Altered voltage sensitivity of mutant OmpC porin channels

Bishop, N.D.; Lea, E.J.A.; Mobasheri, Hamid; Spiro, Stephen

doi:10.1016/0014-5793(95)01535-3

Cited by 14 publications

(6 citation statements)

References 24 publications

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“…Finally, we also provide brief insight into the dynamics of loop L3 which is located in the CR. This loop has been shown to play a key role in gating of the OmpC channels in several studies. − The root-mean-square fluctuation (RMSF) is estimated from the unbiased simulations for all three studied models as shown in Figure A. The RMSF is observed to be lowest in the non-Drude model, slightly higher in the Drude* model, and highest in the Drude model.…”

Section: Resultsmentioning

confidence: 99%

Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field

Prajapati

Mele

Aksoyoglu

et al. 2020

J. Chem. Inf. Model.

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In the past two decades, molecular dynamics simulations have become the method of choice for elucidating the transport mechanisms of ions through various membrane channels. Often, these simulations heavily rely on classical nonpolarizable force fields (FFs), which lack electronic polarizability in the treatment of the electrostatics. The recent advancements in the Drude polarizable FF lead to a complete set of parameters for water, ions, protein, and lipids, allowing for a more realistic modeling of membrane proteins. However, the quality of these Drude FFs remains untested for such systems. Here, we examine the quality of this FF set in two ways, i.e., (i) in simple ionic aqueous solution simulations and (ii) in more complex membrane channel simulations. First, the aqueous solutions of KCl, NaCl, MgCl2, and CaCl2 salts are simulated using the polarizable Drude and the nonpolarizable CHARMM36 FFs. The bulk conductivity has been estimated for both FF sets using applied-field simulations for several concentrations and temperatures in the case of all investigated salts and compared to experimental findings. An excellent improvement in the ability of the Drude FF to reproduce the experimental bulk conductivities for KCl, NaCl, and MgCl2 solutions can be observed but not in the case of CaCl2. Moreover, the outer membrane channel OmpC from the bacterium Escherichia coli has been employed to examine the ability of the polarizable and nonpolarizable FFs to reproduce ion transport-related quantities known from experiment. Unbiased and applied-field simulations have been performed in the presence of KCl using both FF sets. Unlike for the bulk systems of aqueous salt solutions, it has been found that the Drude FF is not accurate in modeling KCl transport properties across the OmpC porin.

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Section: Resultsmentioning

confidence: 99%

Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field

Prajapati

Mele

Aksoyoglu

et al. 2020

J. Chem. Inf. Model.

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“…The present work has identified a channel-forming activity intrinsic to the cytotoxic endonuclease domain of an enzymatic colicin that is indispensable for cytotoxicity. Colicin E9, its derivatives and the E9 DNase were added to the cis compartment to a final concentration of 2 nM or 20 nM and single-channel measurements made at room temperature as described previously 43,44 . Briefly, using reversible Ag/AgCl electrodes and an applied p.d., To determine the range of channel activities exhibited by the E9 DNase, channel data from 8 separate bilayer experiments were analyzed covering ~7000 s of records.…”

Section: Discussionmentioning

confidence: 99%

“…Colicin E9, its derivatives and the E9 DNase were added to the cis compartment to a final concentration of 2 nM or 20 nM and single-channel measurements made at room temperature as described previously 43,44 . Briefly, using reversible Ag/AgCl electrodes and an applied p.d., membrane current was measured using a bilayer amplifier (HAMK2TC, R.A.P.…”

Section: Planar Lipid Bilayers and Single-channel Recordings Bilayersmentioning

confidence: 99%

The cytotoxic domain of colicin E9 is a channel-forming endonuclease

et al. 2002

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Article:Mosbahi, Khédidja, Lemaître, Christelle, Mobasheri, Hamid et al. (6 more authors) (2002) The cytotoxic domain of colicin E9 is a channel-forming endonuclease. Nature Structural Biology. pp. 476-484. ISSN 1545-9985 https://doi.org/10.1038/nsb797 eprints@whiterose.ac.uk https://eprints.whiterose.ac.uk/ Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. TakedownIf you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing eprints@whiterose.ac.uk including the URL of the record and the reason for the withdrawal request. White Rose Consortium ePrints Repositoryhttp://eprints.whiterose.ac.uk/ This is an author produced version of a paper published in Nature Structural Biology. This paper has been peer-reviewed but does not include final publisher proof-corrections or journal pagination.White Rose Repository URL for this paper: http://eprints.whiterose.ac.uk/archive/00001066/ Citation for the published paper Mosbahi, Khédidja and Lemaître, Christelle and Keeble, Anthony H. and Mobasheri, Hamid and Morel, Bertrand and James, Richard and Moore, Geoffrey R. and Lea, Edward J. A. and Kleanthous, Colin (2002) The cytotoxic domain of colicin E9 is a channel-forming endonuclease. Nature Structural Biology, 9 (6). pp. 476-484. Citation for this paperTo refer to the repository paper, the following format may be used: Mosbahi, Khédidja and Lemaître, Christelle and Keeble, Anthony H. and Mobasheri, Hamid and Morel, Bertrand and James, Richard and Moore, Geoffrey R. and Lea, Edward J. A. and Kleanthous, Colin (2002) Colicin E9 is a 60 kDa toxin that is normally released from colicinogenic bacteria in the form of a heterodimeric complex with its 9.5 kDa immunity protein, Im9 (ref. 14). The immunity protein protects the colicin-producing bacterium from the activity of its own toxin but is jettisoned on entry of the colicin into a susceptible cell 15 . Hence, the form of the toxin tested in the bilayer experiments had the immunity protein removed (see Materials andMethods section). Previous work from our laboratory has shown that this form of the toxin retains complete biological activity 14 . Immunity-free colicin E9 (2 nM) was added to the cis chamber of a bilayer apparatus in 10 mM Tris/HCl buffer at pH 7.5, containing 0.1 M NaCl and 10 mM CaCl 2 , and a potential difference (p.d.) applied across the membrane. Random, fluctuating current was observed that showed evidence of opening and closing events with conductance of the order of ~100 pS, although larger conductance states were also seen ( Fig. 1a). In order to identify the region(s) of the protein responsible for this a...

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“…Interestingly, the finding that OmpF and PhoE have an opposite voltage-dependence has provided an explanation for the observation that mutations at conserved residues had opposite effects on the voltage dependence ( Figure 1B): charge removal of negatively charged residues of L3 renders OmpF less voltage-sensitive, but PhoE more voltage-sensitive (30). Mutations of the positively charged amino acids cluster of the barrel wall also conferred an increased voltage-sensitivity to OmpF (30) or OmpC (56,69).…”

Section: Voltage Dependencementioning

confidence: 96%

Solute uptake through general porins

Delcour¹

2003

Front Biosci

110

104

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General diffusion porins are among the few membrane proteins that have been thoroughly investigated by many techniques, including X-ray crystallography, AFM microscopy, computer modeling, electrophysiology and biochemistry. This had led to a good understanding of the process of solute transport per se. However, other aspects of porin function remain enigmatic, such as the molecular basis and physiological relevance of many regulatory processes. After summarizing the most salient structural features, the review provides a description of the techniques used for the functional study of porins. The process of solute transport is presented on the basis of structure-function relationship and modeling studies. Three aspects of regulation are discussed: voltage-dependence, pH sensitivity and modulation by polycations and polyanions. The review ends with a perspective on future porin research, to be targeted at a molecular understanding of the regulatory processes, the deciphering of the physiological context in which these processes take place, and rational drug design.

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Altered voltage sensitivity of mutant OmpC porin channels

Cited by 14 publications

References 24 publications

Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field

Computational Modeling of Ion Transport in Bulk and through a Nanopore Using the Drude Polarizable Force Field

The cytotoxic domain of colicin E9 is a channel-forming endonuclease

Solute uptake through general porins

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