The gramicidin A channel: the energy profile for single and double occupancy in a head-to-head β6.3 3,3 -helical dimer backbone

Dynamic properties of individual water molecules in a hydrophobic pore lined with acyl chains: a molecular dynamics study

Recently, a certain class of synthetic molecules has been shown to form ion channels, the pore of which is lined with hydrophobic acyl chains [M. Sokabe, in: F. Oosawa, H. Hayashi, T. Yoshioka (Eds.), Transmembrane Signaling and Sensation, JSSP/VNU Science Press BV, Tokyo, 1984, p. 119; F. Hayashi, M. Sokabe, M. Takagi, K. Hayashi, U. Kishimoto, Biochim. Biophys. Acta, 510 (1978) 305; M.J. Pregel, L. Jullien, J. Canceill, L. Lacombe, J.M. Lehn, J. Chem. Soc. Perkin Trans., 2 (1995) 417; Y. Tanaka, Y. Kobuke, M. Sokabe, Angew. Chem. Int. Ed. Engl., 34 (1995) 693; M. Sokabe, Z. Qi, K. Donowaki, H. Ishida, K. Okubo, Biophys. J., 70 (1996) A201; H. Ishida, K. Donowaki, Y. Inoue, Z. Qi, M. Sokabe, Chem. Lett. (1997) p. 953]. As an initial step towards understanding the physical mechanisms of ion permeation across such a hydrophobic pore, systematic molecular dynamics simulations were performed to investigate dynamic and energetic properties of water molecules inside the pore using a dimer of alanine-N'-acylated cyclic peptide as a channel model. Dynamic energy profiles for water molecules indicated that the energy barrier at the middle region of the pore is approximately 2-3 kcal/mol higher than that in the cap water region which was defined as a vicinity region of the channel entrance. Energetics analyses demonstrated that the mutual interactions among intrapore water molecules are the major factor to give favorable interaction (negative energy contribution) for themselves. The pore, despite being lined with acyl chains, has a favorable van der Waals interaction with intrapore water molecules. These results may help to explain why water-filled channels can be formed by the hydrophobic helices in natural channels.

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).

How can the aromatic side-chains modulate the conductance of the gramicidin channel? A new approach using non-coded amino acids

In order to elucidate the role of the aromatic side-chains in the mechanism of transduction of monovalent cations through the channel of linear gramicidin, two series of analogues containing non-coded aromatic amino acids were synthesized. In the first series, the four tryptophans were replaced by either four L-3-(8-quinolyl)alanyl or four L-3-(4-quinolyl)alanyl residues and single channel conductance measurements showed that these substitutions led to a strong lowering of the channel conductance, which is attributed to a modification of the orientation of the aromatic side-chains due to an increase of their hydrophobicity. In the second series, the analogues contained both tryptophyl and naphthylalanyl residues in various amounts and positions. The single channel conductance data indicated that the conductance was mainly governed by the number of polar residues (Trp) and not by their positions. The conformational consequences of these results are discussed together with their influence on the energy profile of the gramicidin channel.

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.

Gramicidin A--phospholipid model systems

Gramicidin A forms ion-conducting channels which can traverse the hydrocarbon core of lipid bilayer membranes. The structures formed by gramicidin A are among the best characterized of all membrane-bound polypeptides or proteins. In this review a brief summary is given of the occurrence, conformation, and synthesis of gramicidin A, and of its use as a model for ion transport and the interaction of proteins and lipids in biological membranes.

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.

Theoretical study of potential ion-channels formed by a bundle of alpha-helices: effect of the presence of polar residues along the channel inner wall

In a channel-forming bundle of five alpha-helices of poly-L-alanine, the replacement of all the alanyl side-chains lining the inner wall by serines is shown, by energy optimization, to produce only small modifications of the packing. The stability of the bundle is larger than that of the pure alanyl package, owing to hydrogen bonding between serine hydroxyls and carbonyl oxygens. The energy profile for sodium as well as the water-channel interactions are favored by the presence of the OH groups and by the lability of the seryl side chains. The possible general significance of the results is suggested.

Investigation of the interaction between thallous ions and gramicidin A in dimyristoylphosphatidylcholine vesicles: a thallium-205 NMR equilibrium study

This study reports the first direct observation of multiple occupancy of the gramicidin A channel by Tl+ ions. 205Tl NMR has been used to study the equilibrium binding of Tl+ by gramicidin A incorporated in sonicated dimyristoylphosphatidylcholine vesicles. It is shown that only multiple-channel occupancy can account for the 205Tl chemical shifts measured. The data are analyzed to yield the equilibrium association constants of 450-600 and 5-20 M-1 for the binding of the first and the second ions at 34 degrees C, respectively.

Orientation of gramicidin D incorporated into phospholipid multibilayers: a Fourier transform infrared-attenuated total reflection spectroscopic study

Polarized Fourier transform infrared (FTIR)-attenuated total reflection (ATR) spectroscopy was applied to study the orientation of the linear pentadecapeptide antibiotic gramicidin D incorporated into phospholipid multibilayers, which were cast on a germanium ATR plate from chloroform solution. In DMPC and DPPC multibilayers, the CH2 stretching bands of lipid hydrocarbon chains were slightly shifted to the higher frequency side and bandwidth was increased in the presence of gramicidin. However, in DPPE multibilayers, frequencies and bandwidths of these bands were unaltered. In each case, gramicidin produced little effect on the orientation of lipid hydrocarbon chains, suggesting that gramicidin penetrates into lipid layers without noticeable perturbations. Upon incubation of cast films in contact with water above the gel-liquid-crystalline transition temperature (Tc) of lipids, the reorientation of gramicidin in lipid multibilayers occurred, the degree thereof depending upon the fluidity of the lipid hydrocarbon chains and the amount of surrounding water. In DMPC multibilayers, the helix axis of gramicidin was oriented almost parallel to the lipid hydrocarbon chains after incubation. In DPPC multibilayers, on the other hand, the helix axis of gramicidin was tilted on average about 15 degrees from the lipid hydrocarbon chains after incubation. However, in DPPE multibilayers, which are known to have the most rigid bilayer structures, the reorientation of gramicidin could not be seen.

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.

The gramicidin A channel: comparison of the energy profiles of Na+, K+ and Cs+. Influence of the flexibility of the ethanolamine end chain on the profiles

The energy profiles for single occupancy by Cs+, K+ and Na+ in the gramicidin A channel assumed to be in a head-to-head beta 6.3 3.3 helical dimeric structure, were computed: (A) allowing complete conformational freedom to the ethanolamine end, (B) constraining it to stay in its intrinsically preferred conformation. Whatever the constraint, both the entrance barrier and the central barrier appear in the order Cs+ less than K+ less than Na+. Introducing the flexibility of the tail modifies appreciably the profiles and the location of the extrema along it.

Calculations of electrostatic interactions in biological systems and in solutions

Correlating the structure and action of biological molecules requires knowledge of the corresponding relation between structure and energy. Probably the most important factors in such a structure– energy correlation are associated with electrostatic interactions. Thus the key requirement for quantative understanding of the action of biological molecules is the ability to correlate electrostatic interactions with structural information. To appreciate this point it is useful to compare the electrostatic energy of a charged amino acid in a polar solvent to the corresponding van der Waals energy. The electrostatic free energy, ΔGel, can be approximated (as will be shown in Section II) by the Born formula (ΔGel= –(166Q2/ā) (I – I/E)). Where ΔGelis given in kcal/mol,Qis the charge of the given group, in units of electron charge,āis the effective radius of the group, andEis the dielectric constant of the solvent. With an effective radius of charged amino acids of approximately 2 Å, Born's formula gives about – 80 kcal/mol for their energy in polar solvents whereEis larger than 10. This energy is two orders of magnitude larger than the van der Waals interaction of such groups and their surroundings.