Low conductance states of a single ion channel are not ?closed?

Korchev, Yuri; Bashford, C. L.; Alder, G. M.; Kasianowicz, John J.; Pasternak, C. A.

doi:10.1007/bf00234521

Cited by 70 publications

(63 citation statements)

References 37 publications

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“…The conductances of the bacterial channels are comparable to (or higher than) those of other pores believed to be involved in macromolecule transport, such as the endoplasmic reticulum and nuclear pores referred to above, those activated by leader peptides in the E. coli plasma membrane (4), and the possibly DNA-conducing bacterial and phage proteins mentioned in the Introduction. It should at any rate be considered that the conductance of a channel may be only marginally related to the size of the species that can move through it (58). The mitochondrial porin, VDAC, is also able to conduct genetic material.…”

Section: Discussionmentioning

confidence: 99%

DNA Translocation Across Planar Bilayers Containing Bacillus subtilis Ion Channels

Szabó

Báthori²,

Tombola

et al. 1997

Journal of Biological Chemistry

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The mechanisms by which genetic material crosses prokaryotic membranes are incompletely understood. We have developed a new methodology to study the translocation of genetic material via pores in a reconstituted system, using techniques from electrophysiology and molecular biology. We report here that planar bilayer membranes become permeable to double-stranded DNA (kilobase range) if Bacillus subtilis membrane vesicles containing high conductance channels have been fused into them. The translocation is an electrophoretic process, since it does not occur if a transmembrane electrical field opposing the movement of DNA, a polyanion, is applied. It is not an aspecific permeation through the phospholipid bilayer, since it does not take place if no proteins have been incorporated into the membrane. The transport is also not due simply to the presence of polypeptides in the membrane, since it does not occur if the latter contains gramicidin A or a eukaryotic, multiprotein vesicle fraction exhibiting 30-picosiemens anion-selective channel activity. The presence of DNA alters the behavior of the bacterial channels, indicating that it interacts with the pores and may travel through their lumen. These results support the idea that DNA translocation may take place through proteic pores and suggest that some of the high conductance bacterial channels observed in electrophysiological experiments may be constituents of the DNA translocating machinery in these organisms.

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Section: Discussionmentioning

confidence: 99%

DNA Translocation Across Planar Bilayers Containing Bacillus subtilis Ion Channels

Szabó

Báthori²,

Tombola

et al. 1997

Journal of Biological Chemistry

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“…The rest of the residues are electrically neutral. In view of experimental contexts (23), the protein pore is not allowed to move.…”

Section: Simulation Methodsmentioning

confidence: 99%

Simulation of polymer translocation through protein channels

Muthukumar

Kong

2006

Proc. Natl. Acad. Sci. U.S.A.

128

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A modeling algorithm is presented to compute simultaneously polymer conformations and ionic current, as single polymer molecules undergo translocation through protein channels. The method is based on a combination of Langevin dynamics for coarse-grained models of polymers and the Poisson-Nernst-Planck formalism for ionic current. For the illustrative example of ssDNA passing through the ␣-hemolysin pore, vivid details of conformational fluctuations of the polymer inside the vestibule and ␤-barrel compartments of the protein pore, and their consequent effects on the translocation time and extent of blocked ionic current are presented. In addition to yielding insights into several experimentally reported puzzles, our simulations offer experimental strategies to sequence polymers more efficiently.T ranslocation of polymers through biological channels is very complex involving many machineries and is a fundamental step in many life processes. Although several essential features of translocation are richly documented in systems such as mRNP complex through nuclear pores (1-3), a simple system has only recently been identified for following the single-file passage of one isolated polymer through one channel (4-11). In this system, the channel is constituted by self-assembling heptamers of the Staphylococcus aureus ␣-hemolysin (␣HL) protein. The channel is assembled in a phospholipid bilayer, which offers a physical barrier, and the channel has an opening diameter of Ϸ1.4 nm at the narrowest constriction (12). A single-stranded polynucleotide, such as poly(deoxyadenylate) and poly(deoxycytidylate), is pulled through the channel by an externally applied voltage gradient across the channel in a solution of a strong electrolyte. The idea is that the ionic current through the channel caused by the passage of small ions of the electrolyte is blocked to a certain extent during the event of translocation of the polymer. It has been hoped that the extent and duration of the current blockade are unique signatures of the identity of the polymer, both in terms of the polymer's chemical characteristics and physical length.Even this simplest setup, where identical molecules undergo translocation, has generated several puzzling results. The distribution, P( ), of the duration of blockade of ionic current I b is very broad and appears to exhibit at least two peaks. In addition, there are several levels of ionic current blockade I b for the same molecule. It is standard practice in experimental investigations to combine the histograms of and I b (8). The resultant scatter plots always yield two groups of data even for monodisperse homopolymers.To gain insight into these puzzles, we have developed the following simulation. It is complementary to a flurry of theoretical activity (13-21), based on entropic barrier dynamics (22), all of which lead to a generic P( ) unlike in experiments. Although it is indeed desirable to perform the computation ab initio, the size of the system to be simulated is forbiddingly large to enable such a compu...

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“…In addition, Krasilnikov and others used PEGs to estimate the radii of ion channels from the ability of size-selected PEGs to partition into the channel pore. 11,[19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36] Protein translocation across membranes, which plays a key role in many biological processes, can be facilitated by ion channels. [37][38][39] Other biomolecules can be detected as they transport through ion channels.…”

Section: Introductionmentioning

confidence: 99%

Probing single nanometer-scale pores with polymeric molecular rulers

Henrickson¹,

DiMarzio

Wang³

et al. 2010

The Journal of Chemical Physics

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We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus ␣-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stable modes during the interactions. We show here that polynucleotides can be used to probe structural features of the ␣-hemolysin channel itself. Specifically, both the pore length and channel aperture profile can be estimated. The results are consistent with the channel crystal structure and suggest that polymer-based "molecular rulers" may prove useful in deducing the structures of nanometer-scale pores in general.

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Low conductance states of a single ion channel are not ?closed?

Cited by 70 publications

References 37 publications

DNA Translocation Across Planar Bilayers Containing Bacillus subtilis Ion Channels

DNA Translocation Across Planar Bilayers Containing Bacillus subtilis Ion Channels

Simulation of polymer translocation through protein channels

Probing single nanometer-scale pores with polymeric molecular rulers

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