Skip to main content
SpringerLink
Log in

Transportation behavior of alkali ions through a cell membrane ion channel. A quantum chemical description of a simplified isolated model

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

Quantum chemical model calculations were carried out for modeling the ion transport through an isolated ion channel of a cell membrane. An isolated part of a natural ion channel was modeled. The model channel was a calixarene derivative, hydrated sodium and potassium ions were the models of the transported ion. The electrostatic potential of the channel and the energy of the channel-ion system were calculated as a function of the alkali ion position. Both attractive and repulsive ion-channel interactions were found. The calculations – namely the dependence of the system energy and the atomic charges of the water molecules with respect to the position of the alkali ion in the channel – revealed the molecular-structural background of the potassium selectivity of this artificial ion channel. It was concluded that the studied ion channel mimics real biological ion channel quite well.

Transportation behavior of alkali ions through a cell membrane ion channel

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
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10

Similar content being viewed by others

References

  1. Hille B (2001) Ion channels of excitable membranes, 3rd edn. Sinauer Associates, Sunderland, MA, USA

    Google Scholar 

  2. Aidley DJ, Stanfield PR (1996) Ion channels: molecules in action. Cambridge University Press, Cambridge, UK

    Google Scholar 

  3. Kew JNC (2010) Davies CH (2010) Ion channels: from structure to function. Oxford University Press, Oxford, UK

    Google Scholar 

  4. Gillespie D, Eisenberg RS (2002) Physical descriptions of experimental selectivity measurements in ion channels. Eur Biophys J 31:454–466. doi:10.1007/s00249-002-0239-x

    Article  CAS  Google Scholar 

  5. Hall LT, Hill CD, Cole JH, Städler B, Caruso F, Mulvaney P, Wrachtrup J, Hollenberg LCL (2010) Monitoring ion-channel function in real time through quantum decoherence. PNAS 107:18777–18782. doi:10.1073/pnas.1002562107

    Article  CAS  Google Scholar 

  6. Siwy Z, Ausloos M, Ivanova K (2002) Correlation studies of open and closed state fluctuations in an ion channel: analysis of ion current through a large-conductance locust potassium channel. Phys Rev E 65:031907. doi:10.1103/PhysRevE.65.031907

    Article  Google Scholar 

  7. Guidoni L, Carloni P (2002) Potassium permeation through the KcsA channel: a density functional study. Biochim Biophys Acta 1563:1–6. doi:10.1016/j.bpc.2006.04.008

    Article  CAS  Google Scholar 

  8. Roux B (2002) Computational studies of the Gramicidin channel. Acc Chem Res 35:366–375. doi:10.1021/ar010028v

    Article  CAS  Google Scholar 

  9. Grigorenko BL, Nemukhin AV, Topol IA, Burt SK (2002) Modeling of Biomolecular Systems with the Quantum Mechanical and Molecular Mechanical Method Based on the Effective Fragment Potential Technique: Proposal of Flexible Fragments. J Phys Chem A 106:10663–10672. doi:10.1021/jp026464w

    Article  CAS  Google Scholar 

  10. Vogel C (2002) Modeling transport across biological membranes. Structural Studies Division MRC Laboratory of Molecular Biology, Hills Road, Cambridge. http://polaris.icmb.utexas.edu/people/cvogel/Dogs/mini1_gapjct.doc

  11. Liu JL (2011) A quantum corrected Poisson-Nernst-Planck model for biological ion channels. www.nhcue.edu.tw/∼jinnliu/proj/Device/2011QCPNP.pdf

  12. Abad E, Reingruber J, Sansom MSP (2009) On a novel rate theory for transport in narrow ion channels and its application to the study of flux optimization via geometric effects. J Chem Phys 130(055101):1–18. doi:10.1063/1.3077205

    Google Scholar 

  13. Poznanski RR, Bell J (2000) A dendritic cable model for the amplification of synaptic potentials by an ensemble average of persistent sodium channels. Math Biosci 166:101–121. doi:10.1016/S0025-5564(00)00031-6

    Article  CAS  Google Scholar 

  14. Poznanski RR, Bell J (2000) Theoretical analysis of the amplification of synaptic potentials by small clusters of persistent sodium channels in dendrites. Math Biosci 166:123–147. doi:10.1016/S0025-5564(00)00032-8

    Article  CAS  Google Scholar 

  15. Chen JL, Tsai CH, Chen YY (1995) The application of hidden markov model to the problem of ion channel modeling; National Science Council, NSC 84-2213-E-216-020

  16. Ash WL, Zlomislic MR, Oloo EO, Tieleman DP (2004) Computer simulations of membrane proteins. Biochim Biophys Acta 1666:158–189. doi:10.1016/j.bbamem.2004.04.012

    Article  CAS  Google Scholar 

  17. Tieleman DP, Biggin PC, Smith GR, Sansom MSP (2001) Simulation approaches to ion channel structure–function relationships. Q Rev Biophys 34:473–561. doi:10.1017/S0033583501003729

    Article  CAS  Google Scholar 

  18. Bohmer V (1995) Calixarenes, macrocycles with (almost) unlimited possibilities. Angew Chem Int Ed Engl 34:713–745. doi:10.1002/anie.199507131

    Article  Google Scholar 

  19. Tanaka Y, Kobuke Y, Sokabe M (1995) A non-peptidic ion channel with K+ selectivity. Angew Chem Int Ed 34:693–694. doi:10.1002/anie.199506931

    Article  CAS  Google Scholar 

  20. Chen WH, Nishikawa M, Tan SD, Yamamura M, Satake A, Kobuke Y (2004) Tetracyanoresorcin[4]arene ion channel shows pH dependent conductivity change. Chem Commun (Camb) 7:872–873. doi:10.1039/B312952G

    Article  Google Scholar 

  21. Kulikov OV, Li R, Gokel GW (2009) A synthetic ion channel derived from a metallogallarene capsule that functions in phospholipid bilayers. Angew Chem Int Ed Engl 48:375–377. doi:10.1002/anie.200804099

    Article  CAS  Google Scholar 

  22. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Zakrzewski VG, Montgomery JA Jr, Stratmann RE, Burant JC, Dapprich S, Millam JM, Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi MR, Cammi R, Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J, Ortiz JV, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Gonzalez C, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL, Gonzalez C, Head-Gordon M, Replogle ES, Pople JA (1998) Gaussian 98, Revision A.3. Gaussian Inc, Pittsburgh, PA

    Google Scholar 

  23. Billes F, Mohammed-Ziegler I (2002) Ab initio equilibrium geometry and vibrational spectroscopic study of 25,26,27,28-tetrahydroxycalix[4]arene. Supramol Chem 14:451–459. doi:10.1080/10610270212491

    Article  CAS  Google Scholar 

  24. Furer VL, Borisoglebskaya EI, Kovalenko VI (2005) Band intensity in the IR spectra and conformations of calix[4]arene and thiacalix[4]arene. Spectrochim Acta A 61:355–359. doi:10.1016/j.saa.2004.05.009

    Article  CAS  Google Scholar 

  25. Backes AC, Schatz J, Siehl HU (2002) GIAO-DFT calculated and experimentally derived complexation-induced chemical shifts of calix[4]arene–solvent inclusion complexes. J Chem Soc -Perkin Trans 2:484–488. doi:10.1039/B110078P

    Article  Google Scholar 

  26. Choe JI, Lee SH (2004) Ab Initio Study of the conformational isomers of tetraethyl and triethyl esters of calix[4]arene. B Kor Chem Soc 25:553–556. doi:10.5012/bkcs.2004.25.6.847

    Article  CAS  Google Scholar 

  27. Mäkinen M, Jalkanen JP, Vainiotalo P (2002) Conformational properties and intramolecular hydrogen bonding of tetraethyl resorcarene: an ab initio study. Tetrahedron 58:8591–8596. doi:10.1016/S0040-4020(02)00863-3

    Article  Google Scholar 

  28. Rempe SB, Pratt LR (2000). Ion hydration studies aimed at ion channel selectivity. Theor Chem Mol Phys T-12. Los Alamos. http://www.t12.lanl.gov/projects/rempe.pratt.00.pdf

Download references

Acknowledgments

The authors would like to express their gratitude for the help of Prof. Reiner Saltzer (Institute of Analytical Chemistry, Dresden University of Technology). I. M-Z participated in this work as a former staff member of IR and Raman Laboratory, Chemical Research Center of the Hungarian Academy of Sciences, Budapest.

Author information

Author notes

  1. Ildikó Mohammed-Ziegler

    Present address: Gedeon Richter Plc, H-2510, Esztergomi út 27., Dorog, Hungary

Authors and Affiliations

  1. Department of Physical Chemistry, Budapest University of Technology and Economics, H-1521, Budapest, Budafoki út 8., Hungary

    Ferenc Billes

  2. Hemercy KKT, H-2521 Arany Janos u. 28., Csolnok, Hungary

    Ildikó Mohammed-Ziegler

  3. Institute for Chemical Technologies and Analytics, Vienna University of Technology, A-1060 Vienna, Getreidemarkt 9/164/EC, Austria

    Ferenc Billes & Hans Mikosch

Authors
  1. Ferenc Billes
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ildikó Mohammed-Ziegler
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hans Mikosch
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ildikó Mohammed-Ziegler.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Billes, F., Mohammed-Ziegler, I. & Mikosch, H. Transportation behavior of alkali ions through a cell membrane ion channel. A quantum chemical description of a simplified isolated model. J Mol Model 18, 3627–3637 (2012). https://doi.org/10.1007/s00894-012-1364-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-012-1364-9

Keywords

Search

Navigation