Journal of Computational Electronics

, Volume 7, Issue 1, pp 20–23 | Cite as

Exploration of Na+,K+-ATPase ion permeation pathways via molecular dynamic simulation and electrostatic analysis

  • J. E. Fonseca
  • S. Mishra
  • S. Kaya
  • R. F. Rakowski
Article

Abstract

Biologically-inspired nanodevices can serve as “natural” alternatives to conventional semiconductor devices in many applications from information storage to mechanical rotors. In this work we consider an ATP-powered transmembrane protein, the Na+,K+-ATPase, which has appealing functionality but still lacks an “atomistic” picture capable of elucidating its operation. The vast collection of experimental literature on the Na+,K+-ATPase gives a unique advantage to this protein in developing and validating computational tools. We have performed extensive molecular dynamic simulations of the Na+,K+-ATPase in an accurate biological environment, followed by time-averaged electrostatic analysis, to investigate the ion-binding loci and access/egress pathways that cations may take through the protein as they are transported across the membrane.

Keywords

Na+,K+-ATPase Bionano Homology modeling Electrostatics Molecular dynamics 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Asenov, A., et al.: IEEE Trans. Electron Devices 50, 1837 (2003) CrossRefGoogle Scholar
  2. 2.
    Niemeyer, C.M., Mirkin, C.A.: Nanobiotechnology: Concepts, Applications and Perspectives. Wiley-VCH, Weinheim (2004) Google Scholar
  3. 3.
    van den Heuvel, M., Dekker, C.: Science 317, 333 (2007) CrossRefGoogle Scholar
  4. 4.
    Saraniti, M., et al.: J. Comp. Elec. 5, 405 (2006) CrossRefGoogle Scholar
  5. 5.
    Toyoshima, C., et al.: Nature 432, 361 (2004) CrossRefGoogle Scholar
  6. 6.
    Apell, H.J.: Bioelectrochemistry 63, 149 (2004) CrossRefGoogle Scholar
  7. 7.
    Horisberger, J.D.: Physiology (Bethesda) 19, 377 (2004) Google Scholar
  8. 8.
    Law, R.J., et al.: J. Mol. Graph. Model 24, 157 (2005) CrossRefGoogle Scholar
  9. 9.
    Laskowski, R.A., et al.: J. Appl. Cryst. 26, 283 (1993) CrossRefGoogle Scholar
  10. 10.
    Morth, J.P., et al.: Nature 450, 1043 (2007) CrossRefGoogle Scholar
  11. 11.
    Sweadner, K.J., Donnet, C.: Biochem. J. 356, 685 (2001) Google Scholar
  12. 12.
    Toyoshima, C., et al.: Nature 405, 647 (2000) CrossRefGoogle Scholar
  13. 13.
    Munson, K., et al.: Biochemistry 44, 5267 (2005) CrossRefMathSciNetGoogle Scholar
  14. 14.
    Einholm, A.P., et al.: J. Biol. Chem. 282, 23854 (2007) CrossRefGoogle Scholar
  15. 15.
    Marti-Renom, M.A., et al.: Ann. Rev. Biophys. Biomol. Str. 29, 291 (2000) CrossRefGoogle Scholar
  16. 16.
    Kandt, C., et al.: Methods 41, 475 (2007) CrossRefGoogle Scholar
  17. 17.
    Fonseca, J.E., et al.: Nanotechnology 18, 424022 (2007) CrossRefGoogle Scholar
  18. 18.
    Humphrey, W., et al.: J. Mol. Graph. 14, 33 (1996) CrossRefGoogle Scholar
  19. 19.
    Aksimentiev, A., Schulten, K.: Biophys. J. 88, 3745 (2005) CrossRefGoogle Scholar
  20. 20.
    Li, C., et al.: P. Nat. Ac. Sci. 102, 12706 (2005) CrossRefGoogle Scholar
  21. 21.
    Schneider, H., Scheiner-Bobis, G.: J. Biol. Chem. 272, 16158 (1997) CrossRefGoogle Scholar
  22. 22.
    Capendeguy, O., Horisberger, J.D.: J. Physiol. 565, 207 (2005) CrossRefGoogle Scholar
  23. 23.
    Capendeguy, O., et al.: J. Gen. Physiol. 127, 341 (2006) CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2008

Authors and Affiliations

  • J. E. Fonseca
    • 1
  • S. Mishra
    • 1
  • S. Kaya
    • 1
  • R. F. Rakowski
    • 2
  1. 1.School of EECS, Russ College of Eng. & Tech.Ohio UniversityAthensUSA
  2. 2.Department of Biological SciencesOhio UniversityAthensUSA

Personalised recommendations