Polypeptide gramicidin

Certain microbes synthesize small organic molecules, ionophores, that function as shuttles for the movement of ions across membranes. These ionophores contain hy-drophihc centers that bind specific ions and are surrounded by peripheral hydrophobic regions this arrangement allows the molecules to dissolve effectively in the membrane and diffuse transversely therein. Others, Hke the well-smdied polypeptide gramicidin, form channels. 

The gramicidin family of linear polypeptides represents a biologically viable channel system of related peptides in which specific changes in amino acid composition can be correlated with cation binding selectivity and transport. The parent molecule of this family of polypeptides, gramicidin A, has the amino acid sequence shown in Fig. 1. This relatively simple molecule is probably the best characterized ion channel (both structurally and functionally) and has, to date, been the principal proving-ground for many of our ideas about the molecular nature of ion conduction in membranes. ... 

Most channels behave as simple resistors to current flow when the channel is open, the current through the channel varies linearly with membrane potential (AF — IR). The antibiotic polypeptide gramicidin A forms a cylindrical channel by end-to-end dimerization of two peptides, one in each of the bilayer leaflets. Individual gramicidin channels exhibit a resistance of 8 x 10 over... 

All of these approaches lead to permeable nano-compartments however, biometric membranes are only those resulting from insertion of transmembrane proteins or biopores. ° The small pore-forming polypeptide gramicidin (gA), with a length of 2.6 nm, has been successfully inserted into PMOXA-Z)-PDMS-Z)-PMOXA membranes with thicknesses ranging from... 

The antibiotic tyrothricin is a mixture of about 20% of the linear polypeptide gramicidin (consisting of six structurally related gramicidins) and about 80% of the cyclic polypeptide tyrocidin (consisting of five structurally related tyrocidines, A-E). Only gramicidin is of therapeutic interest. 

The transport of ions into or out of a cell needs to be mediated (that is, involve other species) because charged species do not partition well into the hydrophobic environment of the membrane. There are two mechanisms for ion transport mediation by a carrier molecule or transport through a channel former, a protein that creates a hydrophilic pore through which the ion can pass. An example of a channel former is the polypeptide gramicidin A, which increases the membrane permeability to cations such as ff, K+, and Na. ... 

It has been known for some years that gramicidin forms transmembrane ion channels in lipid bilayers and biological membranes and that these channels are assembled from two molecules of the polypeptide 213). The channels are permeable specifically to small monovalent cations [such as H+, Na+, K+, Rb+, Cs+, Tl+, NH4+, CHjNHj, but not (CH3)2NH2+J and small neutral molecules (such as water, but not urea). They do not allow passage of anions or multivalent cations 21 n. 

Fig. 23. Possible helical models for the gramicidin A ion channel. The polypeptides are represented as helical strips, one molecule being stippled for clarity. Numbers refer to the substituted terminal amino acid residues. Model (i), proposed originally by Urry, is the one now generally accepted...

It should be noted that in forming this dimeric channel structure all the hydrogen bonds are parallel to the channel axis and that the inner surface is lined with the polar polypeptide groups. In addition the various lipophilic side chains coat the outer wall of the structure and are thus in contact with the lipid hydrocarbon chains. The resulting gramicidin A channel is a most efficient means of ion transport with approximately 107 sodium ions traversing the channel per second, under conditions of 1 M NaCl, 100 mV applied potential and a temperature of 25 °C 225). The detailed mechanism by which this can be achieved is under active study 226). 

The data thus clearly shows that, depending on the gramicidin concentration, the structure of the temperature- and pressure-dependent lipid bilayer is significantly altered by the insertion of the polypeptide. It has also been shown... 

Lipmann, F., Gevers, W., Kleinkauf, H., and Roskoski, R. Jr. (1971). Polypeptide synthesis on protein templates the enzymatic synthesis of gramicidin S and tyrocidine. Adv. Enzymol. Relat. Areas Mol. Biol. 35, 1-34. 

Bacitracin and gramicidin are polypeptide antibiotics with activity against gram-positive organisms and against most anaerobic cocci. Systemic toxicity for bacitracin is rare because of poor absorption through the skin. Gramicidin is used only topically... 

The first successful synthesis of a biologically active cyclic peptide, gramicidin S, was accomplished by Schwyzer and Sieber[6,7l via the 4-nitrophenyl ester. The fact that -protected peptide esters can be deprotected to give the peptide active ester salts has made this approach popular not only in the synthesis of sequential polypeptides but also of cyclic peptides. Among the various active esters examined for this purpose, the pentafluorophenyl esters have emerged as the most reactive ones, although a high risk of epimerization is encountered when C-terminal chiral amino acids are involved. 

Beta structures are found in many small peptides. Tire hormone oxytocin (Fig. 2-4), the antibiotics gramicidin S (Fig. 2-4) and valinomycin (Fig. 8-22), and the mushroom peptide antamanide (Box 28-B) are among these. The cyclic structures of these compounds favor formation of antiparallel (3 strands with sharp turns at the ends. Polypeptide antibiotics that have alternating... 

Our approach has been essentially empirical in nature with less emphasis on the theoretical. We have isolated single substances, proved their purity, and determined their covalent structure by classical methods of organic chemistry we have then used these substances of molecular weight ranging from 1,000 to 14,000 as model solutes for the study of conformation and intermolecular interaction. Solutes of special interest have been gramicidin SA (2), bacitracin A (3), polymyxin B, and the tyrocidines A, B, and C (4). All are cyclic antibiotic polypeptides. The first three behave in aqueous solution as reasonably ideal solutes and do not associate, but the tyrocidines associate strongly and are interesting models for the study of association phenomena. Other model solutes of... 

Transport inhibitors, dinitrophenol, DNP, 257 fluorodinitrobenzene, FDNB, 251 gramicidin, 255 N-ethylmaleimide, NEM, 250 ouabain, 259, 260 tetraethyl ammonium, TEA, 253 tetrodotoxin, 254, 256 Trifolium subterranean, migration of, 213, 214 Triple helix formation, 141 Two genes, one polypeptide, 2,59... 

Polypeptide antibiotics, such as gramicidin A and polymyxin B, are capable of increasing the permeability of bacterial membranes. As is to be expected, they change the phase transition, much like cholesterol [130]. These substances induce a tightening of fluid membranes and an increase in the fluidity of rigid membranes. It has been shown that polymyxin B produces phase separation and forms a Dimyris-toylphosphatidylcholine (DMPG)-rich phase in DMPG/DMPC membranes [131]. 

For gramicidin-S (Scott et al., 1967), where the loop involves the bonds of the polypeptide backbone, closure of the ring was effected at the C —C bond of an arbitrarily selected residue, together with the following potential function to close the gap ... 

The hard-sphere potential has also been used to compute the sterically allowed conformations of small polypeptides of known amino acid sequence, viz. an octapeptide loop of ribonuclease (Nemethy and Scheraga, 1965) and the cyclic decapeptide gramicidin-S (Vanderkooi et al., 1966). We shall use the calculation for gramicidin-S to illustrate the method. This decapeptide consists of two identical pentapeptides joined into a ring by peptide bonds, the amino acid sequence being... 

The procedures and calculations described in this chapter provide considerable insight into the factors affecting the conformations of polypeptides and proteins. The computer programs for gramicidin-S, oxytocin, vasopressin, etc., can also be used for larger structures—of the size of ribonuclease and lysozyme—although the required computer time is considerably increased. 

David, S.A., Balaram, P., Mathan, V.I. Interaction of basic amphiphilic polypeptide antimicrobials, gramicidin S, tyrocidin and efrapeptin, with endotoxic lipid A. Med Microbiol Lett 2 (1993) 42-47. 

To date, the most extensively studied natural ionophore is gramicidin,10 a polypeptide antibiotic isolated from the bacterium Bacillus brevis. Indeed, the idea of a channel-like structure for ion transport was inferred from its study. However, unlike channel proteins, which are exclusively composed of L-amino acids, each alternate amino acid in gramicidin has D-stereochemistry. It is composed of 16 residues, 15 of which are amino acids. The structure is summarized below, in which Xxx has the following identities gramicidin A (gA), Trp gB, Phe gC, Tyr gD, a mixture of gA, gB, gC, -80 5 15. 

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