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Electro-nanopores in the lipid membrane. Computer modeling vs experiments

Kingston University, Dept. Computing, Information Systems and Mathematics. Electro-nanopores in the lipid membrane. Computer modeling vs experiments. Malgorzata Kotulska Department of Biomedical Engineering & Instrumentation Wroclaw University of Technology, Poland. Wroclaw.

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Electro-nanopores in the lipid membrane. Computer modeling vs experiments

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  1. Kingston University, Dept. Computing, Information Systems and Mathematics Electro-nanopores in the lipid membrane. Computer modeling vs experiments Malgorzata KotulskaDepartment of Biomedical Engineering & InstrumentationWroclaw University of Technology, Poland

  2. Wroclaw

  3. Wroclaw University of Technology

  4. E ions molecules lipid bilayer with no pore hydrophilic nanopore Membrane reorganization under electric field

  5. Cell electroporation Rapid-freezing electron microscopy of red blood cells before and after brief electric pulses (protoplasmic membrane face). Pore diameter 20-120 nm. DC. Chang and TS. Reese, Biophysical J. 58 (1990 ) Hypo-osmolar conditions – hemolysis (?) ML. Escande-Geraud et al., BBA 939 (1988) 247Iso-osmolar  no effect GV. Gass, LV. Chernomordik, BBA 1023 (1990) 1

  6. Molecular Dynamics Lipid bilayer (2304 lipids) tk = 3680 ps. Red headgroups and blue chains; (yellow and green lipids - periodic images; water not shown) Movie from Tieleman DP., BMC Biochem. 2004, 19; 5:10.

  7. Energetical profile Free energy of the pore JC. Weaver and YA. Chizmandzhev, Bioelectrochem. Bioenerg. 41 (1996) 135

  8. Problems • Basic • Mechanism of electroporation • Shape of electropores (cylindrical or irregular ?) • Applications • Stabilizing of electropore (other than mechanical stress) • Size control in long-lived electropores (e.g. big and stable electropores for DNA delivery) • Control of the sensitivity to electroporation

  9. Monte Carlo simulations – modified Pink’s model H=Hvdw + Hconf + Hdip+ He The rate of heads in standing configuration show rapid head reorientation if E > 0.5 · 108 V/m (250 mV) M. Kotulska, K. Kubica, Physical Review E 72 (2005) 061903 Kotulska M., Kubica K., Koronkiewicz S., Kalinowski S., Bioelectrochemistry 70 (2007) 64

  10. The rate of chains in gel (all-trans) and fluid conformations depends on electric field E if E > 0.5·108 V/m (250 mV) (NL – negative layer, PL – positive layer)

  11. Creation of a hydrophilic pore Kotulska M., Kubica K., in Advances in Planar Lipid Bilayers and Liposomes, vol. 7. ed. A. Leitmannova Liu, Elsevier, 2008

  12. Methods of electroporation • Pulses • Current clamp (M. Robello, A. GliozziBBA982 (1989) 173)

  13. pore formation membrane charging pore fluctuations Electroporation under current-controlled conditions (chronopotentiometry - ChP) Voltage fluctuations under current-clamp, I = 0.2 nA, egg lecithin Kalinowski S., G. Ibron, K. Bryl, Z. Figaszewski. 1998., BBA 1369:204‑212

  14. Applications of chronopotentiometry Modelling ischemic electroporated cell Kalinowski S, Koronkiewicz S, Kotulska M, Kubica K, Bioelectrochemistry 70 (2007) 83-90 Noise 1/f, exponent dependent on physico-chemical conditions M. Kotulska, S. Koronkiewicz, S. Kalinowski, Physical Review E 69 (2004), 031920

  15. CACC electroporation (Chronoamperometry After Current Clamp) Electroporation at current clamp I Delay time; mean potential Um stabilized (at I) Clamping voltage at constant Um Data acquisition (at Um) 1.5 M AlCl3 (DAlCl3 1.3 nm) & 2 M NaCl (DNaCl 0.9 nm) M. Kotulska, Biophysical Journal 92 (2007), 2412-21

  16. Periodograms Periodograms for 2 M NaCl, B = 1.38, Sl = 0.6 nA2/Hz, Dmean = 1.73 nm (crosses, upper curve), 0.2 M NaCl, B = 1.37, Sl = 2.1 nA2/Hz, Dmean = 2.1 nm (diamonds, middle curve), and 1.5 M AlCl3, B = 1.55, Sl = 3.0 nA2/Hz, Dmean = 1.3 nm (squares, bottom curve).

  17. artificial nanopore / maltoporin channel • Bezrukov SM, Winterhalter M.Phys Rev Lett. 2000; 85(1):202 • Siwy Z, Fulinski A., Phys Rev Lett. 2002; 89(15):158101

  18. Models • Self-similar process or 1/f noise Hypotheses: • One long-term process • Sums of Markovian processes • Self-Organized Criticallity

  19. -stableprobability density function (MLE) (Left) Probability density function of the conductance dynamics approximated by MLE as a long‑tailed -stable distribution (= 1.78) and the smoothed data (stars).Confidence interval 0.95 (Right) Tail region in log-log . Data obtained for 1.5 M AlCl3(B= 1.64, G = 2.4 nm) Statistical tests with STABLE program by JP. Nolan.(MLE, sample characteristic function and quantile methods,   [0.03, 0.1]) Kotulska M., Biophysical Journal 92 (2007), 2412-21

  20. fractional Levy stable motion tends to fractional Brownian motion Stability index  depends on the nanopore size. (Data for 2 M NaCl)

  21. Shape evolution (?) Images generated by Fractal Explorer

  22. Feedback effect Memory of the process d = H 1/ (if d > 0 then the memory is long) Memory current-clamp< Memory CACC

  23. Electroporation inmedical applications

  24. Heart DefibrillationELECTROCHEMOTHERAPY(ECT)ELECTROGENETHERAPY(EGT)

  25. Molecular transport into the cell Mir L.M, S. Orlowski, Adv.Drug Deliv. Rev. 35(1999) 107-118

  26. Electroporation in the cell Dev S.B. et al.. IEEE Trans. Plasma Sci. 28 (2000) 206-223

  27. ECT of a squamous cell carcinoma

  28. Mechanisms of anti-cancer effect • Enhanced transport of cytostatic drugs • Radiosensitizing effect of bleomycin • Vascular block

  29. Other pores/channels

  30. Enhanced algorithm for Poisson-Nernst-Planck model Nernst-Planck (Smoluchowski) Poisson Modelling ionic flow through channels Collaboration: Witek Dyrka, Andy Augousti

  31. Characteristics

  32. Optimization • Adaptive gradient-based optimisation of step size: super relaxation • Adjustable relaxation coefficient • Space segmentation

  33. Reducing computational cost Dyrka W., Augousti A.T., Kotulska M.: Ion flux through membrane channels – an enhanced algorithm for Poisson-Nernst-Planck model, submitted to J. Comp. Chemistry.

  34. FKBP12.6 RyR2 Ryanodine receptor calcium channel Collaboration: Jean-Christophe Nebel

  35. T-tubule myocyte sarcolemmal membrame Na/Ca exchanger RyRs L-type channel Efflux Influx SR Ca reuptake pump Ca Ca Ca Relax Contract M. Scoote, A.J. Williams, Cardiovascular Research 56 (2002) 359-372 Ca dependent electromechanical coupling in cardiac myocyte

  36. Diseases resulting from channelopathies • Malignant Hyperthermia (MH), • Central Core Disease (CDD) • Catecholaminergic Polymorphic Ventricular Tachycardia (CPVT). • Hypotheses • Mutations increase Ca2+ leak. • Abnormal cardiac RyR phosphorylation and dissociation of FKBP12.6 may play a role in the pathogenesis of some forms of heart failure (HF), but this presumption needs more experimental support. • Kania M. Kotulska M., A system for modeling the cooperativity ofryanodine receptors in cardiac myocytes, Proc. IFMBE 11 (2005) 1727-83,

  37. What is the pore structure? AJ. Williams, Q. Rev. Bioph. 34, 1 (2001), pp. 61–104. Y. Wang et al. Biophys. J. 89 (2005) 256-265

  38. Thank you for your attention

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