Slow Conformational Dynamics in the Hamster Prion Protein

Biochemistry

Volumn 43, Issue 15, 2004, Pages 4439-4446

  Kuwata, Kazuo ^a   Kamatari, Yuji O ^b   Akasaka, Kazuyuki ^c   James, Thomas L ^d  

^a GIFU UNIVERSITY   (Japan)

^b RIKEN HARIMA INSTITUTE   (Japan)

^c KINKI UNIVERSITY   (Japan)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; NUCLEAR MAGNETIC RESONANCE; PRESSURE EFFECTS; PROTEINS;

ATOMIC RESOLUTION; CONFORMATIONAL CONVERSION; CONFORMATIONAL DYNAMICS; PUTATIVE EXCHANGE;

BIOCHEMISTRY;

PRION PROTEIN; RECOMBINANT PROTEIN;

ARTICLE; CONFORMATIONAL TRANSITION; HAMSTER; MOLECULAR DYNAMICS; NITROGEN NUCLEAR MAGNETIC RESONANCE; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; THERMODYNAMICS;

ANIMALS; CRICETINAE; MESOCRICETUS; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDE FRAGMENTS; PRESSURE; PRIONS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; THERMODYNAMICS; TIME FACTORS;

ANIMALIA; CRICETINAE;

EID: 4744351381     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi036123o     Document Type: Article

References (39)

1. Chazot, G., Broussolle, E., Lapras, C. I., Blättler, T., Aguzzi, A., and Kopp, N. (1996) New Variant of Creutzfeldt-Jakob Disease in a 26-Year-Old French Man. Lancet 347, 1181.
2. Will, R. G., Ironside, J. W., Zeidler, M., Cousens, S. N., Estibeiro, K., Alperovitch, A., Poser, S., Pocchiari, M., Hofman, A., and Smith, P. G. (1996) A New Variant of Creutzfeldt-Jakob Disease in the UK. Lancet. 347, 921-925.
3. Prusiner, S. B. (1982) Novel proteinaceous infectious particles cause scrapie. Science 216, 136-144.
4. Prusiner, S. B. (1991) Molecular Biology of Prion Diseases. Science 252, 1515-1522.
5. Stahl, N., Baldwin, M. A., Teplow, D. B., Hood, L., Gibson, B. W., Burlingame, A. L., and Prusiner, S. B. (1993) Structural studies of the scrapie prion protein using mass spectrometry and amino acid sequencing. Biochemistry 32, 1991-2002.
6. Pan, K.-M., Baldwin, M., Nguyen, J., Gasset, M., Serban, A., Groth, D., Mehlhorn, I., Huang, Z., Fletterick, R. J., Cohen, F. E., and Prusiner, S. B. (1993) Conversion of α-Helices into β-Sheets Features in the Formation of the Scrapie Prion Proteins. Proc. Natl. Acad. Sci. U.S.A. 90, 10962-10966.
7. Riek, R., Hornemann, S., Wider, G., Billeter, M., Glockshuber, R., and Wüthrich, K. (1996) NMR Structure of the Mouse Prion Protein Domain PrP(121-231). Nature 382, 180-182.
8. James, T. L., Liu, H., Ulyanov, N. B., Farr-Jones, S., Zhang, H., Donne, D. G., Kaneko, K., Groth, D., Mehlhorn, I., Prusiner, S. B., and Cohen, F. E. (1997) Solution structure of a 142-residue recombinant prion protein corresponding to the infectious fragment of the scrapieisoform. Proc. Natl. Acad. Sci. U.S.A. 94, 10086-10091.
9. Lopez Garcia, F., Zahn, R., Riek, R., and Wuthrich, K. (2000) NMR structure of the bovine prion protein. Proc. Natl. Acad. Sci. U.S.A. 97, 8334-8339.
10. Calzolai, L., Lysek, D. A., Guntert, P., von Schroetter, C., Riek, R., Zahn, R., and Wuthrich, K. (2000) NMR structures of three single-residue variants of the human prion protein. Proc. Natl. Acad. Sci. U.S.A. 97, 8340-8345.
11. Liu, H., Farr-Jones, S., Ulyanov, N. B., Llinas, M., Marqusee, S., Groth, D., Cohen, F. E., Prusiner, S. B., and James, T. L. (1999) Solution structure of Syrian hamster prion protein rPrP(90-231). Biochemistry 38, 5362-5377.
12. Viles, J. H., Donne, D., Kroon, G., Prusiner, S. B., Cohen, F. E., Dyson, H. J., and Wright, P. E. (2001) Local structural plasticity of the prion protein. Analysis of NMR relaxation dynamics. Biochemistry 40, 2743-2753.
13. Sc? Biochemistry 41, 12277-12283.
14. Luz, Z., and Meiboom, S. (1963) Nuclear Magnetic Resonance Study of the Protolysis of Trimethylammonium Ion in Aqueous Solution - Order of the Reaction with Respect to Solvent. J. Chem. Phys. 39, 366.
15. Prusiner, S. B. (1996) Human Prion Diseases and Neurodegeneration. Curr. Top. Microbiol. Immunol. 207, 1-17.
16. Buevich, A. V., and Baum, J. (1999) Dynamics of unfolded proteins: incorporation of distributions of correlation times in the model free analysis of NMR relaxation data. J. Am. Chem. Soc. 121, 8671-8672.
17. Uversky, V. N. (2002) Natively unfolded proteins: a point where biology waits for physics. Protein Sci. 11, 739-756.
18. Farrow, N. A., Zhang, O., Forman-Kay, J. D., and Kay, L. E. (1995) Comparison of the backbone dynamics of a folded and an unfolded SH3 domain existing in equilibrium in aqueous buffer. Biochemistry 34, 868-878.
19. Mulder, F. A. A., Spronk, C. A., E. M., Slijper, M., Kaptein, R., and Boelens, R. (1996) Improved HSQC Experiments for the Observation of Exchange Broadened Signals. J. Biomolec. NMR. 8, 223-228.
20. van Tilborg, P. J., Mulder, F. A., de Backer, M. M., Nair, M., van Heerde, E. C., Folkers, G., van der Saag, P. T., Karimi-Nejad, Y., Boelens, R., and Kaptein, R. (1999) Millisecond to micro-second time scale dynamics of the retinoid X and retinoic acid receptor DNA-binding domains and dimeric complex formation. Biochemistry 38, 1951-1956.
21. Palmer, A. G., III, Skelton, N. J., Chazin, W. J., Wright, P. E., and Rance, M. (1992) Suppression of the effects of cross-correlation between dipolar and anisotropic chemical shift relaxation mechanisms in the measurement of spin spin relaxation rates. Mol. Phys. 75, 699-711.
22. Millet, O., Loria, J. P., Kroenke, C. D., Pons, M., and Palmer, A. G., 3rd. (2000) The Static Magnetic Field Dependence of Chemical Exchange Linebroadening Defines the NMR Chemical Shift Time Scale. J. Am. Chem. Soc. 122, 2867-2877.
23. Davis, D. G., Perlman, M. E., and London, R. E. (1994) Direct measurements of the dissociation rate constant for inhibitor-enzyme complexes via the T1 rho and T2 (CPMG) methods. J. Magn. Reson. B. 104, 266-275.
24. Shmerling, D., Hegyi, I., Fischer, M., Blättler, T., Brandner, S., Götz, J., Rülicke, T., Flechsig, E., Cozzio, A., von Mering, C., Hangartner, C., Aguzzi, A., and Weissmann, W. (1998) Expression of Amino-Terminally Truncated PrP in the Mouse Leading to Ataxia and Specific Cerebellar Lesions. Cell 93, 203-214.
25. Muramoto, T., DeArmond, S. J., Scott, M., Telling, G. C., Cohen, F. E., and Prusiner, S. B. (1997) Heritable disorder resembling neuronal storage disease in mice expressing prion protein with deletion of an alpha-helix. Nat. Med. 3, 750-755.
26. Perrier, V., Kaneko, K., Safar, J., Vergara, J., Tremblay, P., DeArmond, S. J., Cohen, F. E., Prusiner, S. B., and Wallace, A. C. (2002) Dominant-negative inhibition of prion replication in transgenic mice. Proc. Natl. Acad. Sci. U.S.A. 99, 13079-13084.
27. Zhang, H., Stöckel, J., Mehlhorn, I., Groth, D., Baldwin, M. A., Prusiner, S. B., James, T. L., and Cohen, F. E. (1997) Physical Studies of Conformational Plasticity in a Recombinant Prion Protein. Biochemistry 36, 3543-3553.
28. Hornemann, S., and Glockshuber, R. (1998) A scrapie-like unfolding intermediate of the prion protein domain PrP(121-231) induced by acidic pH. Proc. Nat. Acad. Sci. U.S.A. 95, 6010-6014.
29. Apetri, A. C., and Surewicz, W. K. (2002) Kinetic intermediate in the folding of human prion protein. J. Biol. Chem. 277, 44589-44592.
30. Kaneko, K., Zulianello, L., Scott, M., Cooper, C. M., Wallace, A. C., James, T. L., Cohen, F. E., and Prusiner, S. B. (1997) Evidence for protein X binding to a discontinuous epitope on thecellular prion protein during scrapie prion propagation. Proc. Natl. Acad. Sci. U.S.A. 94, 10069-10074.
31. Garcia, A. E., and Hummer, G. (1999) Conformational dynamics of cytochrome c: correlation to hydrogen exchange. Proteins 36, 175-191.
32. Karplus, M. (2000) Aspects of protein reaction dynamics: deviations from simple behavior. J. Phys. Chem. B. 104, 11-27.
33. Komatsuzaki, T., and Berry, R. S. (2001) Dynamical hierarchy in transition states: why and how does a system climb over the mountain? Proc. Natl. Acad. Sci. U.S.A. 98, 7666-7671.
34. Akasaka, K. (2003) Highly fluctuating protein structures revealed by variable-pressure nuclear magnetic resonance. Biochemistry 42, 10875-10885.
35. 15N NMR. Biochemistry 40, 8665-8671.
36. 15N chemical shifts in BPTI. Protein Sci. 8, 1946-1953.
37. Tai, K., Shen, T., Borjesson, U., Philippopoulos, M., and McCammon, J. A. (2001) Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase. Biophys. J. 81, 715-724.
38. Muramoto, T., Scott, M., Cohen, F., and Prusiner, S. B. (1996) Recombinant scrapie-like prion protein of 106 amino acids is soluble. Proc. Natl. Acad. Sci. U.S.A. 93, 15457-15462.
39. Wille, H., Michelitsch, M. D., Guenebaut, V., Supattapone, S., Serban, A., Cohen, F. E., Agard, D. A., and Prusiner, S. B. (2002) Structural studies of the scrapie prion protein by electron crystallography. Proc. Nat. Acad. Sci. U.S.A. 99, 3563-3568.