Structural studies of amyloids by quenched hydrogen-deuterium exchange by NMR

Methods in Molecular Biology

Volumn 849, Issue , 2012, Pages 185-198

  Vilar, Marçal ^a   Wang, Lei ^b   Riek, Roland ^b  

^a INSTITUTO DE SALUD CARLOS III   (Spain)

^b ETH ZURICH   (Switzerland)

Author keywords

A , synuclein; Amyloid fibrils; H D exchange; NMR

Indexed keywords

ALPHA SYNUCLEIN; AMYLOID; DIMETHYL SULFOXIDE;

ARTICLE; DEUTERIUM HYDROGEN EXCHANGE; HETERONUCLEAR MULTIPLE QUANTUM COHERENCE; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN FOLDING; CHEMISTRY; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN MULTIMERIZATION; PROTEIN SECONDARY STRUCTURE; SOLUBILITY;

AMYLOID; DEUTERIUM EXCHANGE MEASUREMENT; DIMETHYL SULFOXIDE; MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY; SOLUBILITY;

EID: 84864621493     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-551-0_13     Document Type: Article

References (27)

1. Tycko, R. (2000) Solid-state NMR as a probe of amyloid fi bril structure. Curr. Opin. Chem. Biol 4 , 500-506
2. Cohen, A. S., and Calkins, E. (1959) Electron microscopic observations on a fi brous component in amyloid of diverse origins. Nature 183 , 1202-1203
3. Eanes, E. D., Glenner, G. G. (1968) X-ray diffraction studies on amyloid fi laments. J. Histochem. Cytochem. 16 , 673-677
4. Sipe, J.D., Cohen, A. S. (2000) Review: history of the amyloid fi bril. J. Struct. Biol 130 , 88-98
5. Sunde, M., Serpell, L. C., Bartlam, M., Fraser, P. E., Pepys, M. B., Blake, C. C. (1997) Common core structure of amyloid fi brils by synchrotron X-ray diffraction. J. Mol. Biol. 273 , 729-39
6. Shewmaker, F., Wickner, R. B., Tycko, R. (2006) Amyloid of the prion domain of Sup35p has an in-register parallel beta-sheet structure. Proc. Natl. Acad. Sci. USA 103 , 19754-19759
7. van der Wel, P. C., Lewandowski, J. R., Griffi n, R. G. (2007) Solid-state NMR study of amyloid nanocrystals and fi brils formed by the peptide GNNQQNY from yeast prion protein Sup35p. J. Am. Chem. Soc 129 , 5117-5130
8. Hoshino, M., Katou, H., Hagihara, Y., Hasegawa, K., Naiki, H., Goto, Y. (2002) Mapping the core of the beta(2)-microglobulin amyloid fi bril by H/D exchange. Nat. Struct. Biol 9 , 332-336
9. Wasmer, C., Lange, A., Van Melckebeke, H., Siemer, A. B., Riek, R., Meier, B. H. (2008) Amyloid fi brils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core. Science 319, 1523-1526
10. Castellani, F., van Rossum, B., Diehl, A., Schubert, M., Rehbein, K., Oschkinat, H. (2002) Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy. Nature 420 , 98-102
11. Heise, H., Hoyer, W., Becker, S., Andronesi, O. C., Riedel, D., Baldus, M. (2005) Molecularlevel secondary structure, polymorphism, and dynamics of full-length alpha-synuclein fi brils studied by solid-state NMR. Proc. Natl. Acad. Sci. USA. 102 , 15871-15876
12. Nelson, R., Sawaya, M. R., Balbirnie, M., Madsen, A. Oø., Riekel, C., Grothe, R., Eisenberg, D. (2005) Structure of the cross-beta spine of amyloid-like fi brils. Nature 435 , 773-778
13. Alexandrescu, A. T. (2001) An NMR-based quenched hydrogen exchange investigation of model amyloid fi brils formed by cold shock protein A. Pac. Symp. Biocomput 67-78
14. Wang, L., Schubert, D., Sawaya, M. R., Eisenberg, D., Riek, R. (2010) Multidimensional structure-activity relationship of a protein in its aggregated states. Angew. Chem. Int. Ed. Engl 49 , 3904-3908
15. Wang, L., Maji, S. K., Sawaya, M. R., Eisenberg, D, Riek, R. (2008) Bacterial inclusion bodies contain amyloid-like structure. PLoS Biol 6 :e195
16. Vilar, M., Chou, H. T., Lührs, T., Maji, S. K., Riek-Loher, D., Verel, R., Manning, G., Stahlberg, H., Riek, R. (2008) The fold of alpha-synuclein fi brils. Proc. Natl. Acad. Sci. USA 105 , 8637-8642
17. Ritter, C., Maddelein, M. L., Siemer, A. B., Lührs, T., Ernst, M., Meier, B. H., Saupe, S. J., Riek, R. (2005) Correlation of structural elements and infectivity of the HET-s prion. Nature 435 , 844-848
18. Lührs, T., Ritter, C., Adrian, M., Riek-Loher, D., Bohrmann, B., Döbeli, H., Schubert, D., Riek, R. (2005) 3D structure of Alzheimer's amyloid-beta(1-42) fi brils. Proc. Natl. Acad. Sci. USA 102 , 17342-17347
19. Zhang, Y. Z., Paterson, Y., Roder, H. (1995) Rapid amide proton exchange rates in peptides and proteins measured by solvent quenching and two-dimensional NMR. Protein Sci 4, 804-814
20. Englander, S. W. ( http://HX2.Med.Upenn. edu/)
21. Gal, M., Kern, T., Schanda, P., Frydman, L., Brutscher, B. (2009) An improved ultrafast 2D NMR experiment: towards atom-resolved realtime studies of protein kinetics at multi-Hz rates. J. Biomol. NMR 43 , 1-10
22. Hirota-Nakaoka, N., Hasegawa, K., Naiki, H., Goto, Y. (2003) Dissolution of beta2-microglobulin amyloid fi brils by dimethylsulfoxide. J. Biochem 134 , 159-64
23. Grzesiek, S. and Bax, A. (1992) Improved 3D Triple-Resonance NMR Techniques Applied to a 31-kDa Protein. J. Magn. Reson 96 , 432-440
24. Bracken, C., Palmer, A. G. 3rd, and Cavanagh, J. (1997) (H)N(COCA)NH and HN(COCA) NH experiments for 1H-15N backbone assignments in 13C/15N-labeled proteins. J. Biomol. NMR 9 , 94-100
25. Cavanagh, J., Fairbrother, W. J., Palmer, A. G. 3rd, Rance, M., Skelton, N. J. (2007) Protein NMR spectroscopy : principles and practice. Academic Press; San Diego
26. Griffey, R. H., Poulter, C. D., Bax, A., Hawkins, B. L., Yamaizumi, Z., Nishimura, S. (1983) Multiple quantum two-dimensional 1H-15N nuclear magnetic resonance spectroscopy: chemical shift correlation maps for exchangeable imino protons of Escherichia coli tRNAMetf in water. Proc Natl Acad Sci USA 80 , 5895-5897
27. Güntert, P., Dötsch, V., Wider, G., and Wüthrich, K. (1992). Processing of Multi-Dimensional NMR Data with the New Software PROSA. J. Biomol. NMR 2 , 619-629.