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Том 16   Выпуск 2   Год 2021
Лихачев И.В., Быстров В.С.

Сборка фенилаланиновой нанотрубки молекулярно-динамическим манипулятором

Математическая биология и биоинформатика. 2021;16(2):244-255.

doi: 10.17537/2021.16.244.

Список литературы

  1. Calvin M. Chemical evolution: Molecular evolution towards the origin of living systems on the earth and elsewhere. Oxford: Clarendon Press, 1969. doi: 10.1002/jobm.19770170116
  2. Lehninger A.L. Biochemistry. The Molecular Basis of Cell Structure and Function (2nd Edition). New York: Worth Publishers, Inc., 1972.
  3. Sharma P., Rathi B., Rodrigues J., Gorobets N. Self-Assembled Peptide Nanoarchitectures: Applications and Future Aspects. CTMC. 2015:15(13). doi: 10.2174/1568026615666150408105711
  4. Mendes A.C., Baran E.T., Reis R.L., Azevedo H.S. Self-assembly in nature: using the principles of nature to create complex nanobiomaterials. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. 2013;5(6):582–612. doi: 10.1002/wnan.1238
  5. Arya S.K., Solanki P.R., Datta M., Malhotra B.D. Recent advances in self-assembled monolayers based biomolecular electronic devices. Biosens. Bioelectron. 2009;24(9):2810–2817. doi: 10.1016/j.bios.2009.02.008
  6. Pauling L., Corey R.B. Configurations of Polypeptide Chains With Favored Orientations Around Single Bonds: Two New Pleated Sheets. PNAS. 1951;37(11):729–740. doi: 10.1073/pnas.37.11.729
  7. Dalgleish D.G. Biophysical chemistry: Part III ’The behaviour of biological macromolecules: By CR Cantor and PR Schimmel. With two Appendices and Index to Parts I–III. pp 849–1371. WH Freeman, Oxford. 1980. Biochemical Education. 1981;9:157–157. doi: 10.1016/0307-4412(81)90144-8
  8. Tverdislov V.A. Chirality as a primary switch of hierarchical levels in molecular biological systems. Biophysics. 2013;58:128–132. doi: 10.1134/S0006350913010156
  9. Tverdislov V.A., Malyshko E.V. On regularities in the spontaneous formation of structural hierarchies in chiral systems of nonliving and living matter. Phys-Usp. 2019;62:354–363. doi: 10.3367/UFNe.2018.08.038401
  10. Bystrov V.S., Zelenovskiy P.S., Nuraeva A.S., Kopyl S., Zhulyabina O.A., Tverdislov V.A. Chiral Peculiar Properties of Self-Organization of Diphenylalanine Peptide Nanotubes: Modeling Of Structure and Properties. Math. Biol. Bioinf. 2019;14:94–125. doi: 10.17537/2019.14.94
  11. Tishkov V.I. Moscow University Chemistry Bulletin. 2002;43:381–388 (in Russ.).
  12. Semenova E.V., Malyshko E.V., Tverdislov V.A. On the possible interrelation of the chirality of drugs and chiral structures in target biomacromolecules. Russian Journal of Biological Physics and Chemistry. 2019;4(3):346–351.
  13. Beloglazova I.B., Plekhanova O.S., Katkova E.V., Rysenkova K.D., Stambol’skii D.V., Sulimov V.B., Tkachuk V.A. Molecular Modeling as a New Approach to the Development of Urokinase Inhibitors. Bull. Exp. Biol. Med. 2015;158:700–704. doi: 10.1007/s10517-015-2839-3
  14. Sulimov A.V., Kutov D.C., Taschilova A.S., Ilin I.S., Stolpovskaya N.V., Shikhaliev K.S., Sulimov V.B. In Search of Non-covalent Inhibitors of SARS-CoV-2 Main Protease: Computer Aided Drug Design Using Docking and Quantum Chemistry. Supercomputing Frontiers and Innovations. 2020;7. doi: 10.14529/jsfi200305
  15. Orsi M. Self-assembling Biomaterials - 1st Edition. https://www.elsevier.com/books/self-assembling-biomaterials/azevedo/978-0-08-102015-9 (accessed 12.05.2021).
  16. Lee O.S., Stupp S.I., Schatz G.C. Atomistic Molecular Dynamics Simulations of Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers. J. Am. Chem. Soc. 2011;133:3677–3683. doi: 10.1021/ja110966y
  17. Görbitz C.H. Nanotube Formation by Hydrophobic Dipeptides. Chemistry – A European Journal. 2001;7:5153–5159. doi: 10.1002/1521-3765(20011203)7:23<5153::AID-CHEM5153>3.0.CO;2-N
  18. Scanlon S., Aggeli A. Self-assembling peptide nanotubes. Nano Today. 2008;3:22–30. doi: 10.1016/S1748-0132(08)70041-0
  19. Shklovsky J., Beker P., Amdursky N., Gazit E., Rosenman G. Bioinspired peptide nanotubes: Deposition technology and physical properties. Materials Science and Engineering: B. 2010;169:62–66. doi: 10.1016/j.mseb.2009.12.040
  20. Reches M., Gazit E. Controlled patterning of aligned self-assembled peptide nanotubes. Nature Nanotechnology. 2006;1:195–200. doi: 10.1038/nnano.2006.139
  21. Adler-Abramovich L., Gazit E. The physical properties of supramolecular peptide assemblies: from building block association to technological applications. Chem. Soc. Rev. 2014;43:6881–6893. doi: 10.1039/C4CS00164H
  22. Amdursky N., Molotskii M., Aronov D., Adler-Abramovich L., Gazit E., Rosenman G. Blue luminescence based on quantum confinement at peptide nanotubes. Nano Lett. 2009;9:3111–3115. doi: 10.1021/nl9008265
  23. Nuraeva A., Vasilev S., Vasileva D., Zelenovskiy P., Chezganov D., Esin A., Kopyl S., Romanyuk K., Shur V.Ya., Kholkin A.L. Evaporation-Driven Crystallization of Diphenylalanine Microtubes for Microelectronic Applications. Crystal Growth & Design. 2016;16:1472–1479. doi: 10.1021/acs.cgd.5b01604
  24. Zelenovskiy P., Kornev I., Vasilev S., Kholkin A. On the origin of the great rigidity of self-assembled diphenylalanine nanotubes. Phys. Chem. Chem. Phys. 2016;18:29681–29685. doi: 10.1039/C6CP04337B
  25. Bdikin I., Bystrov V., Delgadillo I., Gracio J., Kopyl S., Wojtas M., Mishina E., Sigov A., Kholkin A.L. Polarization switching and patterning in self-assembled peptide tubular structures. Journal of Applied Physics. 2012;111:074104. doi: 10.1063/1.3699202
  26. Bystrov V.S., Bdikin I.K., Heredia A., Pullar R.C., Mishina E.D., Sigov A.S., Kholkin A.L. Piezoelectricity and Ferroelectricity in Biomaterials: From Proteins to Self-assembled Peptide Nanotubes. In: Piezoelectric Nanomaterials for Biomedical Applications. Nanomedicine and Nanotoxicology. Eds. Ciofani G., Menciassi A. Springer, 2012. P. 187–211. doi: 10.1007/978-3-642-28044-3_7
  27. Bystrov V. Computer Simulation Nanostructures: Bioferroelectric Peptide Nanotubes. LAP LAMBERT Academic Publishing. 2016. https://www.morebooks.de/store/gb/book/computer-simulation-nanostructures:-bioferroelectric-peptide-nanotubes/isbn/978-3-659-92397-5 (accessed 12.05.2021).
  28. Bystrov V.S., Paramonova E., Bdikin I., Kopyl S., Heredia A., Pullar R.C., Kholkin A.L. BioFerroelectricity: Diphenylalanine Peptide Nanotubes Computational Modeling and Ferroelectric Properties at the Nanoscale. Ferroelectrics. 2012;440:3–24. doi: 10.1080/00150193.2012.741923
  29. Bystrov V.S., Zelenovskiy P.S., Nuraeva A.S., Kopyl S., Zhulyabina O.A., Tverdislov V.A. Molecular modeling and computational study of the chiral-dependent structures and properties of self-assembling diphenylalanine peptide nanotubes. J. Mol. Model. 2019;25:199. doi: 10.1007/s00894-019-4080-x
  30. Zelenovskiy P.S., Nuraeva A.S., Arkhipov S.G., Vasilev S.G., Bystrov V.S., Gruzdev D.A., Waliczek M., Svitlyk V., Shur V.Ya., Mafra L., Kholkin A.L. Chirality-Dependent Growth of Self-Assembled Diphenylalanine Microtubes. Crystal Growth and Design. 2019;19:6414–6421. doi: 10.1021/acs.cgd.9b00884
  31. Bystrov V.S., Coutinho J., Zelenovskiy P.S., Nuraeva A.S., Kopyl S., Filippov S.V., Zhulyabina O.A., Tverdislov V.A. Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diphenylalanine peptide nanotubes, containing water molecules. J. Mol. Model. 2020;26:326. doi: 10.1007/s00894-020-04564-5
  32. Bystrov V., Coutinho J., Zelenovskiy P., Nuraeva A., Kopyl S., Zhulyabina O., Tverdislov V. Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis. Nanomaterials. 2020;10:1999. doi: 10.3390/nano10101999
  33. Emtiazi G., Zohrabi T., Lee L.Y., Habibi N., Zarrabi A. Covalent diphenylalanine peptide nanotube conjugated to folic acid/magnetic nanoparticles for anti-cancer drug delivery. Journal of Drug Delivery Science and Technology. 2017;41:90–98. doi: 10.1016/j.jddst.2017.06.005
  34. Silva R.F., Araújo D.R., Silva E.R., Ando R.A., Alves W.A. L-diphenylalanine microtubes as a potential drug-delivery system: characterization, release kinetics, and cytotoxicity. Langmuir. 2013;29:10205–10212. doi: 10.1021/la4019162
  35. German H.W., Uyaver S., Hansmann U.H.E. Self-Assembly of Phenylalanine-Based Molecules. J. Phys. Chem. A. 2015;119:1609–1615. doi: 10.1021/jp5077388
  36. Adler-Abramovich L., Vaks L., Carny O., Trudler D., Magno A., Caflisch A., Frenkel D., Gazit E. Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria. Nat. Chem. Biol. 2012;8:701–706. doi: 10.1038/nchembio.1002
  37. Oroz J., Valbuena A., Vera A.M., Mendieta J., Gómez-Puertas P., Carrión-Vázquez M. Nanomechanics of the Cadherin Ectodomain. J. Biol. Chem. 2011;286:9405–9418. doi: 10.1074/jbc.M110.170399
  38. Lemak A.S., Balabaev N.K. A Comparison Between Collisional Dynamics and Brownian Dynamics. Molecular Simulation. 1995;15:223–231. doi: 10.1080/08927029508022336
  39. Lemak A.S., Balabaev N.K. Molecular dynamics simulation of a polymer chain in solution by collisional dynamics method. Journal of Computational Chemistry. 1996;17:1685–1695. doi: 10.1002/(SICI)1096-987X(19961130)17:15<1685::AID-JCC1>3.0.CO;2-L
  40. Likhachev I.V., Balabaev N.K., Galzitskaya O.V. Elastic and Non-elastic Properties of Cadherin Ectodomain: Comparison with Mechanical System. In: Advances in Computer Science for Engineering and Education II. ICCSEEA 2019. Advances in Intelligent Systems and Computing. Eds. Hu Z., Petoukhov S., Dychka I., He M. Springer International Publishing; 2020:555–566. doi: 10.1007/978-3-030-16621-2_52
  41. Glyakina A.V., Likhachev I.V., Balabaev N.K., Galzitskaya O.V. Comparative mechanical unfolding studies of spectrin domains R15, R16 and R17. J. Struct. Biol. 2018;201:162–170. doi: 10.1016/j.jsb.2017.12.003
  42. Glyakina A.V., Likhachev I.V., Balabaev N.K., Galzitskaya O.V. Mechanical stability analysis of the protein L immunoglobulin-binding domain by full alanine screening using molecular dynamics simulations. Biotechnol. J. 2015;10:386–394. doi: 10.1002/biot.201400231
  43. Glyakina A.V., Likhachev I.V., Balabaev N.K., Galzitskaya O.V. Right- and left-handed three-helix proteins. II. Similarity and differences in mechanical unfolding of proteins. Proteins. 2014;82:90–102. doi: 10.1002/prot.24373.
  44. Likhachev I.V., Balabaev N.K. Trajectory analyzer of molecular dynamics. Mat. Biolog. Bioinform. 2007;2:120–129. doi: 10.17537/2007.2.120
  45. Likhachev I.V., Balabaev N.K., Galzitskaya O.V. Available Instruments for Analyzing Molecular Dynamics Trajectories. Open Biochem. J. 2016;10:1–11. doi: 10.2174/1874091X01610010001
  46. HyperChem 8. Tools for Molecular Modeling. Professional Edition For Windows AC Release 8.0 USB (on CD). Gainesville: Hypercube. Inc.; 2011.
Содержание
Оригинальная статья
Мат. биол. и биоинф.
2021;16(2):244-255
doi: 10.17537/2021.16.244
опубликована на рус. яз.

Аннотация (рус.)
Аннотация (англ.)
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