Molecular dynamics study of the fibril elongation of the prion protein fragment PrP106-126

Journal of Theoretical Biology

Volumn 245, Issue 2, 2007, Pages 238-242

  Zhang, Yong ^a   Zhao, Xin ^a   Wang, Peng Ye ^a  

^a INSTITUTE OF PHYSICS   (China)

Author keywords

Fibril elongation; Molecular dynamics; Prion protein; PrP106 126

Indexed keywords

HYDROXYL GROUP; PRION PROTEIN; PRION PROTEIN [106-120]; UNCLASSIFIED DRUG;

ACIDITY; BIOMECHANICS; MOLECULAR ANALYSIS; PH; PROTEIN; SIMULATION;

ACIDITY; ARTICLE; BETA SHEET; FIBER; MICROENVIRONMENT; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTON TRANSPORT; SIMULATION;

COMPUTER SIMULATION; HYDROGEN-ION CONCENTRATION; HYDROXIDES; MODELS, MOLECULAR; ONIUM COMPOUNDS; PEPTIDE FRAGMENTS; PRIONS; PROTEIN STRUCTURE, SECONDARY;

EID: 33847024928     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2006.10.018     Document Type: Article

References (26)

1. Berendsen H.J.C., Postma J.P.M., Gusteren W.F., and Hermans J. Intermolecular Forces (1981), Reidel, Dordrecht
2. Berendsen H.J.C., van Spoel D., and van Drunen R. Comput. Phys. Commun. 91 (1995) 43-56
3. Collins S.J., Lawson V.A., and Masters C.L. Transmissible spongiform encephalopathies. Lancet 363 (2004) 51-61
4. 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
5. Errington J.R., and Debenedetti P.G. Relationship between structural order and the anomalies of liquid water. Nature 409 (2001) 318-321
6. Forloni G., Angeretti N., Chiesa R., Monzani E., Salmona M., Bugiani O., and Tagliavini F. Neurotoxicity of a prion protein fragment. Nature 362 (1993) 543-546
7. Hornemann S., and Glockshuber R. A scrapie-like unfolding intermediate of the prion protein domain PrP121-231 induced by acidic pH. Proc. Natl Acad. Sci. USA 95 (1998) 6010-6014
8. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
9. Kuwata K., Matumoto T., Cheng H., Nagayama K., James T.L., and Roder H. Proc. Natl Acad. Sci. USA 100 (2003) 14790-14795
10. Lindahl E., Hess B., and van der Spoel D. Gromacs 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Modeling 7 (2001) 306-317
11. Ma B., and Nussinov R. Molecular dynamics simulations of alanine rich β-sheet oligomers: insight into amyloid formation. Protein Sci. 11 (2002) 2335-2350
12. C helix 1 in the hydrophilic seeding of prion aggregates. Proc. Natl Acad. Sci. USA 96 (1999) 11293-11298
13. Pan K.M., Baldwin M., Nguyen J., Gasset M., Serban A., Groth D., Mehlehorn I., Huang Z., Fletterick R.J., Cohen F.E., and Prusiner S.B. Conversion of α-helices β-sheets features in the formation of the scrapie prion proteins. Proc. Natl Acad. Sci. USA 90 (1993) 10962-10966
14. Petkova A.T., Ishii Y., Balbach J.J., Antzutkin O.N., Leapman R.D., Delaglio F., and Tycko R. A structural model for alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR. Proc. Natl Acad. Sci. USA 99 (2002) 16742-16747
15. Prusiner S. Prion diseases and the BSE crisis. Science 278 (1996) 245-257
16. Prusiner S. Shattuck lecture: neurodegenerative diseases and prions. N. Engl. J. Med. 344 (2001) 1516-1526
17. Safar J., Roller P.P., Gajdusek D.C., and Gibbs C.J. Thermal stability and conformational transitions of scrapie amyloid (prion) protein correlate with infectivity. Protein Sci. 2 (1993) 2206-2216
18. Salmona M., Malesani P., Gioia L.D., Gorla S., Bruschi M., Molinari A., Vedova R.D., Pedrotti B., Marrari M.A., Awan T., Bugiani O., Forloni G., and Tagliavini F. Molecular determinants of the physicochemical properties of a critical prion protein region comprising residues 106-126. Biochem. J. 342 (1999) 207-214
19. Selvaggini C., Gioia L.D., Cantu L., Ghibaudi E., Diomede L., Passerini F., Forloni G., Tagliavini O.B.F., and Salmona M. Molecular characteristics of a protease-resistant, amyloidogenic and neurotoxic peptide homologous to residues 106-126 of the prion protein. Biochem. Biophys. Res. Commun. 194 (1993) 1380-1386
20. Swietnicki W., Petersen R., Gambetti P., and Surewicz W.K. pH-dependent stability and conformation of the recombinant human prion protein PrP90-231. J. Bio. Chem. 272 (1997) 27517-27520
21. Tagliavini F., Prelli F., Verga L., Giaccone G., Sarma R., Gorevic P., Ghetti B., Passerini F., Ghibaudi E., Forloni G., Salmona M., Bugiani O., and Frangione B. Synthetic peptides homologous to prion protein residues 106-147 form amyloid-like fibrils in vitro. Proc. Natl. Acad. Sci. USA 90 (1993) 9678-9682
22. Tarek M., and Tobias D.J. Role of protein-water hydrogen bond dynamics in the protein dynamical transition. Phys. Rev. Lett. 88 (2002) 138101
23. van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hunenberger, P.H., Kruger, P., Mark, A.E., Scott, W.R.P., Tironi, I.G., 1996. Biomolecular Simulation: The GROMOS96 Manual and Userguide. Hochschulverlag AG an der ETH Zurich, Switzerland, Zurich.
24. Zhang H., Kaneko K., Nguyen J.T., Livshits T.L., Baldwin M.A., Cohen F.E., James T.L., and Prusiner S.B. J. Mol. Biol. 250 (1995) 514-526
25. Zhang Y., Dai L., Iwamoto M., and can Ou-Yang Z. Molecular dynamics study on the conformational transition of prion induced by the point mutation: F198s. Thin Solid Film 449 (2006) 224-228
26. Zhang, Y., Qian, J., Wang, P.-Y., can Ou-Yang, Z., 2007. Molecular dynamical simulations of point mutation occurring at the 198th site of prion protein. J. Comput. Theor. Nanoscience, will appear in 2007.