5-A Fourier map of gramicidin A phased by deuterium-hydrogen solvent difference neutron diffraction

Crystals of ion-free gramicidin A (P212121: a = 24.61, b = 32.28, c = 32.52) have been investigated using neutron diffraction. A difference analysis of crystals soaked in ethanol/H2O as opposed to ethanol-d6/D2O has led to single isomorphous replacement Fourier projections of the structure at 5-A resolution. The gramicidin dimer appears to be a 32-A-long cylinder oriented parallel to the c-axis in these crystals.

Hydrogen bonding involving the ornithine side chain of gramicidin S

The side-chain and backbone hydrogen bonding pattern is identical in the computed minimum-energy conformation of gramicidin S and in the recently determined X-ray crystallographic structure of the hydrated urea complex of this peptide. The identity of hydrogen bonding (except where it is affected by intermolecular interactions in the crystal) and the close agreement of the overall backbone conformation attest to the validity of the conformational energy computations used to determine the unique low-energy conformation of this cyclic peptide.

A difference infrared spectroscopic study of gramicidin A, alamethicin and bacteriorhodopsin in perdeuterated dimyristoylphosphatidylcholine

Difference infrared spectroscopy has been used to study the way in which the intrinsic molecules gramicidin A, alamethicin and bacteriorhodopsin perturb their environment when present within a lipid bilayer structure. Dimyristoylphosphatidylcholine containing perdeuterated chains has been used to enable the lipid chain C-2H stretching absorption band to be separated from the C-H bands arising from the intrinsic polypeptide or protein. The C-2H stretching bands of the phospholipid are sensitive to two different types of chain conformation. The C-2H stretching frequency provides information about the static order of the lipid chains, whilst the half-maximum bandwidth provides a measure of chain librational and torsional motion. From the measurements it is concluded that: (1) Above the lipid phase transition temperature tc, low concentrations of either gramicidin A or alamethicin cause a small decrease in lipid chain gauche isomers whilst bacteriorhodopsin in the lipid bilayer has no effect. At higher concentrations each intrinsic molecule causes an increase to occur in lipid chain gauche isomers. (2) The lipid acyl chain motion, as deduced from the bandwidths is increased by the presence of a low concentration of gramicidin A within the lipid bilayer. The presence of the other intrinsic molecules studied have little effect. A higher concentration of alamethicin causes a decrease in chain motion whilst gramicidin A and bacteriorhodopsin have no effect. (3) Below tc each of the intrinsic molecules when present in the lipid bilayer causes an increase in gauche isomers to occur as well as an increase in the lipid chain motion. A broadening of the lipid phase transition occurs as the concentration of the polypeptide increases.

Single-channel studies on linear gramicidins with altered amino acid sequences. A comparison of phenylalanine, tryptophane, and tyrosine substitutions at positions 1 and 11

The relation between chemical structure and permeability characteristics of transmembrane channels has been investigated with the linear gramicidins (A, B, and C), where the amino acid at position 1 was chemically replaced by phenylalanine, tryptophane or tyrosine. The purity of most of the compounds was estimated to be greater than 99.99%. The modifications resulted in a wide range of conductance changes in NaCl solutions: sixfold from tryptophane gramicidin A to tyrosine gramicidin B. The conductance changes induced by a given amino acid substitution at position 1 are not the same as at position 11. The only important change in the Na+ affinity was observed when the first amino acid was tyrosine. No major conformational changes of the polypeptide backbone structure could be detected on the basis of experiments with mixtures of different analogues and valine gramicidin A (except possibly with tyrosine at position 1), as all the compounds investigated could form hybrid channels with valine gramicidin A. The side chains are not in direct contact with the permeating ions. The results were therefore interpreted in terms of modifications of the energy profile for ion movement through the channel, possibly due to an electrostatic interaction between the dipoles of the side chains and ions in the channel.

GM1 micelles modify the transport properties of the ionophore gramicidin D in artificial planar bilayers

We have analyzed the effects induced in different phospholipid planar bilayers by monosialoganglioside micelles containing the ionophore gramicidin D. The membrane conductance increases after the addition of GM1 micelles at various ionophore/ganglioside ratios. We believe this fact may be ascribed to gramicidin molecules that incorporate into the bilayer together with gangliosides. In the presence of micelles the mean lifetime and the amplitude of the gramicidin single channel did not present relevant modifications when dioleoylphosphatidylcholine or phosphatidylserine were used to form the bilayer. Calcium proved to trigger the interaction between phosphatidylethanolamine membranes and GM1 micelles containing gramicidin. In this case the ionic pore presents a longer lifetime and a lower amplitude with respect to pure gramicidin. We suggest that different properties developed by gramicidin may depend on structural organization of gangliosides when incorporated into the phospholipid bilayer.

A simple and sensitive procedure for measuring isotope fluxes through ion-specific channels in heterogenous populations of membrane vesicles

In this paper, we describe a simple and highly sensitive manual assay for isotope fluxes through ion-conducting pathways, particularly cation-specific channels, in heterogenous populations of small membrane vesicles. We measure uptake of tracer of the ion of interest, against a large chemical gradient of the same ion. As a result of the imposed chemical gradient, a transient electrical diffusion potential is set up across the membranes of those vesicles which are highly permeable to the ion of interest. The isotope tends to equilibrate with the diffusion potential and is therefore concentrated selectively and transiently into those vesicle containing the channels. Furthermore, when performed in this way, the time course of tracer equilibration occurs over several minutes, rather than the sub-second range expected for tracer equilibration into channel-containing vesicles in the absence of an opposing chemical gradient of the permeant ion. The use of the procedure is demonstrated for three Na-conducting channels: gramicidin D incorporated into phospholipid vesicles, amiloride-blockable Na channels in toad bladder microsomes, and veratridine-activated tetrodotoxin-blockable Na channels in rat brain synaptic membranes. For all three cases, it proved simple to measure a specific 22Na uptake, in a minute time range, using very low concentrations of the channel-containing vesicles. By comparison with isotope flux measurements performed without an opposing Na gradient, the power of the present assay derives from both the very large gain in sensitivity and the convenient time course.

The effects of bilayer thickness and tension on gramicidin single-channel lifetime

Measurements have been made of gramicidin single-channel lifetimes in monoacylglycerol bilayers chosen so that their thickness ranged from above to below the length of the gramicidin channel. Contact angles, electrical capacities and bulk-phase interfacial tensions have also been determined for these systems. The mean channel lifetime decreased with the hydrocarbon thickness of the membrane until the latter reached 2.2 nm, after which the lifetime was relatively constant. A theoretical model has been proposed which relates the mean channel lifetime (or dissociation constant) to both the thickness and the tension of the bilayers. The analysis of the present results and of those of previous studies has led to the idea that aggregates of water molecules may play an important rôle in the dissociation of the gramicidin channel.

Complexation and phase transfer of nucleotides by gramicidin S

Gramicidin S (GrS), an amphiphilic cyclosymmetric decapeptide produced by Bacillus brevis G-B and Nagano, binds nucleotides in water to yield a complex which partitions into organic solvents. The observed phase-transfer efficiencies at a given pH increase in the order AMP less than ADP less than ATP. The lipophilic complexes have well-defined stoichiometries, which were determined to be 1:1 for ADP-GrS at pH 7 and ATP-GrS at pH 3 and 1:2 for ATP-GrS at pH 7. The interaction is primarily ionic, involving coordination of the ornithine N delta H3+ groups of the peptide and the phosphoryl groups of the nucleotide, with little contribution from the nucleoside moiety. Exchange of organic and inorganic phosphates was also found to be mediated by GrS. The nucleotide complexes are sparingly soluble in water and self-associate extensively in CHCl3, most likely by cross-beta-aggregation, to yield large, ribbonlike aggregates which give rise to broad NMR resonances. Structures for the 1:1 and 1:2 complexes are proposed. In the latter, two GrS molecules envelop the nucleotide, orienting their apolar faces externally in opposite directions, while the lateral faces retain considerable polar character and direct aggregation in organic media. The 1:1 complex possesses a single apolar face and is less lipophilic. Binding constants were estimated by simulation of the extraction data. For the 1:1 complexes, K1:1 congruent to 4 X 10(4) M-1 for either ADP or ATP. Phase transfer of the ATP complex at pH 7 could be modeled either by stochastically independent binding to two noninteracting sites on the nucleotide with K1 approximately K2 approximately K1:1 or by a sequential process with K1 approximately K1:1 and K2/K1 less than 100. It is concluded that the apparent selectivity of GrS for ATP over ADP is a consequence of the greater lipophilicity and tendency to aggregate of the 1:2 complex, rather than an intrinsically higher binding affinity for triphosphates. GrS is, to our knowledge, the first peptide known to possess phase-transfer activity toward nucleotides; this is, in addition, the first molecular recognition process in which GrS is demonstrated to participate in vitro at physiologically active concentrations.

Infrared spectra of the Gramicidin A transmembrane channel: the single-stranded-beta 6-helix

IR spectra are reported for preparations of Gramicidin A and malonyl Gramicidin A incorporated as the channel state in phospholipid structures. In this preparation Gramicidin A has already been shown to be unequivocally in the single-stranded beta-helical conformation. The result is an amide I frequency of 1633 +/- 1 cm-1. This demonstrates that the single-stranded beta-helix has an amide I frequency that has previously been considered to be diagnostic of antiparallel double-stranded beta-helix and of beta-sheet structures.

Supramolecular organization of lysophosphatidylcholine-packaged Gramicidin A

Heat derived gramicidin A'/L-alpha-lysophosphatidylcholine complexes were separated on a sucrose gradient to form two fractions: Fraction A which had an approximately constant Gramicidin A' to phospholipid ratio of 8 to 10 lipid molecules per Gramicidin A' molecule and Fraction B which had a larger but variable ratio. Fluorescence and circular dichroism studies confirmed Fraction A to be a lipid-incorporated channel state. Electron microscopic studies, using uranyl acetate negative staining, showed fraction A to be a membranous state with the formation of bilayer vesicles, that is, the interaction of peptide and phospholipid micelles causes the lipid to reorganize into a bilayer structure. Freeze-fracture replicas of the channel incorporated state demonstrated the presence of a supramolecular organization of particles exhibiting a tendency to form rows with a 50-60 A periodicity along the row and with 70-80 A distance between rows. An idealized working model for the incorporated state is presented.

Polypeptide clearing in model membranes: an analysis of the partition of gramicidin a' between cadmium ion induced gel and liquid-crystalline phases in vesicles of phosphatidic acid and phosphatidylcholine

Using a simple model for a biological membrane we examine cation-induced gel phase formation and the depletion of polypeptide from the gel phase. The model system consists of vesicles of phosphatidic acid and phosphatidylcholine which contain gramicidin A'. By use of electron spin resonance to monitor lipid phase behavior, Cd2+ is found to induce gel and liquid-crystal phase coexistence over a wide range of lipid composition. Quenching of gramicidin A' tryptophanyl fluorescence by spin-labeled phosphatidic acid or spin-labeled phosphatidylcholine is analyzed to obtain the partition coefficient, Kp, for gramicidin A' between gel and liquid-crystal phases. The value of Kp = 3 favoring the liquid-crystal phase indicates a partial clearing of the membrane-bound polypeptide from Cd2+-induced gel phase regions of the membrane.

First observation of a beta-turn conformation fused with the oxy-analogue of an alpha-turn: the molecular structure of a model peptide of the C-terminal part of gramicidin A

The molecular structure of N-tert-butyloxycarbonyl-D-leucyl-L-phenylalanyl ethanolamide (t-Boc-D-Leu-L-Phe-EA), a protected analogue of the C-terminal dipeptide of the membrane-active linear antibiotic gramicidin A, has been determined by X-ray diffraction. One of the two independent molecules in the asymmetric unit is characterized by a chain reversal stabilized by an intramolecular, three-centre, double hydrogen bonding. It represents the first experimental evidence for a beta-turn conformation fused with the oxy-analogue of an alpha-turn.

Entropy effects on the ion-diffusion rate in transmembrane protein channels

We treat the transport of univalent cations through pore-like protein channels in biological membranes analytically, using two models (A + B) for the channel and the ion-channel interaction. A Lennard-Jones-type repulsion between the ions and the pore wall is introduced. We also include Van der Waals- and coulomb-type interactions between polar ligands of the pore-forming protein (e.g., carbonyl groups directed towards the axis of the channel) and the migrating particles. In model A, the polar groups are assumed to occur in pairs of dipoles pointing in opposite directions (as in the gramicidin A channel), while in model B the channel is treated as a pore with a radially isotropic charge distribution. In both models the ion-channel interaction leads to the occurrence of periodic potentials, corresponding to quasi-equilibrium and transition state sites of the ion in the pore. The diffusion rate can be calculated employing rate-theoretical concepts on the basis of microscopic parameters. It is demonstrated that the anomaly (inversion of the normal mass effect) for the transport rates of different ions can be related to differences in the activation entropy. The latter quantity is estimated analytically for both models. As a test, we performed numerical calculations with parameters based on the gramicidin A model. The results are in good agreement with experimental data and data from computer simulations. This shows that simple analytic expressions are well suited for predicting trends in the ionic conductivity of protein channels on the basis of microscopic interactions.

Gramicidin A induces lysolecithin to form bilayers

Heat-induced association of Gramicidin A with lysolecithin micelles results in the formation of lipid bilayer structures. The capacity of the Gramicidin A peptide to transform the lysolecithin lipid structure from micelle to bilayer is considered in terms of molecular packing mechanisms and relevance to membrane processes in general. The resulting lipid-bilayer-packaged channel system has particular usefulness in characterizing channel structure and mechanism.

Thallium-205 NMR determination of the thermodynamics of the interaction between the thallous ion and gramicidin dimers incorporated into micelles

A study has been made of the thermodynamics of the interaction between the thallous ion and gramicidin dimers incorporated into micelles using thallium-205 NMR spectroscopy. The chemical shift data obtained are interpreted interms of a model in which the dimer has only one tight binding site. The variation of the binding constant over the temperature range 303-323 K is used to determine the changes in enthalpy and entropy of binding giving values of -11.3 kcal/mole and -16 e.u. at 303 K, respectively.

Effect of anions on the cation selectivity of gramicidin-containing liposomes

An osmotic method was used to study the salt permeability induced by gramicidin A in liposomes. Sequences of cation permeation were obtained for iodide, salycilate, acetate and formate salts in liposomes below and above their transition temperature. Salycilate and formate salts, unlike acetate and iodide salts, exhibit the same sequences for cation selectivity in liposomes below and above their transition temperature. These results can be explained by assuming three mechanisms for salt permeation across gramicidin-containing liposomes: (i) the anion moves by the lipid part of the membrane whereas the cation moves by the gramicidin channel, (ii) movement of the undissociated acid species occurs through the lipid part of the membrane followed by cation-proton exchange via the gramicidin channel and (iii) the cation and anion may move simultaneously via the gramicidin channel. When the movement of the anion or undissociated acid across the lipid part of the membrane is not rate limiting the permeation process, the cation selectivity obtained agrees with the cation selectivity of the gramicidin A channel, as determined by others using independent measurements.

Dielectric relaxation studies of ionic processes in lysolecithin-packaged gramicidin channels

Dielectric permitivities have been determined for suspensions of lysolecithin packaged malonyl gramicidin channels over the frequency range of 5 kHz to 900 MHz and under conditions of approximately equimolar concentrations (approximately 10mM) of channels and salts. The salts were lithium chloride, sodium chloride and thallium acetate. A relaxation process unique to the thallium acetate-channel system was observed which on analysis gave rise to a relaxation time at 25 degrees of 120 msec. The permitivity data, as well as a comparison of binding constants, indicate that the relaxation process results from TI+ being bound within the channel and more specifically from an intrachannel ion translocation with a rate constant of approximately 4 x 10(6) sec-1 and with an energy of activation of less than 6.7 kcal/mole. These data compare favorably with data from conductance studies on planar bilayers and with ion and carbon-13 nuclear magnetic studies on the lysolecithin packaged malonyl gramicidin channels which combine to indicate that the relaxation process is due to the jump of the thallium ion across a central barrier.

Single channels of 9, 11, 13, 15-destryptophyl-phenylalanyl-gramicidin A

Analysis of the single-channel behavior of an analogue of gramicidin A in which all four tryptophyl residues are substituted by phenylalanyl suggests that the nature of the side chains may play an important role in the ion translocation process. Indeed, while infrared spectroscopy indicates that both peptides have very similar backbone conformations, they have different single-channel characteristics. The unit conductance of the analogue is much smaller than that of the natural product. Moreover, contrary to gramicidin A, it is voltage dependent.

Low-frequency motion in membranes. The effect of cholesterol and proteins

Nuclear magnetic resonance (NMR) relaxation techniques have been used to study the effect of lipid-protein interactions on the dynamics of membrane lipids. Proton enhanced (PE) 13C-NMR measurements are reported for the methylene chain resonances in red blood cell membranes and their lipid extracts. For comparison similar measurements have been made of phospholipid dispersions containing cholesterol and the polypeptide gramicidin A+. It is found that the spin-lattice relaxation time in the rotating reference frame (T1 rho) is far more sensitive to protein, gramicidin A+ or cholesterol content than is the laboratory frame relaxation time (T1). Based on this data it is concluded that the addition of the second component to a lipid bilayer produces a low-frequency motion in the region of 10(5) to 10(7) Hz within the membrane lipid. The T1 rho for the superimposed resonance peaks derived from all parts of the phospholipid chain are all influenced in the same manner suggesting that the low frequency motion involves collective movements of large segments of the hydrocarbon chain. Because of the molecular co-operativity implied in this type of motion and the greater sensitivity of T1 rho to the effects of lipid-protein interactions generally, it is proposed that these low-frequency perturbations are felt at a greater distance from the protein than those at higher frequencies which dominate T1.

Intermolecular interactions of gramicidin A' transmembrane channels incorporated into lysophosphatidylcholine lipid systems

Fluorescence studies are reported on gramicidin A' incorporated into lysophosphatidylcholine phospholipid structures. The shift in the emission maximum during incorporation and the quenching of fluorescence by I- and by acrylamide of the incorporated state obtained after prolonged heating are consistent with the presence of the channel state comprised of two single-stranded beta 6 -helices associated head-to-head (formyl end-to-formyl end). The quantum yield for the incorporated state, when gramicidin A' is within the lipid matrix, is very low and indicates the occurrence of intermolecular Trp-Trp interactions. Possible interactions between channels within the lipid matrix are discussed utilizing Trp-Trp contacts.

On the relative lipid membrane permeability of Na+ and Ca2+. A physical basis for the messenger role of Ca2+

Calcium ion is demonstrated to bind in the gramicidin A transmembrane channel at a site that is displaced outward about 1.5 A from that of the sodium ion. The calcium ion is also shown to exchange rapidly with the solution such that the impermeability of the channel to calcium ion is due to the proximity of the lipid which limits solvation energy. Also at its binding site, calcium is shown to be able to draw into binding a peptide carbonyl which is not drawn into coordination by the sodium ion. These results demonstrate aspects of calcium ion transport and interaction which are considered central to its role as a cellular messenger.

Orientation of gramicidin A transmembrane channel. Infrared dichroism study of gramicidin in vesicles

Polarized infrared spectroscopy has been used to investigate the orientation of gramicidin A incorporated in dimyristoylphosphatidylcholine liposomes. Dichroism measurements of the major lipid (C = O ester, PO2-, CH2) and peptide (amide A, I, II) bands were performed on liposomes (with or without gramicidin) oriented by air-drying. The mean orientation of the lipid groups and of the pi LD helix chain in the gramicidin has been determined. It can be inferred from infrared frequencies of gramicidin that the dominant conformation of the peptide in liposomes cannot be identified to the antiparallel double-helical dimer found in organic solution. No shift in lipid frequencies was observed upon incorporation of gramicidin in the liposomes. However, a slight reorganization of the lipid hydrocarbon chains which become oriented more closely to the normal to the bilayer is evidenced by a change in the dichroism of the CH2 vibrations. The infrared dichroism results of gramicidin imply a perpendicular orientation of the gramicidin transmembrane channel with the pi LD helix axis at less than 15 degrees with respect to the normal to the bilayer.

The influence of n-alkanols and cholesterol on the duration and conductance of gramicidin single channels in monoolein bilayers

The mean lifetime of gramicidin A channels in bilayers formed from monoolein and squalane was sharply reduced by the absorption of a range of n-alkanols and cholesterol. Results are shown for n-hexanol, n-octanol, n-decanol, n-dodecanol, n-tetradecanol, n-hexadecanol, n-octadecanol and cholesterol. The longer chain n-alkanols were apparently more effective than the shorter members and cholesterol was the most effective of the substances examined. The single channel conductance was also affected, though to a much lesser extent than the mean channel lifetime, the n-alkanols producing increases and cholesterol a decrease. It is suggested that membrane fluidity changes are not likely to be primarily responsible for the reductions in channel lifetimes but that the bilayer tension, which is known to be increased by n-octanol, could be significant.