Abstract
The distance measurement method based on Fourier deconvolution of dipolar coupling in spin-labeled EPR spectra provides a new way of examining the structure and function of biological macromolecules. In this chapter, we describe a new approach that has been developed for effective and reasonably accurate data analysis, followed by discussions of several successful applications to interesting biological problems on membrane-associated proteins. This method of EPR spectroscopic ruler has emerged as a powerful tool to investigate the functions of membrane-associated proteins.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Ban, N., Nissen, P., Hansen, J., Capel, M., Moore, P., and Steitz, T. (1999). Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit. Nature 400, 841–847.
Bennett, M., and Scheller, R. (1994). A molecular description of synaptic vesicle membrane trafficking. Ann. Rev. Biochem. 63, 63–100.
Berger, B., Wilson, D. B., Wolf, E., Tonchev, T., Mille, M., and Kim, P. S. (1995). Predicting coiled coils by use of pairwise residue correlations. Proc. Natl. Acad. Sci. USA 92, 8259–8263.
Broadie, K., Prokop, A., Bellen, H., O’Kane, C., Schulze, K., and Sweeney, S. (1995). Syntaxin and synaptobrevin function downstream of vesicle docking in Drosophila. Neuron 15, 663–673.
Cate, J., Yusupov, M., Yusupova, G., Earnest, T., and Noller, H. (1999). X-ray crystal structures of 70S ribosome functional complexes. Science 285, 2095–2104.
Chapman, E., An, S., Barton, N., and Jahn, R. (1994). SNAP-25, a t-SNARE which binds to both syntaxin and synaptobrevin via domains that may form coiled coils. J. Biol. Chem. 269, 27427–27432.
Clemons, W., May, J., Wimberly, B., McCutcheon, J., Capel, M., and Ramakrishnan, V. (1999). Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution. Nature 400, 833–840.
Creighton, T. (1983). “Proteins”, Freeman, New York, NY.
Edman, K., Nollert, P., Royant, A., Belrhali, H., Pebay-Peyroula, E., Hajdu, J., Neutze, R. and Landau, E. M. (1999). High-resolution X-ray structure of an early intermediate in the bacteriorhodopsin photocycle. Nature 401, 822–826.
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, 768–770.
Fasshauer, D., Bruns, D., Shen, B., Jahn, R., and Briinger, A. T. (1997a). A structural change occurs upon binding of syntaxin to SNAP-25. J. Biol. Chem. 272, 4582–4590.
Fasshauer, D., Otto, H., Eliason, W., Jahn, R., and Brünger, A. T. (1997b). Structural changes are associated with soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor complex formation. J Biol. Chem. 272, 28036–28041.
Gerstein, M. (1998). Patterns of protein-fold usage in eight microbial genomes: a comprehensive structural census. Proteins 33, 518–534.
Grigorieff, N., Ceska, T. A., Downing, K. H., Baldwin, J. M. and Henderson, R. (1996). Electron crystallographic refinement of the structure of bacteriorhodopsin. J. Mol. Biol. 259, 393–421.
Hanson, P., Roth, R., Morisaki, H., Jahn, R., and Heuser, J. (1997). Structure and conformational changes in NSF and its membrane receptor complexes visualized by quick-freeze/deep-etch electron microscopy. Cell 90, 523–535.
Haupts, U., Tittor, J., and Oesterhelt, D. (1997) Closing in on bacteriorhodopsin: progress in understanding the molecule. Ann. Rev. Biophys. Biomol. Struct. 28, 367–399.
Hayashi, T., McMahon, H., Yamasaki, S., Binz, T., Hata, Y., Südhof, T., and Nieman, H. (1994). Synaptic vesicle membrane fusion complex: action of clostridial neurotoxins on assembly. EMBO J. 13, 5051–5061.
Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, R., Beckmann, E. and Downing, K. H. (1990). Model for the structure of bacteriorhodopsin based on high-resolution electron cryomicroscopy. J. Mol. Biol. 213, 899–929.
Hubbell W. L., and Altenbach C. (1994). Investigation of structure and dynamics in membrane proteins using site-directed spin labelling. Curr. Opin. Struct. Biol. 4, 566–573.
Hustedt, E., and Beth, A. (1999). Nitroxide spin-spin interactions: applications to protein structure and dynamics. Ann. Rev. Biophys. Biomol. Struct. 28, 129–153.
Iwata, S., Ostermeier, C., Ludwig, B., and Michel, H. (1995). Structure at 2.8 A resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 376, 660–669.
Jardetzky, O. (1966). Simple allosteric model for membrane pumps. Nature 211, 969–970.
Kee, Y., Lin, R., Hsu, S., and Scheller, R. (1995). Distinct domains of syntaxin are required for synaptic vesicle fusion complex formation and dissociation. Neuron 14, 991–998.
Lanyi, J. K. (1995). Bacteriorhodopsin as a model for proton pumps. Nature 375, 461–463.
Lin, R., and Scheller, R. (1997). Structural organization of the synaptic exocytosis core complex. Neuron 19, 1087–1094.
Luecke, H., Schobert, B., Richter, H.T., Cartailler, J. P. and Lanyi, J. K. (1999) Structural changes in bacteriorhodopsin during ion transport at 2 Angstrom resolution. Science 286, 255–260.
Lupas, A. (1996). Prediction and analysis of coiled-coil structures. Methods Enzymol. 266, 513–525.
Marqusee S., Robbins V., Baldwin R. (1989). Unusually stable helix formation in short alanine-based peptides. Proc. Natl. Acad. Sci. USA 86, 5286–5290.
Milligan, D. L., and Koshland, D. E. (1991). Intrasubunit signal transduction by the aspartate chemoreceptor. Science 254, 1651–1654.
Nickel, W., Weber, T., McNew, J. A., Parlati, F., Sollner, T. H., and Rothman, J. E. (1999). Content mixing and membrane integrity during membrane fusion driven by pairing of isolated v-SNAREs and t-SNAREs. Proc. Natl. Acad. Sci. USA 96, 12571–12576.
Niemann, H., Blasi, J., and Jahn, R. (1994). Clostridial neurotoxins: New tools for dissecting exocytosis. Trends Cell Biol. 4, 179–185.
Ottemann, K. M., Thorgeirsson, T., Kolodziej, A., 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.
Ottemann, K. M., Xiao, W., Shin, Y.-K., and Koshland, D. E. (1999). A piston model for transmembrane signaling of the aspartate receptor. Science 285, 1751–1754.
Otto, H., Hanson, P., and Jahn, R. (1997). Assembly and disassembly of a ternary complex of synaptobrevin, syntaxin, and SNAP-25 in the membrane of synaptic vesicles. Proc. Natl. Acad. Sci. USA 94, 6197–6201.
Parlati, F., Weber, T., McNew, J., Westermann, B., Sollner, T., and Rothman, J. E. (1999) Rapid and efficient fusion of phospholipid vesicles by the alpha-helical core of a SNARE complex in the absence of an N-terminal regulatory domain. Proc. Natl. Acad. Sci. USA 96, 12565–12570.
Pebay-Peyroula, E., Rummel, G., Rosenbusch, J., and Landau, E. (1997). X-ray structure of bacteriorhodopsin at 2.5 angstroms from microcrystals grown in lipidic cubic phases. Science 277, 1676–1681.
Perozo, E., Cortes, D. M., and Cuello, L. G. (1999). Structural rearrangements underlying K+-channel activation gating. Science 285: 73–78.
Poirier, M., Hao, J., Malkus, P., Chan, C., Moore, M., King, D., and Bennett, M. (1998a) Protease resistance of syntaxin SNAP-25 VAMP complexes. J. Biol. Chem. 273, 11370–11377.
Poirier, M., Xiao, W., Macosko, J., Chan, C., Shin, Y.-K., and Bennett, M. (1998b). The synaptic SNARE complex is a parallel four-stranded helical bundle. Nature Struct. Biol. 5, 765–769.
Rabenstein, M., and Shin, Y.-K. (1995). Determination of the distance between two spin labels attached to a macromolecule. Proc. Natl. Acad. Sci. USA 92, 8239–8243.
Spudich, J. L. and Lanyi, J. K. (1996). Shuttling between two protein conformations: the common mechanism for sensory transduction and ion transport. Curr. Opin. Cell. Biol. 8, 452–457.
Subramaniam S., Gerstein M., Oesterhelt D. and Henderson R. (1993). Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin. EMBOJ. 12, 1–8.
Südhof, T. (1995). The synaptic vesicle cycle: a cascade of protein-protein interactions. Nature 375, 645–653.
Sutton, R. B., Fasshauer, D., Jahn, R., and Brünger, A. T. (1998). Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 angstrom resolution. Nature 395, 347–353.
Tanford, C. (1983). Translocation pathway in the catalysis of active transport. Proc. Natl. Acad. Sci. USA 80, 3701–3705.
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. J. Mol. Biol. 273, 951–957.
Unwin, N. (1995). Acetylcholine receptor channel imaged in the open state. Nature 373, 37–43.
Vonck, J. (1996). A three-dimensional difference map of the N intermediate in the bacteriorhodopsin photocycle: part of the F helix tilts in the M to N transition. Biochemistry 35, 5870–5878.
Weber, T., Zemeiman, B., McNew, J., Westermann, B., Gmachi, M., Panarti, F., Sóliner, T., and Rothman, J. E. (1998). SNAREpins: Minimal machinery for membrane fusion. Cell 92, 759–772.
Weimbs, T., Low, S., Chapin, S., Mostov, K., Bucher, P., and Hofmann, K. (1997). A conserved domain is present in different families of vesicular fusion proteins: a new superfamily. Proc. Natl. Acad. Sci. U S A 94, 3046–3051.
Weimbs, T., Mostov, K., Low, S., and Hofinan, K. (1998). A model for structural similarity between different SNARE complexes based on sequence relationships. Trends Cell Biol. 8, 260–262.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Kluwer Academic / Plenum Publishers, New York
About this chapter
Cite this chapter
Xiao, W., Shin, YK. (2002). EPR Spectroscopic Ruler: the Method and its Applications. 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_5
Download citation
DOI: https://doi.org/10.1007/0-306-47109-4_5
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4757-0575-1
Online ISBN: 978-0-306-47109-4
eBook Packages: Springer Book Archive