Menu
Publications
2024
2023
2022
2021
2020
2019
2018
2017
2016
2015
2014
2013
2012
2011
2010
2009
2008
2007
2006
2005
2004
2003
2002
2001
Editor-in-Chief
Nikiforov
Vladimir O.
D.Sc., Prof.
Partners
doi: 10.17586/2226-1494-2018-18-4-595-605
COMPUTER MODELING OF INTERACTION OF LYSINE DENDRIMER WITH EPITHALON PEPTIDES
Read the full article
';
Article in Russian
For citation: Khamidova D.N., Popova A.V., Bezrodnyi V.V., Mikhtanyuk S.E., E.V. Popova, Neelov I.M., Leermakers F. Computer modeling of interaction of lysine dendrimer with epithalon peptides. Scientific and Technical Journal of Information Technologies, Mechanics and Optics, 2018, vol. 18, no. 4, pp. 595–605 (in Russian). doi: 10.17586/2226-1494-2018-18-4-595-605
Abstract
For citation: Khamidova D.N., Popova A.V., Bezrodnyi V.V., Mikhtanyuk S.E., E.V. Popova, Neelov I.M., Leermakers F. Computer modeling of interaction of lysine dendrimer with epithalon peptides. Scientific and Technical Journal of Information Technologies, Mechanics and Optics, 2018, vol. 18, no. 4, pp. 595–605 (in Russian). doi: 10.17586/2226-1494-2018-18-4-595-605
Abstract
Subject of Study.Dendrimers are hyperbranched polymeric molecules that regularly branch from a single center. Dendrimers are used in biomedical applications to deliver drugs and genetic material to cells. The present work considers the study of the formation of lysine dendrimer complexes with therapeutic tetrapeptides and the equilibrium properties of the complex. Two systems were studied consisting of one second-generation lysine dendrimer and 16 tetrapeptides. In the first case, the system consisted of a dendrimer and 16 free molecules of Epithalon peptide. In the second case, the system consisted of a dendrimer and 16 chemically bound to its ends Epithalon peptide molecules. Method. The study was carried out by computer simulation by the molecular dynamics method. Main Results. The sizes and internal structure of the complex and conjugate of peptide molecules with dendrimer were compared. It is found that in the case of free Epithalon, peptide molecules are adsorbed not only on the surface but can also penetrate into the dendrimer to form a stable complex with it. In the case of a conjugate, the peptides penetrate less into the dendrimer, but, being mainly on the dendrimer surface, they compress the dendrimer inwards, forming a more compact structure than the structure of complex. Practical Relevance. Such complexes and conjugates can be used in the future to deliver various therapeutic peptides and other drug molecules to target organs
Keywords: lysine dendrimers, Epithalon peptide, computer simulation, molecular dynamics method
Acknowledgements. This work was financially supported by the Government of the Russian Federation (grant 08-08). All calculations were carried out on the supercomputer "Lomonosov" in supercomputer center of Moscow State University.
References
Acknowledgements. This work was financially supported by the Government of the Russian Federation (grant 08-08). All calculations were carried out on the supercomputer "Lomonosov" in supercomputer center of Moscow State University.
References
1. Kozina L.S., Arutjunyan A.V., Stvolinsky S.L., Khavinson V.Kh. The valuation of biological activity of regulatory peptides in model experiments in vitro. Advances in Gerontology, 2008, vol. 21, no. 1, pp. 68–73. (in Russian)
2. Khavinson V.K., Bondarev I.E., Butyugov A.A. Epithalon peptide induces telomerase activity and telomere elongation in human somatic cells. Bulletin of Experimental Biology and Medicine, 2003, vol. 135, no. 6, pp. 590–592. doi: 10.1023/A:1025493705728
3. Khavinson V.K., Shataeva L.K. Model of complementary interaction of oligopeptides with double helix DNA. Meditsinskii Akademicheskii Zhurnal, 2005, vol. 5, pp. 15–23. (in Russian)
4. Falkovich S., Markelov D., Neelov I., Darinskii A. Are structural properties of dendrimers sensitive to the symmetry of branching? Computer simulation of lysine dendrimers. Journal of Chemical Physics, 2013, vol. 139, no. 7, art. 064903. doi: 10.1063/1.4817337
5. Neelov I.M., Markelov D.A., Falkovich S.G., Ilyash M.Yu., Okrugin B.M., Darinskii A.A. Mathematical simulation of lysine dendrimers: Temperature dependences. Polymer Science - Series C, 2013, vol. 55, no. 1, pp. 154–161. doi: 10.1134/S1811238213050032
6. Neelov I., Falkovich S., Markelov D., Paci E., Darinskii A., Tenhu H. Molecular dynamics of lysine dendrimers. Computer simulation and NMR. In: Dendrimers in Biomedical Applications. London, Royal Society of Chemistry, 2013, pp. 99–114.
7. Markelov D.A., Falkovich S.G., Neelov I.M., Ilyash M.Yu., Matveev V.V., Lahderanta E., Ingman P., Darinskii A.A. Molecular dynamics simulation of spin-lattice NMR relaxation in poly-L-lysine dendrimers. Manifestation of the semiflexibility effect. Physical Chemistry and Chemical Physics, 2015, vol. 17, pp. 3214–3226. doi: 10.1039/c4cp04825c
8. Neelov I., Ilyash M., Falkovich S., Darinskii A. Computer simulation of lysine dendrimers by molecular dynamics method. In Synthesis, Characterization and Modelling of Nano-Sized Structures. Nova Science Publisher, 2016, pp. 147–156.
9. Shavykin O.V., Popova E.V., Darinskii A.A., Neelov I.M., Leermakers F. Computer simulation of local mobility in dendrimers with asymmetric branching by Brownian dynamics method. Scientific and Technical Journal of Information Technologies, Mechanics and Optics, 2016, vol. 16, no. 5, pp. 893–902. doi: 10.17586/2226-1494-2016-16-5-893-902
10. Shavykin O.V., Neelov I.M., Darinskii A.A. Is the manifestation of the local dynamics in the spin-lattice NMR relaxation in dendrimers sensitive to excluded volume interactions? Physical Chemistry Chemical Physics, 2016, vol. 18, no. 35, pp. 24307–24317. doi: 10.1039/c6cp01520d
11. Okrugin B.M., Neelov I.M., Borisov O.V., Leermakers F.A.M. Structure of asymmetrical peptide dendrimers: insights given by self-consistent field theory.Polymer, 2017, vol. 125, pp. 292–302. doi: 10.1016/j.polymer.2017.07.060
12. Shavykin O.V., Leermakers F.A.M., Neelov I.M., Darinskii A.A. Self-assembly of lysine-based dendritic surfactants modeled by the self-consistent field approach. Langmuir, 2018, vol. 34, no. 4, pp. 1613–1626. doi: 10.1021/acs.langmuir.7b03825
13. Neelov I.M., Janaszewska A., Klajnert B., Bryszewska M., Makova N., Hicks D., Pearson H., Vlasov G.P., Ilyash M.Yu., Vasilev D.S., Dubrovskaya N.M., Tumanova N.L., Zhuravin I.A., Turner A.J., Nalivaeva N.N. Molecular properties of lysine dendrimers and their interactions with Ab-peptides and neuronal cells.Current Medical Chemistry, 2013, vol. 20, no. 1, pp. 134–143. doi: 10.2174/09298673130113
14. Klajnert B., Bryszewska M., Cladera J. Molecular interactions of dendrimers with amyloid peptides: pH dependence. Biomacromolecules, 2006, vol. 7, no. 7, pp. 2186–2191. doi: 10.1021/bm060229s
15. Ilyash M.Yu., Khamidova D.N., Okrugin B.M., Neelov I.M. Computer simulation of lysine dendrimers and their interactions with amyloid peptides.WSEAS Transaction on Biology and Biomedicine, 2015, vol. 12, pp. 79–86.
16. Popova E., Okrugin B., Neelov I. Molecular dynamics simulation of interaction of short lysine brush and oppositely charged Semax peptides. Natural Science, 2016, vol. 8, no. 12, pp. 499–510. doi: 10.4236/ns.2016.812051
17. Popova E.V., Shavykin O.V., Neelov I.M., Leemakers F. Molecular dynamics simulation of lysine dendrimer and semax peptides interaction.Scientific and Technical Journal of Information Technologies, Mechanics and Optics, 2016, vol. 16, no. 4, pp. 716–724. (in Russian) doi: 10.17586/2226-1494-2016-16-4-716-724
18. Popova E.V., Khamidova D.N., Neelov I.M., Komilov F.S., Leermakers F. Computer simulation of interaction of lysine dendrimers with stack of amyloid peptides. Scientific and Technical Journal of Information Technologies, Mechanics and Optics, 2017, vol. 17, no. 6, pp. 1033–1044 (in Russian). doi: 10.17586/2226-1494-2017-17-6-1033-1044
19. Neelov I., Popova E. Molecular dynamics simulation of complex formation by lysine dendrigraft of second generation and semax peptide.International Journal of Materials, 2017,vol. 4, pp. 16–21.
20. Neelov I., Popova E., Khamidova D., Komilov F. Interaction of lysine dendrimers of 2nd and 3rd generation with stack of amyloid peptides. Molecular dynamics simulation. International Journal of Biology and Biomedical Engineering, 2017, vol. 11, pp. 95–100.
21. Neelov I., Popova E., Khamidova D., Tarasenko I. Interaction of lysine dendrimers and Semax peptides. Molecular dynamics simulation. International Journal of Biology and Biomedical Engineering, 2017, vol. 2, pp. 6–12.
22. Popova E., Khamidova D., Neelov I., Komilov F. Lysine dendrimers and their complezxes with therapeutic and amyloid peptides. Computer simulation. Dendrimers. Fundamentals and Applications. IntechOpen, 2018, pp. 29–45. doi: 10.5772/intechopen.71052
23. Hess B., Kutzner C., Van Der Spoel D., Lindahl E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 2008, vol. 4, no. 3, pp. 435–447. doi: 10.1021/ct700301q
24. Hornak V., Abel R., Okur A., Strockbine D., Roitberg A., Simmerling C. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins: Structure Function and Genetics, 2006, vol. 65, no. 3, pp. 712–725. doi: 10.1002/prot.21123
25. Gotlib Y.Y., Balabaev N.K., Darinskii A.A., Neelov I.M. Investigation of local motions in polymers by the method of molecular dynamics. Macromolecules, 1980, vol. 13, no. 3, pp. 602–608. doi: 10.1021/ma60075a023
26. Gotlib Ya.Yu., Darinsky A.A., Klushin L.I., Neelov I.M. Properties of kinetic element and local mobility of polymer chains. Acta Polymerica, 1984, vol. 35, no. 2, pp. 124–129. doi: 10.1002/actp.1984.010350203
27. Darinskii A.A., Gotlib Yu.Ya., Lyulin A.V., Neelov I.M. Computer simulation of local dynamics of polymer chain in the orienting field of the LC type. Vysokomoleculyanye Soedineniya, Seriya A, 1991, vol. 33, no. 6, pp. 1211–1220. (In Russian)
28. Darinskii A., Gotlib Yu., Lukyanov M., Neelov I. Computer simulation of the molecular motion in LC and oriented polymers. Progress in Colloid & Polymer Science, 1993, vol. 91, pp. 13–15.
29. Darinskii A., Lyulin A., Neelov I. Computer simulations of molecular motion in liquid crystals by the method of Brownian dynamics. Macromolecular Theory and Simulations, 1993, vol. 2, pp. 523–530. doi: 10.1002/mats.1993.040020402
30. Neelov I.M., Binder K. Brownian dynamics of grafted polymer brushes. Macromolecular Theory and Simulations, 1995, vol. 4, no. 1, pp. 119–136. doi: 10.1002/mats.1995.040040108
31. Neelov I.M., Binder K. Brownian dynamics of grafted polymer chains: time dependent properties. Macromolecular Theory and Simulations, 1995, vol. 4, no. 6, pp. 1063–1084. doi: 10.1002/mats.1995.040040605
32. Balabaev N.K., Darinskii A.A., Neelov I.M., Lukasheva N.V., Emri I. Molecular dynamics simulation of a two-dimensional polymer melt. Polymer Science Series C, 2002, vol. 44, no. 7, pp. 781–790.
33. Neelov I.M., Adolf D.B., Lyulin A.V., Davies G.R. Brownian dynamics simulation of linear polymers under elongational flow: bead-rod model with hydrodynamic interactions.Journal of Chemical Physics,2002, vol. 117, no. 8, pp. 4030–4041. doi: 10.1063/1.1493187
34. Neelov I.M., Adolf D.B., McLeish T.C.B., Paci E. Molecular dynamics simulation of dextran extension by constant force in single molecule AFM. Biophysical Journal, 2006, vol. 91, no. 10, pp. 3579–3588. doi: 10.1529/biophysj.105.079236
35. Yudin V.E., Dobrovolskaya I.P., Neelov I.M. et al.Wet spinning of fibers made of chitosan and chitin nanofibrils. Carbohydrate Polymers, 2014, vol. 108, no. 1, pp. 176–182. doi: 10.1016/j.carbpol.2014.02.090
36. Neelov I.M., Mistonova A.A., Khvatov A.Y., Bezrodny V.V. Molecular dynamic simulation of peptide polyelectrolytes. Scientific and Technical Journal of Information Technologies, Mechanics and Optics, 2014, no. 4, pp. 169–175. (In Russian).
37. Gowdy J., Batchelor M., Neelov I., Paci E. Nonexponential kinetics of loop formation in proteins and peptides: A signature of rugged free energy landscapes? Journal of Physical Chemistry B, 2017, vol. 121, no. 41, pp. 9518–9525. doi: 10.1021/acs.jpcb.7b07075
38. Ennari J., Elomaa M., Neelov I., Sundholm F. Modelling of water-free and water containing solid polyelectrolytes. Polymer, 2000, vol. 41, no. 3, pp. 985–990. doi: 10.1016/S0032-3861(99)00235-9
39. Ennari J., Neelov I., Sundholm F. Comparison of cell multipole and Ewald summation methods for solid polyelectrolyte. Polymer, 2000, vol. 41, no. 6, pp. 2149–2155. doi: 10.1016/S0032-3861(99)00382-1
40. Ennari J., Neelov I., Sundholm F. Molecular dynamics simulation of the PEO sulfonic acid anion in water. Computational and Theoretical Polymer Science, 2000, vol. 10, no. 5, pp. 403–410.
41. Ennari J., Neelov I., Sundholm F. Molecular dynamics simulation of the structure of PEO based solid polymer electrolytes. Polymer, 2000, vol. 41, no. 11, pp. 4057–4063.
42. Ennari J., Neelov I., Sundholm F. Estimation of the ion conductivity of a PEO-based polyelectrolyte system by molecular modeling. Polymer, 2001, vol. 42, no. 3, pp. 8043–8050.
43. Ennari J., Neelov I., Sundholm F. Modelling of gas transport properties of polymer electrolytes containing various amount of water. Polymer, 2004, vol. 45, no. 12, pp. 4171–4179. doi: 10.1016/j.polymer.2004.03.096
44. Neelov I.M., Adolf D.B. Brownian dynamics simulations of dendrimers under elongational flow: bead-rod model with hydrodynamic interactions. Macromolecules, 2003, vol. 36, no. 18, pp. 6914–6924. doi: 10.1021/ma030088b
45. Sheridan P.F., Adolf D.B., Lyulin A.V., Neelov I., Davies G.R. Computer simulations of hyperbranched polymers: the influence of the Wiener index on the intrinsic viscosity and radius of gyration. Journal of Chemical Physics, 2002, vol. 117, no. 16, pp. 7802–7812. doi: 10.1063/1.1507774
46. Neelov I.M., Adolf D.B. Brownian dynamics simulation of hyperbranched polymers under elongational flow. Journal of Physical Chemistry B, 2004, vol. 108, no. 10, pp. 7627–7636. doi: 10.1021/jp030994q
47. Mazo M.A., Shamaev M.Y., Balabaev N.K., Darinskii A.A., Neelov I.M. Conformational mobility of carbosilane dendrimer: molecular dynamics simulation. Physical Chemistry Chemical Physics, 2004, vol. 6, no. 6, pp. 1285–1289.
48. Sadovnichy V., Tikhonravov A., Voevodin V., Opanasenko V. "Lomonosov": supercomputing at Moscow State University. In: Contemporary High Performance Computing: From Petascale Toward Exascale. Boca Raton, USA, CRC Press, 2013, pp. 283–307.
