Structure, dynamics, and stability of assemblies of the human prion fragment SNQNNF

Biochemical and Biophysical Research Communications

Volumn 366, Issue 3, 2008, Pages 800-806

  De Simone, Alfonso ^a   Pedone, Carlo ^a,b   Vitagliano, Luigi ^a  

^a CNR   (Italy)

^b UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

Amyloid structure; Molecular dynamics; Prion hydration; Prion protein; Steric zipper

Indexed keywords

PRION PROTEIN; SERYLASPARAGINYLGLUTAMINYLASPARAGINYLASPARAGINYLPHENYLALANINE; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; MOLECULAR SIZE; POINT MUTATION; PRION DISEASE; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; SIMULATION;

BINDING SITES; COMPUTER SIMULATION; DIMERIZATION; MODELS, CHEMICAL; MODELS, MOLECULAR; PRIONS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 37549007231     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2007.12.047     Document Type: Article

References (35)

1. Bousset L., and Melki R. Similar and divergent features in mammalian and yeast prions. Microbes Infect. 4 (2002) 461-469
2. Aguzzi A., and Polymenidou M. Mammalian prion biology: one century of evolving concepts. Cell 116 (2004) 313-327
3. Prusiner S.B. Prions. Proc. Natl. Acad. Sci. USA 95 (1998) 13363-13383
4. Weissmann C. The state of the prion. Nat. Rev. Microbiol. 2 (2004) 861-871
5. Chiti F., and Dobson C.M. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem. 75 (2006) 333-366
6. Riek R., Hornemann S., Wider G., Billeter M., Glockshuber R., and Wuthrich K. NMR structure of the mouse prion protein domain PrP(121-321). Nature 382 (1996) 180-182
7. DeMarco M.L., and Daggett V. From conversion to aggregation: protofibril formation of the prion protein. Proc. Natl. Acad. Sci. USA 101 (2004) 2293-2298
8. Langedijk J.P., Fuentes G., Boshuizen R., and Bonvin A.M. Two-rung model of a left-handed beta-helix for prions explains species barrier and strain variation in Transmissible Spongiform Encephalopathies. J. Mol. Biol. 360 (2006) 907-920
9. Govaerts C., Wille H., Prusiner S.B., and Cohen F.E. Evidence for assembly of prions with left-handed beta-helices into trimers. Proc. Natl. Acad. Sci. USA 101 (2004) 8342-8347
10. Tattum M.H., Cohen-Krausz S., Thumanu K., Wharton C.W., Khalili-Shirazi A., Jackson G.S., Orlova E.V., Collinge J., Clarke A.R., and Saibil H.R. Elongated oligomers assemble into mammalian PrP amyloid fibrils. J. Mol. Biol. 357 (2006) 975-985
11. Lu X., Wintrode P.L., and Surewicz W.K. Beta-sheet core of human prion protein amyloid fibrils as determined by hydrogen/deuterium exchange. Proc. Natl. Acad. Sci. USA 104 (2007) 1510-1515
12. Nelson R., Sawaya M.R., Balbirnie M., Madsen A.O., Riekel C., Grothe R., and Eisenberg D. Structure of the cross-beta spine of amyloid-like fibrils. Nature 435 (2005) 773-778
13. Sawaya M.R., Sambashivan S., Nelson R., Ivanova M.I., Sievers S.A., Apostol M.I., Thompson M.J., Balbirnie M., Wiltzius J.J., McFarlane H.T., Madsen A.O., Riekel C., and Eisenberg D. Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature 447 (2007) 453-457
14. Berendsen H.J.C., van der Spoel D., and van Drunen R. GROMACS: "a message-passing parallel molecular dynamics implementation". Comp. Phys. Commun. 91 (1995) 43-56
15. Silveira J.R., Raymond G.J., Hughson A.G., Race R.E., Sim V.L., Hayes S.F., and Caughey B. The most infectious prion protein particles. Nature 437 (2005) 257-261
16. Kaneko K., Zulianello L., Scott M., Cooper C.M., Wallace A.C., James T.L., Cohen F.E., and Prusiner S.B. Evidence for protein X binding to a discontinuous epitope on the cellular prion protein during scrapie prion propagation. Proc. Natl. Acad. Sci. USA 94 (1997) 10069-10074
17. Samaia H.B., Mari J.J., Vallada H.P., Moura R.P., Simpson A.J., and Brentani R.R. A prion-linked psychiatric disorder. Nature 390 (1997) 241
18. Brandl M., Weiss M.S., Jabs A., Suhnel J., and Hilgenfeld R. C-H...pi-interactions in proteins. J. Mol. Biol. 307 (2001) 357-377
19. Gazit E. A possible role for pi-stacking in the self-assembly of amyloid fibrils. FASEB J. 16 (2002) 77-83
20. Esposito L., Pedone C., and Vitagliano L. Molecular dynamics analyses of cross-beta-spine steric zipper models: beta-sheet twisting and aggregation. Proc. Natl. Acad. Sci. USA 103 (2006) 11533-11538
21. Zheng J., Ma B., Tsai C.J., and Nussinov R. Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys. J. 91 (2006) 824-833
22. Supattapone S., Bosque P., Muramoto T., Wille H., Aagaard C., Peretz D., Nguyen H.O., Heinrich C., Torchia M., Safar J., Cohen F.E., DeArmond S.J., Prusiner S.B., and Scott M. Prion protein of 106 residues creates an artificial transmission barrier for prion replication in transgenic mice. Cell 96 (1999) 869-878
23. Anfinsen C.B. Principles that govern the folding of protein chains. Science 181 (1973) 223-230
24. Guo J.T., Jaromczyk J.W., and Xu Y. Analysis of chameleon sequences and their implications in biological processes. Proteins 67 (2007) 548-558
25. Collinge J. Prion diseases of humans and animals: their causes and molecular basis. Annu. Rev. Neurosci. 24 (2001) 519-550
26. Jones E.M., and Surewicz W.K. Fibril conformation as the basis of species- and strain-dependent seeding specificity of mammalian prion amyloids. Cell 121 (2005) 63-72
27. Vanik D.L., Surewicz K.A., and Surewicz W.K. Molecular basis of barriers for interspecies transmissibility of mammalian prions. Mol. Cell 14 (2004) 139-145
28. Toyama B.H., Kelly M.J., Gross J.D., and Weissman J.S. The structural basis of yeast prion strain variants. Nature 449 (2007) 233-237
29. A. De Simone, L. Esposito, C. Pedone, L. Vitagliano, Insights into stability and toxicity of amyloid-like oligomers by replica exchange molecular dynamics analyses, submitted for publication.
30. Tsai M.T., Su Y.C., Chen Y.H., and Chen C.H. Lack of evidence to support the association of the human prion gene with schizophrenia. Mol. Psychiatry 6 (2001) 74-78
31. Gorfe A.A., and Caflisch A. Ser170 controls the conformational multiplicity of the loop 166-175 in prion proteins: implication for conversion and species barrier. FASEB J (2007)
32. Humphrey W., Dalke A., and Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 14 (1996) 33-38 27-28
33. De Simone A., Dodson G.G., Verma C.S., Zagari A., and Fraternali F. Prion and water: tight and dynamical hydration sites have a key role in structural stability. Proc. Natl. Acad. Sci. USA 102 (2005) 7535-7540
34. De Simone A., Zagari A., and Derreumaux P. Structural and hydration properties of the partially unfolded States of the prion protein. Biophys. J. 93 (2007) 1284-1292
35. De Simone A., Spadaccini R., Temussi P.A., and Fraternali F. Toward the understanding of MNEI sweetness from hydration map surfaces. Biophys. J. 90 (2006) 3052-3061