Linear Gramicidin Research Articles

Formation of non-beta 6.3-helical gramicidin channels between sequence-substituted gramicidin analogues

Using the linear gramicidins as an example, we have previously shown how the statistical properties of heterodimeric (hybrid) channels (formed between the parent [Val1]gramicidin A (gA) and a sequence-altered analogue) can be used to assess whether the analogue forms channels that are structurally equivalent to the parent channels (Durkin, J. T., R. E. Koeppe II, and O. S. Andersen. 1990. J. Mol. Biol. 211:221-234). Generally, the gramicidins are tolerant of amino acid sequence alterations. We report here an exception. The optically reversed analogue, gramicidin M- (gM-) (Heitz, F., G. Spach, and Y. Trudelle. 1982. Biophys. J. 40:87-89), forms channels that are the mirror-image of [Val1]gA channels; gM- should thus form no hybrid channels with analogues having the same helix sense as [Val1]gA. Surprisingly, however, gM- forms hybrid channels with the shortened analogues des-Val1-[Ala2]gA and des-Val1-gC, but these channels differ fundamentally from the parent channels: (a) the appearance rate of these heterodimers is only approximately 1/10 of that predicted from the random assortment of monomers into conducting dimers, indicating the existence of an energy barrier to their formation (e.g., monomer refolding into a new channel-forming conformation); and (b), once formed, the hybrid channels are stabilized approximately 1,000-fold relative to the parent channels. The increased stability suggests a structure that is joined by many hydrogen bonds, such as one of the double-stranded helical dimers shown to be adopted by gramicidins in organic solvents (Veatch, W. R., E. T. Fossel, and E. R. Blout. 1974. Biochemistry. 13:5249-5256).

On the supramolecular organization of gramicidin channels. The elementary conducting unit is a dimer

The question, whether the conducting channels formed by the linear gramicidins are dimers (as is generally believed) or tetramers (as has been recently proposed [Stark G., M. Strässle, and Z. Takacz. 1986. J. Membr. Biol. 89:23-37; Strässle, M., G. Stark, M. Wilhelm, P. Daumas, F. Heitz, and R. Lazaro. 1989. Biochim. Biophys. Acta. 980:305-314]) has been addressed in single-channel experiments. The experimental approach was based on the ability of electrophysiological (single-channel) experiments to resolve the number of hybrid channel types that could form between gramicidin A or C and O-pyromellityl-gramicidin A or C (in which a pyromellitic acid residue has been esterified to the ethanolamine-OH group [Apell, H.-J., E. Bamberg, H. Alpes, and P. Läuger. 1977. J. Membr. Biol. 31:171-188]). The presence of the bulky, negatively charged pyromellityl group at the channel entrances endows the hybrid channels with characteristically different features and thus facilitates the resolution of the different hybrid channel types. Only two hybrid channel types were detected, indicating that the conducting channels are membrane-spanning dimers. There was likewise no evidence for lateral association between conducting channels and nonconducting monomers. These results can be reconciled with those of Stark et al. (op. cit.) if gramicidin channel formation involves a (slow) folding into beta 6.3-helical monomers followed by the dimerization step.

Changes in conformation and antimicrobial properties caused by replacement ofD-amino acids with α-aminoisobutyric acid in the gramicidin backbone: synthesis and circular dichroic studies

In an attempt to mimic the stable helical structures of proteins with possible pore-forming ability in membranes, the linear gramicidin backbone has been changed by inserting achiral α-aminoisobutyric acids (Aib) in place of all of the alternatively sequenced D-amino acids. The conformation and biological activity of the synthetic gramicidin A and B analogues have been studied. CD measurements have been used to determine the conformation in solution. The original conformation of gramicidin clearly changes and its antimicrobial activity is reduced in Aib analogues. Although α-helical motifs can be clearly distinguished in analogues, the CD spectra show inherent complexities. The possibility of superposition of different conformations is considered. The potential pore-forming ability of analogues is briefly discussed.

Amino acid sequence modulation of gramicidin channel function: effects of tryptophan-to-phenylalanine substitutions on the single-channel conductance and duration

Linear gramicidins with one, two, or three Trp----Phe substitutions in the gramicidin A sequence form beta 6.3-helical channels that have widely varying conductances and average durations. The variations in single-channel conductance and average duration are uncoupled. The single-channel conductance decreases as a monotonic function of the number of Trp----Phe substitutions, and the relative conductance decrease induced by a given Trp----Phe substitution is only weakly affected by substitutions at other positions. These results suggest that each Trp influences the conductance independently, most likely through electrostatic interactions between the Trp dipole(s) and the permeant ion (as was deduced previously for aromatic side-chain substitutions at position one [Koeppe, R. E., Mazet, J.-L., & Andersen, O. S. (1990) Biochemistry 29 (2), 512-520]). Trp----Phe substitutions exert a complex, nonadditive influence on average duration as well as the energetics of heterodimer formation. These changes are presumably due to sequence-specific differences in the channel's surface chemistry--which may be related to ability of the Trp indole NH moieties to form hydrogen bonds with the lipid backbone oxygens and/or interfacial H2O.

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.

An alternative to Urry's model for the gramicidin transmembrane channels

AbstractIt is suggested that the conducting transmembrane channels formed by the linear gramicidins A, B and C may be head‐to‐head (formyl end‐to‐formyl end) dimers of double‐stranded parallel β‐helices. This possibility is not in conflict with any of the various experimental findings bearing on the molecular organization of the channels and represents a plausible alternative to Urry's model of a head‐to‐head dimer of single‐stranded β6.3‐helices.

Nonribosomal biosynthesis of peptide antibiotics

Peptide antibiotics are known to contain non-protein amino acids, D-amino acids, hydroxy acids, and other unusual constituents. In addition they may be modified by N-methylation and cyclization reactions. Their biosynthetic origin has been connected in many cases to an enzymatic system referred to as the 'thiotemplate multienzymic mechanism'. This mechanism includes the activation of the constituent residues as adenylates on the enzymic template, the acylation of specific template thiol groups, epimerization or N-methylation at this thioester stage, and polymerization in the sequence directed by the multienzymic structure with the aid of 4'-phosphopantetheine as a cofactor, including possible cyclization or terminal modification reactions. The reaction sequences leading to gramicidin S, tyrocidine, cyclosporine, bacitracin, polymyxin, actinomycin, enniatin, beauvericin, delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine and linear gramicidin are discussed. The structures of the multienzymes, their genetic organization, the biological functions of these peptides and results on related systems are discussed.

Distinction between dipolar and inductive effects in modulating the conductance of gramicidin channels

The ion permeability of transmembrane channels formed by the linear gramicidins is altered by amino acid sequence substitutions. We have previously shown that the polarity of the side chain at position one is important in modulating a channel's conductance and ion selectivity [Russel et al. (1986) Biophys. J. 49, 673-686]. Changes in polarity could alter ion permeability by (through-space) ion-dipole interactions or by (through-bond) inductive electron shifts. We have addressed this question by investigating the permeability characteristics of channels formed by gramicidins where the NH2-terminal amino acid is either phenylalanine or one of a series of substituted phenylalanines: p-hydroxy-, p-methoxy-, o-fluoro-, m-fluoro-, or p-fluorophenylalanine. The electron-donating or -withdrawing nature, as quantified by the Hammett constant, ranges from -0.37 to +0.34 for these side chains. Channels formed by these gramicidins show a more than 2.5-fold variation in their Na+ conductance, but the conductance variations do not rank in the order of the Hammett constants of the side chains. Inductive effects cannot therefore be of primary importance in the modulation of the gramicidin single-channel conductance by these side chains. The results support previous suggestions that electrostatic interactions between side chain dipoles and permeating ions can modify the energy profile for ion movement through the gramicidin channel and thus alter the conductance.

Energetics of gramicidin hybrid channel formation as a test for structural equivalence: Side-chain substitutions in the native sequence

To determine whether amino acid side-chain substitutions in linear gramicidins alter the structure of membrane-spanning channels formed by the modified peptides, we have developed a quantitative measure of structural equivalence of the peptide backbone among gramicidin channels based on functional (single-channel) measurements. The experiments exploit the fact that gramicidin channels are symmetrical dimers, and that channels formed by different gramicidin analogues can be distinguished on the basis of their single-channel current amplitudes or durations. It is thereby possible to determine whether hybrid channels can form between chemically dissimilar peptides, i.e. whether the peptides can adapt to each other. Further, since the relative rates of channel formation as well as the relative concentrations of pure and hybrid channel types can be measured in the same membrane, these experiments provide a quantitative measure of the energetic cost of hybrid channel formation relative to the formation of the pure channels. For a wide variety of different side-chains, we find that substitutions as extreme as glycine to phenylalanine at position 1, at the join between the two monomers in a membrane-spanning dimer, incur no energetic cost for channel formation, which implies that channels formed by each of the modified peptides are structurally equivalent. In addition, the average durations of the hybrid channels (except those having tyrosine or hexafluorovaline at position 1) are intermediate to the average durations of the respective pure channel types, thus providing further evidence for structural equivalence among channels formed by sequence-substituted gramicidins.

Single channels and surface potential of linear gramicidins

The single channel data for 4 different linear gramicidins containing either 4 Trp, 4 Phe, 4 Tyr or TyrBzl have been analyzed on the basis of 3 barriers-2 sites model. They form 2 families which differ by their single channel behavior and thus different energy profiles of the channel. A relationship between the surface potential and the entry barrier is proposed.

Gramicidin A analogs: influence of the substitution of the tryptophans by naphthylalanines

The synthesis of 4 linear gramicidins bearing both polar and non-polar aromatic side chains is described. From the single channels data, it appears that the relative positions of these residues has little or no influence on the conductance and that this conductance is governed mainly by the number of tryptophan residues. It is also shown that the effect of the bulkiness of the apolar aromatic side chain can be neglected.

Mixed monolayers of linear gramicidins and phospholipid. Surface pressure and surface potential studies

The behavior of two gramicidins incorporated into lipid monolayers is analyzed on the basis of the force and surface potential area curves. It is shown that the position of the gramicidins (helical axis parallel or perpendicular to the interface) depends on the monolayer pressure and that these molecules are not miscible with dioleoylphosphatidylcholine. Surface potential measurements suggest the existence of a relationship between the single channel characteristics and the surface potential and indicate that the tryptophans are essential for lowering the lipid surface potential in agreement with the single channel behaviour of both gramicidin A and gramicidin M.

Linear gramicidin activates neutrophil functions and the activation is blocked by chemotactic peptide receptor antagonist

The activation of functional responses in rabbit peritoneal neutrophils by gramicidin and the chemotactic peptide, N-formyl-methionyl-leucyl-phenylalanine methyl ester, was studied. Gramicidin activated superoxide generation, lysosomal enzyme release and a decrease in fluorescence of chlortetracycline-loaded cells, as for the chemotactic peptide. The maximum intensities of the responses by gramicidin were lower than that by chemotactic peptide. Responses by both these peptides could be inhibited by t-butyloxycarbonyl-methionyl-leucyl-phenylalanine, a chemotactic peptide receptor antagonist. Gramicidin gave responses at low doses comparable to that of the chemotactic peptide.

Linear gramicidins at the air-water interface

The behavior of four linear gramicidins, which differ by the nature of their 9, 11, 13, and 15 aromatic residues, together with a covalent "head to tail" retro GA-DAla-GA dimer, has been examined at the air-water interface. It is shown that all four "monomers" have almost the same molecular area, which is compatible with either a single-stranded or a double-stranded helical model, whereas it is suggested that retro GA-DAla-GA could adopt another conformation. The surface potential measurements agree with those of different groups of molecules characterized by their single-channel behaviors.

Membranous phosphoglyceride-linked biosynthesis of pentadeca peptide, linear gramicidin, by Bacillus brevis ATCC 8185

A peptide antibiotic, linear gramicidin A, from Bacillus brevis ATCC 8185 was biosynthesized with a cell-free preparation. An ethanolamine donor required for masking of a carboxyl terminal in this linear peptide was detected. Phosphatidylethanolamine, one of phosphoglycerides and a major structural element of membranes in bacterial cells, was verified to be the primary donor of terminal ethanolamine in the total synthesis of the peptide. This paper suggests that one of the non-ribosomal peptidyl products undergoes tight linkage to a component of cellular membranes.

DNA‐supercoiling is affected in vitro by the peptide antibiotics tyrocidine and gramicidin

Tyrocidine, a peptide antibiotic produced by Bacillus brevis (ATCC 8185), relaxes superhelical DNA in a biphasic manner and induces 'packaging' of the DNA at higher concentrations. This was concluded from studies using the sensitive 4,5',8-trimethylpsoralen photobinding technique [Sinden, R. R., Carlson, J. O. & Pettijohn, D.-E. (1980) Cell 21, 773-783]. Relaxed DNA is not affected by tyrocidine whereas linearized molecules become packaged. The linear gramicidin synthesized by the same strain reverses the tyrocidine-induced relaxation as well as the packaging, an observation which might be of biological relevance.

Single-channel studies on linear gramicidins with altered amino acid side chains. Effects of altering the polarity of the side chain at position 1 in gramicidin A

The modulation of gramicidin A single-channel characteristics by the amino acid side chains was investigated using gramicidin A analogues in which the NH2 terminal valine was chemically replaced by other amino acids. The replacements were chosen such that pairs of analogues would have essentially isosteric side chains of different polarities at position 1 (valine vs. trifluorovaline or hexafluorovaline; norvaline vs. S-methyl-cysteine; and norleucine vs. methionine). Even though the side chains are not in direct contact with the permeating ions, the single-channel conductances for Na+ and Cs+ are markedly affected by the changes in the physico-chemical characteristics of the side chains. The maximum single-channel conductance for Na+ is decreased by as much as 10-fold in channels formed by analogues with polar side chains at position 1 compared with their counterparts with nonpolar side chains, while the Na+ affinity is fairly insensitive to these changes. The relative conductance changes seen with Cs+ were less than those seen with Na+; the ion selectivity of the channels with polar side chains at position 1 was increased. Hybrid channels could form between compounds with a polar side chain at position 1 and either valine gramicidin A or their counterparts with a nonpolar side chain at position 1. The structure of channels formed by the modified gramicidins is thus essentially identical to the structure of channels formed by valine gramicidin A. The polarity of the side chain at position 1 is an important determinant of the permeability characteristics of the gramicidin A channel. We discuss the importance of having structural information when interpreting the functional consequences of site-directed amino acid modifications.

Effect of linear gramicidin on sporulation and intracellular ATP pools of Bacillus brevis

When Bacillus brevis ATCC 8185 was subjected to nutritional shiftdown from a rich medium to one completely devoid of a nitrogen source, sporulation could be stimulated by the addition of linear gramicidin. Gramicidin-induced sporulation occurred after a considerably longer lag period than the earlier described tyrocidine-induced process (Ristow and Paulus 1982) but involved similar associated biochemical changes, such as extracellular protease production, rapid incorporation of radioactive precursors into RNA, and dipicolinate synthesis. The increased incorporation of [3H]leucine into tyrocidine was a characteristic element in gramicidin-induced sporulation, not being observed when spore formation was accelerated by limited nitrogen supplementation. Nitrogen supplementation (0.02-0.01% nutrient broth) caused a slow and gradual increase in dipicolinate production, in contrast to the sudden, rapid rise of dipicolinate synthesis provoked by the addition of gramicidin or tyrocidine. The induction of sporulation by gramicidin occurred at very low peptide concentrations (0.03 microM), which also brought about an acute depletion of intracellular ATP. In sporulation accelerated by nutrient broth, no depression of ATP level was observed and nonionophoric analogues of gramicidin were unable to substitute for gramicidin in inducing sporulation.

Semisynthesis of linear gramicidins using diphenyl phosphorazidate (DPPA)

Sequential HPLC analysis has been used to optimize a synthetic scheme for the preparation of semisynthetic position 1 analogues of the channel-forming pentadecapeptide, gramicidin A. Diphenyl phosphorazidate (DPPA) was more efficient than dicyclohexylcarbodiimide (DCC) for the coupling of N-formyl amino acids to des(formyl-valyl) gramicidin A. The DPPA coupling proceeds rapidly, and with high yield, at 0 degree. The absence of significant (less than 0.1%) racemization is demonstrated by the lack of electrophysiologically active formyl-L-valine gramicidin A in preparations of formyl-D-valine gramicidin A. This scheme has proved useful for the preparation of microgram to gram amounts of position-1-substituted gramicidin analogues suitable for crystallography and electrophysiology. Details of the techniques for the preparation of these highly purified analogues are discussed.

Effect of Gramicidin S on the Transcription System of the Producer Bacillus brevis Nagano

The effect of the peptide antibiotic gramicidin S, produced by Bacillus brevis Nagano, was tested on the transcription system of the producer by using in vivo, semi in vitro and in vitro systems for studies of RNA synthesis. The effects of other peptide antibiotics (linear gramicidin, tyrocidine and tyrothricin) were also tested for comparison. It was found that (a) RNA polymerase isolated from either gramicidin S-producing or non-producing strains had a similar structure and requirements and that (b) the presence of gramicidin S caused a very strong inhibition of the in vitro transcription system. We present evidence that this inhibition is most probably through formation of a complex between the antibiotic and the DNA. In vivo studies indicate that transcription during growth and sporulation is not affected by gramicidin S and the implication is made that gramicidin S inhibits transcription during germination and outgrowth.