Gramicidin dimerization

Fig. 5.5 Gramicidin dimers double helix form [12] (left) and end-to-end form [13] (right)...

Figure 6. Schematic representation of the intramolecular linked gramicidin dimer showing flipping of the (R,R)-dioxolane ring into and out of the conduction pore. Reproduced with permission from Stankovic, C. J. Heinemann, S. H. Schreiber, S. L., J. Am. Chem. Soc. 1990, 112, 3703.

Veatch and coworkers proposed a different class of gramicidin dimers, constituting double stranded helices (cf. Section 5.3.)292,293 This model has been included in recent discussions of the mechanism of gramicidin channel formation17,291. ... 

Fig. 52. Schematic diagram of an antiparallel-(3-double-helical gramicidin dimer with seven residues per turn and even ends . The dotted lines denote hydrogen bonds [Reproduced from Veatch, W. R., et al. Biochemistry 13,...

Fig. 1 (left) Schematic structure of a gramicidin dimer in a phospholipid bilayer, (right) Bilayer conductance exhibited by gramicidin... 

The gramicidin channel, formed by dimerization of two molecules in a loose helical conformation (Fig. 3), has been studied extensively as a model system. The helical dimer spans the membrane to produce a channel through the hollow center of the helix with anionic sites or regions to facilitate cation transport. The channel transmits only univalent cations. Divalent calcium ion blocks ion flow through the channel. The channel exhibits the anomalous mole fraction effect. Both univalent thallous ion and sodium ion are very permeable when gramicidin dimers... 

FIGURE 10.41 (a) Gramicidin forms a double helix in organic solvents a helical dimer is the preferred strnctnre in lipid bilayers. The strnctnre is a head-to-head, left-handed helix, with the carboxy-termini of the two monomers at the ends of the strnctnre. (b) The hydrogen-bonding pattern resembles that of a parallel /3-sheet. 

A. Side view of channel spanning the lipid layer of a planar lipid bilayer, The structure is comprised of two monomers, each in a left-handed, single stranded p -helical conformation, and joined together at the head or formyl end by means of six, intermolecular hydrogen bonds. The two formyl protons are seen at the center of the structure in this view. Replacement of these protons by methyls destabilizes the conducting dimer as shown with N-acetyl desformyl Gramicidin A (Fig. 3D). 

For a more complete treatment of the derivations and determination of experimental rate constants (to be discussed briefly below) refer to Ref. 46 for Gramicidin A and Ref. 47 for the malonyl dimer of Gramicidin A. (Malonyl Gramicidin A is formed by deformylation of Gramicidin A and then joining to amino ends together using the malonyl moiety, —CO—CH2—CO—, to form the covalent dimer.)... 

X-ray diffraction studies on gramicidin commenced as early as 1949 218-219> and this early work pointed to a helical structure 220). Recent work by Koeppe et al. 221) on gramicidin A crystallised from methanol (/%) and ethanol (.P212121) has shown that the helical channel has a diameter of about 5 A and a length of about 32 A in both cases. The inclusion complexes of gramicidin A with CsSCN and KSCN (P212121) have channels that are wider (6-8 A) and shorter (26 A) than the uncomplexed dimer 221 222). Furthermore there are two cation binding sites per channel situated either 2.5 A from either end of the channel or 2.5 A on each side of its centre 222) Unfortunately these data do not permit a choice to be made from the helical models (i)—(iv) and it is not certain if the helical canals studied are the same as those involved in membrane ion transport. 

Fig. 24. Proposed structure of the Gramicidin A dimer showing the intramolecular and intermolecular hydrogen bonding arrangement. Numbers refer to the amino acid residues Peptide side groups are omitted for clarity.

Fig. 25. Top view of a space-filling model of the proposed Gramicidin A dimer structure, showing the transmembrane channel. [Photograph courtesy of D. A. Haydon]...

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). 

Fluorescence quantum yield and emission maximum determinations as a function of peptide concentration may also permit the detection of peptide self-aggregation at concentrations below 10-4 M, because the peptide fluorophore is likely to be located in a different environment in the peptide aggregate. For example, the concentration-dependent changes in the tryptophan fluorescence emission maximum of mellitin were monitored to determine the equilibrium dissociation constant and thermodynamic parameters of the monomer-tetramer self-association reaction of this peptide. 25 Similarly, measurement of the changes in the tryptophan fluorescence intensity of gramicidin A as a function of its concentration permitted the determination of an average monomer-dimer equilibrium con-stant. 26 ... 

An example of a channel- or pore-forming antibiotic is gramicidin A (9.57), a peptide consisting of 15 amino acids. It induces the transmembrane transport of protons, alkali-metal ions, and thallium ions at concentrations as low as 10 ° M, even though it is unable to complex these ions in solution. Gramicidin also forms several dimers with itself. 

The expected channel shown in Figure 12 is of a bimolecular structure. The rigid channel mouth may prohibit the consecutive long alkyl chains from assembling themselves and to prevent lipid molecules from invading the area. The space thus provided may accommodate water molecules to make the domain sufficiently hydrophilic to pass ions. Such a domain would recognize its counterpart located in another lipid layer to make a tail-to-tail dimer of 8, i.e. a symmetric transmembrane channel, as in the case of Gramicidin A dimer. ... 

The linear peptide gramicidin A (15 residues) dimerizes in biological and synthetic membranes in a head-to-head manner30 to give channels of about 5 A in diameter and 32 A in length. These channels are specific for alkali metal cations, and show high transport rates, e.g. 107 Na+ ions s l, a value close to the ion fluxes found for the Na+ channel of nerve cells. Each structural unit appears to contain two channels, each of which contains two binding sites for cations. 

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