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Том 6   Выпуск 1   Год 2011
Данилкович Алексей Викторович, Соболев Егор Васильевич, Тихонов Дмитрий Анатольевич, Шадрина Татьяна Евгеньевна, Удовиченко Игорь Петрович

Молекулярная динамика комплексов самоорганизующихся ионных пептидов (RADA)4

Математическая биология и биоинформатика. 2011;6(1):92-101.

doi: 10.17537/2011.6.92.

Список литературы

  1. Zhang S. Fabrication of novel biomaterials through molecular self-assembly. Nature Biotechnology. 2003;21:1171-1178. doi: 10.1038/nbt874
  2. Hsieh PCH, Davis ME, Gannon J, MacGillivray C, Lee RT. Controlled delivery of PDGF-BB for myocardial protection using injectable self-assembling peptide nanofibers. Journal of Clinical Investigations. 2006;116(1):237-248. doi: 10.1172/JCI25878
  3. Ellis-Behnke RG, Liang Y-X, You S-W, Tay DKC, Zhang S, So K-F, Schneider GE. Nano neuro knitting: Peptide nanofiber scaffold for brain repair and axon regeneration with functional return of vision. Proceedings of National Academy of Sciences of the USA. 2006;103(13):5054-5059. doi: 10.1073/pnas.0600559103
  4. Goldschmidt L, Teng PK, Riek R, Eisenberg D. Identifying the amylome, proteins capable of forming amyloid-like fibrils. Proceedings of National Academy of Sciences of the USA. 2010;107(8):3487-3492. doi: 10.1073/pnas.0915166107
  5. Harper JD, Lansbury PT. Jr. Models of amyloid seeding in Alzheimer’s disease and scrapie: mechanistic truths and physiological consequences of the time-dependent solubility of amyloid proteins. Annual Review of Biochemistry. 1997;66:385-407. doi: 10.1146/annurev.biochem.66.1.385
  6. Lambert MP. Diffusible, nonfibrillar ligands derived fromAb1– 42 are potent central nervous system neurotoxins. Proceedings of National Academy of Sciences of the USA. 1998;95:6448-6453. doi: 10.1073/pnas.95.11.6448
  7. Walsh DM, Lomakin A, Benedek GB, Condron MM, Teplow DB. Amyloid b-protein fibrillogenesis—detection of a protofibrillar intermediate. Journal of Biological Chemistry. 1997;272:22364-22372. doi: 10.1074/jbc.272.35.22364
  8. Haass C, Selkoe DJ. Soluble protein oligomers in neurodegeneration: lessons from the Alzheimer’s amyloid Ab-peptide. Nature Review Molecular & Cellular Biology. 2007;8:101-112. doi: 10.1038/nrm2101
  9. Carulla N, Zhou M, Arimon M, Gairi M, Giralt E, Robinson CV, Dobson CM. Experimental characterization of disordered and ordered aggregates populated during the process of amyloid fibril formation. Proceedings of National Academy of Sciences of the USA. 2009;106:7828-7833. doi: 10.1073/pnas.0812227106
  10. Goldsbury C, Kistler J, Aebi U, Arvinte T, Cooper GJS. Watching amyloid fibrils grow by time-lapse atomic force microscopy. Journal of Molecular Biology. 1999;285:33-39. doi: 10.1006/jmbi.1998.2299
  11. Marek P, Abedini A, Song BB, Kanungo M, Johnson ME, Gupta R, Zaman W, Wong SS, Raleigh DP. Aromatic interactions are not required for amyloid fibril formation by islet amyloid polypeptide but do influence the rate of fibril formation and fibril morphology. Biochemistry (Moscow). 2007;46:3255-3261. doi: 10.1021/bi0621967
  12. Zhang S, Rich A. Direct convertion of a oligopeptide from β-sheet to an α-helix: A model for amyloid formation. Proceedings of National Academy of Sciences of the USA. 1997;94:23-28. doi: 10.1073/pnas.94.1.23
  13. Williamson JA, Miranker AD. Direct detection of transient a-helical states in islet amyloid polypeptide. Protein Sciences. 2007;16:110-117. doi: 10.1110/ps.062486907
  14. Danilkovich AV, Tikhonov DA, Sobolev EV, Shadrina TE, Udovichenko IP. Considering usage of different force-fields for molecular dynamic studies of the ionic peptides and their dimers. The Mathematical Biology and Bioinformatics. 2011;6(1):53-62. doi: 10.17537/2011.6.53
  15. Macindoe G, Mavridis L, Venkatraman V, Devignes MD, Ritchie DW. HexServer: an FFT-based protein docking server powered by graphics processors. Nucleic Acids Research. 2010;38:445-449. doi: 10.1093/nar/gkq311
  16. Tovchigrechko A, Vakser IA. Development and testing of an automated approach to protein docking. Proteins. 2005;60(2):296-301. doi: 10.1002/prot.20573
  17. HyperChem® Computational Chemistry. Practical Guide – Theory and Method, HC 70-00-04-00. Gainesville: Hypercube Inc, 2002; 350 p.
  18. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ. The Amber biomolecular simulation programs. Journal of Computational Chemistry. 2005;26(16):1668-1688. doi: 10.1002/jcc.20290
  19. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, and Klein ML. Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics. 1983;79(2):926-935. doi: 10.1063/1.445869
  20. Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry. 2003;24(16):1999-2012. doi: 10.1002/jcc.10349
  21. Lee MC, Duan Y. Distinguish protein decoys by using a scoring function based on a new Amber force field, short molecular dynamics simulations, and the generalized Born solvent model. Proteins. 2004;55:620-634. doi: 10.1002/prot.10470
  22. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983;12:2577-2637.
  23. Onufriev A, Bashford D, Case DA. Modification of the Generalized Born Model Suitable for Macromolecules. Journal of Physical Chemistry B. 2000;104(15):3712-3720. doi: 10.1021/jp994072s
Содержание
Оригинальная статья
Мат. биол. и биоинф.
2011;6(1):92-101
doi: 10.17537/2011.6.92
опубликована на рус. яз.

Аннотация (рус.)
Аннотация (англ.)
Полный текст (рус., pdf)
Список литературы

 
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