Electrostatic properties and macroscopic electrodiffusion in OmpF porin and mutants

Aguilella‐Arzo, Marcel; García-Celma, Juan J.; Cervera, Javier; Alcaraz, Antonio; Aguilella, Vicente M.

doi:10.1016/j.bioelechem.2006.04.005

Cited by 43 publications

(96 citation statements)

References 33 publications

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“…The property of porins in distinguishing charged ions, known as ion selectivity, have been studied extensively and is greatly affected by the electrostatics due to the presence of acidic and basic amino acid in the pore constriction zone of E. coli OmpF (Aguilella-Arzo et al, 2007;Benz et al, 1985;Lou et al, 1996;Phale et al, 2001;Saint et al, 1996). Recent crystal structure (Dhakshnamoorthy et al, 2009) and molecular dynamics study (Im and Roux, 2002a;Schirmer and Phale, 1999) of E. coli OmpF revealed that cations and anions follow separate pathway along the entire length of channel, indicating residues other than those present in the constriction zone might participate in the ion permeation (Vrouenraets and Miedema, 2010).…”

Section: Ion-selectivity Of S Typhi Ompfmentioning

confidence: 99%

Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi

Balasubramaniam

Arockiasamy

Kumar

et al. 2012

Journal of Structural Biology

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Section: Ion-selectivity Of S Typhi Ompfmentioning

confidence: 99%

Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi

Balasubramaniam

Arockiasamy

Kumar

et al. 2012

Journal of Structural Biology

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“…33 Aside from the commented disparity between bulk and pore water due to the confined geometry and the electrostatic interaction with protein residues, another interesting criticism pays attention to the nature of water in aqueous solutions, stressing that Booth's original model was developed for pure water and not for an electrolyte solution. 39 Keeping in mind that electrophysiological experiments with ion channels are typically performed at decimolar salt concentrations, the average number of ions inside the OmpF channel studied here is so small (two-three ions) 29 that we can overlook the above criticism. Only in this sense, such a diluted electrolyte should not differ too much from pure water.…”

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confidence: 97%

Dielectric saturation of water in a membrane protein channel

Aguilella‐Arzo

Andrio

Aguilella

et al. 2009

Phys. Chem. Chem. Phys.

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Water molecules in confined geometries like nanopores and biological ion channels exhibit structural and dynamical properties very different from those found in free solution. Protein channels that open aqueous pores through biological membranes provide a complex spatial and electrostatic environment that decreases the translational and rotational mobility of water molecules, thus altering the effective dielectric constant of the pore water. By using the Booth equation, we study the effect of the large electric field created by ionizable residues of an hour-glass shaped channel, the bacterial porin OmpF, on the pore water dielectric constant, e w . We find a space-dependent significant reduction (down to 20) of e w that may explain some ad hoc assumptions about the dielectric constant of the protein and the water pore made to reconcile model calculations with measurements of permeation properties and pK a 's of protein residues. The electric potential calculations based on the OmpF protein atomic structure and the Booth field-dependent dielectric constant show that protein dielectric constants ca. 10 yield good agreement with molecular dynamics simulations as well as permeation experiments.

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“…27 The fixed charge distribution is obtained from the 3D structure and free solution ionic diffusion coefficients are used. 30 The model calculations show the total current (green) and the individual currents carried by each ion (K þ in red and Cl À in blue). Positive values of I K and negative values of I Cl correspond, respectively, to uphill transport of the respective ion.…”

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confidence: 99%

Electrical pumping of potassium ions against an external concentration gradient in a biological ion channel

Queralt-Martín

García-Giménez

Aguilella

et al. 2013

Applied Physics Letters

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We show experimentally and theoretically that significant currents can be obtained with a biological ion channel, the OmpF porin of Escherichia coli, using zero-average potentials as driving forces. The channel rectifying properties can be used to pump potassium ions against an external concentration gradient under asymmetric pH conditions. The results are discussed in terms of the ionic selectivity and rectification ratio of the channel. The physical concepts involved may be applied to separation processes with synthetic nanopores and to bioelectrical phenomena. Ratchet systems have the ability of rectifying unbiased fluctuations into directed transport. 1-3 Both synthetic and biological nanochannels may show non-zero electrical currents driven by zero-average time dependent forces. [4][5][6][7] The electrical rectification is on the basis of the observed phenomena 4,5,8,9 and the potential applications concern separation processes and energy conversion. 10-12 Electrical rectification and ratchet phenomena can also be of relevance for signal averaging of weak electric fields and cell plasticity because ion channels, together with ion pumps and gap junction complexes, play a crucial role in cell communication and control. [13][14][15][16] In this Letter, we present measurements and model calculations of the rectifying properties of a biological ion channel (the outer membrane protein F, OmpF, a porin expressed in Escherichia coli bacteria 17 ). We consider the pH-controlled net current induced by zero-average oscillating potentials and the electrical pumping of potassium ions against an external concentration gradient, a phenomenon previously reported in synthetic nanopores. 4,5 We show that the complex interplay between the current rectification and the channel ionic selectivity is crucial for understanding the uphill transport of ions. The results are of relevance for the mechanisms regulating the transport through ion channels, [17][18][19] for electric signal transduction in cell cycle and embryogenesis, 14,16 and for building ionic circuits in the emerging field of nanofluidics. 6,[20][21][22][23][24][25] The set-up used in the experiments is shown schematically in Fig. 1. A single OmpF ion channel is reconstituted on a planar lipid bilayer and communicates the two halves of a conductivity cell filled with KCl solutions of concentrations c cis (side of protein addition) and c trans . pH cis and pH trans denote the corresponding pH values. A detailed description of the reconstitution procedure can be found elsewhere. 17,26 The electric potential V is positive when it is higher at the trans side of the membrane cell. An Axopatch 200B amplifier (Molecular Devices, Sunnyvale, CA) in the voltage-clamp mode is used for measuring both V and the electric current (I) through the channel. I is positive when it flows from solution trans to solution cis in Fig. 1.The OmpF porin contains both basic (positive) and acidic (negative) residues, 27 and thus, the net charge of the channel depends on the ionization state of th...

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Electrostatic properties and macroscopic electrodiffusion in OmpF porin and mutants

Cited by 43 publications

References 33 publications

Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi

Asymmetric pore occupancy in crystal structure of OmpF porin from Salmonella typhi

Dielectric saturation of water in a membrane protein channel

Electrical pumping of potassium ions against an external concentration gradient in a biological ion channel

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