References
- 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
- Lehninger A.L. Biochemistry. The Molecular Basis of Cell Structure and Function (2nd Edition). New York: Worth Publishers, Inc., 1972.
- Sharma P., Rathi B., Rodrigues J., Gorobets N. Self-Assembled Peptide Nanoarchitectures: Applications and Future Aspects. CTMC. 2015:15(13). doi: 10.2174/1568026615666150408105711
- 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
- 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
- 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
- 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
- Tverdislov V.A. Chirality as a primary switch of hierarchical levels in molecular biological systems. Biophysics. 2013;58:128–132. doi: 10.1134/S0006350913010156
- 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
- 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
- Tishkov V.I. Moscow University Chemistry Bulletin. 2002;43:381–388 (in Russ.).
- 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.
- 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
- 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
- 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).
- 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
- 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
- Scanlon S., Aggeli A. Self-assembling peptide nanotubes. Nano Today. 2008;3:22–30. doi: 10.1016/S1748-0132(08)70041-0
- 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
- Reches M., Gazit E. Controlled patterning of aligned self-assembled peptide nanotubes. Nature Nanotechnology. 2006;1:195–200. doi: 10.1038/nnano.2006.139
- 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
- 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
- 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
- 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
- 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
- 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
- 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).
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Lemak A.S., Balabaev N.K. A Comparison Between Collisional Dynamics and Brownian Dynamics. Molecular Simulation. 1995;15:223–231. doi: 10.1080/08927029508022336
- 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
- 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
- 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
- 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
- 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.
- Likhachev I.V., Balabaev N.K. Trajectory analyzer of molecular dynamics. Mat. Biolog. Bioinform. 2007;2:120–129. doi: 10.17537/2007.2.120
- 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
- HyperChem 8. Tools for Molecular Modeling. Professional Edition For Windows AC Release 8.0 USB (on CD). Gainesville: Hypercube. Inc.; 2011.
|
|
|