β2-microglobulin amyloid fragment organization and morphology and its comparison to Aβ suggests that amyloid aggregation pathways are sequence specific

Biochemistry

Volumn 47, Issue 8, 2008, Pages 2497-2509

  Zheng, Jie ^a   Jang, Hyunbum ^b   Nussinov, Ruth ^b,c  

^a The University of Akron   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

AGGLOMERATION; BINDING SITES; MOLECULAR DYNAMICS; OLIGOMERS;

ELECTROSTATIC REPULSION; MICROGLOBULINS;

PROTEINS;

AMYLOID; ASPARAGINE; BETA 2 MICROGLOBULIN; OLIGOMER; AMYLOID BETA PROTEIN; PEPTIDE FRAGMENT; POLYMER;

ARTICLE; ELECTRICITY; FIBER; MOLECULAR DYNAMICS; MORPHOLOGY; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN AGGREGATION; SIMULATION; WILD TYPE; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; ENZYME SPECIFICITY; HUMAN; HYDROPHOBICITY; METABOLISM; PHYSIOLOGY; PRECIPITATION; PROTEIN FOLDING; PROTEIN QUATERNARY STRUCTURE; PROTEIN SECONDARY STRUCTURE; SIGNAL TRANSDUCTION; THEORETICAL MODEL;

AMINO ACID SEQUENCE; AMYLOID; AMYLOID BETA-PROTEIN; BETA 2-MICROGLOBULIN; COMPUTER SIMULATION; HUMANS; HYDROPHOBICITY; MODELS, MOLECULAR; MODELS, THEORETICAL; PEPTIDE FRAGMENTS; POLYMERS; PRECIPITATION; PROTEIN FOLDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; SIGNAL TRANSDUCTION; SUBSTRATE SPECIFICITY;

EID: 39749090561     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi7019194     Document Type: Article

References (45)

1. Meredith, S. C. (2006) Protein denaturation and aggregation. Cellular responses to denatured and aggregated proteins, Ann. N.Y. Acad. Sci. 1066, 181-221.
2. Bucciantini, M., Calloni, G., Chid, F., Formigli, L., Nosi, D., Dobson, C. M., and Stefani, M. (2004) Prefibrillar amyloid protein aggregates share common features of cytotoxicity, J. Biol. Chem. 279, 31374-31382.
3. Lashuel, H. A., and Lansbury, P. T. (2006) Are amyloid diseases caused by protein aggregates that mimic bacterial pore-forming toxins? Q. Rev. Biophys. 39, 167-201.
4. Gosal, W. S., Morten, I. J., Hewitt, E. W., Smith, D. A., Thomson, N. H., and Radford, S. E. (2005) Competing pathways determine fibril morphology in the self-assembly of [β]2-microglobulin into amyloid, J. Mol. Biol. 351, 850-864.
5. Lashuel, H. A., Hartley, D., Petre, B. M., Walz, T., and Lansbury, P. T. (2002) Amyloid pores from pathogenic mutations, Nature (London, U.K.) 418, 291.
6. Lashuel, H. A., Petre, B. M., Wall, J., Simon, M., Nowak, R. J., Walz, T., and Lansbury, J. P. T. (2002) α-Synuclein, especially the Parkinson's disease-associated mutants, forms pore-like annular and tubular protofibrils, J. Mol. Biol. 322, 1089-1102.
7. Mousseau, N., and Derreumaux, P. (2005) Exploring the early steps of amyloid peptide aggregation by computers, Acc. Chem. Res. 38, 885-891.
8. Makabe, K., McElheny, D., Tereshko, V., Hilyard, A., Gawlak, G., Yan, S., Koide, A., and Koide, S. (2006) Atomic structures of peptide self-assembly mimics, Proc. Natl. Acad. Sci. U.S.A. 103, 17753-17758.
9. Ma, B., and Nussinov, R. (2002) Stabilities and conformations of Alzheimer's β-amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects, Proc. Natl. Acad. Sci. U.S.A. 99, 14126-14131.
10. Armen, R. S., Bernard, B. M., Day, R., Alonso, D. O. V., and Daggett, V. (2005) Characterization of a possible amyloidogenic precursor in glutamine-repeat neurodegenerative diseases, Proc. Natl. Acad. Sci. U.S.A. 102, 13433-13438.
11. Nguyen, H. D., and Hall, C. K. (2006) Spontaneous fibril formation by polyalanines: Discontinuous molecular dynamics simulations, J. Am. Chem. Soc. 128, 1890-1901.
12. Pellarin, R., and Caflisch, A. (2006) Interpreting the aggregation kinetics of amyloid peptides, J. Mol. Biol. 360, 882-892.
13. Zheng, J., Ma, B., Tsai, C.-J., and Nussinov, R. (2006) Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35, Biophys. J. 91, 824-833.
14. Wu, C., Lei, H., and Duan, Y. (2005) Elongation of ordered peptide aggregate of an amyloidogenic hexapeptide NFGAIL observed in molecular dynamics simulations with an explicit solvent, J. Am. Chem. Soc. 127, 13530-13537.
15. Buchete, N.-V., and Hummer, G. (2007) Structure and dynamics of parallel {β}-sheets, hydrophobic core, and loops in Alzheimer's A{β} fibrils, Biophys. J. 92, 3032-3039.
16. Huet, A., and Derreumaux, P. (2006) Impact of the mutation A21G (Flemish variant) on Alzheimer's {β}-amyloid dimers by molecular dynamics simulations, Biophys. J. 91, 3829-3840.
17. Baumketner, A., Bernstein, S. L., Wyttenbach, T., Bitan, G., Teplow, D. B., Bowers, M. T., and Shea, J.-E. (2006) Amyloid β-protein monomer structure: A computational and experimental study, Protein Sci. 15, 420-428.
18. Jang, H., Zheng, J., and Nussinov, R. (2007) Models of {β}-amyloid ion-channels in the membrane suggest that channel formation in the bilayer is a dynamic process, Biophys. J. 93, 1938-1949.
19. Maenaka, K., and Jones, E. Y. (1999) MHC superfamily structure and the immune system, Curr. Opin. Struct. Biol. 9, 745-753.
20. Chen, Y., and Dokholyan, N. V. (2005) A single disulfide bond differentiates aggregation pathways of [β]2-microglobulin, J. Mol. Biol. 354, 473-482.
21. Kad, N. M., Thomson, N. H., Smith, D. P., Smith, D. A., and Radford, S. E. (2001) [β]2-Microglobulin and its deamidated variant, N17D, form amyloid fibrils with a range of morphologies in vitro, J. Mol. Biol. 313, 559-571.
22. Jones, S., Manning, J., Kad, N. M., and Radford, S. E. (2003) Amyloid-forming peptides from [β]2-microglobulin: Insights into the mechanism of fibril formation in vitro, J. Mol. Biol. 325, 249-257.
23. Ivanova, M. I., Gingery, M., Whitson, L. J., and Eisenberg, D. (2003) Role of the C-terminal 28 residues of β-2 microglobulin in amyloid fibril formation, Biochemistry 42, 13536-13540.
24. Iwata, K., Fujiwara, T., Matsuki, Y., Akutsu, H., Takahashi, S., Naiki, H., and Goto, Y. (2006) 3-D structure of amyloid protofilaments of β2-microglobulin fragment probed by solid-state NMR, Proc. Natl. Acad. Sci. U.S.A. 103, 18119-18124.
25. Ivanova, M. I., Sawaya, M. R., Gingery, M., Attinger, A., and Eisenberg, D. (2004) An amyloid-forming segment of β2-microglobulin suggests a molecular model for the fibril, Proc. Natl. Acad. Sci. U.S.A. 101, 10584-10589.
26. Tessier, P. M., and Lindquist, S. (2007) Prion recognition elements govern nucleation, strain specificity, and species barriers, Nature (London, U.K.) 447, 556-561.
27. Kale, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K., and Schulten, K. (1999) NAMD2: Greater scalability for parallel molecular dynamics, J. Comput. Phys. 151, 283-312.
28. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem. 4, 187-217.
29. Lawrence, M. C., and Colman, P. M. (1993) Shape complementarity at protein/protein interfaces, J. Mol. Biol. 234, 946-950.
30. Im, W., Lee, M. S., and Brooks, C. L., III. (2003) Generalized born model with a simple smoothing function, J. Comput. Chem. 24, 1691-1702.
31. Im, W., Feig, M., and Brooks, C. L., III. (2003) An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins, Biophys. J. 85, 2900-2918.
32. Tsai, H.-H., Zanuy, D., Haspel, N., Gunasekaran, K., Ma, B., Tsai, C.-J., and Nussinov, R. (2004) The stability and dynamics of the human calcitonin amyloid peptide DFNKF, Biophys. J. 87, 146-158.
33. Zanuy, D., Ma, B., and Nussinov, R. (2003) Short peptide amyloid organization: Stabilities and conformations of the islet amyloid peptide NFGAIL, Biophys. J. 84, 1884-1894.
34. Nishino, M., Sugita, Y., Yoda, T., and Okamoto, Y. (2005) Structures of a peptide fragment of [β]2-microglobulin studied by replica-exchange molecular dynamics simulations: Towards the understanding of the mechanism of amyloid formation, FEBS Lett. 579, 5425-5429.
35. Petkova, A. T., Ishii, Y., Balbach, J. J., Antzutkin, O. N., Leapman, R. D., Delaglio, F., and Tycko, R. (2002) A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR, Proc. Natl. Acad. Sci. U.S.A. 99, 16742-16747.
36. Ferguson, N., Becker, J., Tidow, H., Tremmel, S., Sharpe, T. D., Krause, G., Flinders, J., Petrovich, M., Berriman, J., Oschkinat, H., and Fersht, A. R. (2006) General structural motifs of amyloid protofilaments, Proc. Natl. Acad. Sci. U.S.A. 103, 16248-16253.
37. Naito, A., and Kawamura, I. (2007) Solid-state NMR as a method to reveal structure and membrane interaction of amyloidogenic proteins and peptides, Biochim. Biophys. Acta 1768, 1900-1912.
38. Zheng, J., Ma, B., and Nussinov, R. (2006) Consensus features in amyloid fibrils: Sheet-sheet recognition via a (polar or nonpolar) zipper structure, Phys. Biol. 3, 1-4.
39. Masuda, Y., Irie, K., Murakami, K., Ohigashi, H., Ohashi, R., Takegoshi, K., Shimizu, T., and Shirasawa, T. (2005) Verification of the turn at positions 22 and 23 of the [β]-amyloid fibrils with Italian mutation using solid-state NMR, Bioorg. Med. Chem. 13, 6803-6809.
40. Han, W., and Wu, Y. D. (2005) A strand-loop-strand structure is a possible intermediate in fibril elongation: Long time simulations of amyloid-β peptide (10-35), J. Am. Chem. Soc. 127, 15408-15416.
41. Tarus, B., Straub, J. E., and Thirumalai, D. (2006) Dynamics of Asp23-Lys28 salt-bridge formation in A[β]10-35 monomers, J. Am. Chem. Soc. 128, 16159-16168.
42. Petkova, A. T., Yau, W. M., and Tycko, R. (2006) Experimental constraints on quaternary structure in Alzheimer's β-amyloid fibrils, Biochemistry 45, 498-512.
43. Luhrs, T., Ritter, C., Adrian, M., Riek-Loher, D., Bohrmann, B., Dobeli, H., Schubert, D., and Riek, R. (2005) 3-D structure of Alzheimer's amyloid-{β}(1-42) fibrils, Proc. Natl. Acad. Sci. U.S.A. 102, 17342-17347.
44. Zheng, J., Jang, H., Ma, B., Tsai, C.-J., and Nussinov, R. (2007) Modeling the Alzheimer a{β}17-42 fibril architecture: Tight intermolecular sheet-sheet association and intramolecular hydrated cavities, Biophys. J. 93, 3046-3057.
45. Humphrey, W., Dalke, A., and Schulten, K. (1996) VMD: Visual molecular dynamics, J. Mol. Graphics 14, 33-38.