Spontaneous formation of annular structures observed in molecular dynamics simulations of polyglutamine peptides

Computational Biology and Chemistry

Volumn 30, Issue 3, 2006, Pages 215-218

  Marchut, Alexander J ^a   Hall, Carol K ^a  

^a North Carolina State University   (United States)

Author keywords

Molecular dynamics; Polyglutamine; Protein aggregation

Indexed keywords

AMINES; AMINO ACIDS; LATTICE CONSTANTS; MATHEMATICAL MODELS; MOLECULAR DYNAMICS; NANOTUBES; PROTEINS;

ANNULAR STRUCTURES; INTERMEDIATE-RESOLUTION PROTEIN MODEL; LARGE BETA SHEETS; POLYGLUTAMINE;

POLYPEPTIDES;

NANOTUBE; PEPTIDE; POLYGLUTAMINE;

ARTICLE; BRAIN DISEASE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HUMAN; HUNTINGTON CHOREA; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE;

BRAIN DISEASES; COMPUTER SIMULATION; HUMANS; HUNTINGTON DISEASE; MODELS, MOLECULAR; NANOTUBES; PEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY;

EID: 33747032067     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2006.01.003     Document Type: Article

References (20)

1. Alder B.J., and Wainwright T.E. Studies in molecular dynamics. I. General method. J. Chem. Phys. 31 (1959) 459
2. Bates G. Huntingtin aggregation and toxicity in huntington's disease. Lancet 361 (2003) 1642
3. Bellemans A., Orban J., and Belle D.V. Molecular dynamics of rigid and non-rigid necklaces of hard disks. Mol. Phys. 39 (1980) 781
4. Burke M.G., Woscholski R., and Yaliraki S.N. Differential hydrophobicity drives self-assembly in huntington's disease. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 13928
5. Ding F., Borreguero J.M., Buldyrey S.V., Stanley H.E., and Dokholyan N.V. Mechanism for the alpha-helix to beta-hairpin transition. Proteins 53 (2003) 220
6. Ding T.T., Lee S.-J., Rochet J.-C., and Lansbury J.P.T. Annular alpha-synuclein protofibrils are produced when spherical protofibrils are incubated in solution or bound to brain-derived membranes. Biochemistry 41 (2002) 10209
7. Finke J.M., Cheung M.S., and Onuchic J.N. A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory. Biophys. J. 87 (2004) 1900
8. Lashuel H.A., Petre B.M., Wall J., Simon M., Nowak R.J., Walz T., and Lansbury P.T. Alpha-synuclein, especially the Parkinson's disease-associated mutants, forms pore-like annular and tubular protofibrils. J. Mol. Biol. 322 (2002) 1089
9. Nguyen H.D., and Hall C.K. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 16180
10. Nguyen H.D., Marchut A.J., and Hall C.K. Solvent effects on the conformational transition of a model polyalanine peptide. Protein Sci. 13 (2004) 2909
11. Perutz M.F., Finch J.T., Berriman J., and Lesk A. Amyloid fibers are water-filled nanotubes. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 5591
12. Rapaport D.C. Molecular dynamics study of a polymer chain. J. Chem. Phys. 71 (1979) 3299
13. Smith A.V., and Hall C.K. Bridging the gap between homopolymer and protein models: a discontinuous molecular dynamics study. J. Chem. Phys. 113 (2000) 9331
14. Smith A.V., and Hall C.K. Alpha-helix formation: discontinuous molecular dynamics on an intermediate resolution model. Proteins: Struct. Funct. Genet. 44 (2001) 344
15. Smith A.V., and Hall C.K. Assembly of a tetrameric alpha-helical bundle: computer simulations on an intermediate resolution protein model. Proteins: Struct. Funct. Genet. 44 (2001) 376
16. Smith A.V., and Hall C.K. Protein folding versus aggregation: computer simulations on an intermediate resolution protein model. J. Mol. Biol. 312 (2001) 187
17. Smith S.W., Freeman B.D., and Hall C.K. Molecular dynamics for polymeric fluids using discontinuous potentials. J. Comput. Phys. 134 (1997) 16
18. Starikov E.B., Lerach H., and Wanker E.E. Folding of oligoglutamines: a theoretical approach based upon thermodynamics and molecular mechanics. J. Biomol. Struct. Dyn. 17 (1999) 409
19. Wacker J.L., Zareie M.H., Fong H., Sarikaya M., and Muchowski P.J. Hsp70 and Hsp40 attenuate formation of spherical and annular polyglutamine oligomers by partitioning monomer. Nat. Struct. Mol. Biol. 11 (2004) 1215
20. Wanker E.E. Protein aggregation and pathogenesis of huntington's disease: mechanisms and correlations. Biol. Chem. 381 (2000) 937