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Distance Measurements in Biological Systems by EPR pp 185–247Cite as

Determination of Protein Folds and Conformational Dynamics Using Spin-Labeling EPR Spectroscopy

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Part of the book series: Biological Magnetic Resonance ((BIMR,volume 19))

Abstract

The near completion of a large number of genome sequencing projects is ushering in a new perspective on how research in biological and biomedical sciences will be conducted in the future, both at the conceptual and experimental levels. The rush is on to transform the molecular blueprints of life into global views of the biochemical and physiological circuitry that interconnect to form entire organisms. The evolutionary histories, now available as multiple sequence alignments, will be complemented with pictures of evolving structures. In this post genomic era, the process of scientific discovery will be the result of large-scale parallel measurements to answer questions formulated from a genomic perspective.

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References

  • Abragam, A. (1961). Principles of Nuclear Magnetism. Oxford: Oxford University Press.

    Google Scholar 

  • Altenbach, C., Cai, K., Khorana, H. G. and Hubbell, W. L. (1999a) Structural features and light-dependent changes in the sequence 306322 extending from helix VII to the palmitoylation sites in rhodopsin: a site-directed spin-labeling study. Biochemistry 38, 7931–7.

    Article  PubMed  CAS  Google Scholar 

  • Altenbach, C., Klein-Seetharaman, J., Hwa, J., Khorana, H. G. and Hubbell, W. L. (1999b). Structural features and light-dependent changes in the sequence 59–75 connecting helices I and II in rhodopsin: a site-directed spin-labeling study. Biochemistry 38, 7945–9.

    Article  PubMed  CAS  Google Scholar 

  • Altenbach, C., Marti, T., Khorana, H. G. and Hubbell, W. L. (1990). Transmembrane protein structure: spin labeling of bacteriorhodopsin mutants. Science 248, 1088–92.

    Article  PubMed  CAS  Google Scholar 

  • Altenbach, C., Yang, K., Farrens, D. L., Farahbakhsh, Z. T., Khorana, H. G. and Hubbell, W. L. (1996). Structural features and light-dependent changes in the cytoplasmic interhelical E-F loop region of rhodopsin: a site-directed spin-labeling study. Biochemistry 35, 12470–8.

    Article  PubMed  CAS  Google Scholar 

  • Armstrong, C. M. (1971). Interaction of tetraethylammonium ion derivatives with the potassium channels of giant axons. Journal of General Physiology 58, 413–37.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Berengian, A. R., Bova, M. P. and Mchaourab, H. S. (1997). Structure and function of the conserved domain in aA-crystallin. Site-directed spin labeling identifies a beta-strand located near a subunit interface. Biochemistry 36, 9951–7.

    Article  PubMed  CAS  Google Scholar 

  • Berengian, A. R., Parfenova, M. and Mchaourab, H. S. (1999). Site-directed spin labeling study of subunit interactions in the a-crystallin domain of small heat-shock proteins. Comparison of the oligomer symmetry in aA-crystallin, HSP 27, and HSP 16.3. Journal of Biological Chemistry 274, 6305–14.

    Article  PubMed  CAS  Google Scholar 

  • Bova, M. P., Ding, L. L., Horwitz, J. and Fung, B. K. (1997). Subunit exchange of aA-crystallin. Journal of Biological Chemistry 272, 29511–7.

    Article  PubMed  CAS  Google Scholar 

  • Bowie, J. U. (1997). Helix packing in membrane proteins. Journal of Molecular Biology 272, 780–9.

    Article  PubMed  CAS  Google Scholar 

  • Burley, S. K., Almo, S. C., Bonanno, J. B., Capel, M., Chance, M. R., Gaasterland, T., Lin, D., Sali, A., Studier, F. W. and Swaminathan, S. (1999). Structural genomics: beyond the human genome project. Nature Genetics 23, 151–7.

    Article  PubMed  CAS  Google Scholar 

  • Burr, M. and Koshland, D. E. (1964). Use of “reporter groups” in structure. function studies of proteins. Biochemistry 52, 1017–1024.

    CAS  Google Scholar 

  • Caffrey, M., Cai, M., Kaufman, J., Stahl, S. J., Wingfield, P. T., Covell, D. G., Gronenbom, A. M. and Clore, G. M. (1998). Three-dimensional solution structure of the 44 kDa ectodomain of SIV gp41. EMBO Journal 17, 4572–84.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Chan, D. C., Fass, D., Berger, J. M. and Kim, P. S. (1997). Core structure of gp41 from the HIV envelope glycoprotein. Cell 89, 263–73.

    Article  PubMed  CAS  Google Scholar 

  • Chang, Z., Primm, T. P., Jakana, J., Lee, I. H., Serysheva, I., Chiu, W., Gilbert, H. F. and Quiocho, F. A. (1996). Mycobacterium tuberculosis 16-kDa antigen (Hsp16.3) functions as an oligomeric structure in vitro to suppress thermal aggregation. Journal of Biological Chemistry 271, 7218–23.

    Article  PubMed  CAS  Google Scholar 

  • Chervitz, S. A. and Falke, J. J. (1996). Molecular mechanism of transmembrane signaling by the aspartate receptor: a model. Proceedings of the National Academy of Sciences of the United States of America 93, 2545–50.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Chothia, C. (1984). Principles that determine the structure of proteins. Annual Review of Biochemistry 53, 537–72.

    Article  PubMed  CAS  Google Scholar 

  • Chothia, C. and Finkelstein, A. V. (1990). The classification and origins of protein folding patterns. Annual Review of Biochemistry 59, 1007–39.

    Article  PubMed  CAS  Google Scholar 

  • Chothia, C., Hubbard, T., Brenner, S., Barns, H. and Murzin, A. (1997). Protein folds in the all-beta and all-a classes. Annual Review of Biophysics & Biomolecular Structure 26, 597–627.

    Article  CAS  Google Scholar 

  • Cornette, J. L., Cease, K. B., Margalit, H., Spouge, J. L., Berzofsky, J. A. and DeLisi, C. (1987). Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. Journal of Molecular Biology 195, 659–85.

    Article  PubMed  CAS  Google Scholar 

  • Cuello, L. G., Romero, J. G., Cortes, D. M. and Perozo, E. (1998). pH-dependent gating in the Streptomyces lividans K+ channel. Biochemistry 37, 3229–36.

    Article  PubMed  CAS  Google Scholar 

  • de Jong, W. W., Caspers, G. J. and Leunissen, J. A. (1998). Genealogy of the a-crystallin-small heat-shock protein superfamily. International Journal of Biological Macromolecules 22, 151–62.

    Article  PubMed  Google Scholar 

  • Donnelly, D., Overington, J. P. and Blundell, T. L. (1994). The prediction and orientation of a-helices from sequence alignments: the combined use of environment-dependent substitution tables, Fourier transform methods and helix capping rules. Protein Engineering 7, 645–53.

    Article  PubMed  CAS  Google Scholar 

  • Doyle, D. A., Cabral, J. M., Pfuetzner, R. A., Kuo, A., Gulbis, J. M., Cohen, S. L., Chait, B. T. and MacKinnon, R. (1998). The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280, 69–77.

    Article  PubMed  CAS  Google Scholar 

  • Eaton, G. R. and Eaton, S. S. (1989). Resolved electron-electron spin-spin splittings in EPR spectra. In Biological Magnetic Resonance, vol. 8 (ed. L. J. Berliner and J Reuben ), pp. 340–397. New York: Plenum.

    Google Scholar 

  • Faber, H. R. and Matthews, B. W. (1990). A mutant T4 lysozyme displays five different crystal conformations. Nature 348, 263–6.

    Article  PubMed  CAS  Google Scholar 

  • Fajer, P. G. (2000) EPR in Peptide and Protein Analysis. In Encyclopedia of Analytical Chemistry (ed. R.A. Meyers) John Wiley and Sons, Ltd. In press.

    Google Scholar 

  • Falke, J. J., Bass, R. B., Butler, S. L., Chervitz, S. A. and Danielson, M. A. (1997). The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes. Annual Review of Cell & Developmental Biology 13, 457–512.

    Article  CAS  Google Scholar 

  • Farahbakhsh, Z. T., Hideg, K. and Hubbell, W. L. (1993). Photoactivated conformational changes in rhodopsin: a time-resolved spin label study. Science 262, 1416–9.

    Article  PubMed  CAS  Google Scholar 

  • Farrens, D. L., Altenbach, C., Yang, K., Hubbell, W. L. and Khorana, H. G. (1996). Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science 274, 768–70.

    Article  PubMed  CAS  Google Scholar 

  • Freed, J. H. and Schneider, D. J. (1989). Calculating slow motional magnetic resonance spectra: A user’s guide. In Biological Magnetic Resonance, vol. 8 (ed. L. J. a. R. Berliner, J. ), pp. 1–76. New York: Plenum.

    Google Scholar 

  • Froncisz, W. and J.S., H. (1982). The loop-gap resonator: A new microwave lumped circuit ESR sample structure. J. Magn. Reson. 47, 515–522.

    CAS  Google Scholar 

  • Gaasterland, T. (1998a). Structural genomics taking shape. Trends in Genetics 14, 135.

    Article  PubMed  CAS  Google Scholar 

  • Gaasterland, T. (1998b). Structural genomics: bioinformatics in the driver’s seat. Nature Biotechnology 16, 625–7.

    Article  PubMed  CAS  Google Scholar 

  • Gerstein, M., Lesk, A. M. and Chothia, C. (1994). Structural mechanisms for domain movements in proteins. Biochemistry 33, 6739–49.

    Article  PubMed  CAS  Google Scholar 

  • Gross, A., Columbus, L., Hideg, K., Altenbach, C. and Hubbell, W. L. (1999). Structure of the KcsA potassium channel from Streptomyces lividans: a site-directed spin labeling study of the second transmembrane segment. Biochemistry 38, 10324–35.

    Article  PubMed  CAS  Google Scholar 

  • Haley, D. A., Horwitz, J. and Stewart, P. L. (1998). The small heat-shock protein, aB-crystallin, has a variable quatemary structure. Journal of Molecular Biology 277, 27–35.

    Article  PubMed  CAS  Google Scholar 

  • Hanson, P., Millhauser, G., Formaggio, F., Crisma, M. and Toniolo, C. (1996). Esr Characterization of Hexameric, Helical Peptides Using Double Toac Spin Labeling. Journal of the American Chemical Society 118, 7618–7625.

    Article  CAS  Google Scholar 

  • Havel, T. F. (1991). An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. Progress in Biophysics & Molecular Biology 56, 43–78.

    Article  CAS  Google Scholar 

  • He, M. M., Sun, J. and Kaback, H. R. (1996). Cysteine-scanning mutagenesis of transmembrane domain XII and the flanking periplasmic loop in the lactose permease of EScherichia coli. Biochemistry 35, 12909–14.

    Article  PubMed  CAS  Google Scholar 

  • He, M. M., Voss, J., Hubbell, W. L. and Kaback, H. R. (1997). Arginine 302 (helix IX) in the lactose permease of Escherichia coli is in close proximity to glutamate 269 (helix VIII) as well as glutamate 325. Biochemistry 36, 13682–7.

    Article  PubMed  CAS  Google Scholar 

  • Heginbotham, L., Kolmakova Partensky, L. and Miller, C. (1998). Functional reconstitution of a prokaryotic K+ channel. Journal of General Physiology 111, 741–9.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Heginbotham, L., LeMasurier, M., Kolmakova-Partensky, L. and Miller, C. (1999). Single streptomyces lividans K+ channels: functional asymmetries and sidedness of proton activation. Journal of General Physiology 114, 551–60.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Heginbotham, L., Lu, Z., Abramson, T. and MacKinnon, R. (1994). Mutations in the K+ channel signature sequence. Biophysical Journal 66, 1061–7.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, F., Beckmann, E. and Downing, K. H. (1990). Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. Journal of Molecular Biology 213, 899–929.

    Article  PubMed  CAS  Google Scholar 

  • Horwitz, J. (1993). The function of a-crystallin. Investigative Ophthalmology & Visual Science 34, 10–22.

    CAS  Google Scholar 

  • Hubbell, W. L. and Altenbach, C. (1994). Site-directed spin labeling of membrane proteins. In Membrane protein structure. Experimental approaches (ed. S. H. White ). New York, NY: Oxford Univ. Press.

    Google Scholar 

  • Hubbell, W. L., Gross, A., Langen, R. and Lietzow, M. A. (1998). Recent Advances in Site-Directed Spin Labeling of Proteins. Current Opinion in Structural Biology 8, 649–656.

    Article  PubMed  CAS  Google Scholar 

  • Hubbell, W. L., Mchaourab, H. S., Altenbach, C. and Lietzow, M. A. (1996). Watching proteins move using site-directed spin labeling. Structure 4, 779–83.

    Article  PubMed  CAS  Google Scholar 

  • Hustedt, E. J., Smirnov, A. I., Laub, C. F., Cobb, C. E. and Beth, A. H. (1997). Molecular Distances From Dipolar Coupled Spin-Labels–the Global Analysis of Multifrequency Continuous Wave Electron Paramagnetic Resonance Data. Biophysical Journal 72, 1861–1877.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Hyde, J. S. and Subczynski, W. K. (1989). Spin label oxymetry. In Biological Magnetic Resonance, vol. 8 (ed. L. J. a. R. Berliner, J. ), pp. 399–425. New York: Plenum.

    Google Scholar 

  • Janin, J., and Chothia, C. (1980). Packing of a-helices onto beta-pleated sheets and the anatomy of a/ß proteins. J. Mol. Biol 143, 95–128.

    Article  PubMed  CAS  Google Scholar 

  • Kaback, H. R. and Wu, J. H. (1999). What to do while awaiting crystals of a membrane transport protein and thereafter. Accounts of Chemical Research 32, 805–813.

    Article  CAS  Google Scholar 

  • Kabsch, W. and Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–637.

    Article  PubMed  CAS  Google Scholar 

  • Kim, K. K., Yokota, H. and Kim, S. H. (1999). Four-helical-bundle structure of the cytoplasmic domain of a serine chemotaxis receptor. Nature 400, 787–92.

    Article  PubMed  CAS  Google Scholar 

  • Kim, S. H. (1998). Shining a light on structural genomics. Nature Structural Biology 5, 643–5.

    Article  PubMed  CAS  Google Scholar 

  • Koteiche, H. A., Berengian, A. R. and Mchaourab, H. S. (1998). Identification of protein folding patterns using site.directed spin labeling. Structural characterization of a beta-sheet and putative substrate binding regions in the conserved domain of a A-crystallin. Biochemistry 37, 12681–8.

    Article  PubMed  CAS  Google Scholar 

  • Koteiche, H. A. and Mchaourab, H. S. (1999). Folding pattern of the acrystallin domain in aA-crystallin determined by site-directed spin labeling. Journal of Molecular Biology 294, 561–77.

    Article  PubMed  CAS  Google Scholar 

  • Kuroki, R., Weaver, L. H. and Matthews, B. W. (1993). A covalent enzyme-substrate intermediate with saccharide distortion in a mutant T4 lysozyme. Science 262, 2030–3.

    Article  PubMed  CAS  Google Scholar 

  • Langen, R., Cai, K., Altenbach, C., Khorana, H. G. and Hubbell, W. L. (1999). Structural features of the C-terminal domain of bovine rhodopsin: a site-directed spin-labeling study. Biochemistry 38, 7918–24.

    Article  PubMed  CAS  Google Scholar 

  • Langen, R., Isas, J. M., Luecke, H., Haigler, H. T. and Hubbell, W. L. (1998). Membrane-mediated assembly of annexins studied by site-directed spin labeling. Journal of Biological Chemistry 273, 22453–7.

    Article  PubMed  CAS  Google Scholar 

  • Liu, Y., Holmgren, M., Jurman, M. E. and Yellen, G. (1997). Gated access to the pore of a voltage-dependent K+ channel. Neuron 19, 175–84.

    Article  PubMed  Google Scholar 

  • Luecke, H., Schobert, B., Richter, H. T., Cartailler, J. P. and Lanyi, J. K. (1999). Structure of bacteriorhodopsin at 1.55 A resolution. Journal of Molecular Biology 291, 899–911.

    Article  PubMed  CAS  Google Scholar 

  • Matthews, B. W. (1995). Studies on protein stability with T4 lysozyme. Advances in Protein Chemistry 46, 249–78.

    Article  PubMed  CAS  Google Scholar 

  • Mchaourab, H. S., Berengian, A. R. and Koteiche, H. A. (1997a). Site-directed spin-labeling study of the structure and subunit interactions along a conserved sequence in the a-crystallin domain of heat-shock protein 27. Evidence of a conserved subunit interface. Biochemistry 36, 14627–34.

    Article  PubMed  CAS  Google Scholar 

  • Mchaourab, H. S., Lietzow, M. A., Hideg, K. and Hubbell, W. L. (1996). Motion of spin-labeled side chains in T4 lysozyme. Correlation with protein structure and dynamics. Biochemistry 35, 7692–704.

    Article  PubMed  CAS  Google Scholar 

  • Mchaourab, H. S., Oh, K. J., Fang, C. J. and Hubbell, W. L. (1997b). Conformation of T4 lysozyme in solution. Hinge-bending motion and the substrate-induced conformational transition studied by site-directed spin labeling. Biochemistry 36, 307–16.

    Article  PubMed  CAS  Google Scholar 

  • Michon, J. and Rassat, A. (1974). Rotational correlation time determination of nitroxide biradical aplication to solution studies. J. Amer. Chem. Soc. 96, 335–337.

    Article  CAS  Google Scholar 

  • Milburn, M. V., Prive, G. G., Milligan, D. L., Scott, W. G., Yeh, J., Jancarik, J., Koshland, D. E., Jr. and Kim, S. H. (1991). Three-dimensional structures of the ligand-binding domain of the bacterial aspartate receptor with and without a ligand. Science 254, 1342–7.

    Article  PubMed  CAS  Google Scholar 

  • Montelione, G. T. and Anderson, S. (1999). Structural genomics: keystone for a Human Proteome Project. Nature Structural Biology 6, 11–2.

    Article  PubMed  CAS  Google Scholar 

  • Ogawa, S. and McConnell, H. M. (1967). Spin-label study of hemoglobin conformations in solution. Proceedings of the National Academy of Sciences of the United States of America 58, 19–26.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Ogawa, S., McConnell, H. M. and Horwitz, A. (1968). Overlapping conformation changes in spin-labeled hemoglobin. Proceedings of the National Academy of Sciences of the United States of America 61, 4015.

    Article  Google Scholar 

  • Oh, K. J., Zhan, H., Cui, C., Hideg, K., Collier, R. J. and Hubbell, W. L. (1996). Organization of diphtheria toxin T domain in bilayers: a site-directed spin labeling study. Science 273, 810–2.

    Article  PubMed  CAS  Google Scholar 

  • Ottemann, K. M., Thorgeirsson, T. E., Kolodziej, A. F., Shin, Y. K. and Koshland, D. E. (1998). Direct Measurement of Small Ligand-Induced Conformational Changes in the Aspartate Chemoreceptor Using Epr. Biochemistry 37, 7062–7069.

    Article  PubMed  CAS  Google Scholar 

  • Ottemann, K. M., Xiao, W. Z., Shin, Y. K. and Koshland, D. E. (1999). A piston model for transmembrane signaling of the aspartate receptor. Science 285, 1751–1754.

    Article  PubMed  CAS  Google Scholar 

  • Pebay-Peyroula, E., Rummel, G., Rosenbusch, J. P. and Landau, E. M. (1997). X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science 277, 1676–81.

    Article  PubMed  CAS  Google Scholar 

  • Perozo, E., Cortes, D. M. and Cuello, L. G. (1998). Three-dimensional architecture and gating mechanism of a K+ channel studied by EPR spectroscopy. Nature Structural Biology 5, 459–69.

    Article  PubMed  CAS  Google Scholar 

  • Perozo, E., Cortes, D. M. and Cuello, L. G. (1999). Structural rearrangements underlying K+-channel activation gating. Science 285, 73–8.

    Article  PubMed  CAS  Google Scholar 

  • Poirier, M. A., Xiao, W., Macosko, J. C., Chan, C., Shin, Y. K. and Bennett, M. K. (1998). The synaptic SNARE complex is a parallel four-stranded helical bundle. Nature Structural Biology 5, 765–9.

    Article  PubMed  CAS  Google Scholar 

  • Rabenstein, M. D. and Shin, Y. K. (1995). Determination of the distance between two spin labels attached to a macromolecule. Proceedings of the National Academy of Sciences of the United States of America 92, 8239–43.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Rabenstein, M. D. and Shin, Y. K. (1996). HIV-1 gp41 tertiary structure studied by EPR spectroscopy. Biochemistry 35, 13922–8.

    Article  PubMed  CAS  Google Scholar 

  • Rees, D. C., DeAntonio, L. and Eisenberg, D. (1989). Hydrophobic organization of membrane proteins. Science 245, 510–3.

    Article  PubMed  CAS  Google Scholar 

  • Rink, T., Riesle, J., Oesterhelt, D., Gerwert, K. and Steinhoff, H. J. (1997). Spin-labeling studies of the conformational changes in the vicinity of D36, D38, T46, and E161 of bacteriorhodopsin during the photocycle. Biophysical Journal 73, 983–93.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Robinson, B. H., Haas, D. A. and Mailer, C. (1994). Molecular dynamics in liquids: spin-lattice relaxation of nitroxide spin labels. Science 263, 490–3.

    Article  PubMed  CAS  Google Scholar 

  • Salwinski, L. and Hubbell, W. L. (1999). Structure in the channel forming domain of colicin El bound to membranes: the 402–424 sequence. Protein Science 8, 562–72.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Schrempf, H., Schmidt, O., Kummerlen, R., Hinnah, S., Muller, D., Betzler, M., Steinkamp, T. and Wagner, R. (1995). A prokaryotic potassium ion channel with two predicted transmembrane segments from Streptomyces lividans. EMBO Journal 14, 5170–8.

    PubMed Central  PubMed  CAS  Google Scholar 

  • Shin, Y. K., Levinthal, C., Levinthal, F. and Hubbell, W. L. (1993). Colicin E 1 binding to membranes: time-resolved studies of spin-labeled mutants. Science 259, 960–3.

    Article  PubMed  CAS  Google Scholar 

  • Steinhoff, H. J. and Hubbell, W. L. (1996). Calculation of electron paramagnetic resonance spectra from Brownian dynamics trajectories: application to nitroxide side chains in proteins. Biophysical Journal 71, 2201–12.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Steinhoff, H. J., Mollaaghababa, R., Altenbach, C., Hideg, K., Krebs, M., Khorana, H. G. and Hubbell, W. L. (1994). Time-resolved detection of structural changes during the photocycle of spin-labeled bacteriorhodopsin. Science 266, 105–7.

    Article  PubMed  CAS  Google Scholar 

  • Subramaniam, S. and Henderson, R. (1999). Electron crystallography of bacteriorhodopsin with millisecond time resolution. Journal of Structural Biology 128, 19–25.

    Article  PubMed  CAS  Google Scholar 

  • Sun, J., Voss, J., Hubbell, W. L. and Kaback, H. R. (1999). Proximity between periplasmic loops in the lactose permease of Escherichia coli as determined by site-directed spin labeling. Biochemistry 38, 3100–5.

    Article  PubMed  CAS  Google Scholar 

  • Sutton, R. B., Fasshauer, D., Jahn, R. and Brunger, A. T. (1998). Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 A resolution. Nature 395, 347–53.

    Article  PubMed  CAS  Google Scholar 

  • Terwilliger, T. C., Waldo, G., Peat, T. S., Newman, J. M., Chu, K. and Berendzen, J. (1998). Class-directed structure determination foundation for a protein structure initiative. Protein Science 7, 1851–6.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Thorgeirsson, T. E., Xiao, W., Brown, L. S., Needleman, R., Lanyi, J. K. and Shin, Y. K. (1997). Transient channel-opening in bacteriorhodopsin: an EPR study. Journal of Molecular Biology 273, 951–7.

    Article  PubMed  CAS  Google Scholar 

  • Ujwal, M. L., Jung, H., Bibi, E., Manoil, C., Altenbach, C., Hubbell, W. L. and Kaback, H. R. (1995). Membrane topology of helices VII and XI in the lactose permease of Escherichia coli studied by lacY-phoA fusion analysis and site-directed spectroscopy. Biochemistry 34, 14909–17.

    Article  PubMed  CAS  Google Scholar 

  • Unger, V. M., Hargrave, P. A., Baldwin, J. M. and Schertler, G. F. (1997). Arrangement of rhodopsin transmembrane a-helices. Nature 389, 2036.

    Google Scholar 

  • Voss, J., He, M. M., Hubbell, W. L. and Kaback, H. R. (1996). Site-directed spin labeling demonstrates that transmembrane domain XII in the lactose permease of Escherichia coli is an a-helix. Biochemistry 35, 12915–8.

    Article  PubMed  CAS  Google Scholar 

  • Voss, J., Hubbell, W. L., Hemandez-Borrell, J. and Kaback, H. R. (1997). Site-directed spin-labeling of transmembrane domain VII and the 4B1 antibody epitope in the lactose permease of Escherichia coli. Biochemistry 36, 15055–61.

    Article  PubMed  CAS  Google Scholar 

  • Voss, J., Hubbell, W. L. and Kaback, H. R. (1995a). Distance determination in proteins using designed metal ion binding sites and site-directed spin labeling: application to the lactose permease of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 92, 12300–3.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Voss, J., Hubbell, W. L. and Kaback, H. R. (1998). Helix packing in the lactose permease determined by metal-nitroxide interaction. Biochemistry 37, 211–6.

    Article  PubMed  CAS  Google Scholar 

  • Voss, J., Salwinski, L., Kaback, H. R. and Hubbell, W. L. (1995b). A method for distance determination in proteins using a designed metal ion binding site and site-directed spin labeling: evaluation with T4 lysozyme. Proceedings of the National Academy of Sciences of the United States of America 92, 12295–9.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Wahl, P. and Weber, G. (1967). Fluorescence depolarization of rabbit gamma globulin conjugates. Journal of Molecular Biology 30, 371–82.

    Article  PubMed  CAS  Google Scholar 

  • Wang, Q., Voss, J., Hubbell, W. L. and Kaback, H. R. (1998). Proximity of helices VIII (Ala273) and IX (Met299) in the lactose permease of Escherichia coli. Biochemistry 37, 4910–5.

    Article  PubMed  Google Scholar 

  • Weber, T., Zemelman, B. V., McNew, J. A., Westermann, B., Gmachl, M., Parlati, F., Sollner, T. H. and Rothman, J. E. (1998). SNAREpins: minimal machinery for membrane fusion. Cell 92, 759–72.

    Article  PubMed  CAS  Google Scholar 

  • Weimbs, T., Low, S. H., Chapin, S. J., Mostov, K. E., Bucher, P. and Hofmann, K. (1997). A conserved domain is present in different families of vesicular fusion proteins: a new superfamily. Proceedings of the National Academy of Sciences of the United States of America 94, 3046–51.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Weissenhorn, W., Dessen, A., Harrison, S. C., Skehel, J. J. and Wiley, D. C. (1997). Atomic structure of the ectodomain from HIV-1 gp41. Nature 387, 426–30.

    Article  PubMed  CAS  Google Scholar 

  • Wu, J., Voss, J., Hubbell, W. L. and Kaback, H. R. (1996). Site-directed spin labeling and chemical crosslinking demonstrate that helix V is close to helices VII and VIII in the lactose permease of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 93, 10123–7.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Yeh, J. I., Biemann, H. P., Prive, G. G., Pandit, J., Koshland, D. E., Jr. and Kim, S. H. (1996). High-resolution structures of the ligand binding domain of the wild-type bacterial aspartate receptor. Journal of Molecular Biology 262, 186–201.

    Article  PubMed  CAS  Google Scholar 

  • Zhao, M., Zen, K. C., Hubbell, W. L. and Kaback, H. R. (1999). Proximity between G1u126 and Arg144 in the lactose permease of Escherichia coli. Biochemistry 38, 7407–12.

    Article  PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA

    Hassane S. Mchaourab

  2. Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, Charlottesville, VA, 22906, USA

    Eduardo Perozo

Authors
  1. Hassane S. Mchaourab
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  2. Eduardo Perozo
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Editors and Affiliations

  1. Ohio State University, Columbus, Ohio, USA

    Lawrence J. Berliner

  2. Department of Chemistry and Biochemistry, University of Denver, 80208, Denver, Colorado, USA

    Gareth R. Eaton  & Sandra S. Eaton  & 

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© 2002 Kluwer Academic / Plenum Publishers, New York

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Mchaourab, H.S., Perozo, E. (2002). Determination of Protein Folds and Conformational Dynamics Using Spin-Labeling EPR Spectroscopy. In: Berliner, L.J., Eaton, G.R., Eaton, S.S. (eds) Distance Measurements in Biological Systems by EPR. Biological Magnetic Resonance, vol 19. Springer, Boston, MA. https://doi.org/10.1007/0-306-47109-4_4

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  • DOI: https://doi.org/10.1007/0-306-47109-4_4

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4757-0575-1

  • Online ISBN: 978-0-306-47109-4

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