakshmi, K. and Brudvig, G.: Pulsed electron paramagnetic resonance methods for macromolecular structure determination. Curr. Opin. Struct. Biot. 11, 523-531 (2003).
2. Berliner L.J., Eaton G.R., and Eaton S.S.: Distance Measurements in Biological Systems by EPR (Kluwer Academic/Plenum Publishers, New York, 2000).
3. Hirsh, D.J., Beck, W.F., Innes, J.B. and Brudvig, G.W.: Using saturation-recovery EPR to measure distances in proteins: applications to photosystem II. Biochemistry 31, 532-541 (1992).
4. Hirsh, D.J., Beck, W.F., Lynch, J.B., Que, L., Jr. and Brudvig, G.W.: Using saturation-recovery EPR to measure exchange couplings in proteins: application to ribonucleotide reductase. J. Am. Chem. Soc. 114, 7475-7481 (1992).
5. MacArthur, R.: Component B binding tothe soluble methanemonooxygenase hydroxylase by saturation-recovery EPR spectroscopy of spin-labeled MMOB.J. Am. Chem. Soc. 124, 13392-13393 (2002).
6. Clegg, R.M.: Fluorescence resonance energy transfer. in Fluorescence Imaging Spectroscopy and Microscopy Vol. 137 (eds. Wang, X.F. and Herman, B.) 179-251 (Wiley, New York, 1996).
7. Stryer, L.: Fluorescence energy transfer as a spectroscopic ruler. Annu. Rev. Biochem. 47, 819-846 (1978).
8. Forster, T.: Delocalized excitation and excitation transfer. in Modern Quantum Chemistry Vol. 3 (ed. Sinanoglu, O.) 93-137 (Academic Press Inc., New York, 1965).
9. Borbat, P.B. and Freed, J.H.: Double-quantum ESR and distance measurements. in Distance Measurements in Biotogicat Systems by EPR Vol. 19 (eds. Berliner, L.J., Eaton, G.R. and Eaton, S.S.) 383-456 (Kluwer Academic/Plenum Publishers, New York, 2000).
10. Raitsimring, A.: ''2 + 1" pulse sequence as applied for distance and spatial distribution measurements of paramagnetic centers. in Distance Measurements in Biotogicat Systems by EPR Vol. 19 (eds. Berliner, L.J., Eaton, G.R. and Eaton, S.S.) 461-490 (Kluwer Academic/Plenum Publishers, New York, 2000).
11. Jeschke, G., Pannier, M. and Spiess, H.W.: Distance measurements in biological systems by EPR. in Distance Measurements in Biotogicat Systems by EPR Vol. 19 (eds. Berliner, L.J., Eaton, G.R. and Eaton, S.S.) 493-511 (KluwerAcademic/Plenum Publishers, New York, 2000).
12. Berliner L.J.: Spin Labeling 444 (Springer, New York, 2007).
13. Berliner L.J.: Spin Labeling II: Theory and Applications (Academic Press, New York, 1979).
14. Berliner L.J.: Spin Labetting 605 (Academic Press, New York, 1976).
15. Bloembergen, N.: The interaction of nuclear spins in a crystalline lattice. Physica (The Hague) 15, 386-426 (1949).
16. Bloembergen, N., Purcell, E.M. and Pound, R.V.: Relaxation effects in nuclear magnetic resonance absorption. Phys. Rev. 73, 679-712 (1948).
17. Bloembergen, N., Shapiro, S., Pershan, P.S. and Artman, J.O.: Cross relaxation in spin systems. Phys. Rev. 114, 445-459 (1959).
18. Abragam, A.: Overhauser effect in nonmetals. Phys. Rev. 98, 1729-35 (1955).
19. Kulikov, A.V. and Likhtenstein, G.I.: Adv. Mot. Retax. Interact. Processes 10, 47-79 (1977).
20. Goodman, G. and Leigh, J.S. Jr.: Distance between the visible copper and cytochrome a in bovine heart cytochrome oxidase. Biochemistry 24, 2310-2317 (1985).
21. Rakowsky, M., More, K., Kulikov, A., Eaton, G. and Eaton, S.: Time-domain electron paramagnetic resonance as a probe of electron-electron spin-spin interaction in spin-labeled low-spin iron porphyrins. J. Am. Chem. Soc. 117, 2049-2057 (1995).
22. Eaton, G.R. and Eaton, S.S.: Relaxation times oforganicradicalsand transition metal ions. in Distance Measurements in Biotogicat Systems by EPR Vol. 19 (eds. Berliner, L.J., Eaton, G.R. and Eaton, S.S.) 29-154 (Kluwer Academic/Plenum Publishers, New York, 2000).
23. Debus, R.J., Feher, G. and Okamura, M.Y.: Iron-depleted reaction centers from Rhodopseudomonas sphaeroides R-26.1: characterization and reconstitution with Fe2+, Mn2+, Co2+, Ni2+, Cu2+ and Zn2+. Biochemistry 25, 2276-2287 (1986).
24. Zhou, Y., Bowler, B., Lynch, K., Eaton, S. and Eaton, G.: Interspin distances in spin-labeled metmyoglobin variants determined by saturation recovery EPR. Biophys. J. 79, 1039-1052 (2000).
25. Seiter, M., Budker, V., Du, J.-L., Eaton, G.R. and Eaton, S.S.: Interspin distances determined by time domain EPR ofspin-labeled high-spin methemoglobin. Inorg.Chim. Acta 273, 354-366 (1998).
26. Hirsh, D.J. and Brudvig, G.W.: Long-range electron spin-spin interactions in the bacterial photosynthetic reaction center. J. Phys. Chem. 97, 13216-13222 (1993).
27. Portis, A.M.: Electronic structure of F centers: saturation of the electron spin resonance. Phys. Rev. 91, 1071-1078 (1953).
28. Castner, T.G. Jr.: Saturation of the paramagnetic resonance of a V center. Phys. Rev. 115, 1506-1515 (1959).
29. Galli, C., Innes, J., Hirsh, D. and Brudvig, G.: Effects of dipole-dipole interactions on microwave progressive power saturation of radicals in proteins. J. Magn. Reson. B 110, 284-287 (1996).
30. Voss, J., Hubbell, W.L. and Kaback, H.R.: Distance determination in proteins using designed metal ion binding sites and site-directed spin labeling: application to the lactose permease of Escherichia coti. Proc. Natt. Acad. Sci. USA 92, 12300-12303 (1995).
31. Roberts, J.D.: ABCs of FT-NMR (University Science Books, Sausalito, CA, 2000).
32. Harris, R.K.: Nuctear Magnetic Resonance Spectroscopy: A Physicochemicat View (Wiley, New York, 1986).
33. Weil, J.A., Bolton, J.R. and Wertz, J.E.: Etectron Paramagnetic Resonance: Elementary Theory and Practicat Apptications 568 (Wiley, New York, 1994).
34. Symons, M.M.C.: Chemicat and Biochemicat Aspects of Etectron-Spin Resonance Spectroscopy 190 (John Wiley, New York, 1978).
35. Hyde, J.S., Swartz, H.M. and Antholine, W.E.: in Spin Labeting II: Theory and Apptications (ed. Berliner, L.J.) 71-113 (Academic Press, New York, 1979).
36. Hyde, J.S.: Saturation recovery methodology. in Time-domain Etectron Spin Resonance (eds. Kevan, L. and Schwartz, R.N.) 1-30 (Wiley, New York, 1979).
37. Yamauchi, T., Mino, H., Matsukawa, T., Kawamori, A. and Ono, T.: Parallel polarization electron paramagnetic resonance studies of the S1-state manganese cluster in the photosynthetic oxygen-evolving system. Biochemistry 36, 7520-7526 (1997).
38. Bizzarri, A.R. and Cannistraro, S.: Solvent modulation of the structural heterogeneity in FeIII myoglobin samples: a low temperature EPR investigation. Eur. Biophys. J. 22, 259-267 (1993).
39. Berthold, D.A., Babcock, G.T. and Yocum, C.F.: A highly resolved, oxygen-evolving photosystem II preparation from spinach thylakoid membranes. FEBS Lett. 134, 231-234 (1981).
40. Pikal-Cleland, K.A., Rodriguez-Hornedo, N., Amidon, G.L. and Carpenter, J.F.: Protein denaturation during freezing and thawing in phosphate buffer systems: monomeric and tetrameric beta-galactosidase. Arch. Biochem. Biophys. 384, 398-406 (2000).
41. Eaton, S.S. and Eaton, G.R.: Irradiated fused-quartz standard sample for time-domain EPR. J. Magn. Reson. A 102, 354-356 (1993).
42. Sahlin, M.: Magnetic interaction between the tyrosyl free radical and the antiferromagnetically coupled iron center in ribonucleotide reductase. Biochemistry 26, 5541-5548 (1987).
43. Allen, J.P., Feher, G., Yeates, T.O., Komiya, H. and Rees, D.C.: Structure of the reaction center from Rhodobacter sphaeroides R-26: protein-cofactor (quinones and Fe2+) interactions. Proc. Natl. Acad. Sa. USA 85, 8487-8491 (1988).
44. Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J. and Iwata, S.: Architecture of the photosynthetic oxygen-evolving center. Science 303, 1831-1838 (2004).
45. Loll, B., Kern, J., Saenger, W., Zouni, A. and Biesiadka, J.: Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II. Nature (London, United Kingdom) 438, 1040-1044 (2005).
46. Hirsh, D.J.: Using Saturation-recovery EPR to Measure Distances and Exchange Couplings in Proteins PhD thesis, Yale University (1993).
47. Du, J.-L., Eaton, G.R. and Eaton, S.S.: Temperature, orientation, and solvent dependence ofelectron spin-lattice relaxation rates for nitroxyl radicals in glassy solvents and doped solids. J. Magn. Reson. A 115, 213-221 (1995).
48. Eaton, S.S. and Eaton, G.R.: Determination of distances based on T and Tm effects. in Distance Measurements in Biological Systems by EPR Vol. 19 (eds. Berliner, L.J., Eaton, G.R. and Eaton, S.S.) 348-378 (Kluwer Academic/Plenum Publishers, New York, 2000).