Skip to main content
SpringerLink
Log in

Modeling of the Lipid Bilayer Mimicking the Inner Mitochondrial Membrane

  • STRUCTURE OF MACROMOLECULAR COMPOUNDS
  • Published:
Crystallography Reports Aims and scope Submit manuscript

Abstract

The model of the lipid bilayer mimicking the inner mitochondrial membrane was constructed. Each layer of the lipid bilayer model consists of 51 dilinoleoyl phosphatidylethanolamine molecules, 36 dilinoleoyl phosphatidylcholine molecules, 35 tetraoleoyl cardiolipin molecules, and 6 dilinoleoyl phosphatidylinositol molecules. This model was analyzed by molecular dynamics simulation (20 000 ps). The mobility of different lipids and groups of atoms involved in the lipids is described. This model can be used to study the lipid component of the inner mitochondrial membrane.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.

Similar content being viewed by others

REFERENCES

  1. B. Alberts, A. Johnson, J. Lewis, et al., Molecular Biology of the Cell (Garland Science, New York, 2002). https://doi.org/10.1093/aob/mcg023

  2. R. B. Gennis, Biomembranes: Molecular Structure and Function (Springer, New York, 1989). https://doi.org/10.1007/978-1-4757-2065-5

    Book  Google Scholar 

  3. S.-I. Hakomori and Y. Igarashi, J. Biochem. 118 (6), 1091 (1995). https://doi.org/10.1093/oxfordjournals.jbchem.a124992

    Article  Google Scholar 

  4. N. Khatibzadeh, S. Gupta, B. Farrell, et al., Soft Matter 8 (32), 8350. (2012). https://doi.org/10.1039/C2SM25263E

    Article  ADS  Google Scholar 

  5. T. Koike, G. Ishida, M. Taniguchi, et al., Biochim. Biophys. Acta Mol. Basis Dis. 1406 (3), 327 (1998). https://doi.org/10.1016/S0925-4439(98)00019-2

    Article  Google Scholar 

  6. O. Nadiv, M. Shinitzky, H. Manu, et al., Biochem. J. 298 (2), 443 (1994). https://doi.org/10.1042/bj2980443

    Article  Google Scholar 

  7. S. P. H. Alexander, A. Mathie, and J. A. Peters, Br. J. Pharmacol. 164, Spec. Iss.: Guide to Recept. Channels, 5th Ed., p. S137 (2011). https://doi.org/10.1111/j.1476-5381.2011.01649_1.x

    Book  Google Scholar 

  8. P. Siekevitz, Sci. Am. 197 (1), 131 (1957). https://doi.org/10.1038/scientificamerican0757-131

    Article  ADS  Google Scholar 

  9. K. A. Waters, B. Meehan, J. Huang, et al., Pediatr. Res. 45 (2), 166 (1999). https://doi.org/10.1203/00006450-199902000-00002

    Article  Google Scholar 

  10. S. Namura, J. Zhu, K. Fink, et al., J. Neurosci. 18 (10), 3659 (1998). https://doi.org/10.1523/JNEUROSCI.18-10-03659.1998

    Article  Google Scholar 

  11. K. Takuma, S. S. Yan, D. M. Stern, et al., J. Pharmacol. Sci. 97 (3), 312 (2005). https://doi.org/10.1254/jphs.cpj04006x

    Article  Google Scholar 

  12. A. Wenzel, C. Grimm, M. Samardzija, et al., Prog. Retin. Eye Res. 24 (2), 275 (2005). https://doi.org/10.1016/j.preteyeres.2004.08.002

    Article  Google Scholar 

  13. S. M. Krams, H. Egawa, M. B. Quinn, et al., Transplantation 59 (4), 621 (1995).

    Article  Google Scholar 

  14. D. P. Lane and S. Benchimol, Gene. Dev. 4 (1), 1 (1990). https://doi.org/10.1101/gad.4.1.1

    Article  Google Scholar 

  15. M. Hollstein, D. Sidransky, B. Vogelstein, et al., Science 253 (5015), 49 (1991). https://doi.org/10.1126/science.1905840

    Article  ADS  Google Scholar 

  16. D. Gonzalez, I. Bejarano, C. Barriga, et al., Curr. Signal Transduction Ther. 5 (2), 181 (2010). https://doi.org/10.2174/157436210791112172

    Article  Google Scholar 

  17. Y. A. Vladimirov, E. Proskurnina, and A. Alekseev, Biochemistry (Moscow) 78 (10), 1086 (2013). https://doi.org/10.1134/S0006297913100027

    Article  Google Scholar 

  18. G. Vladimirov, A. Vikulina, D. Volodkin, et al., Chem. Phys. Lipids 214, 35 (2018). https://doi.org/10.1016/j.chemphyslip.2018.05.007

    Article  Google Scholar 

  19. Y. A. Vladimirov, C. Sarisozen, G. K. Vladimirov, et al., Pharm. Res. 34 (6), 1264 (2017). https://doi.org/10.1007/s11095-017-2143-1

    Article  Google Scholar 

  20. J. Comte, B. Maĭsterrena, and D. C. Gautheron, Biochim. Biophys. Acta Biomembr. 419 (2), 271 (1976). https://doi.org/10.1016/0005-2736(76)90353-9

    Article  Google Scholar 

  21. S. Jo, T. Kim, V. G. Iyer, et al., J. Comput. Chem. 29 (11), 1859 (2008). https://doi.org/10.1002/jcc.20945

    Article  Google Scholar 

  22. D. A. Case, T. E. Cheatham, III, T. Darden, et al., J. Comput. Chem. 26 (16), 1668 (2005). https://doi.org/10.1002/jcc.20290

    Article  Google Scholar 

  23. R. Salomon-Ferrer, A. W. Götz, D. Poole, et al., J. Chem. Theor. Comput. 9 (9), 3878 (2013). https://doi.org/10.1021/ct400314y

    Article  Google Scholar 

  24. J. B. Klauda, R. M. Venable, J. A. Freites, et al., J. Phys. Chem. B 114 (23), 7830 (2010). https://doi.org/10.1021/jp101759q

    Article  Google Scholar 

  25. M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford Univ.Ppress, New York, 1991). https://doi.org/10.2307/2938686

    MATH  Google Scholar 

  26. P. J. Steinbach, Proteins: Struct., Funct., Bioinf. 57 (4), 665 (2004). https://doi.org/10.1002/prot.20247

    Article  Google Scholar 

  27. M. A. Marchenkova, Y. A. Dyakova, E. Y. Tereschenko, et al., Langmuir 31 (45), 12426 (2015). https://doi.org/10.1021/acs.langmuir.5b03155

    Article  Google Scholar 

Download references

Funding

The study was financially supported by the Russian Science Foundation (project no. 19-14-00244, molecular dynamics simulations) and the Ministry of Science and Higher Education of the Russian Federation within the framework of the state assignment for the Federal Scientific Research Centre “Crystallography and Photonics” of the Russian Academy of Sciences (analysis of the results of molecular modeling).

Author information

Authors and Affiliations

  1. Pirogov Russian National Research Medical University, 117997, Moscow, Russia

    A. A. Yurchenko, A. R. Gusel’nikova & Yu. A. Vladimirov

  2. Lomonosov Moscow State University, 119991, Moscow, Russia

    P. D. Korotkova, A. B. Shumm & Yu. A. Vladimirov

  3. Lebedev Physical Institute, Russian Academy of Sciences, 119991, Moscow, Russia

    A. B. Shumm

  4. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, 119333, Moscow, Russia

    V. I. Timofeev & Yu. A. Vladimirov

  5. Department of NBICS Nature-Like Technologies, National Research Centre “Kurchatov Institute”, 123182, Moscow, Russia

    V. I. Timofeev

  6. Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, 119991, Moscow, Russia

    Yu. A. Vladimirov

Authors
  1. A. A. Yurchenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. P. D. Korotkova
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. A. R. Gusel’nikova
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. A. B. Shumm
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. V. I. Timofeev
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yu. A. Vladimirov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to A. A. Yurchenko or V. I. Timofeev.

Ethics declarations

The authors declare no conflict of interest, financial or otherwise.

Additional information

Translated by T. Safonova

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yurchenko, A.A., Korotkova, P.D., Gusel’nikova, A.R. et al. Modeling of the Lipid Bilayer Mimicking the Inner Mitochondrial Membrane. Crystallogr. Rep. 66, 1006–1009 (2021). https://doi.org/10.1134/S1063774521060432

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1063774521060432

Search

Navigation