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Protein structure by solid-state NMR spectroscopy

Published online by Cambridge University Press:  17 March 2009

S. J. Opella
Affiliation:
Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104U.S.A.
P. L. Stewart
Affiliation:
Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104U.S.A.
K. G. Valentine
Affiliation:
Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104U.S.A.

Extract

The three-dimensional structures of proteins are among the most valuable contributions of biophysics to the understanding of biological systems (Dickerson & Geis, 1969; Creighton, 1983). Protein structures are utilized in the description and interpretation of a wide variety of biological phenomena, including genetic regulation, enzyme mechanisms, antibody recognition, cellular energetics, and macroscopic mechanical and structural properties of molecular assemblies. Virtually all of the information currently available about the structures of proteins at atomic resolution has been obtained from diffraction studies of single crystals of proteins (Wyckoff et al, 1985). However, recently developed NMR methods are capable of determining the structures of proteins and are now being applied to a variety of systems, including proteins in solution and other non-crystalline environments that are not amenable for X-ray diffraction studies. Solid-state NMR methods are useful for proteins that undergo limited overall reorientation by virtue of their being in the crystalline solid state or integral parts of supramolecular structures that do not reorient rapidly in solution. For reviews of applications of solid-state NMR spectroscopy to biological systems see Torchia and VanderHart (1979), Griffin (1981), Oldfield et al. (1982), Opella (1982), Torchia (1982), Gauesh (1984), Torchia (1984) and Opella (1986). This review describes how solid-state NMR can be used to obtain structural information about proteins. Methods applicable to samples with macroscopic orientation are emphasized.

Type
Research Article
Copyright
Copyright © Cambridge University Press 1987

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References

REFERENCES

Abragam, A. (1961). The Principles of Nuclear Magnetism. Oxford.Google Scholar
Arnott, S. & Dover, S. D.. (1967). Refinement of bond angles of an α-helix. J. Mol. Biol. 30, 209212.CrossRefGoogle ScholarPubMed
Asbeck, F., Beyreuther, K., Kohler, H. Von Wettstein, G., & Braunitzer, G. (1969). Virusproteine IV Die Konstitution des Hullproteins des Phagen fd. Hoppe-Seyler's Z. Physiol. Chem 350, 10471066.Google Scholar
Banner, D. W., Nave, C., & Marvin, D. A.. (1981). Structure of the protein and DNA in fd filamentous bacterial virus. Nature 289, 814816.CrossRefGoogle ScholarPubMed
Blinc, R., Mali, M., Osredkar, R., Seliger, J., and Ehrenberg, L. (1974). 14N quadrupole resonance in polyglycine. Chem. Phys. Lett. 28, 158159.CrossRefGoogle Scholar
Braun, W., Bosch, C., Brown, L. R., Go, N. & Wüthrich, K. (1981). Combined use of proton-proton overhauser enhancements and a distance geometry algorithm for determination of polypeptide conformations. Application to micelle-bound glucagon. Biochem. biophys. Acta 667, 377396.Google Scholar
Brown, L. R., Braun, W., Kumar, A. & Wüthrich, K. (1982). High resolution nuclear magnetic resonance studies of the conformation and orientation of melittin bound to a lipid-water interface. Biophys. J. 37, 319328.CrossRefGoogle ScholarPubMed
Brunger, A. T., Clore, G. M., Gronenborn, A. M.. & Karplus, M. (1986). Threedimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc. natn. Acad. Sci. U.S.A. 83, 38013805.CrossRefGoogle ScholarPubMed
Colnago, L. A., Valentine, K. G.. & Opella, S. J.. (1987). Dynamics of fd coat protein in the bacteriophage. Biochemistry 26, 847854.CrossRefGoogle ScholarPubMed
Creighton, T. E.. (1983). Proteins. New York: Freeman.Google Scholar
Cross, T. A., DiVerdi, J. A.. & Opella, S. J.. (1982). Strategy for nitrogen NMR of biopolymers. J. Am. chem. Soc. 104, 17591761.CrossRefGoogle Scholar
Cross, T. A., Frey, M. H.. & Opella, S. J.. (1983a). 15N spin exchange in a protein. J. Am. chem. Soc. 105, 74717473.CrossRefGoogle Scholar
Cross, T. A.. & Opella, S. J.. (1983). Protein structure by solid state NMR. J. Am. chem. Soc. 105, 306308.CrossRefGoogle Scholar
Cross, T. A.. & Opella, S. J.. (1985). Protein structure by solid state NMR: residues 40–45 of fd coat protein. J. molec. Biol. 182, 367381.CrossRefGoogle Scholar
Cross, T. A., Opella, S. J., Stubbs, G. & Caspar, D. L. D.. (1983b). 31P nuclear magnetic resonance of the RNA in tobacco mosaic virus. J. molec. Biol. 170, 10371043.CrossRefGoogle ScholarPubMed
Cross, T. A., Tsang, P. & Opella, S. J.. (1983c). Comparison of protein and DNA structure in fd and Pf1 bacteriophages. Biochemistry 22, 721726.CrossRefGoogle ScholarPubMed
Day, L. A.. & Wiseman, R. L.. (1978). A comparison of DNA packaging in the virions of fd, Xf, and Pf1. In The Single-Stranded DNA Phages (ed. Denhardt, D. T., Dressier, D & Ray, D. S.) Cold Spring Harbor Laboratory, pp. 605625.Google Scholar
Dickerson, R. E.. & Geis, I. (1969). The Structure and Action of Proteins. Menlo Park: Benjamin/Cummings.Google Scholar
Edmonds, D. T.. & Speight, P. A.. (1971). Nitrogen quadrupole resonance in amino acids. Phys. Lett. A 34, 325326.CrossRefGoogle Scholar
Feldman, R. J., Brooks, B. R.. & Lee, B. (1986). Tools for each Age: understanding Protein Architecture Through Simulated Unfolding, Bethesda, Division of Computer Research and Technology, N.I.H.Google Scholar
Frey, M. H.. & Opella, S. J.. (1980). High resolution features of 13C NMR spectra of solid amino acids and peptides. J. chem. Soc. Chem. Comm. pp. 474475.CrossRefGoogle Scholar
Frey, M. H.. & Opella, S. J.. (1984). 13C spin exchange in amino acids and peptides. J. Am. chem. Soc. 106, 49424945.CrossRefGoogle Scholar
Frey, M. H., Opella, S. J., Rockwell, A. L.. & Gierasch, L. M.. (1985). Solid state NMR of cyclic pentapeptides. J. Am. chem. Soc 107, 19461951.CrossRefGoogle Scholar
Fyfe, C. A.. (1983). Solid state NMR for Chemists Guelph: C.F.C. Press.Google Scholar
Gall, C. M., Cross, T. A., DiVerdi, J. A.. & Opella, S. J.. (1982). Protein dynamics by solid-state NMR: aromatic rings of the coat protein in fd bacteriophage. Proc. natn. Acad. Sci. U.S.A. 79, 101105.CrossRefGoogle ScholarPubMed
Ganesh, K. N.. (1984). Biological applications of high resolution solid-state NMR spectroscopy. Appl. Spectrosc. Rev. 20, 107157.CrossRefGoogle Scholar
Griffin, R. G.. (1981). Solid state nuclear magnetic resonance of lipid bilayers. Meth. Enzym. 72, 108174.CrossRefGoogle ScholarPubMed
Griffin, R. G.. Powers, L. & Persham, P. (1978). Head-group conformation in phospholipids: a phosphorus-31 nuclear magnetic resonance study of oriented monodomain dipalmitoyl phosphatidylcholine bilayers. Biochemistry 17, 27182722.CrossRefGoogle Scholar
Gurd, F. R. N.. & Rothgeb, T. M.. (1979). Motions in proteins. Adv. prot. Chem 33, 73165.CrossRefGoogle Scholar
Haeberlen, U. (1976). High Resolution NMR in Solids. Selective Averaging. Academic Press, NY.Google Scholar
Harbison, G. S., Jelinski, L. W., Stark, R. E., Torchia, D. A., Herzfeld, J. & Griffin, R. G.. (1984). 15N chemical shift and 15N-13C dipolar tensors for the peptide bond in [1-13C]glycyl [lsN]glycine hydrochloride monohydrate. J. magn. Reson. 60, 7982.Google Scholar
Havel, T. F.. & Wüthrich, K. (1985). An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution. J. Mol. Biol. 182, 281294.CrossRefGoogle ScholarPubMed
Herzberg, O. & Sussman, J. L.. (1983). Protein model building by the use of a constrained–restrained least-squares procedure. J. appl. Cryst. 16, 144150.CrossRefGoogle Scholar
Hexem, J. G., Frey, M. H.. & Opella, S. J.. (1981). Influence of 14N on 13C NMR spectra of solids, J. am. Soc. 103, 224226.CrossRefGoogle Scholar
Hexem, J. G., Frey, M. H.. & Opella, S. J.. (1982). Molecular and structural information from the 14N–13C dipolar coupling manifested in high resolution 13C NMR spectra of solid. J. chem. Phys. 77, 38473856.CrossRefGoogle Scholar
Hirs, C. H. W.. & Timasheff, S. N.. (eds.) (1986). Enzyme structure. Meth. Enzym. 131, 3653.Google Scholar
Hohener, A., Mueller, L. & Ernst, R. R.. (1979). Dipole-coupled carbon-13 spectra as a source of structural information on liquid crystals. Mol. Phys 38, 909922.CrossRefGoogle Scholar
Jeener, J., Meier, B. H., Bachmann, P. & Ernst, R. R.. (1979). Investigation of exchange processes by two-dimensional NMR spectroscopy. J. chem. Phys. 71, 45464553.CrossRefGoogle Scholar
Kaptein, R., Zuiderweg, E. R. P., Scheek, R. M., Boelens, R. & van Gunsteren, W. F.. (1985). A protein structure from nuclear magnetic resonance data: lac repressor headpiece. J. molec. Biol. 182, 179182.CrossRefGoogle ScholarPubMed
Kricheldorf, H. R.. & Muller, D. (1983). Secondary structure of peptides. 3. 13C NMR cross polarization/magic angle spinning spectroscopic characterization of solid polypeptides. Macromolecules 16, 615628.CrossRefGoogle Scholar
Kricheldorf, H. R., Mutter, M., Maser, F., Muller, D. & Forster, D. (1983). Secondary structure of peptides. 4. 13C-NMR CP/MAS investigation of solid oligoand poly(L-alanines). Biopolymers 2, 13571372.CrossRefGoogle Scholar
Lee, R. W. K.. & Oldfield, E. (1982). Nuclear magnetic resonance of hemeprotein crystals: structure of the heme in physeter catodon ferrimyoglobin and an analysis of hyperfine shifts. J. biol. Chem. 257, 50235029.CrossRefGoogle Scholar
Lesk, A. M.. & Hardman, K. D.. (1985). Computer-generated pictures of proteins. Meth. Enzym. 115, 381390.CrossRefGoogle ScholarPubMed
Lewis, B. A., Harbison, G. S., Herzfeld, J. & Griffin, R. G.. (1985). NMR structural analysis of a membrane protein: bacteriorhodopsin peptide backbone orientation and motion. Biochemistry 24, 46714679.CrossRefGoogle ScholarPubMed
Makowski, L. (1984). Structural diversity in filamentous bacteriophages. In Biological Macromolecules and Assemblies, vol. 1, The Viruses, (ed. McPherson, A), pp. 203253. York: Wiley.Google Scholar
Makowski, L. & Caspar, D. L. D.. (1981). The symmetries of filamentous phage particles. J. molec. Biol. 145, 611617.Google Scholar
Maret, G. & Dransfeld, K. (1985). Biomolecules and polymers in high steady magnetic fields. In Topics in Applied Physics (ed. Herloch, F.) 57, pp. 142204. Springer-Verlag.Google Scholar
Marvin, D. A.. & Hohn, B. (1969). Filamentous bacterial viruses, Bact. Rev. 33, 172209.CrossRefGoogle ScholarPubMed
Marvin, D. A., Pigram, W. J., Wiseman, R. L., Wachtel, E. J.. & Marvin, F. J.. (1974). Filamentous bacterial viruses XII molecular architecture of the class I (fd, If1, Ike) virion. J. Mol. Biol. 88, 581600.CrossRefGoogle Scholar
McLaughlin, A. C., Cullis, P. R., Hemminga, M. A., Hoult, D. I., Radda, G. K., Ritchie, G. A., Seeley, P. J.. & Richards, R. E.. (1975). Application of 31P NMR to model and biological membrane systems. FEBS Lett. 57, 213217.CrossRefGoogle ScholarPubMed
Mehring, M. (1983). Principles of High Resolution NMR in solids, 2nd ed.Berlin: Springer-Verlag.CrossRefGoogle Scholar
Moult, J., Yonath, A., Traub, W., Smilansky, A., Podjarny, A., Rabinovich, D., & Saya, A. (1976). The structure of Triclinic Lysozyme at 2·5 A Resolution. J. Mol. Biol. 100, 179195.CrossRefGoogle ScholarPubMed
Naito, A., Ganapathy, S. & McDowell, C. A.. (1982). 14N Quadrupole effects in CP-MAS 13C NMR spectra of organic compounds in the solid state. J. Magn. Reson. 48, 367381.Google Scholar
Nakashima, Y. & Konigsberg, W. (1974). Reinvestigation of a region of fd bactenophage coat protein sequence. J. Mol. Biol. 88, 598600.CrossRefGoogle ScholarPubMed
Nall, B. T., Rothwell, W. P., Waugh, J. S.. & Rupprecht, A. (1981). Stuctural studies of A-form sodium deoxyribonucleic acid: phosphorus-31 nuclear magnetic resonance of oriented fibers. Biochemistry 20, 18811887.CrossRefGoogle Scholar
Nave, C., Fowler, A. G., Malsey, S., Marvin, D. A., Siegrist, H., & Wachtel, E. J.. (1979). Macromolecular Structural Transition in Pf1 Filamentous Bacterial Virus. Nature 281, 232234.CrossRefGoogle ScholarPubMed
Oldfield, E., Kinsey, R. A.. & Kintanar, A. (1982). Recent advances in the study of bacteriorhodopsin dynamic structure using high-field solid-state nuclear magnetic resonance spectroscopy. Meth. Enzym. 88, 310324.CrossRefGoogle Scholar
Oldfield, E. & Rothgeb, T. M.. (1980). NMR of individual sites in protein crystals. Magnetic ordering effects. J. Am. chem. Soc. 102, 36353637.CrossRefGoogle Scholar
Opella, S. J.. (1982). Solid state NMR of biological systems. A. Rev. phys. Chem. 33, 533562.CrossRefGoogle Scholar
Opella, S. J.. (1986). Protein dynamics by solid state nuclear magentic resonance. Meth. Enzym. 131, 327361.CrossRefGoogle Scholar
Opella, S. J.. & Gierasch, L. M.. (1985). Solid state nuclear magnetic resonance of peptides. In The Peptides: Analysis, Synthesis, Biology, vol. 7 (ed. Udenfriend, S, Meienhofer, H and Hruby, V), pp. 405436.Google Scholar
Opella, S. J.. & Waugh, J. S.. (1977). Two-dimensional 13C NMR of highly oriented polyethylene. J. Chem. Phys. 66, 49194924.CrossRefGoogle Scholar
Pease, L. G., Frey, M. H.. & Opella, S. J.. (1981). Observation of conformationally distinct proline residues in two cyclic peptides by solid-state nuclear magnetic resonance. J. Am. chem. Soc. 103, 467468.CrossRefGoogle Scholar
Phillips, D. C.. (1966). The three-dimensional structure of an enzyme molecule. Sci. Am. 215 (5), 7890.CrossRefGoogle ScholarPubMed
Pines, A., Gibby, M. G.. & Waugh, J. S.. (1973). Proton-enhanced NMR of dilute spins in solids. J. chem. Phys 59, 569590.CrossRefGoogle Scholar
Ramachandran, G. N.. & Sasisekharan, V. (1968). Conformation of polypeptides and proteins. Adv. protein Chem. 23, 283437.CrossRefGoogle ScholarPubMed
Richardson, J. S.. (1981). The anatomy and taxonomy of protein structure. Adv. protein Chem. 34, 167–139.Google Scholar
Rothgeb, T. M.. & Oldfield, E. (1981). Nuclear magnetic resonance of heme protein crystals: General Aspects. J. biol. Chem. 256, 14321446.CrossRefGoogle ScholarPubMed
Sadiq, G. F., Greenbaum, S. G.. & Bray, P. J.. (1981). 14N nuclear quadrupole resonance in N-acetyl amino acids. Org. magn. Reson 17, 191193.CrossRefGoogle Scholar
Saito, H., Tabeta, R., Asakura, T., Iwanaga, Y., Shoji, A., Ozaki, T. & Ando, I. (1984). High-resolution 13C NMR study of silk fibroin in the solid state by crosspolarization-magic angle spinning method. Macromolecules 17, 14051412.CrossRefGoogle Scholar
Saito, H., Tabeta, R., Shoji, A., Ozaki, T. & Ando, I. (1983). Conformational characterization of polypeptides in the solid state as viewed from the conformationdependent 13C chemical shifts. Macromolecules 16, 10501057.CrossRefGoogle Scholar
Schiksnis, R. A., Bogusky, M., Tsang, P. & Opella, S. J.. (1987). Structure and dynamics of the Pf1 filamentous bacteriophages coat protein in micelles. Biochemistry (in the Press).CrossRefGoogle Scholar
Seelig, J. & Niederberger, W. (1974). Deuterium labeled lipids as structural probes in liquid crystalline bilayers. J. Am. Chem. Soc. 96, 20692072.CrossRefGoogle Scholar
Shindo, H. (1984). Solid-state phosphorus-31 NMR: Theory and application to nucleic acids. In Phosphorus-31 NMR Principles and Applications (ed. Gorenstein, D. G.) pp. 401422. New York: Academic Press.Google Scholar
Spiess, H. W.. (1982a). NMR in oriented polymers. In Developments in Oriented Polymers-1. (ed. Ward, I. M.), pp. 4770. London: Appl. Sci. Publ.Google Scholar
Spiess, H. W.. (1982b). Rotation of molecules and nuclear spin relaxation. NMR Basic Princ. Prog. 15, 55214.Google Scholar
Stark, R. E., Haberkorn, R. A.. & Griffin, R. G.. (1978). 14N NMR determination of NH bond lengths in solids. J. chem. Phys. 68, 19961997.CrossRefGoogle Scholar
Stark, R. E., Jelinski, L. W., Ruben, D. J., Torchia, D. A.. & Griffin, R. G.. (1983). 13C chemical shift and 13C–15N dipolar tensors for the peptide bond: [1 - 13C]glycyl [15N]glycine HC1·H2O. J. magn. Reson. 55, 266273.Google Scholar
Stewart, P. L., Valentine, K. G.. & Opella, S. J.. (1987). Structural analysis of solid state NMR measurements of peptides and proteins. J. magn. Reson. 71, 4561.Google Scholar
Subramanian, E. & Lalitha, V. (1983). Crystal structure of a tripeptide L-alanylglycyl-glycine and its relevance to the poly(glycine)-II type of conformation. Biopolymers 22, 833838.CrossRefGoogle Scholar
Taki, T., Yamashita, S., Satoh, M., Shibata, A., Yamashita, T., Tabeta, R. & Saito, H. (1981). 13C chemical shifts of solid polypeptides by cross polarization/magic angle spinning (CP/MAS) NMR spectroscopy: conformation-dependent 13C shifts characteristic of a-helix and β-sheet forms. Chem. Lett. pp. 18031806.CrossRefGoogle Scholar
Thomas, G. J., Prescott, B. & Day, L. (1983). Structure, similarity, differences, and variability in the filamentous viruses fd, If1, IKe, Pf1, and Xf. J. Mol. Biol. 165, 321356.CrossRefGoogle ScholarPubMed
Torbet, J. & Maret, G. (1979). Fibres of highly oriented Pf1 bacteriophage produced in a strong magnetic field. J. Mol. Biol. 134, 843845.CrossRefGoogle Scholar
Torbet, J. & Maret, G. (1981). High-field magnetic birefringence study of the structure of rod like phages Pf1 and fd in solution. Biopolymers 20, 26572669.CrossRefGoogle Scholar
Torchia, D. A.. (1982). Solid state NMR studies of molecular motion in collagen fibrils. Meth. Enzym. 82, 174186.CrossRefGoogle Scholar
Torchia, D. A.. (1984). Solid state NMR studies of protein internal dynamics. Ann. Rev. Biophys. Bioeng. 13, 124144.Google ScholarPubMed
Torchia, D. A.. & VanderHart, D. L.. (1979). High-power double-resonance studies of fibrous proteins, proteoglycans, and model membranes. Top. Carbon-13 NMR Spectrosc. 3, 325360.Google Scholar
Tsang, P. and Opella, S. J.. (1986). Pf1 virus particle dynamics. Biopolymers 25, 18591864.CrossRefGoogle ScholarPubMed
Tycko, R. & Opella, S. J.. (1986). High resolution 14N overtone spectroscopy. J. Am. chem. Soc. 108, 35313532.CrossRefGoogle Scholar
Tycko, R., Stewart, P. L.. & Opella, S. J.. (1986). Peptide plane orientations determined by fundamental and overtone 14N NMR. J. Ant. chem. Soc. 108, 54195425.CrossRefGoogle Scholar
Valentine, K. G., Schneider, D. M., Leo, G. C., Colnago, L. A.. & Opella, S. J.. (1985). Structure and dynamics of fd coat protein. Biophys. J. 49, 3638.CrossRefGoogle Scholar
Vold, R. R., Brandes, R., Tsang, P., Kearns, D. R., Vold, R. L.. & Rupprecht, A. (1986). Deuterium NMR spectra and librational motions of the base pairs in oriented calf thymus DNA. J. Am. Chem. Soc. 108, 302303.CrossRefGoogle Scholar
Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids. New York: Wiley.CrossRefGoogle Scholar
Wyckoff, H. W., Hirs, C. H. W.. & Timasheff, S. N.. (1985). Diffraction methods for biological macromolecules. Part A and Part B. Meth. Enzym. 114, 115, Orlando, Academic Press.Google Scholar
Zumbulyadis, N., Henrichs, P. M.. & Young, R. H.. (1981). Quadrupole effects in the magic-angle-spinning spectra of spin– 1/2 nuclei. J. Chem. Phys 75, 16031611.CrossRefGoogle Scholar