The gramicidin A channel: Role of the ethanolamine end chain on the energy profile for single occupancy by Na +

Conformation of the acylation site of palmitoylgramicidin in lipid bilayers of dimyristoylphosphatidylcholine

Gramicidin A(gA) can be palmitoylated by means of an ester linkage to the OH group of the terminal ethanolamine that sits at the membrane-water interface in the functional gA channel. We have investigated palmitoyl-gA as a model transmembrane acylprotein. Ethanolamine-d(4) (NH(2)CD(2)CD(2)OH) was incorporated into gA by total synthesis, and a portion of the labeled gA was palmitoylated. Solid-state (2)H-NMR spectra of acyl- and nonacyl-gA in hydrated dimyristoylphosphatidylcholine (DMPC) bilayers were compared. The spectra for both oriented and nonoriented samples at 4 and at 40 degrees C indicate that the ethanolamine of gA is highly mobile prior to acylation, but essentially immobile after palmitoylation. The (2)H quadrupolar splittings allow the conformation of the ethanolamine group in acyl-gA to be determined. By combining our data with the previously determined quadrupolar splittings for deuterium labels on the palmitoyl chain [Vogt, T.C.B., Killian, J.A., & de Kruijff, B. (1994) Biochemistry 33, 2063-2070], we also propose a model for the acyl chain. The ethanolamine group rotates over Leu(10) and toward the outside of the gA channel's cylinder upon acylation, so that the attached acyl chain passes between the side chains of Trp(9) and Leu(10). To accommodate the acyl chain, the six-membered portion of the indole ring of Trp(9) is displaced by about 0.9 angstroms, by means of 1-2 degree rotations in chi(1) and chi(2).

On the helix sense of gramicidin A single channels

In order to resolve whether gramicidin A channels are formed by right- or left-handed beta-helices, we synthesized an optically reversed (or mirror image) analogue of gramicidin A, called gramicidin A-, to test whether it forms channels that have the same handedness as channels formed by gramicidin M- (F. Heitz et al., Biophys. J. 40:87-89, 1982). In gramicidin M- the four tryptophan residues have been replaced with phenylalanine, and the circular dichroism (CD) spectrum therefore reflects almost exclusively contributions from the polypeptide backbone. The CD spectrum of gramicidin M- in dimyristoylphosphatidylcholine vesicles is consistent with a left-handed helical backbone folding motif (F. Heitz et al., Biophys. Chem. 24:149-160, 1986), and the CD spectra of gramicidins A and A- are essentially mirror images of each other. Based on hybrid channel experiments, gramicidin A- and M- channels are structurally equivalent, while gramicidin A and A- channels are nonequivalent, being of opposite helix sense. Gramicidin A- channels are therefore left-handed, and natural gramicidin A channels in phospholipid bilayers are right-handed beta 6.3-helical dimers.

The channel properties of possible gramicidin dimers

Extending previous work (Sung & Jordan, 1987 a, Biophys. J. 51, 661-672; 1988, Biophys. J.54, 519-526), we describe channel properties of five possible gramicidin dimers by studying dimerization energies and axial electrical potentials. Unlike the head-to-head dimer (the predominant channel former), both tail-to-tail and head-to-tail dimers with the same beta-helical monomer structure as the head-to-head dimer only form four intermonomer hydrogen bonds and are much less stable. Were channels formed from these dimers to be observed, their electrical potential profiles suggest that they should be cation selective, probably conduct less than the head-to-head dimer, have a central cation binding site, bind cations preferentially if crystallizable, and in the case of the head-to-tail dimer, rectify. Like the antiparallel double stranded helical dimer (a possible minor conducting pathway) the parallel double stranded helical dimer has 28 interstrand hydrogen bonds, but its hydrogen bond network is quite distorted and it is much less stable. If it formed, its electrical potential profile suggests that it would be cation selective, bind anions preferentially if crystallizable, rectify, and at high enough voltages, might exhibit a conductance greater than that of the antiparallel form.

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.

Energy profiles in the gramicidin A channel

Gramicidin A (GA) is a linear pentadecapeptide made of alternating D and L residues, in which the N-and C-terminals are blocked by a formyl group (head) and an ethanolamine end (tail), respectively (Sarges & Witkop, 1964):

The interaction of Cl- with a gramicidin-like channel

Molecular dynamics simulations have been used to study the interaction of Cl- with a gramicidin-like channel. The results suggest that there is a high-energy barrier at the entrance of the channel, which would correspond to a permeability 10(-9)-times that of a cation of the same size. This could account for the cationic selectivity of the gramicidin channel and indicates that valence selectivity is kinetically controlled.

Experimental and theoretical study of gramicidin P, an analog of gramicidin A with a methylamine C-terminal

Gramicidin P (a gramicidin A in which the ethanolamine C-terminus is replaced by methylamine) was synthesized and shown to have the same single-channel conductance behavior as gramicidin A. The results are discussed in connection with the energy profile computed in the presence of water in comparison with the corresponding profile for gramicidin A.

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.

The effect of the amino-acid side chains on the energy profiles for ion transport in the gramicidin A channel

Computations on the energy profiles for Na+ in the gramicidin A (GA) channel have been extended by introducing the effect, previously neglected, of the amino acid side chains of GA, fixed in their most stable conformations. The calculations have been performed in two approximations: 1) with the ethanolamine tail fixed in its most stable conformation, 2) with the tail allowed to optimize its conformation upon the progression of the ion. In both approximations the overall shape of the energy profile is very similar to that obtained in the absence of the side chains. One observes, however, a general lowering of the profile upon the adjunction of the side chains. The analysis of the factors responsible for this energy lowering indicates that it is due essentially to the electrostatic and polarisation components of the interaction which interplay differently, however, in the different parts of the channel. A particular role is attributed in this respect to the tryptophan residues of GA. The role of the 4 tryptophans present, Trp 15, 13, 11 and 9, is individualized by stripping of one of them at a time. The strongest effect on the energy deepening is due to Trp 13 and is particularly prominent in the entrance zone at 14.5A from the center of the channel. The result indicates the possibility of investigating theoretically the effect on the energy profiles of the substitution of the "natural" side chain by others.