Systematic examination of polymorphism in amyloid fibrils by molecular-dynamics simulation

Biophysical Journal

Volumn 100, Issue 9, 2011, Pages 2234-2242

  Berryman, Joshua T ^a   Radford, Sheena E ^b   Harris, Sarah A ^b  

^a UNIVERSITY OF LUXEMBOURG   (Luxembourg)

^b UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79959713610     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.02.060     Document Type: Article

References (54)

1. Fändrich, M. 2007. On the structural definition of amyloid fibrils and other polypeptide aggregates. Cell. Mol. Life Sci. 64:2066-2078. (Pubitemid 350092423)
2. Chiti, F., and C. M. Dobson. 2006. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem. 75:333-366. (Pubitemid 44118036)
3. Fowler, D. M., A. V. Koulov,..., J. W. Kelly. 2007. Functional amyloid-from bacteria to humans. Trends Biochem. Sci. 32:217-224.
4. Glover, J. R., A. S. Kowal,..., S. Lindquist. 1997. Self-seeded fibers formed by Sup35, the protein determinant of [PSI+], a heritable prion-like factor of S. cerevisiae. Cell. 89:811-819. (Pubitemid 27516184)
5. Serpell, L. C. 2000. Alzheimer's amyloid fibrils: structure and assembly. Biochim. Biophys. Acta. 1502:16-30. (Pubitemid 30433852)
6. Antzutkin, O. N., R. D. Leapman,..., R. Tycko. 2002. Supramolecular structural constraints on Alzheimer's β-amyloid fibrils from electron microscopy and solid-state nuclear magnetic resonance. Biochemistry. 41:15436-15450. (Pubitemid 36008156)
7. Toyama, B. H., M. J. Kelly,..., J. S. Weissman. 2007. The structural basis of yeast prion strain variants. Nature. 449:233-237. (Pubitemid 47402368)
8. Jiménez, J. L., E. J. Nettleton,..., H. R. Saibil. 2002. The protofilament structure of insulin amyloid fibrils. Proc. Natl. Acad. Sci. USA. 99:9196-9201. (Pubitemid 34764590)
9. Krishnan, R., and S. L. Lindquist. 2005. Structural insights into a yeast prion illuminate nucleation and strain diversity. Nature. 435:765-772. (Pubitemid 40839721)
10. Castilla, J., D. Gonzalez-Romero,..., C. Soto. 2008. Crossing the species barrier by PrP (Sc) replication in vitro generates unique infectious prions. Cell. 134:757-768.
11. Berryman, J. T., S. E. Radford, and S. A. Harris. 2009. Thermodynamic description of polymorphism in Q-and N-rich peptide aggregates revealed by atomistic simulation. Biophys. J. 97:1-11.
12. Miller, Y., B. Ma, and R. Nussinov. 2010. Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states. Proc. Natl. Acad. Sci. USA. 107:9490-9495.
13. Miller, Y., B. Ma, and R. Nussinov. 2009. Polymorphism of Alzheimer's Aβ17-42 (p3) oligomers: the importance of the turn location and its conformation. Biophys. J. 97:1168-1177.
14. Miller, Y., B. Ma,..., R. Nussinov. 2010. Hollow core of Alzheimer's Aβ42 amyloid observed by cryoEM is relevant at physiological pH. Proc. Natl. Acad. Sci. USA. 107:14128-14133.
15. Wei, G. H., A. I. Jewett, and J. E. Shea. 2010. Structural diversity of dimers of the Alzheimer amyloid-β (25-35) peptide and polymorphism of the resulting fibrils. Phys. Chem. Chem. Phys. 12:3622-3629.
16. Sawaya, M. R., S. Sambashivan,..., D. Eisenberg. 2007. Atomic structures of amyloid cross-β spines reveal varied steric zippers. Nature. 447:453-457. (Pubitemid 46816731)
17. Wiltzius, J. J., M. Landau,..., D. Eisenberg. 2009. Molecularmechanisms for protein-encoded inheritance. Nat. Struct. Mol. Biol. 16:973-978.
18. Macke, T. J., and D. A. Case. 1997. Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids. N. B. Leontes and J. Santa Lucia, Jr., editors. American Chemical Society, Washington, DC. 379-393.
19. Hovmöller, S., T. Zhou, and T. Ohlson. 2002. Conformations of amino acids in proteins. Acta Crystallogr. D Biol. Crystallogr. 58:768-776. (Pubitemid 34557286)
20. Case, D. A., T. E. Cheatham, 3rd,..., R. J. Woods. 2005. The Amber biomolecular simulation programs. J. Comput. Chem. 26:1668-1688. (Pubitemid 43076180)
21. Cornell, W. D., P. Cieplak,..., P. A. Kollman. 1995. A 2nd generation force-field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
22. Jorgensen, W. L., J. Chandrasekhar,..., M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
23. MacKerell, A. D., D. Bashford,..., M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616. (Pubitemid 128576688)
24. Phillips, J. C., R. Braun,..., K. Schulten. 2005. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26:1781-1802. (Pubitemid 43078511)
25. Tsui, V., and D. A. Case. 2000-2001. Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers 56:275-291. (Pubitemid 34105875)
26. DeLano, W. L. 2002. The PyMOL Molecular Graphics System. DeLano Scientific, Palo Alto, CA.
27. Lawrence, M. C., and P. M. Colman. 1993. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234:946-950. (Pubitemid 24027225)
28. Collaborative Computational Project, Number 4. 1994. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50:760-763.
29. Collinge, J., and A. R. Clarke. 2007. A general model of prion strains and their pathogenicity. Science. 318:930-936. (Pubitemid 350098981)
30. Madine, J., E. Jack,..., D. A. Middleton. 2008. Structural insights into the polymorphism of amyloid-like fibrils formed by region 20-29 of amylin revealed by solid-state NMR and X-ray fiber diffraction. J. Am. Chem. Soc. 130:14990-15001.
31. Nelson, R., M. R. Sawaya,..., D. Eisenberg. 2005. Structure of the crossβ spine of amyloid-like fibrils. Nature. 435:773-778. (Pubitemid 40839722)
32. Marshall, K. E., M. R. Hicks,..., L. C. Serpell. 2010. Characterizing the assembly of the Sup35 yeast prion fragment, GNNQQNY: structural changes accompany a fiber-to-crystal switch. Biophys. J. 98:330-338.
33. Landschulz, W. H., P. F. Johnson, and S. L. McKnight. 1988. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science. 240:1759-1764.
34. Deechongkit, S., H. Nguyen,..., J. W. Kelly. 2004. Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics. Nature. 430:101-105. (Pubitemid 38915233)
35. Chou, K. C., M. Pottle,..., H. A. Scheraga. 1982. Structure of β-sheets. Origin of the right-handed twist and of the increased stability of antiparallel over parallel sheets. J. Mol. Biol. 162:89-112.
36. Thompson, M. J., S. A. Sievers,..., D. Eisenberg. 2006. The 3D profile method for identifying fibril-forming segments of proteins. Proc. Natl. Acad. Sci. USA. 103:4074-4078.
37. Zheng, J., B. Ma, and R. Nussinov. 2006. Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure. Phys. Biol. 3:1-4.
38. Steinmetz, M. O., Z. Gattin,..., R. A. Kammerer. 2008. Atomic models of de novo designed cc β-Met amyloid-like fibrils. J. Mol. Biol. 376:898-912.
39. Verel, R., I. T. Tomka,..., B. H. Meier. 2008. Polymorphism in an amyloid-like fibril-forming model peptide. Angew. Chem. Int. Ed. Engl. 47:5842-5845.
40. Tjernberg, L., W. Hosia,..., J. Johansson. 2002. Charge attraction and β propensity are necessary for amyloid fibril formation from tetrapeptides. J. Biol. Chem. 277:43243-43246. (Pubitemid 35285710)
41. Fishwick, C. W. G., A. J. Beevers,..., N. Boden. 2003. Structures of helical β-tapes and twisted ribbons: the role of side-chain interactions on twist and bend behavior. Nano Lett. 3:1475-1479. (Pubitemid 37518155)
42. Geddes, A. J., K. D. Parker,..., E. Beighton. 1968. "Crossβ " conformation in proteins. J. Mol. Biol. 32:343-358.
43. Fändrich, M., J. Meinhardt, and N. Grigorieff. 2009. Structural polymorphism of Alzheimer Aβ and other amyloid fibrils. Prion. 3:89-93.
44. Miller, Y., B. Ma, and R. Nussinov. 2010. Polymorphism in Alzheimer Aβ amyloid organization reflects conformational selection in a rugged energy landscape. Chem. Rev. 110:4820-4838.
45. Deng, W., A. Cao, and L. Lai. 2008. Distinguishing the crossβ spine arrangements in amyloid fibrils using FRET analysis. Protein Sci. 17:1102-1105. (Pubitemid 351749216)
46. Conchillo-Solé, O., N. S. de Groot,..., S. Ventura. 2007. AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides. BMC Bioinformatics. 8:65-81.
47. Trovato, A., F. Seno, and S. C. Tosatto. 2007. The PASTA server for protein aggregation prediction. Protein Eng. Des. Sel. 20:521-523. (Pubitemid 350135561)
48. Tartaglia, G. G., and M. Vendruscolo. 2008. The Zyggregator method for predicting protein aggregation propensities. Chem. Soc. Rev. 37:1395-1401.
49. Tartaglia, G. G., A. Cavalli,..., A. Caflisch. 2005. Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Protein Sci. 14:2723-2734. (Pubitemid 41395598)
50. Bryan, Jr., A. W., M. Menke,..., B. Berger. 2009. BETASCAN: probable β-amyloids identified by pairwise probabilistic analysis. PLOS Comput. Biol. 5:e1000333.
51. Maurer-Stroh, S., M. Debulpaep,..., F. Rousseau. 2010. Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat. Methods. 7:237-242.
52. Fernandez-Escamilla, A. M., F. Rousseau,..., L. Serrano. 2004. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat. Biotechnol. 22:1302-1306. (Pubitemid 39336784)
53. Goldschmidt, L., P. K. Teng,..., D. Eisenberg. 2010. Identifying the amylome, proteins capable of forming amyloid-like fibrils. Proc. Natl. Acad. Sci. USA. 107:3487-3492.
54. Goux, W. J., L. Kopplin,..., D. A. Kirschner. 2004. The formation of straight and twisted filaments from short τ peptides. J. Biol. Chem. 279:26868-26875. (Pubitemid 38812520)