Gramicidin dimer model

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. ... 

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... 

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. 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]...

Fig. 6. Minimum interaction energies of K+ and Na+ with gramicidin A as a function of their position along the channel axis. The top two curves 1911 are calculated according to a model proposed by Gresh et.al. with blocked ethanolamine end chain. The more attractive curves 165-166> are determined using the pair potential method. The gramicidin A dimer ranges from about —14 A to +14 A...

Figure 2. Schematic models of gramicidin A dimers (A) head-to-head helical dimer (B) tail-to-tail helical dimer (C) antiparallel double-stranded helix (D) parallel double-stranded helix. (Reproduced with permission from reference 301. Copyright 1986 Biophysical Society.)...

Gramicidin A. Gramicidin A (gA) is a small 15-residue antibiotic peptide formed as a dimer in a head-to-head (HH) or a double-helical (DH) conformation. " Because of its simplicity and reduced dimensions, the gA structure has been studied extensively and simulated as a model for ion channels,and has emerged as a benchmark for simulation approaches. " The structure exposes its hydrophobic sidechains to the lipid membrane that embeds the protein. The molecular structure of gA has been known for three decades,and has been recently resolved with NMR spectroscopyThe relation of the structure seen spectroscopically to that... 

Figure 3 Balls and sticks model of the gramicidin A dimer (orthographic projection)...

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