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Molecular Dynamics and Spin-Lattice NMR Relaxation in \(\alpha\)- and \(\varepsilon\)-Polylysine

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Abstract

The NMR relaxation method is widely used in various biomedical applications. Investigation of model homopeptides is an important step for understanding of structure and NMR properties of more complex branched peptides based on lysine monomers, for example, dendrimers, dendrigrafts and dendritic polymer brushes. In this paper, we perform molecular dynamics simulation of two linear lysine peptides with the same number of lysine monomers but with different connection between them through \(\alpha\)- or \(\varepsilon\)-peptide bonds. We obtained that the end-to-end distance and radius of gyration are smaller and radial density near the center of mass is essentially larger and decrease faster with radial distance for \(\alpha\)-lysine peptide than for \(\varepsilon\)-lysine peptide. Orientational mobility of \(\hbox {CH}_2\) groups in both peptides could be described by second order orientational autocorrelation function and by spin-lattice NMR relaxation time. We calculated both functions and found that the relaxation of vector in side chains of \(\alpha\)-lysine peptide is slightly faster in comparison with mobility of \(\hbox {CH}_2\) groups in main chain of \(\varepsilon\)-lysine peptide. Thus the big difference between the relaxation rates of these two types of \(\hbox {CH}_2\) groups in lysine dendrimers obtained recently both in NMR and in simulation is mainly due to dendrimer effect and not due to difference in position (side or main chain) of \(\hbox {CH}_2\) group in short linear lysine fragments. This result allows to use NMR for discrimination between \(\alpha\)-lysine and \(\varepsilon\)-lysine peptides as well as between linear lysine peptides (or their mixtures) and lysine dendrimers.

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References

  1. G. Sitterley, BioFiles 3(8), 12 (2008)

    Google Scholar 

  2. S. Shima, H. Sakai, Agric. Biol. Chem. 41(9), 1807–1809 (1977). https://doi.org/10.1271/bbb1961.41.1807

    Article  Google Scholar 

  3. D. Mazia, G. Schatten, W. Sale, J. Cell Biol. 66(1), 198–200 (1975). https://doi.org/10.1083/jcb.66.1.198

    Article  Google Scholar 

  4. M. Hyldgaard, T. Mygind, B.S. Vad, M. Stenvang, D.E. Otzen, R.L. Meyer, Appl. Environ. Microbiol. 80(24), 7758–7770 (2014). https://doi.org/10.1128/AEM.02204-14

    Article  Google Scholar 

  5. A.H. Chheda, M.R. Vernekar, Int. Food Res. J. 22(1), 23–30 (2015). https://doi.org/10.1016/j.fbio.2014.05.005

    Article  Google Scholar 

  6. T. Park, J. Gwan, K. Ji Hoon, S. Wan, Adv. Drug Deliv. Rev. 58(4), 467–486 (2006). https://doi.org/10.1016/j.addr.2006.03.007

    Article  Google Scholar 

  7. A.T. Petkova, G. Buntkowsky, F. Dyda, R.D. Leapman, W.M. Yau, R. Tycko, J. Mol. Biol. 335(1), 247–260 (2004). https://doi.org/10.1016/j.jmb.2003.10.044

    Article  Google Scholar 

  8. M. Tischler, D. Nasu, M. Empting, S. Schmelz, D.W. Heinz, P. Rottmann, H. Kolmar, G. Buntkowsky, D. Tietze, O. Avrutina, Angew. Chem. Int. Edn. 51(15), 3708–3712 (2012). https://doi.org/10.1002/anie.201108983

    Article  Google Scholar 

  9. V.I. Chizhik, M.S. Tagirov, Appl. Magn. Reson. 49, 533–536 (2018). https://doi.org/10.1007/s00723-018-1021-2

    Article  Google Scholar 

  10. F. Mohamed, M. Hofmann, B. Potzschner, N. Fatkullin, E.A. Rossler, Macromolecules 48(10), 3294–3302 (2015). https://doi.org/10.1021/acs.macromol.5b00486

    Article  ADS  Google Scholar 

  11. Y.Y. Gotlib, M.I. Lifshits, V.A. Shevelev, Proton magnetic relaxation in concentrated polystyrene solutions. Polym. Sci. USSR 17, 1563–1573 (1975). https://doi.org/10.1016/0032-3950(75)90323-8

    Article  Google Scholar 

  12. Y.Y. Gotlib, M.I. Lifshits, V.A. Shevelev, Polym. Sci. USSR 17, 2132–2142 (1975). https://doi.org/10.1016/0032-3950(75)90112-4

    Article  Google Scholar 

  13. Y.Y. Gotlib, M.I. Lifshits, V.A. Shevelev, I.S. Lishanskii, I.V. Balanina, Polym. Sci. USSR 20, 467–475 (1978). https://doi.org/10.1016/0032-3950(78)90061-8

    Article  Google Scholar 

  14. Y.Y. Gotlib, Y.Y. Svetlov, I.A. Torchinskii, Polym. Sci. USSR 21, 1145–1152 (1979). https://doi.org/10.1016/0032-3950(79)90012-1

    Article  Google Scholar 

  15. Y.Y. Gotlib, I.M. Neyelov, I.A. Torchinskii, V.A. Shevelev, Polym. Sci. USSR 31, 1976–1983 (1989). https://doi.org/10.1016/0032-3950(89)90414-0

    Article  Google Scholar 

  16. Y.Y. Gotlib, I.A. Torchinski, V.A. Shevelev, Macromol. Theory Simul. 2, 13–20 (1993). https://doi.org/10.1002/mats.1993.040020102

    Article  Google Scholar 

  17. Y.Y. Gotlib, I.A. Torchinskii, V.A. Shevelev, Polym. Sci. Ser. A 38, 1287–1292 (1996)

    Google Scholar 

  18. Y.Y. Gotlib, I.A. Torchinskii, V.A. Shevelev, Polym. Sci. Ser. A 39, 1328–1332 (1997)

    Google Scholar 

  19. Y.Y. Gotlib, I.A. Torchinskii, V.A. Shevelev, Polym. Sci. Ser. A 43, 1066–1073 (2001)

    Google Scholar 

  20. Y.Y. Gotlib, I.A. Torchinskii, V.A. Shevelev, Polym. Sci. Ser. A 44, 206–214 (2002)

    Google Scholar 

  21. R. Kimmich, N. Fatkullin, in Advances in Polymer Science (Springer, Berlin, 2004) pp. 1–113. https://doi.org/10.1007/978-3-540-40000-4_5

    Google Scholar 

  22. YuYa. Gotlib, A.A. Darinskii, I.M. Neelov, Vysokomol. Soyed A18(7), 1528–1533 (1976). https://doi.org/10.1016/0032-3950(76)90303-8

    Article  Google Scholar 

  23. Y.Y. Gotlib, A.A. Darinskii, I.M. Neyelov, Vysocomol. Soed. A20, 42–50 (1978). https://doi.org/10.1016/0032-3950(78)90110-7

    Article  Google Scholar 

  24. C. Cai, Z.Y. Chen, Macromolecules 31(18), 6393–6396 (1998). https://doi.org/10.1021/ma9807419

    Article  ADS  Google Scholar 

  25. Y.Y. Gotlib, D.A. Markelov, Polym. Sci. Ser. A 46, 815–832 (2004). https://doi.org/10.1134/s0965545x07100112

    Article  Google Scholar 

  26. Yu Ya. Gotlib, D.A. Markelov, Polym. Sci. Ser. A 49(10), 1137–1154 (2007). https://doi.org/10.1134/s0965545x07100112

    Article  Google Scholar 

  27. L.F. Pinto, J. Correa, M. Martin-Pastor, R. Riguera, E. Fernandez-Megia, J. Am. Chem. Soc. 135, 1972–1977 (2013). https://doi.org/10.1021/ja311908n

    Article  Google Scholar 

  28. L.F. Pinto, R. Riguera, E. Fernandez-Megia, J. Am. Chem. Soc. 135, 11513–11516 (2013). https://doi.org/10.1021/ja4059348

    Article  Google Scholar 

  29. D.A. Markelov, M. Dolgushev, Y.Y. Gotlib, A. Blumen, J. Chem. Phys. 140, 244904 (2014). https://doi.org/10.1063/1.4884024

    Article  ADS  Google Scholar 

  30. O. Shavykin, I. Neelov, A. Darinskii, Phys. Chem. Chem. Phys. 18(35), 24307–24317 (2016). https://doi.org/10.1039/c6cp01520d

    Article  Google Scholar 

  31. D.A. Markelov, A.N. Shishkin, V.V. Matveev, A.V. Penkova, E. Lähderanta, V.I. Chizhik, Macromolecules 49, 9247–9257 (2016). https://doi.org/10.1021/acs.macromol.6b01502

    Article  ADS  Google Scholar 

  32. M. Dolgushev, S. Schnell, D.A. Markelov, Appl. Magn. Reson. 48, 657–671 (2017). https://doi.org/10.1007/s00723-017-0897-6

    Article  Google Scholar 

  33. D.A. Markelov, M. Dolgushev, E. Lahderanta, Annu. Rep. NMR Spectrosc. 91, 1–66 (2017). https://doi.org/10.1016/bs.arnmr.2016.11.001

    Article  Google Scholar 

  34. I.M. Neelov, A. Janaszewska, B. Klajnert, M. Bryszewska, N.Z. Makova, D. Hicks, H.A. Pearson, G.P. Vlasov, M.Y. Ilyash, D.S. Vasilev, N.M. Dubrovskaya, N.L. Tumanova, I.A. Zhuravin, A.J. Turner, N.N. Nalivaeva, Curr. Med. Chem. 20, 134–143 (2013). https://doi.org/10.2174/0929867311302010013

    Article  Google Scholar 

  35. I. Neelov, S. Falkovich, D. Markelov, E. Paci, A. Darinskii, H. Tenhu, in Dendrimers in Biomedical Applications (The Royal Society of Chemistry, London, 2013), pp. 99–114

    Chapter  Google Scholar 

  36. S. Falkovich, D. Markelov, I. Neelov, A. Darinskii, J. Chem. Phys. 139, 064903 (2013). https://doi.org/10.1063/1.4817337

    Article  ADS  Google Scholar 

  37. I.M. Neelov, D.A. Markelov, S.G. Falkovich, M.Y. Ilyash, B.M. Okrugin, A.A. Darinskii, Polym. Sci. Ser. C 55, 154–161 (2013). https://doi.org/10.1134/s1811238213050032

    Article  Google Scholar 

  38. D.A. Markelov, S.G. Falkovich, I.M. Neelov, M.Y. Ilyash, V.V. Matveev, E. Lähderanta, P. Ingman, A.A. Darinskii, Phys. Chem. Chem. Phys. 17, 3214–3226 (2015). https://doi.org/10.1039/c4cp04825c

    Article  Google Scholar 

  39. Z. Kadlecova, Y. Rajendra, M. Matasci, L. Baldi, D.L. Hacker, F.M. Wurm, H.-A. Klok, J. Control. Release 169(3), 276–288 (2013). https://doi.org/10.1016/j.jconrel.2013.01.019

    Article  Google Scholar 

  40. J. Ennari, I. Neelov, F. Sundholm, Comput. Theor. Polym. Sci. 10, 403–410 (2000). https://doi.org/10.1016/s1089-3156(00)00006-4

    Article  Google Scholar 

  41. I. Neelov, K. Binder, Macromol. Theory Simul. 4(6), 1063–1084 (1995). https://doi.org/10.1002/mats.1995.040040605

    Article  Google Scholar 

  42. A. Darinsky, A. Lyulin, I. Neelov, Macromol. Theory Simul. 2(4), 523–530 (1993). https://doi.org/10.1002/mats.1993.040020402

    Article  Google Scholar 

  43. I. Neelov, D. Adolf, T. McLeish, T. McLeish, E. Paci, Biophys. J. 91(10), 3579–3588 (2006). https://doi.org/10.1529/biophysj.105.079236

    Article  ADS  Google Scholar 

  44. A. Darinskii, Y. Gotlib, A. Lyulin, I. Neelov, Vysokomolek. Soed. Ser. A 33(6),  1211–1220 (1991)

    Google Scholar 

  45. J. Ennari, I. Neelov, F. Sundholm, Polymer 45, 4171–4179 (2004). https://doi.org/10.1016/j.polymer.2004.03.096

    Article  Google Scholar 

  46. J. Gowdy, M. Batchelor, I. Neelov, J. Phys. Chem. B 121(41), 9518–9525 (2017). https://doi.org/10.1021/acs.jpcb.7b07075

    Article  Google Scholar 

  47. D.N. Theodorou, U.W. Suter, Macromolecules 18, 1206–1214 (1985). https://doi.org/10.1021/ma00148a028

    Article  ADS  Google Scholar 

  48. G. Rudnick, G. Gaspari, J. Phys. A 4, L191 (1986). https://doi.org/10.1088/0305-4470/19/4/004

    Article  Google Scholar 

  49. A. Abragam, The Principles of Nuclear Magnetism (Oxford University Press, Oxford, 1983)

    Google Scholar 

  50. V.I. Chizhik, Y.S. Chernyshev, A.V. Donets, V.V. Frolov, A.V. Komolkin, M.G. Shelyapina, Magnetic Resonance and Its Applications (Springer, Cham, 2014)

    Book  Google Scholar 

  51. M.H. Levitt, Spin Dynamics: Basics of NMR, 2nd edn. (John Wiley & Sons, Chichester, England, 2008)

    Google Scholar 

  52. N.N. Sheveleva, D.A. Markelov, M.A. Vovk, M.E. Mikhailova, I.I. Tarasenko, I.M. Neelov, E. Lähderanta, Sci. Rep. 8, 8916–8922 (2018). https://doi.org/10.1038/s41598-018-27063-3

    Article  ADS  Google Scholar 

  53. V. Sadovnichy, A. Tikhonravov, V. Voevodin, V. Opanasenko, in Contemporary High Performance Computing: from Petascale toward Exascale (Chapman and Hall/CRC, New York, 2013), pp. 283–307

    Google Scholar 

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Acknowledgements

This work was partially supported by RFBR (Grant No 19-03-00715) and by subsidy of Government of Russian Federation (Grant 08-08). The research is carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University [53] and Computer Resources Center of Saint Petersburg State University.

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  1. Universitet ITMO Megafakul’tet fotoniki, St. Petersburg, Russian Federation

    V. V. Bezrodnyi, O. V. Shavykin, S. E. Mikhtaniuk & I. M. Neelov

  2. St. Petersburg State University, 7/9 Universitetskaya nab., 199034, St. Petersburg, Russia

    D. A. Markelov

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  1. V. V. Bezrodnyi
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Correspondence to O. V. Shavykin.

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Bezrodnyi, V.V., Shavykin, O.V., Mikhtaniuk, S.E. et al. Molecular Dynamics and Spin-Lattice NMR Relaxation in \(\alpha\)- and \(\varepsilon\)-Polylysine. Appl Magn Reson 51, 1669–1679 (2020). https://doi.org/10.1007/s00723-020-01260-8

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