Gramicidin A Channel Research Articles

Local Anesthetics Affect Gramicidin A Channels via Membrane Electrostatic Potentials.

The effects of local anesthetics (LAs), including aminoamides and aminoesters, on the characteristics of single gramicidin A (GA) channels in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayers were studied. Aminoamides, namely lidocaine (LDC), prilocaine (PLC), mepivacaine (MPV), and bupivacaine (BPV), reduced the conductance of GA channels. Aminoesters influenced the current fluctuations induced by GA differently; procaine (PC) did not affect the fluctuations, whereas tetracaine (TTC) distinctly reduced the conductance of single GA channels. Using electrophysiological technique, we estimated the changes in the membrane boundary potential at the adsorption of LAs; LDC, PLC, MPV, BPV, and TTC substantially increased, while PC did not affect it. To elucidate which component of the membrane boundary potential, the surface or dipole potential, is responsible for the observed effects of LAs, we employed a fluorescence assay. We found that TTC led to a significant increase in the membrane dipole potential, whereas the adsorption of LDC, PLC, MPV, BPV, and PC did not produce any changes in the membrane dipole potential. We concluded that aminoamides affected the surface potential of lipid bilayers. Together, these data suggest that the effects of LAs on the conductance of single GA channels are caused by their influence on membrane electrostatic potentials; the regulation of GA pores by aminoamides is associated with the surface potential of membranes, whereas TTC modulation of channel properties is predominantly due to changes in dipole potential of lipid bilayers. These data might provide some significant implications for voltage-gated ion channels of cell membranes.

Modeling and Simulation of Thermo-Fluid-Electrochemical Ion Flow in Biological Channels

Abstract In this articlewe address the study of ion charge transport in the biological channels separating the intra and extracellular regions of a cell. The focus of the investigation is devoted to including thermal driving forces in the well-known velocity-extended Poisson-Nernst-Planck (vPNP) electrodiffusion model. Two extensions of the vPNP system are proposed: the velocity-extended Thermo-Hydrodynamic model (vTHD) and the velocity-extended Electro-Thermal model (vET). Both formulations are based on the principles of conservation of mass, momentum and energy, and collapse into the vPNP model under thermodynamical equilibrium conditions. Upon introducing a suitable one-dimensional geometrical representation of the channel,we discuss appropriate boundary conditions that depend only on effectively accessible measurable quantities. Then, we describe the novel models, the solution map used to iteratively solve them, and the mixed-hybrid flux-conservative stabilized finite element scheme used to discretize the linearized equations. Finally,we successfully apply our computational algorithms to the simulation of two different realistic biological channels: 1) the Gramicidin-A channel considered in [12]; and 2) the bipolar nanofluidic diode considered in [45].

An artificial primitive mimic of the Gramicidin-A channel.

Gramicidin A (gA) is the simplest known natural channel, and important progress in improving conduction activity has previously been obtained with modified natural gAs. However, simple artificial systems mimicking the gA functions are unknown. Here we show that gA can be mimicked using a simple synthetic triazole or 'T-channel' forming compound (TCT), having similar constitutional functions as the natural gAs. As in gA channels, the carbonyl moieties of the TCT, which point toward the T-channel core and surround the transport direction, are solvated by water. The net-dipolar alignment of water molecules along the chiral pore surfaces influences the conduction of protons/ions, envisioned to diffuse along dipolar hydrophilic pathways. Theoretical simulations and experimental assays reveal that the conduction through the T-channel, similar to that in gA, presents proton/water conduction, cation/anion selectivity and large open channel-conductance states. T-channels--associating supramolecular chirality with dipolar water alignment--represent an artificial primitive mimic of gA.

Hydrogel-Stabilized Droplet Bilayers for High Speed Solution Exchange

Many applications utilizing artificial lipid bilayers require the ability to exchange the bilayer's solution environment. However, because of the instability of the bilayer, the rate of solution exchange is limited, which significantly hinders the measurement rate and throughput. We have developed an artificial bilayer system that can withstand high flow speeds, up to 2.1 m/s, by supporting the bilayer with a hydrogel. We demonstrated the ability to measure during flow by measuring the conductance of gramicidin-A channels while switching between solutions of two different compositions, recording a time to measure 90% change in current of approximately 2.7 seconds at a flow rate of 0.1 m/s. We also demonstrated a potential application of this system by measuring the conductance modulation of the rat TRPM8 ion channel by an agonist and antagonist at varying concentrations, obtaining 7-point IC50 and EC50 values in approximately 7 minutes and 4-point values within 4 minutes.

Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation

Proton transport is one of the most important and interesting phenomena in living cells. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins. We describe proton dynamics quantum mechanically via a density functional approach while implicitly model other solvent ions as a dielectric continuum to reduce the number of degrees of freedom. The densities of all other ions in the solvent are assumed to obey the Boltzmann distribution. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic level. We formulate a total free energy functional to put proton kinetic and potential energies as well as electrostatic energy of all ions on an equal footing. The variational principle is employed to derive nonlinear governing equations for the proton transport system. Generalized Poisson-Boltzmann equation and Kohn-Sham equation are obtained from the variational framework. Theoretical formulations for the proton density and proton conductance are constructed based on fundamental principles. The molecular surface of the channel protein is utilized to split the discrete protein domain and the continuum solvent domain, and facilitate the multiscale discrete/continuum/quantum descriptions. A number of mathematical algorithms, including the Dirichlet to Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The Gramicidin A (GA) channel is used to demonstrate the performance of the proposed proton transport model and validate the efficiency of proposed mathematical algorithms. The electrostatic characteristics of the GA channel is analyzed with a wide range of model parameters. The proton conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and validates the proposed model.

Molecular dynamics study of gramicidin a in lipid bilayer: Structure and lateral pressure profile

AbstractThe structure and lateral pressure profile of the 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphatidylcholine (DMPC) and 1,2‐distearoyl‐sn‐glycero‐3‐phosphatidylcholine (DSPC) lipid bilayers in the absence and presence of gramicidin A (GA) are studied by molecular dynamics simulation. Due to the hydrophobic mismatch between the GA and DSPC lipid bilayer, the chain conformation became disordered, and the hydrophobic thickness around the GA largely decreased to fit the length of hydrophobic core region of the GA. The polar headgroup of lipid was found to orient toward the membrane normal as the lipid approaches the GA. The surface tension around the polar headgroup region in the DMPC/GA membrane decreased due to the decrease of electrostatic interactions between the headgroups. The larger lateral pressure in the hydrophobic region of the DSPC/GA membrane causes the reduction of pore radius around the GA channel entrance, suggesting the decrease of ion accessibility to the GA channel entrance. © 2012 Wiley Periodicals, Inc.

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

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 double-stranded β-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 β-helix structure is maintained due to the stabilization of the channel by water molecules and cations.

Channel and nonchannel forms of spin-labeled gramicidin in membranes and their equilibria.

Channel and nonchannel forms of gramicidin A (GA) were studied by ESR in various lipid environments using new mono- and double-spin-labeled compounds. For GA channels, we demonstrate here how pulse dipolar ESR can be used to determine the orientation of the membrane-traversing molecule relative to the membrane normal and to study subtle effects of lipid environment on the interspin distance in the spin-labeled gramicidin channel. To study nonchannel forms of gramicidin, pulse dipolar ESR was used first to determine interspin distances corresponding to monomers and double-helical dimers of spin-labeled GA molecules in the organic solvents trifluoroethanol and octanol. The same distances were then observed in membranes. Since detection of nonchannel forms in the membrane is complicated by aggregation, we suppressed any dipolar spectra from intermolecular interspin distances arising from the aggregates by using double-labeled GA in a mixture with excess unlabeled GA. In hydrophobic mismatching lipids (L(β) phase of DPPC), gramicidin channels dissociate into free monomers. The backbone structure of the monomeric form is similar to a monomeric unit of the channel dimer. In addition to channels and monomers, the double-helical conformation of gramicidin is present in some membrane environments. In the gel phase of saturated phosphatidylcholines, the fraction of double helices increases in the following order: DLPC < DMPC < DSPC < DPPC. The equilibrium DHD/monomer ratio in DPPC was determined. In membranes, the double-helical form is present only in aggregates. In addition, we studied the effect of N-terminal substitution in the GA molecule upon channel formation. This work demonstrates how pulsed dipolar ESR may be utilized to study complex equilibria of peptides in membranes.

Selectivity on Ion Transport across Bilayer Lipid Membranes in the Presence of Gramicidin A

Ion transport from one aqueous (W1) to another (W2) across bilayer lipid membranes (BLM) containing gramicidin A (GA) was investigated by recording current fluctuations, when various alkali metal chlorides and potassium salts were used as supporting electrolytes. The magnitude of the single-channel current at a given membrane potential depended on not only the cationic species, but also on the anionic species, and then it decreased with an increase in the diameter of the anion when the diameter of the anion was larger than the pore size of the GA channel. The baseline of the recording current, however, increased with an increase in the diameter of the anion, and its height depended on the concentration of GA in the BLM. The results indicate that GA serves as not only a channel-forming compound, but also as a carrier compound in the BLM.

Molecular dynamics simulations of the gramicidin A-dimyristoylphosphatidylcholine system with an ion in the channel pore region.

To investigate the process of ion permeation in an ion channel systematically, we performed molecular dynamics (MD) simulations on a gramicidin A (GA)-phospholipid model system with an ion in the channel pore region. Each of the three types of ions (Ca2+, Na+ Cl-) was placed at five different positions along the channel axis by replacing a water molecule. MD simulations were performed on each system at constant pressure and constant temperature. The MD trajectories showed that the Ca2+ and Na+ ions could stably fluctuate in the pore region, but the Cl- ion was pushed out because of the unfavorable interaction with the channel. This result is consistent with experimental data. It was also found that the conformation of the GA channel underwent a significant change due to the presence of the ion, and the two ends of the GA monomer were more flexible than its middle region. In particular, the dramatic change of local pore radius near the ion indicated this kind of deformation. The strong interaction between the ion and carbonyl oxygen atoms of GA was the major contributor to this change. Furthermore, it was found that the ethanolamine group of the GA molecule was the most flexible group in the GA channel and often observed to block the entrance of GA. These results imply that the deformation of channel structure plays a very important factor in ion permeation, and the ethanolamine group may play a key role in regulating ion entry into the pore. In conclusion, our results indicate that the ion has a dominant influence on the structure of the GA channel and that the flexibility of the ion channel is a crucial factor in the ion permeation process.

Formamidinium-induced dimer stabilization and flicker block behavior in homo- and heterodimer channels formed by gramicidin A and N-acetyl gramicidin A

Compared to the N-formyl gramicidin A (GA), the N-acetyl gramicidin A (NAG) channel has unchanged conductance in 1 M NH4+ (gamma NN/gamma GG = 1, conductance ratio) but reduced conductance in 1 M K+ (gamma NN/gamma GG = 0.6) methylammonium (gamma NN/gamma GG = 0.3), and formamidinium (gamma NN/gamma GG = 0.1) solutions. Except with formamidinium, "flicker blocks" are evident even at low cutoff frequencies. For all cations studied, channel lifetimes of N-acetyl homodimers (NN) are approximately 50-fold shorter than those of the GA homodimer (GG). The novel properties of GA channels in formamidinium solution (supralinear current-voltage relations and dimer stabilization (Seoh and Busath, 1993)) also appear in NN channels. The average single channel lifetime in 1 M formamidinium solution at 100 mV is 6-7-fold longer than in K+ and methylammonium solutions and, like in the GA channel, significantly decreases with increasing membrane potential. Experiments with mixtures of the two peptides, GA and NAG, showed three main conductance peaks. Oriented hybrids were formed utilizing the principle that monomers remain in one leaflet of the bilayer (O'Connell et al., 1990). With GA at the polarized side and NAG at the grounded side, at positive potentials (in which case hybrids were designated GN) and at negative potentials (in which case hybrids were designated NG), channels had the same conductances and channel properties at all potentials studied. Flicker blocks were not evident in the hybrid channels, which suggests that both N-acetyl methyl groups at the junction of the dimer are required to cause flickers. Channel lifetimes in hybrids are only approximately threefold shorter than those of the GG channels, and channel conductances are similar to those of GG rather than NN channels. We suggest that acetyl-acetyl crowding at the dimeric junction in NN channels cause dimer destabilization, flickers, and increased selectivity in N-acetyl gramicidin channels.

The double pi pi 5.6 helix of gramicidin A predominates in unsaturated lipid membranes.

The structure of the channel-forming polypeptide gramicidin A (GA) incorporated into phosphatidyl-choline (PC) liposomes has been studied as a function of the degree of unsaturation of the acyl chains of PC. The initial conformational state of GA in reconstituted bilayers is determined by the solvent in which the peptide and the lipid are initially co-dissolved, whereas the equilibrium conformational state (after heat incubation) is affected by the lipid structure rather than by the nature of the solvent. The conformational equilibrium of GA has been studied in liposomes prepared from PC having a variable number of double bonds in the fatty acid moiety, by circular dichroism and Fourier transform infrared. Liposomes were prepared from trifluoroethanol or ethanol solutions and incubated at 68 degrees C. GA was shown to retain the conformation of the right-handed pi-->6.3 pi<--6.3 helix in PC with saturated acyl chains and with one double bond, whereas in dilinoleoyl-PC, having two double bond in each chain, the thermodynamically preferred structures are left-handed antiparallel and parallel double pi pi 5.6 helices. Natural soybean PC also favours left-handed pi pi 5.6 helical structures of GA (approximately 75%). This finding is discussed in terms of the role of PC unsaturation in the dynamic properties of the lipid matrix. Differences between observed FTIR spectra of the increases decreases pi pi 5.6 helix in solution (and to a larger extent in the membrane) and the calculated IR spectra can be interpreted as resulting from deviation of the real structure from the theoretically derived ideal helix. The data obtained provide grounds for better understanding of a GA channel functioning in lipids of variable degrees of unsaturation.

The effect of microwave radiation on the stability and formation of gramicidin‐A channels in lipid bilayer membranes

The effects of microwaves on the single-channel kinetics of gramicidin-A channels in lipid bilayer membranes were examined. Attempts were made to separate thermal and athermal effects by accurate measurements of temperature at the site of the membrane and by relating the measured parameters to their previously characterized temperature dependence. It was found that microwave radiation does not affect single-channel conductance or channel life time to a degree that is significantly different from that expected of a purely thermal effect. On the other hand, the rate of channel formation is decreased during exposure, which is opposite to that expected of a purely thermal effect. The mechanism of this effect is discussed in terms of the dimerization process of channel formation.

Interaction of K+ ion with the solvated gramicidin A transmembrane channel

Using Urry's gramicidin A (GA) atomic coordinates and ab into calculations, the interaction energies of a K+ ion with GA are examined. From these energies the values of the fitting parameters are obtained for 6-12-1 atom-atom pair potentials. The potential of the GA channel as experienced by the ion is analyzed in detail. An energy profile of the K+ ion in the GA channel is obtained by analyzing iso-energy maps. Using Monte Carlo simulations, the energy profiles of the K+ ion with the solvated GA channel are analyzed and the hydration structures in the presence of the K+ ion are studied.

Ion transport through membranes: A computer experiment

Gramicidin-A is a linear pentadecapeptide antibiotic, which forms transmembrane channels; these have a number of interesting conductance characteristics [1, 2 and Refs. therein], as for example high specific ion fluxes (a single channel carries about 10 7 sodium ions/sec at 25 °C, 1 M NaCl and 100 mV transmembrane d.d.p.) have a remarkable ion selectivity among the monovalent cations. The permeability ratios with respect to sodium were found to be in following order H +(150) > NH 4 + (8.9) > Cs +(5.8) > Rb +(5.5) > K +(3.9) > Na + (1.0) > Li + (0.33). The channel is impermeable to anions and to divalent cations and it exhibits saturation and maxima in conductance as a function of ion concentration, voltage dependence of single channel currents, ion competition and block, and concentration dependence of permeability ratios. These conductance properties make the Gramicidin-A channel in some respects similar to the Na + and K + transmembrane channels responsible for the excitability of nerve and muscle cells; this enhances the interest in the Gramicidin channel. The Gramicidin-A channel seems to have two binding sites for monovalent cations, as suggested by NMR experiments using 13C marked Gramicidin molecules [2]. The free energy profile for the transport of Na + has also been determined [3]. A number of possible structural models for the Gramicidin channel have been considered [4] involving single helices [5, 6], or double helices [4, 7]. in Urry's model, which seems in agreement with a number of experimental works, two left-handed β 6,3 3,6 Gramicidin helices are held together at their N-termini (heads) by hydrogen bonding to form a channel with a length of 26 Å and a pore diameter of 4 Å. A qualitative mechanism of ion transport and ion selectivity has been proposed [8], arising from the liberation of the carbonyl oxygen into the channel, lining with it negative charges. The general picture of the phenomenon, however, is far from complete. Indeed, other molecular conformations could contribute to the conduction process [4] and even small variations in the conformation of the Gramicidin channel could affect the energetics of channel-ion interactions [1]. In order to help our understanding at the molecular level of some of the above problems concerning the interaction between the Gramicidin-A channel and ions and the role played by water in the ion transport process, we have undertaken computer simulation experiments on this system, assuming Urry's model for the channel. As for similarly large systems previously investigated [9, 10], our initial effort has been directed to the evaluation of pair potentials for the interactions between atoms of the residues and of the backbone, and sodium ion/water molecule. This step, which makes possible Monte Carlo and molecular dynamics simulations, required about one thousand three hundred ab initio computations even considering the Na + ion only. In addition, more than four hundred ab initio computations have been carried out to evaluate pair potentials relative to the interaction between Na +/water molecule and the phospholipid lysophosphatidylethanolamine, which is used to simulate the membrane moiety of the system. Results of Monte Carlo simulations based on the above models and pair potentials are presented [11].