The sequence dependence of fiber organization. A comparative molecular dynamics study of the islet amyloid polypeptide segments 22-27 and 22-29

Journal of Molecular Biology

Volumn 329, Issue 3, 2003, Pages 565-584

  Zanuy, David ^a   Nussinov, Ruth ^b,c  

^a NATIONAL CANCER INSTITUTE   (United States)

^b SAIC FREDERICK INC   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

Amyloid conformation; Islet amyloid peptide; Molecular dynamics simulation; Protein unfolding; sheet

Indexed keywords

AMYLOID PROTEIN; AROMATIC COMPOUND; ASPARAGINYLPHENYLALANYLGLYCYLALANYLISOLEUCYLLEUCYLSERYLSERINE; HYDROGEN; POLYPEPTIDE; PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL STRUCTURE; FIBER; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN STRUCTURE; RELIABILITY; STRUCTURE ANALYSIS;

EID: 0038274079     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00491-1     Document Type: Article

References (28)

1. Wanker E.E. Protein aggregation in Huntington's and Parkinson's disease: implications for therapy. Mol. Med. Today. 6:2000;387-391.
2. Gazit E. The "correct folded" state of proteins: is it a metastable state? Angew. Chem. Int. Ed. 41:2002;257-259.
3. Chiti F., Taddei N., Baroni F., Capanni C., Stefani M., Ramponi G., Dobson C.M. Kinetic partitioning of protein folding and aggregation. Nature Struct. Biol. 9:2002;137-143.
4. Kisilevsky R. Amyloidogenesis: unquestioned answers and unanswered questions. J. Struct. Biol. 130:2000;99-108.
5. Sunde M., Blake C.F.F. From the globular to the fibrous state: protein structure and structural conversion in amyloid formation. Quart. Rev. Biophys. 31:1998;1-39.
6. Rochet J.C., Lansbury P.T. Jr. Amyloid fibrillogenesis: themes and variations. Curr. Opin. Struct. Biol. 10:2000;60-68.
7. Pardick S.B., Miranker A.D. Islet amyloid polypeptide: identification of long-range contacts and local order on the fibrillogenesis pathway. J. Mol. Biol. 308:2001;783-794.
8. Kirkitadze M.D., Condron M.M., Teplow D.B. Identification and characterization of key kinetic intermediates in amyloid β-protein fibrillogenesis. J. Mol. Biol. 312:2001;1103-1119.
9. Westermark P., EngstrØm U., Johnson K.H., Westermark G.T. Islet amyloid polypeptide: pinpointing amino acid residues linked to amyloid fibril formation. Proc. Natl Acad. Sci. USA. 87:1990;5036-5040.
10. Tenidis K., Waldner M., Bernhagen J., Fischle W., Bergmann M., Weber M., et al. Identification of penta- and hexapeptide of islet amyloid polypeptide (IAPP) with amyloidogenic and cytotoxic properties. J. Mol. Biol. 295:1999;1055-1071.
11. Zanuy D., Ma B., Nussinov R. Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophys. J. 84:2003;1884-1894.
12. Azriel R., Gazit E. Analysis of the minimal amyloid-forming fragment of the islet amyloid polypeptide. J. Biol. Chem. 276:2001;34156-34161.
13. Ma B., Nussinov R. Molecular dynamics simulations of alanine rich β-sheet oligomers: insights into amyloid formation. Protein Sci. 11:2002;2335-2350.
14. 10-35): sequence effects. Proc. Natl Acad. Sci. USA. 99:2002;14126-14131.
15. Kapuriotu A., Schmauder A., Tenidis K. Structure-based design and study of non-amyloidogenic, double N-methylated IAPP amyloid core sequences as inhibitors of IAPP amyloid formation and cytotoxicity. J. Mol. Biol. 315:2002;339-350.
16. Scrhocci L.A., Chen Y., Waschuk S., Wang F., Cheung S., Darabie A.A., et al. Design of peptide-based inhibitors of human islet amyloid polypeptide fibrillogenesis. J. Mol. Biol. 318:2002;697-706.
17. Reches M., Porat Y., Gazit E. Amyloid fibril formation by pentapeptide and tetrapeptide fragments of human calcitonin. J. Biol. Chem. 277:2002;35475-35480.
18. Mazor Y., Gilead S., Itai B., Gazit E. Identification and characterization of a novel molecular-recognition and self-assembly domain within the islet amyloid polypeptide. J. Mol. Biol. 322:2002;1013-1024.
19. Brown D.R. Prion protein peptides: optimal toxicity and peptide blockade of toxicity. Mol. Cell. Neurosci. 15:2000;66-78.
20. Petkova A.T., Ishii Y., Balbach J.J., Antzutkin O.N., Leapman R.D., Delagio F., 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.
21. Balbirnie M., Grothe R., Eisenberg D.S. An amyloid-forming peptide from the yeast prion Sup35 reveals a dehydrated ? β-sheet structure for amyloid. Proc. Natl Acad. Sci. USA. 98:2001;2375-2380.
22. Scherzinger E., Sittler A., Schweiger K., Heiser V., Lurz R., Hasenbank R., et al. Self-assembly of polyglutamine-containing huntingtin fragments into amyloid-like fibrils: implications for Huntington's disease pathology. Proc. Natl Acad. Sci. USA. 96:1999;4604-4609.
23. Perutz M.F., Finch J.T., Lesk A. Amyloid fibers are water-filled nanotubes. Proc. Natl Acad. Sci. USA. 99:2002;5591-5595.
24. Brooks R.B., Bruccoleri R.E., Olafson B.D., Sate D.J., Swaminathan S., Karplus M. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem. 4:1983;187-217.
25. MacKerell J.A.D., Bashford D., Bellott M., Dunbrack R.L. Jr, Evanseck J., Field M.J., et al. All-hydrogen empirical potential for molecular modeling and dynamics studies of proteins using the CHARMM22 force field. J. Phys. Chem., ser. B. 102:1998;3586-3616.
26. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:1982;926-935.
27. Bursulaya B.D., Brooks C.L. III. Folding free energy surface of three-stranded β-sheet protein. J. Am. Chem. Soc. 121:1999;9946-9951.
28. Ryckaert J.P., Ciccoti G., Berendsen H.J.C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:1977;327-341.