Gramicidin A channel

C. and D. Monoolein/hexadecane membranes, 100 mV applied potential 1 M RbCl and 23 °C. Note that, during the time period of an average Gramicidin A channel (above), the N-acetyl desformyl Gramicidin A channel turns on and off many times and that the conductance step is smaller. The N-acetyl methyl replacing the formyl proton also crowds and destabilizes the head to head junction and results in less favorable lateral coordination of the cation at the junction. Reproduced with permission from Ref.111... 

Fig. 13. Location of calcium ion binding site in the Gramicidin A channel —. For comparison, the sodium ion binding site is included...

A. lCBr titration of Enniatin B in methanol. Since exchange of cation between solution and carrier is relatively rapid only one signal is seen per chemically distinct carbonyl. The titration shows the magnitude of the chemical shift observed. Since Enniatin B may be considered a cyclic analogue of Gramicidin A, these chemical shifts indicate the magnitudes of chemical shifts that can be expected in the Gramicidin A channel (see Fig. 6 and 13) for direct interaction of carbonyl with cation. 

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). 

Cukierman, S. (2000) Proton mobilities in water and in different stereoisomers of covalently linked gramicidin A channels. Biophysical Journal, 78, 1825-1834. 

Roux, B. (1990) Theoretical study of ion transprot in the gramicidin A channel. Harvard University, Cambridge, MA. 

Ionophores are classified as either channel or carrier ionophores. Channel ionophores form channels across the membrane through which ions can diffuse down a concentration gradient. The nature of the channel depends on the ionophore, for example, gramicidin A channels are formed by two gramicidin molecules, N-terminus to N-terminus, each molecule forming a left-handed helix (Figure 7.1(a)). Carrier ionophores pick up an ion on one side of the membrane, transport it across, and release it into the fluid on the other side of the membrane. They usually transport specific ions. For example, valinomycin transports K+ but not Na+ Li+ ions (Figure 7.1(b)). 

It is not easy to directly compare the two models which were discussed in the previous sections. The only interactions which were studied with both techniques are those of a gramicidin A channel with Na+ and K+. In Fig. 6 the results of these studies 165 , I66,i89,i9i) are compare(j. The largest differences can be observed at the two ends of the channel. This is due to the fact that the ethanolamine tails were fixed in different con-... 

Cotten, M., Tian, C., Busath, D. D., et al. (1999) Modulating dipoles for structure-function correlations in the gramicidin A channel. Biochemistry, 38, 9185-9197. 

Liu, Z., Xu, Y, Tang, P. (2006). Steered molecular dynamics simulations of Na permeation across Gramicidin A channel. The Journal of Physical Chemistry, 110, 12789—12795. 

M. G. Kurnikova, R. D. Coalson, P. Graf, and A. Nitzan. A lattice relaxation algorithm for Three-Dimensional Poisson-Nernst-Planck theory with application to ion transport through the Gramicidin A channel Biophys. J.. 76 642-656,1999. 

R. Pomes and B. Roux. Structure and dynamics of a proton wire A theoretical study of translocation along the single-file water chain in the gramicidin A channel. Biophys.]., 71 19-39,2002. 

FIGURE 3 Molecular model of the gramicidin A channel. The two monomers are placed head-to-head with their N termini in near contact. (From Ury, D. W., Jing, T. L., Luan, C. H., and Waller, M. (1988). Current Topics in Membranes and Transport, 33,51-90.)... 

Lattice Relaxation Algorithm for Three-Dimensional Poisson-Nernst-Planck Theory with Application to Ion Transport Through the Gramicidin A Channel. 

Gramicidin A Channel as a Test Ground for Molecular Dynamics Force Fields. 

T. B. Wolf and B. Roux, Protein Struct., Eunct. and Genet., 24(1), 92 (1996). Structure, Energetics, and Dynamics of Lipid-Protein Interactions A Molecular Dynamics Study of Gramicidin A Channel in a DMPC Bilayer. 

Dimensional Poisson-Nernst-Planck Theory Studies Influence of Membrane Electrostatics on Gramicidin A Channel Conductance. 

Alfredo AE, Cardenas RD, Kumikova MG. Three-dimensional Poisson-Nemst-Planck theory studies influence of membrane electrostatics on Gramicidin A channel conductance. Biophys J 2000 79(l) 80-93. 

The above-described algorithm was developed and tested successfully on several simple model systems. The method was further tested on the more challenging gramicidin A channel our results correspond well with the published results in Refs. 154 and 155. The main conclusion from our work is that the EAS-MG approach leads to one order-of-magnitude improvement in... 

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