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  • Channel forming peptide  (2)
  • K+ channels  (1)
  • Membrane helix packing  (1)
  • 1
    Electronic Resource
    Electronic Resource
    Springer
    European biophysics journal 21 (1992), S. 117-128 
    ISSN: 1432-1017
    Keywords: Ion channel ; Peptaibol ; Channel forming peptide ; Planar bilayer
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The zervamicins (Zrv) are a family of 16 residue peptaibol channel formers, related to the 20 residue peptaibol alamethicin (Alm), but containing a higher proportion of polar sidechains. Zrv-1113 forms multi-level channels in planar lipid (diphytanoyl phosphatidylcholine) bilayers in response to cis positive voltages. Analysis of the voltage and concentration dependence of macroscopic conductances induced by Zrv-IIB suggests that, on average, channels contain ca. 13 peptide monomers. Analysis of single channel conductance levels suggests a similar value. The pattern of successive conductance levels is consistent with a modified helix bundle model in which the higher order bundle are distorted within the plane of the bilayer towards a “torpedo” shaped cross-section. The kinetics of intro-burst switching between adjacent conductance levels are shown to be approximately an order of magnitude faster for Zrv-IIB than for Alm. The channel forming properties of the related naturally occurring peptaibols, Zrv-Leu and Zrv-IC, have also been demonstrated, as have those of the synthetic apolar analogue Zrv-Al-16. The experimental studies on channel formation are combined with the known crystallographic structures of Zrv-Al-16 and Zrv-Leu to develop a molecular model of Zrv-II3 channels.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    European biophysics journal 28 (1999), S. 489-498 
    ISSN: 1432-1017
    Keywords: Key words Monte Carlo simulated annealing ; Simulation ; Membrane helix packing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The aim of this study is to investigate if the packing motifs of native transmembrane helices can be produced by simulations with simple potentials and to develop a method for the rapid generation of initial candidate models for integral membrane proteins composed of bundles of transmembrane helices. Constituent residues are mapped along the helix axis in order to maintain the amino acid sequence-dependent properties of the helix. Helix packing is optimized according to a semi-empirical potential mainly composed of four components: a bilayer potential, a crossing angle potential, a helix dipole potential and a helix-helix distance potential. A Monte Carlo simulated annealing protocol is employed to optimize the helix bundle system. Necessary parameters are derived from theoretical studies and statistical analysis of experimentally determined protein structures. Preliminary testing of the method has been conducted with idealized seven Ala20 helix bundles. The structures generated show a high degree of compactness. It was observed that both bacteriorhodopsin-like and δ-endotoxin-like structures are generated in seven-helix bundle simulations, within which the composition varies dependent upon the cooling rate. The simulation method has also been employed to explore the packing of N = 4 and N = 12 transmembrane helix bundles. The results suggest that seven and 12 transmembrane helix bundles resembling those observed experimentally (e.g., bacteriorhodopsin, rhodopsin and cytochrome c oxidase subunit I) may be generated by simulations using simple potentials.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    European biophysics journal 20 (1991), S. 229-240 
    ISSN: 1432-1017
    Keywords: Ion channel ; Channel forming peptide ; α-helix ; Electrostatics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Channel forming peptides (CFPs) are amphipathic peptides, of length ca. 20 residues, which adopt an α-helical conformation in the presence of lipid bilayers and form ion channels with electrophysiological properties comparable to those of ion channel proteins. We have modelled CFP channels as bundles of parallel trans-bilayer helices surrounding a central ion-permeable pore. Ion-channel interactions have been explored via accessible surface area calculations, and via evaluation of changes in van der Waals and electrostatic energies as a K+ ion is translated along the length of the pore. Two CFPs have been modelled: (a) zervamicin-A1-16, a synthetic apolar peptaibol related to alamethicin, and (b) δ-toxin from Staphylococcus aureus. Both of these CFPs have previously been shown to form ion channels in planar lipid bilayers, and have been shown to have predominantly helical conformations. Zervamicin-A1-16 channels were modelled as bundles of 4 to 8 parallel helices. Two related helix bundle geometries were explored. K+channel interactions have been shown to involve exposed backbone carbonyl oxygen atoms. δ-Toxin channels were modelled as bundles of 6 parallel helices. Residues Q3, D11 and D18 generate favourable K+-channel interactions. Rotation of W15 about its Cβ-Cγ bond has been shown to be capable of occluding the central pore, and is discussed as a possible model for sidechain conformational changes in relation to ion channel gating.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1432-1424
    Keywords: K+ channels ; delayed rectifier ; neuroblastoma cells ; membrane lipids ; voltage-gated channels
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary A voltage-sensitive K+ channel with characteristics of the delayed rectifier was studied in NG108-15 cells using the cell-attached patch-clamp technique. The primary conductance of the channel was 18 pS, but occasional openings to a subconductance state were observed. The average latency to first opening of the channel was about 4 msec. Based on about 20,000 channel openings, the open time probability density function (pdf) required at least three exponentials (time constants of about 0.2, 3 and 9 msec) to achieve an adequate fit to the data. The closed time pdf required at least six exponentials to describe the data (time constants ranging from 0.093 to 440 msec). Thus, the channel exists in at least three open and six closed states. The ensemble average describing the inactivation of the channel was well fit by two exponentials with time constants of 170 msec and 4.2 sec. To examine the effect of changes in membrane lipid composition on the properties of the channel, the phospholipids of the cells were enriched with polyunsaturated fatty acids. In patches from 20:4-enriched cells the conductance, mean first latency, and open-time pdf were similar to control cells. However, the open state probability was increased from 0.25 to 0.44 and the mean closed time was decreased from 20 to 9 msec. The closed time pdf exhibited a higher proportion of closing events associated with short time constants, i.e., the probability of the channel closing into a long-lived closed state was decreased. The decay phase of the ensemble average also was changed; the proportion of the curve described by the slower time constant was almost doubled. Thus, the delayed rectifier from NG108-15 cells can exist in at least three open and six closed states, and changes in membrane lipid composition may have subtle effects on the gating kinetics of the channel.
    Type of Medium: Electronic Resource
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