Stability of the gramicidin-A channel structure in view of nanofiltration: a computational and experimental study

Abstract

The secondary, ternary and quaternary structures of the biological ion channel Gramicidin-A are investigated by means of UV-visible and fluorescence spectroscopies, and by computational simulations in water/methanol solvent with various molar ratios. Both experiments and molecular dynamics calculations show that the two considered conformations, i.e. the head-to-head and doublestranded b-helix dimers, behave differently with regard to their stability as a function of the methanol content in the water/methanol mixture. To sum-up, calculations show that the double-stranded dimer is stabilized by methanol, even at low content, while the head-to-head dimer conformation breaks into two monomers which remain however coupled whatever the water/methanol mixture. In pure water and low methanol content, the resulting single b-helix structure is maintained due to the stabilization of the channel by water molecules and cations.

BSA and lysozyme adsorption on homoionic montmorillonite: Influence of the interlayer cation

“…When proteins containing Trp are going through structural or environmental modifications, changes in their photophysical properties can be observed as for example a shift of the fluorescence emission spectrum (Vivian and Callis, 2001;Bonhenry et al, 2011 (Figure 2a) IC. On the contrary, the fluorescence emission spectra of LYS are not significantly shifted when it is adsorbed on Mt independently of IC (Figure 2a).…”

On the perfect diameter condition to optimize the antibiotic nanoencapsulation: case of gramicidin

“…a) GA insertion. Recently [25] we demonstrated the possible encapsulation of gA inside hydrophobic solid state nanopore. Depending on the nanopore radius, the protein encapsulation can yield different behaviors leading to different stable states.…”

“…Concerning ions, parameters from Beglov and Roux [41][42] were taken into account for monovalent ions and from Marchand and Roux [43] for divalent ions. All simulations started from the same protein structure (RCSB Protein Data Bank ID code: 1JNO) [25]. The modeling of the biological system contained one gA channel and 72 DMPC lipids.…”

“…Recently, it has been proved that track-etched membrane can be functionalized adequately in order to create inside small nanopores whose radii can be modulated as a function of the awaiting properties [23]. The atomic layer deposition technique allows obtaining a perfect geometry inside the pore while the last trimethylsilanisation functionalization allows reproducing a strong hydrophobic media aims at stabilizing the transmembrane channel [25][26][27]. The quality and the control of the inner part of the nanopore could thus be managed and could yield to the creation of biomimetic nanopore when ionic channel will be translocated inside the nanopore.…”

“…Based on full atom molecular dynamics simulations, we study the role of the geometry on the encapsulation of a small protein channel with antibiotic properties, i.e. gramicidin [25]. In this monomeric form, the primary structure of the gramicidine A (gA) is a linear polypeptide of 15 hydrophobic amino acids.…”