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  • 1
    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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  • 2
    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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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    European biophysics journal 21 (1992), S. 281-298 
    ISSN: 1432-1017
    Keywords: Ion channel ; Nicotinic receptor ; α-helix bundle ; Molecular modelling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The ion channel of the nicotinic acetylcholine receptor (nAChR) is believed to be lined by transmembrane M2 helices. A “4-8-12” sequence motif, comprising serine (S) or threonine (T) residues at positions 4, 8 and 12 of M2, is conserved between different members, anion and cation selective, of the nAChR superfamily. Parallel bundles of 4-8-12 motif-containing helices are considered as simplified models of ion channels. The relationship between S and T sidechain conformations and channelion interactions is explored via evaluation of interaction energies of K+ and of Cl− ions with channel models. Energy calculations are used to determine optimal ξ2 (Cα-C\-Oγ-Hγ) values in the presence of K+ or Cl− ions. 4-8-12 motif-containing bundles may form favourable interactions with either cations or anions, dependent upon the ξ2 values adopted. Parallel-helix and tilted-helix bundles are considered, as are heteromeric models designed to mimic the Torpedo nAChR. The main conclusion of the study is that conformational flexibility at ξ2 enables both S and T residues to form favourable interactions with anions or cations. Consequently, there is apparently no difference between S and T residues in their interactions with permeant ions, which suggests that the presence of T vs. S residues within the 4-8-12 motif is not a major mechanism whereby anion/cation selectivity may be generated. The implications of these studies with respect to more elaborate models of nAChR and related receptors are considered.
    Type of Medium: Electronic Resource
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  • 4
    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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  • 5
    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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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    European biophysics journal 22 (1993), S. 269-277 
    ISSN: 1432-1017
    Keywords: Amphipathic α-helix ; Channel-forming peptide ; Hydrophilic surface map ; Membrane protein ; Simulated annealing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Ion channels may be formed by bundles of amphipathic α-helices aligned parallel to one another and spanning a lipid bilayer membrane, with the hydrophilic faces of the helices lining a central pore. In order to provide insight into the packing of such helices in bundles, a method has been developed to evalute hydrophilic surface maps of amphipathic α-helices and to display these surfaces in a readily interpretable form. The procedure is based upon empirical energy calculations of interactions of a water molecule with an amphipathic α-helix. The method has been applied to three channel-forming peptides: Staphylococcal δ-toxin; alamethicin; and a synthetic leucine- and serine-containing peptide. Particular emphasis is placed upon the effects of sidechain conformational flexibility on hydrophilic surface maps. Å family of models of the δ-toxin; helix is generated by a simulated annealing procedure. The results of hydrophilic surface map analyses provide more exact definition of the centre of the hydrophilic face of amphipathic helices, and of the variation of the position of the centre in response to changes in sidechain conformation. This information is used to define families of preliminary models for a given ion channel, as is illustrated for δ-toxin.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 414 (2001), S. 156-159 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Water continues to surprise us. Intuitively, one would not expect water to enter a narrow hydrophobic pore, such as that formed by a carbon nanotube, because of both the tube's narrowness and its 'oily', water-repellent properties. Such chemical common sense stems from our experience of the ...
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 385 (1997), S. 390-391 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Several bacterial toxins work by punching a hole in the membrane of their target cell. This produces a protein-lined ion channel (or pore), which dissipates the electrochemical gradients across the membrane and results in the death of the cell under attack. To do the job, a toxin has to reach its ...
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1432-2234
    Keywords: Key words: K+ channel ; Glycoporin ; LamB ; ScrY ; Conductance
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. The Poisson-Boltzmann equation was solved numerically for models of the pore regions of the Shaker K+ channel and of two glycoporins (LamB and ScrY) to yield electrostatic potential profiles along the pore axes. From these potential profiles, single-channel current-voltage (I–V) relations were calculated. The importance of a proper treatment of the ionisation state of two rings of aspartate sidechains at the mouth of the K+ channel pore emerged from such calculations. The calculated most likely state, in which only two of the eight aspartate sidechains were deprotonated, yielded better agreement with experimental conductance data. An approximate calculation of single-channel conductances based simply on pore geometry yielded very similar conductance values for the two glycoporins. This differed from an␣experimentally determined conductance ratio of ScrY:LamB=10:1. Preliminary electrostatics calculations appeared to reproduce the observed difference in conductance between the two glycoporins, confirming that single-channel conductance is determined by electrostatic as well as geometric considerations.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    New York : Wiley-Blackwell
    Biopolymers 39 (1996), S. 503-515 
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In the middle of the S6 helix in voltage-gated potassium channels there is a highly conserved Pro-Val-Pro motif, while the equivalent M2 helix of inward rectifier potassium channels contains a conserved glycine residue in a comparable position. The structural implications of these conserved motifs are of interest given the evidence that S6 and M2 are components of the lining of their respective pores. Multiple sequence alignment and TM helix prediction methods were used to define consensus regions for S6 and M2. Ensembles of 50 structures for each helix were generated by simulated annealing and restrained molecular dynamics. Time-dependent fluctuations of S6 and M2 were investigated by long time scale molecular dynamics simulations on representative members of each ensemble carried out in vacuo in the presence and absence of a hydrophobic potential that mimics a lipid bilayer. The results are discussed in terms of the structural basis of the kink in S6 and M2 and of a putative functional role for flexible helices as “molecular swivels.” © 1996 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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