Water structure in the Gramicidin A transmembrane channel

The interaction energy and the structure of water molecules either inside the Gramicidin A transmembrane channel or at its two extremities is examined with the use of iso-energy maps and Monte Carlo simulations. The shape of the channel as experienced by water is analyzed in detail. Variations in the hydration structure due to the presence of a Na+ ion placed at several positions along the channel are simulated, analyzed and discussed. Preliminary data on Li+ and K+ interacting with Gramicidin A and the system of water molecules are reported. The Gramicidin A atomic coordinates have been taken from Urry's recent papers.     

Water Structure in the Gramicidin A Transmembrane Channel

Abstract

The interaction energy and the structure of water molecules either inside the Gramicidin A transmembrane channel or at its two extremities is examined with the use of iso-energy maps and Monte Carlo simulations. The shape of the channel as experienced by water is analyzed in detail. Variations in the hydration structure due to the presence of a Na+ ion placed at several positions along the channel are simulated, analyzed and discussed. Preliminary data on Li+ and K+ interacting with Gramicidin A and the system of water molecules are reported. The Gramicidin A atomic coordinates have been taken from Urry's recent papers.     

Open channel noise. V. Fluctuating barriers to ion entry in gramicidin A channels.

We have measured the fluctuations in the current through gramicidin A (GA) channels in symmetrical solutions of monovalent cations of various concentrations, and compared the spectral density values with those computed using E. Frehland's theory for noise in discrete transport systems (Frehland, E. 1978. Biophys. Chem. 8:255-265). The noise for the transport of NH4+ and Na+ ions in glycerol-monooleate/squalene membranes could be accounted for entirely by "shot noise" in the process of transport through a single-filing pore with two ion binding sites. However, in confirmation of results in a previous paper (Sigworth, F. J., D. W. Urry, and K. U. Prasad. 1987. Biophys. J. 52:1055-1064) currents of Cs+ showed a substantial excess noise at low ion concentrations, as did currents of K+ and Rb+. The excess noise was increased in thicker membranes. The observations are accounted for by a theory that postulates fluctuations of the entry rates of ions into the channel on a time scale of approximately 1 microsecond. These fluctuations occur preferentially when the channel is empty; the presence of bound ions stabilizes the "high conductance" conformation of the channel. The fluctuations are sensed to different degrees by the various ion species, and their kinetics depend on membrane thickness.     

Gramicidins A, B, and C form structurally equivalent ion channels.

The membrane structure of the naturally occurring gramicidins A, B, and C was investigated using circular dichroism (CD) spectroscopy and single-channel recording techniques. All three gramicidins form channels with fairly similar properties (Bamberg, E., K. Noda, E. Gross, and P. L?uger. 1976. Biochim. Biophys. Acta. 419:223-228.). When incorporated into lysophosphatidylcholine micelles, however, the CD spectrum of gramicidin B is different from that of gramicidin A or C (cf. Prasad, K. U., T. L. Trapane, D. Busath, G. Szabo, and D. W. Urry. 1983. Int. J. Pept. Protein Res. 22:341-347.). The structural identity of the channels formed by gramicidin B has, therefore, been uncertain. We find that when gramicidins A and B are incorporated into dipalmitoylphosphatidylcholine vesicles, their CD spectra are fairly similar, suggesting that the two channel structures could be similar. In planar bilayers, gramicidins A, B, and C all form hybrid channels with each other. The properties of the hybrid channels are intermediate to those of the symmetric channels, and the appearance rates of the hybrid channels (relative to the symmetric channels) corresponds to what would be predicted if all three gramicidin molecules were to form structurally equivalent channels. These results allow us to interpret the different behavior of channels formed by the three gramicidins solely on the basis of the amino acid substitution at position 11.     

Conformation of the gramicidin A channel in phospholipid vesicles: a fluorine-19 nuclear magnetic resonance study

The membrane conformation of the peptide ionophore gramicidin A is shown by 19F NMR to be described by the N-terminal to N-terminal beta LD helical dimer model proposed by Urry [Urry, D.W. (1971) Proc. Natl. Acad. Sci. U.S.A. 68, 672-676]. Fully active analogues of gramicidin with 19F labels at both the N- and C-termini are prepared synthetically. Labeled peptides are incorporated into small unilamellar vesicles of dimyristoylphosphatidylcholine. Measurements of the accessibility of the labels to either aqueous or lipophilic paramagnetic probes show that the N-terminus of gramicidin is located in the membrane interior and the C-terminus is at the membrane surface. Of the specific models proposed for the structure of gramicidin, these data are consistent only with that of Urry. The C-terminal 19F NMR peak in vesicles actually consists of three overlapping peaks. Experiments with the aqueous shift reagent Tm3+ show that C-terminal 19F nuclei in the inner and in the outer leaflets of vesicles resonate at different frequencies. The outer leaflet peak in turn consists of two overlapping peaks, possibly due to a local rearrangement of the C-terminal label.     

The gramicidin A channel: energetics and structural characteristics of the progression of a sodium ion in the presence of water

The distribution of water molecules in the Gramicidin A (GA) channel is determined by theoretical computations, and the role of this water on the energetics of the system upon progression of a sodium cation through the channel is investigated. In the absence of the ion, water molecules form a chain along the channel, hydrogen bonded to one another and to the L carbonyl oxygens, while others stay at the entrances of the channel, hydrogen-bonded to the free carbonyl oxygens of the L-Tryptophan residues. According to the definition adopted for the "inside" and the "outside" of the channel, it is found to contain at most 7 or 9 water molecules. When a hydrated sodium cation approaches and enters the channel, the structural properties corresponding to the minimized total energy of the system GA-water-Na+ indicate a reorganization, but not a destruction, of the chain of water molecules. The "energy profile" for the system GA-Na+-(22 waters) is analyzed in terms of its components and in comparison to the corresponding intrinsic profile computed earlier in vacuo. It appears that the presence of water does not unduely modify the pathway or the qualitative features of the energetics of the cation passage, except at the entrance, where the partial and progressive dehydration of the cation plays an important role. The presence and characteristics of the minimum found earlier at 10.5 A from the center are conserved.     

Molecular dynamics study of the KcsA channel at 2.0-A resolution: stability and concerted motions within the pore

The stability of the KcsA channel accommodating more than one ion in the pore has been studied with molecular dynamics. We have used the very last X-ray structure of the KcsA channel at 2.0-A resolution determined by Zhou et al. [Nature 414 (2001) 43]. In this channel, six of the seven experimentally evidenced sites have been considered. We show that the protein remains very stable in the presence of four K+ ions (three in the selectivity filter and one in the cavity). The locations and the respective distances of the different K+ ions and water molecules (W), calculated within our KWKWKK sequence, also fits well with the experimental observations. The analysis of the K+ ions and water molecules displacements shows concerted file motions on the simulated time scale (approximately 1 ns), which could act as precursor to the diffusion of K+ ions inside the channel. A simple one-dimensional dynamical model is used to interpret the concerted motions of the ions and water molecules in the pore leading ultimately to ion transfer.     

Structure and dynamics of ion transport through gramicidin A.

Molecular dynamics calculations in which all atoms were allowed to move were performed on a water-filled ion channel of the polypeptide dimer gramicidin A (approximately 600 atoms total) in the head-to-head Urry model conformation. Comparisons were made among nine simulations in which four different ions (lithium, sodium, potassium, and cesium) were each placed at two different locations in the channel as well as a reference simulation with only water present. Each simulation lasted for 5 ps and was carried out at approximately 300 K. The structure and dynamics of the peptide and interior waters were found to depend strongly on the ion tested and upon its location along the pore. Speculations on the solution and diffusion of ions in gramicidin are offered based on the observations in our model that smaller ions tended to lie off axis and to distort the positions of the carbonyl oxygens more to achieve proper solvation and that the monomer-monomer junction was more distortable than the center of the monomer. With the potential energy surface used, the unique properties of the linear chain of interior water molecules were found to be important for optimal solvation of the various ions. Strongly correlated motions persisting over 25 A among the waters in the interior single-file column were observed.     

短杆菌肽通道内离子K~＋，Na~＋，Li~＋与水的相关性

基于右手螺旋短杆菌肽Ａ离子通道模型,利用分子动力学计算机模拟方法研究了通道内离子Ｋ＋,Ｎａ＋,Ｌｉ＋与水分子的相关性．     

Gramicidin single-channel properties show no solvent-history dependence.

The structure of membrane-associated gramicidins can depend on the solvent in which they were dissolved prior to membrane incorporation (LoGrasso, P. V., F. Moll, and T. A. Cross 1988. Biophys. J. 54:259-267; Killian, J. A., K. U. Prasad, D. Hains, and D. W. Urry. 1988. Biochemistry. 27:4848-4855). The peptide's solvent history might thus affect the functional characteristics of gramicidin channels (op. cit.). We tested this proposal by examining the properties (conductance, conductance dispersity, and average duration) of channels formed by [Val1]gramicidin A that had been dissolved in eight different solvents. The peptide was incorporated into lipid bilayers either by addition to the aqueous phase (and subsequent adsorption to the membrane) or by cosolubilization with the membrane-forming phospholipid. When the peptide was cosolubilized with the phospholipid, the channel properties did not vary with the solvent used. When the peptide was dissolved in chloroform, benzene, or trifluoroethanol and added through the aqueous phase, the channel properties differed from those found when gramidicin was dissolved in methanol, ethanol, dioxane, dimethylsulfoxide, or ethylacetate. The changes observed with the former three solvents were reproduced by adding them to the aqueous phase, and are therefore due to the ability of these solvents to partition into the membrane and alter the channels' behavior.     

Quantum mechanical calculations of charge effects on gating the KcsA channel

A series of ab initio (density functional) calculations were carried out on side chains of a set of amino acids, plus water, from the (intracellular) gating region of the KcsA K(+) channel. Their atomic coordinates, except hydrogen, are known from X-ray structures [D.A. Doyle, J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, R. MacKinnon, The structure of the potassium channel: molecular basis of K(+) conduction and selectivity, Science 280 (1998) 69-77; R. MacKinnon, S.L. Cohen, A. Kuo, A. Lee, B.T. Chait, Structural conservation in prokaryotic and eukaryotic potassium channels, Science 280 (1998) 106-109; Y. Jiang, A. Lee, J. Chen, M. Cadene, B.T. Chait, R. MacKinnon, The open pore conformation of potassium channels. Nature 417 (2001) 523-526], as are the coordinates of some water oxygen atoms. The 1k4c structure is used for the starting coordinates. Quantum mechanical optimization, in spite of the starting configuration, places the atoms in positions much closer to the 1j95, more tightly closed, configuration. This state shows four water molecules forming a "basket" under the Q119 side chains, blocking the channel. When a hydrated K(+) approaches this "basket", the optimized system shows a strong set of hydrogen bonds with the K(+) at defined positions, preventing further approach of the K(+) to the basket. This optimized structure with hydrated K(+) added shows an ice-like 12 molecule nanocrystal of water. If the water molecules exchange, unless they do it as a group, the channel will remain blocked. The "basket" itself appears to be very stable, although it is possible that the K(+) with its hydrating water molecules may be more mobile, capable of withdrawing from the gate. It is also not surprising that water essentially freezes, or forms a kind of glue, in a nanometer space; this agrees with experimental results on a rather different, but similarly sized (nm dimensions) system [K.B. Jinesh, J.W.M. Frenken, Capillary condensation in atomic scale friction: how water acts like a glue, Phys. Rev. Lett. 96 (2006) 166103/1-4]. It also agrees qualitatively with simulations on channels [A. Anishkin, S. Sukharev, Water dynamics and dewetting transitions in the small mechanosensitive channel MscS, Biophys. J. 86 (2004) 2883-2895; O. Beckstein, M.S.P. Sansom, Liquid-vapor oscillations of water in hydrophobic nanopores, Proc. Natl Acad. Sci. U. S. A. 100 (2003) 7063-7068] and on featureless channel-like systems [J. Lu, M.E. Green, Simulation of water in a pore with charges: application to a gating mechanism for ion channels, Prog. Colloid Polym. Sci. 103 (1997) 121-129], in that it forms a boundary on water that is not obvious from the liquid state. The idea that a structure is stable, even if individual molecules exchange, is well known, for example from the hydration shell of ions. We show that when charges are added in the form of protons to the domains (one proton per domain), the optimized structure is open. No stable water hydrogen bonds hold it together; an opening of 11.0 A appears, measured diagonally between non-neighboring domains as glutamine 119 carbonyl O-O distance. This is comparable to the opening in the MthK potassium channel structure that is generally agreed to be open. The appearance of the opening is in rather good agreement with that found by Perozo and coworkers. In contrast, in the uncharged structure this diagonal distance is 6.5 A, and the water "basket" constricts the uncharged opening still further, with the ice-like structure that couples the K(+) ion to the gating region freezing the entrance to the channel. Comparison with our earlier model for voltage gated channels suggests that a similar mechanism may apply in those channels.     

Attenuation of proton currents by methanol in a dioxolane-linked gramicidin A channel in different lipid bilayers.

The mobility of protons in a dioxolane-linked gramicidin A channel (D1) is comparable to the mobility of protons in aqueous solutions (Cukierman, S., E. P. Quigley, and D. S. Crumrine. 1997. Biophys. J. 73:2489-2502). Aliphatic alcohols decrease the mobility of H+ in aqueous solutions. In this study, the effects of methanol on proton conduction through D1 channels were investigated in different lipid bilayers and at different HCl concentrations. Methanol attenuated H+ currents in a voltage-independent manner. Attenuation of proton currents was also independent of H+ concentrations in solution. In phospholipid bilayers, methanol decreased the single channel conductance to protons without affecting the binding affinity of protons to bilayers. In glycerylmonooleate membranes, the attenuation of single channel proton conductances qualitatively resembled the decrease of conductivities of HCl solutions by methanol. However, in both types of lipid bilayers, single channel proton conductances through D1 channels were considerably more attenuated than the conductivities of different HCl solutions. This suggests that methanol modulates single proton currents through D1 channels. It is proposed that, on average, one methanol molecule binds to a D1 channel, and attenuates H+ conductance. The Gibbs free energy of this process (DeltaG0) is approximately 1.2 kcal/mol, which is comparable to the free energy of decrease of HCl conductivity in methanol solutions (1.6 kcal/mol). Apolar substances like urea and glucose that do not transport protons in HCl solutions and do not permeate D1 channels decreased solution conductivity and single channel conductance by a considerably larger proportion than methanol. Cs+ currents through D1 channels were considerably less (fivefold) attenuated by methanol than proton currents. It is proposed that methanol partitions inside the pore of gramicidin channels and delays the transfer of protons between water and methanol molecules, causing a significant attenuation of the single channel proton conductance. Gramicidin channels offer an interesting experimental model to study proton hopping along a single chain of water molecules interrupted by a single methanol molecule.     

Gramicidin cation channel: an experimental determination of the right-handed helix sense and verification of beta-type hydrogen bonding

Due to the difficulty of obtaining protein/lipid cocrystals for diffraction studies, structural research on intrinsic membrane proteins and polypeptides has been largely restricted to indirect experimental techniques. Hence, many fundamental questions associated with peptide/lipid systems remain unanswered. In particular, the handedness of the gramicidin A transmembrane ion channel incorporated into lipid bilayers has been an open question for nearly two decades. In this study, solid-state 15N NMR spectroscopy is employed to probe directly the secondary structure of the polypeptide backbone. Recent determinations of the 15N chemical shift anisotropy tensor with respect to the molecular frame enable the quantitative evaluation of the 15N chemical shift resonances obtained from oriented dimyristoylphosphatidylcholine (DMPC) bilayer samples containing specific site 15N labeled gramicidin. This direct structural approach verifies the beta-sheet hydrogen-bonding pattern proposed by Urry [Urry, D. W. (1971) Proc. Natl. Acad. Sci. U.S.A. 68, 672-676] and determines that in our DMPC bilayer preparations the gramicidin channel is right-handed. Additional structural information is provided by the 15N chemical shift data in the form of orientational constraints on the C alpha-C alpha axis orientation of individual peptides relative to the helix axis. The significance of these solid-state NMR results lies in the direct determination of the helix sense and the verification of the beta-type hydrogen bonding, in the development of the solid-state NMR methods for obtaining such information, and in emphasizing the importance of having direct structural data at atomic resolution.     

Energy profile of Cs+ in gramicidin A in the presence of water. Problem of the ion selectivity of the channel

The effect of water present at the mouth and inside the channel of Gramicidin A on the energy profile calculated for a caesium ion is determined. The total optimal interaction energy computed for the system GA-Cs+-(22 waters) leads to an energy profile characterized by a deep minimum at 11 A followed by an entrance energy barrier of 7 Kcal/mol expanding until 9 A from the center. After this point, a second minimum less deep than the previous one is observed, itself followed by a central barrier. The shape of the profile at the entrance is governed by the balance between the progressive desolvation process of the ion and the increase of favorable hydrogen bond interactions implying both the water molecules and GA. The comparison of this energy profile with that obtained in vacuo shows that the presence of water molecules does not modify the pathway of the ion which, owing to its size, is constrained essentially to remain on the channel axis. The comparison Na+ versus Cs+ indicates that although the phenomena involved are globally the same, differences between the two profiles appear due firstly to the difference in the affinity of the two ions for water and secondly to their respective size. This last difference implies that the number of water molecules present in the interior of the channel during the cation progression is reduced roughly by one in the case of caesium. The desolvation barrier computed for Cs+ is half the corresponding value for Na+, a result in agreement with the observed selectivity.     

Real-time fluorimetric analysis of gramicidin D- and alamethicin-induced K+ efflux from Sf9 and Cf1 insect cells.

Gramicidin D and alamethicin are pore-forming peptides which exhibit lethal properties against a large spectrum of cells. Despite a wealth of experimental data from artificial membranes, the time course and quantitative analysis of the activity of these ionophores are not well described in living cells. In the present study, the newly described fluorescent dye CD-222 was used to monitor extracellular potassium ion concentration and report the effects of these antibiotics on the K+ permeability of the plasma membrane of Spodoptera frugiperda (Sf9) and Choristoneura fumiferana (Cf1) insect cells. Both peptides induced a rapid efflux of intracellular K+ as a consequence of ion channel formation in the cell membrane. K+ efflux began without any measurable delay. While the final extracellular K+ concentration was unaffected by ionophore concentration, the rate of K+ efflux was dose dependent. Using a model describing the partition of the peptides in lipid membranes, the K+ efflux kinetic parameters were determined for both cell types and both pore formers. The proposed stoichiometry for the channel formed by gramicidin in living cells is in good agreement with the two-monomers model based on data from artificial membrane systems. The K+-permeable channel formed by alamethicin in insect cells appears to involve three monomers.     

Proton conduction in gramicidin A and in its dioxolane-linked dimer in different lipid bilayers.

Gramicidin A (gA) molecules were covalently linked with a dioxolane ring. Dioxolane-linked gA dimers formed ion channels, selective for monovalent cations, in planar lipid bilayers. The main goal of this study was to compare the functional single ion channel properties of natural gA and its covalently linked dimer in two different lipid bilayers and HCl concentrations (10-8000 mM). Two ion channels with different gating and conductance properties were identified in bilayers from the product of dimerization reaction. The most commonly observed and most stable gramicidin A dimer is the main object of this study. This gramicidin dimer remained in the open state most of the time, with brief closing flickers (tau(closed) approximately 30 micros). The frequency of closing flickers increased with transmembrane potential, making the mean open time moderately voltage dependent (tau(open) changed approximately 1.43-fold/100 mV). Such gating behavior is markedly different from what is seen in natural gA channels. In PEPC (phosphatidylethanolamine-phosphatidylcholine) bilayers, single-channel current-voltage relationships had an ohmic behavior at low voltages, and a marked sublinearity at relatively higher voltages. This behavior contrasts with what was previously described in GMO (glycerylmonooleate) bilayers. In PEPC bilayers, the linear conductance of single-channel proton currents at different proton concentrations was essentially the same for both natural and gA dimers. g(max) and K(D), obtained from fitting experimental points to a Langmuir adsorption isotherm, were approximately 1500 pS and 300 mM, respectively, for both the natural gA and its dimer. In GMO bilayers, however, proton affinities of gA and the dioxolane-dimer were significantly lower (K(D) of approximately 1 and 1.5 M, respectively), and the g(max) higher (approximately 1750 and 2150 pS, respectively) than in PEPC bilayers. Furthermore, the relationship between single-channel conductance and proton concentration was linear at low bulk concentrations of H+ (0.01-2 M) and saturated at concentrations of more than 3 M. It is concluded that 1) The mobility of protons in gramicidin A channels in different lipid bilayers is remarkably similar to proton mobilities in aqueous solutions. In particular, at high concentrations of HCl, proton mobilities in gramicidin A channel and in solution differ by only 25%. 2) Differences between proton conductances in gramicidin A channels in GMO and PEPC cannot be explained by surface charge effects on PEPC membranes. It is proposed that protonated phospholipids adjacent to the mouth of the pore act as an additional source of protons for conduction through gA channels in relation to GMO bilayers. 3) Some experimental results cannot be reconciled with simple alterations in access resistance to proton flow in gA channels. Said differences could be explained if the structure and/or dynamics of water molecules inside gramicidin A channels is modulated by the lipid environment and by modifications in the structure of gA channels. 4) The dioxolane ring is probably responsible for the closing flickers seen in the dimer channel. However, other factors can also influence closing flickers.     

Energetics of K+ permeability through Gramicidin A by forward-reverse steered molecular dynamics

The estimation of ion channel permeability poses a considerable challenge for computer simulations because of the significant free energy barriers involved, but also offers valuable molecular information on the ion permeation process not directly available from experiments. In this article we determine the equilibrium free energy barrier for potassium ion permeability in Gramicidin A in an efficient way by atomistic forward-reverse non-equilibrium steered molecular dynamics simulations, opening the way for its use in more complex biochemical systems. Our results indicate that the tent-shaped energetics of translocation of K+ ions in Gramicidin A is dictated by the different polarization responses to the ion of the external bulk water and the less polar environment of the membrane.     

Comparison of fluorescence energy transfer and quenching methods to establish the position and orientation of components within the transverse plane of the lipid bilayer. Application to the gramicidin A--bilayer interaction.

Fluorescence quenching and resonance energy transfer methods have been used to investigate the position of fluorophores in the lateral and transverse planes of the lipid bilayer. A series of n-(9-anthroyloxy) fatty acids (n = 2, 6, 9, and 12) have been used as energy-transfer acceptors so that apparent transfer distances from a membrane-bound donor (N-stearoyltryptophan) have a transverse as well as a lateral component. Both theory and experiment show that the energy-transfer method is not precise enough to discriminate between the positions of the fluorophores in the transverse plane of the bilayer. The n-(9-anthroyloxy) fatty acids are also susceptible to quenching by the indole moiety of tryptophan. The relative quenching efficiency can provide a semiquantitative measure of the position of quenching molecules in the lipid bilayer. The quenching techniques are applied to the determination of the orientation of gramicidin A in lipid bilayers. The tryptophan residues of gramicidin appear to be located near the membrane surface in agreement with the head-to-head dimeric structure proposed by D. W. Urry et al. [(1971) Proc. Natl. Acad. Sci. U.S.A. 68, 672--676].     

Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the human immunodeficiency virus HIV-1

Molecular dynamics (MD) simulations have been carried out on bundles of the channel-forming transmembrane (TM) domain of the viral protein U (VPU(1-27) and VPU(6-27)) from the human immunodeficiency virus (HIV-1). Simulations of hexameric and pentameric bundles of VPU(6-27) in an octane/water membrane mimetic system suggested that the pentamer is the preferred oligomer. Accordingly, an unconstrained pentameric helix bundle of VPU(1-27) was then placed in a hydrated palmitoyl-oleyl-3-n-glycero-phosphatidylethanolamine (POPE) lipid bilayer and its structural properties calculated from a 3-ns MD run. Some water molecules, initially inside the channel lumen, were expelled halfway through the simulation and the bundle adopted a conical structure reminiscent of previous MD results obtained for VPU(6-27) in an octane/water system. The pore constriction generated may correspond to a closed state of the channel and underlies the relocation of the W residue toward the pore lumen. The relative positions of the helices with respect to the bilayer and their interactions with the lipids are discussed. The observed structure is stabilized via specific interactions between the VPU helices and the carbonyl oxygen atoms of the lipid molecules, particularly at the Q and S residues.