Investigationof molecular diffusion through a peptide-induced nano sized pore in the membrane of vesicle using simulation

Abstract

Peptide induces nanopores in the lipid membranes of giant unilamellar vesicles (GUVs) which have been explained by the leakage of water soluble fluorescent probes from inside of GUVs to outside through the pores. In this thesis, at first a single nanopore is designed in the membrane of GUV and then the molecular transport, from outside to inside of GUV through the nanopore, of various fluorescent probes such as calcein, Texas-Red Dextran 3000 (TRD-3k), TRD-10k and TRD-40k is investigated using COMSOL simulation. The molecular transport is also investigated by varying the sizes of GUVs as 16, 18, 20, 25, 28 and 40 µm. The time course of the fluorescence intensity of the GUV follows a single exponential growth function from where the rate constant of molecular transport is calculated. The rate of molecular transport, kmt, is decreases with the increase of the size of probes. The kmt values are obtained to be 0.2708  0.0002, 0.1388  0.0002, 0.0743  0.0003 and 0.0401  0.0001 s-1 for calcein, TRD-3k, TRD-10k and TRD-40k, respectively using pore radius 25 nm and GUV diameter 20 µm. Similarly, the kmt values are obtained to be 0.3146  0.0012, 0.1637  0.0004, 0.0876  0.0003 and 0.0475  0.0002 s-1 for calcein, TRD-3k, TRD-10k and TRD-40k, respectively using pore radius 25 nm and GUV diameter 16 µm. The average kmt values for calcein are obtained to be 0.3150  0.0012, 0.2452  0.0007 and 0.2048  0.0011 s-1 for 18, 25 and 28 m GUV, respectively. The simulation results reasonably supported the reported experimental results. Based on the Fick’s law of diffusion it was developed an analytical treatment for the rate constant of molecular transport for a single nanopore that agrees with the simulation results. The molecular transport, from outside to inside of GUV through the multiple nanopores, of various fluorescent probes are also investigated using COMSOL simulation. For the TRD-10k, it was found the kmt values as 0.0307  0.0001 s¬-1 for single pore, 0.0651  0.0001 s¬-1 for double pore, 0.0997  0.0001 s¬-1 for triple pore and 0.1388  0.0003 s¬-1 for quadra pore. These investigations might be helpful to elucidate the mechanism of pore formation using various membrane-active agents in the lipid membranes of vesicles and biomembranes of cells.