Rapid screening of membrane protein activity: electrophysiological analysis of OmpF reconstituted in proteoliposomes

Solvent-free planar lipid bilayers were formed in an automatic manner by bursting of giant unilamellar vesicles (GUVs) after gentle suction application through micron-sized apertures in a borosilicate glass substrate. Incubation of GUVs with the purified ion channel protein of interest yielded proteoliposomes. These proteoliposomes allow for immediate recording of channel activity after GUV sealing. This approach reduces the time-consuming, laborious and sometimes difficult protein reconstitution processes normally performed after bilayer formation. Bilayer recordings are attractive for investigations of membrane proteins not accessible to patch clamp analysis, like e.g. proteins from organelles. In the presented work, we show the example of the outer membrane protein OmpF from Escherichia coli. We reconstituted OmpF in proteoliposomes and observed the characteristic trimeric conductance levels and the typical gating induced by pH and transmembrane voltage. Moreover, OmpF is the main entrance for beta-lactam antibiotics and we investigated translocation processes of antibiotics and modulation of OmpF by spermine. We suggest that the rapid formation of porin containing lipid bilayers is of potential for the efficient electrophysiological characterization of the OmpF protein, for studying membrane permeation processes and for the rapid screening of antibiotics.     

A pH-tunable nanofluidic diode: electrochemical rectification in a reconstituted single ion channel

We report pH-dependent electrochemical rectification in a protein ion channel (the bacterial porin OmpF) reconstituted on a planar phospholipid membrane. The measurements performed at single-channel level show that the electric current is controlled by the protein fixed charge and it can be tuned by adjusting the local pH. Under highly asymmetric pH conditions, the channel behaves like a liquid diode. Unlike other nanofluidic devices that display also asymmetric conductance, here the microscopic charge distribution of the system can be explored by using the available high-resolution (2.4 A) channel crystallographic structure. Continuum electrostatics calculations confirm the hypothesized bipolar structure of the system. The selective titration of the channel residues is identified as the underlying physicochemical mechanism responsible for current rectification.     

Water diffusion through a membrane protein channel: a first passage time approach

Water diffusion through OmpF, a porin in the outer membrane of Escherichia coli, is studied by molecular dynamics simulation. A first passage time approach allows characterizing the diffusive properties of a well-defined region of this channel. A carbon nanotube, which is considerably more homogeneous, serves as a model to validate the methodology. Here we find, in addition to the expected regular behavior, a gradient of the diffusion coefficient at the channel ends, witness of the transition from confinement in the channel to bulk behavior in the connected reservoirs. Moreover, we observe the effect of a kinetic boundary layer, which is the counterpart of the initial ballistic regime in a mean square displacement analysis. The overall diffusive behavior of water in OmpF shows remarkable similarity with that in a homogeneous channel. However, a small fraction of the water molecules appears to be trapped by the protein wall for considerable lengths of time. The distribution of trapping times exhibits a broad power law distribution psi(tau) approximately tau (-2.4), up to tau=10 ns, a bound set by the length of the simulation run. We discuss the effect of this distribution on the dynamic properties of water in OmpF in terms of incomplete sampling of phase space.     

Electrostatic properties and macroscopic electrodiffusion in OmpF porin and mutants

The bacterial porin OmpF found in the outer membrane of E. coli is a wide channel, characterized by its poor selectivity and almost no ion specificity. It has an asymmetric structure, with relatively large entrances and a narrow constriction. By applying continuum electrostatic methods we determine the ionization states of titratable amino acid residues in the protein and calculate self-consistently the electric potential 3-D distribution within the channel. The average electrostatic properties are then represented by an effective fixed charge distribution along the pore which is the input for a macroscopic electrodiffusion model. The theoretical predictions agree with measurements performed under different salt gradients and pH. The sensitivity of reversal potential and conductance to the direction of the salt gradient and the solution pH is captured by the model. The theory is also able to explain the influence of the lipid membrane charge. The same methodology is satisfactorily applied to some OmpF mutants involving slight structural changes but a large number of net charges. The correlation found between atomic structure and ionic selectivity shows that the transport characteristics of wide channels like OmpF and its mutants are mainly regulated by the collective action of a large number of residues, rather than by the specific interactions of residues at particular locations.     

AC conductance of transmembrane protein channels. The number of ionized residue mobile counterions at infinite dilution

Simultaneous measurements of the AC and DC conductances of alpha-hemolysin (alphaHL) ion channels and outer membrane protein F (OmpF) porins in dilute ionic solutions is described. AC conductance measurements were performed by applying a 10 mV rms AC voltage across a suspended planar bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine in the absence and presence of the protein and detecting the AC current response using phase-sensitive lock-in techniques. The conductances of individual alphaHL channels and OmpF porins were measured in symmetric KCl solutions containing between 5 and 1000 mM KCl. The AC and DC conductances of each protein were in agreement for all solution conditions, demonstrating the reliability of the AC method in single-channel recordings. Linear plots of conductance versus bulk KCl concentration for both proteins extrapolate to significant nonzero conductances (0.150 +/- 0.050 nS and 0.028 +/- 0.008 nS for OmpF and alphaHL, respectively) at infinite KCl dilution. The infinite dilution conductances are ascribed to mobile counterions of the ionizable residues within the protein lumens. A method of analyzing the plots of conductance vs KCl concentration is introduced that allows the determination of the concentration of mobile counterions associated with ionizable groups without knowledge of either the protein geometry or the ion mobilities. At neutral pH, an equivalent of 3 mobile counterions (K+ or Cl-) is estimated to contribute to the conductivity of the alphaHL channel.     

Chemosensing Ensembles for Monitoring Biomembrane Transport in Real Time

The efficacy of drugs and biomolecules relies on their ability to pass through the bilayer. The development of methods to directly and sensitively monitor these membrane transport processes has remained an experimental challenge. A macrocyclic host (p‐sulfonatocalix[4]arene or cucurbit[7]uril) and a fluorescent dye (lucigenin or berberine) are encapsulated as a chemosensing ensemble inside liposomes, which allows for a direct, real‐time fluorescence monitoring of the passage of unlabeled bioorganic analytes. This in vitro assay is transferable to different channel proteins and analytes, has potential for fluorescence‐based screening, e.g., of channel modulators, and yields the absolute kinetics of translocation. Using this new biophysical method, we observed for the first time direct rapid translocation of protamine, an antimicrobial peptide, through the bacterial transmembrane protein OmpF.     

Divalent cations reduce the pH sensitivity of OmpF channel inducing the pK(a) shift of key acidic residues

In contrast to the highly-selective channels of neurophysiology employing mostly the exclusion mechanism, different factors account for the selectivity of large channels. Elucidation of these factors is essential for understanding the permeation mechanisms in ion channels and their regulation in vivo. The interaction between divalent cations and a protein channel, the bacterial porin OmpF, has been investigated paying attention to the channel selectivity and its dependence on the solution pH. Unlike the experiments performed in salts of monovalent cations, the channel is now practically insensitive to pH, being anion selective all over the pH range considered. Electrostatic calculations based on the available structural data suggest that the binding of divalent cations has two main effects: (i) the pK(a) values of key ionizable groups differ significantly from those of the isolated groups in solution and (ii) the cation binding has a decisive impact on the effective electric charge regulating the channel selectivity. A simple molecular model based on statistical thermodynamics provides additional qualitative explanations to the experimental findings that could also be useful for other related systems like synthetic nanopores, ion exchange membranes, and polyelectrolyte multilayers.     

Facilitated permeation of antibiotics across membrane channels--interaction of the quinolone moxifloxacin with the OmpF channel

The facilitated influx of moxifloxacin through the most abundant channel in the outer cell wall of gram-negative bacteria was investigated. Molecular modeling provided atomic details of the interaction with the channel surface, revealed the preferred orientation of the antibiotic along its pathway, and gave an estimated time necessary for translocation. High-resolution conductance measurements on single OmpF trimers allowed the passages of individual moxifloxacin molecules to be counted. The average mean residence time of 50 micros is in agreement with the predicted strong interaction from the modeling. In contrast, control measurements with nalidixic acid, a hydrophobic antibiotic that rather permeates across the lipid membrane, revealed a negligible interaction. The spectral overlap of tryptophan with moxifloxacin was suitable for a FRET study of the protein-antibiotic interaction. Combining molecular dynamics simulations with selective quenching identified an interaction of moxifloxacin with Trp61 inside the OmpF channel, whereas nalidixic acid showed preferential interaction with Trp214 on the channel exterior. An understanding of the detailed molecular interactions between the antibiotic and its preferred channel may be used to develop new antibiotics with improved uptake kinetics.     

Impedance spectroscopy of OmpF porin reconstituted into a mercury-supported lipid bilayer

The channel-forming protein OmpF porin was incorporated in a biomimetic membrane consisting of a lipid bilayer tethered to a mercury electrode via a thiolipid, and it was investigated in aqueous KCl by electrochemical impedance spectroscopy. The impedance spectra, recorded from 1 x 10(-2) to 1 x 10(5) Hz over a potential range of 0.7 V, were fitted to an equivalent circuit consisting of four RC meshes. The dependence of the resulting circuit elements upon the applied potential was interpreted on the basis of a general approximate approach based on a model of the electrified interphase and on the kinetics of the translocation of potassium and chloride ions across the lipid bilayer, assisted by the OmpF porin.     

Electrophysiological Characterization of Transport Across Outer‐Membrane Channels from Gram‐Negative Bacteria in Presence of Lipopolysaccharides

Multi‐drug resistance in Gram‐negative bacteria is often associated with low permeability of the outer membrane. To investigate the role of membrane channels in the uptake of antibiotics, we present an approach using fusion of native outer membrane vesicles (OMVs) into a planar lipid bilayer, allowing characterization of membrane protein channels in their native environment. Two major membrane channels from E. coli, OmpF and OmpC, were overexpressed from the host and the corresponding OMVs were collected. Each OMV fusion surprisingly revealed only single or few channel activities. The asymmetry of the OMVs translates after fusion into the lipid membrane with the lipopolysaccharides (LPS) dominantly present at the side of OMV addition. Compared to the conventional reconstitution method, the channels fused from OMVs containing LPS have similar conductance but a much broader distribution and significantly lower permeation. We suggest using outer membrane vesicles for functional and structural studies of membrane channels in the native membrane.     

Characterization of the refolding and reassembly of an integral membrane protein OmpF porin by low-angle laser light scattering photometry coupled with high-performance gel chromatography

The refolding and reassembly of an integral membrane protein OmpF porin denatured in sodium dodecylsulfate (SDS) into its stable species by the addition of n-octyl-beta-D-glucopyranoside (OG) have been studied by means of circular dichroism (CD) spectroscopy and low-angle laser light scattering photometry coupled with high-performance gel chromatography. The minimal concentration where change in the secondary structure was induced by the addition of OG was found to be 6.0 mg/ml in CD experiments. A species unfolded further than the SDS-denatured form of this protein was observed at an early stage (5-15 min) of refolding just above the minimal OG concentration. In addition, the CD spectrum of protein species obtained above the minimal OG concentration showed that the protein is composed of a beta-structure which is different from the native structure of this protein. In light scattering experiments, no changes in molecular assemblies were observed when the OG concentration was below its minimal refolding concentration determined by CD measurements. Above the minimal concentration, a compact monomeric species was observed when denatured OmpF porin was incubated for 5 min at 25 degrees C in a refolding medium containing 1 mg/ml SDS and 7 mg/ml OG, and then injected into columns equilibrated with the refolding medium. After an incubation of 24 h before injection into the columns, predominant dimerization of this protein was observed in addition to incorrect aggregation.     

Small‐Molecule Permeation across Membrane Channels: Chemical Modification to Quantify Transport across OmpF

Biological channels facilitate the exchange of molecules across membranes, but general tools to quantify transport are missing. Electrophysiology is the method of choice to study the functional properties of channels. However, analyzing the current fluctuation of channels typically does not identify successful transport, that is, distinguishing translocation from binding. To distinguish both processes, we added an additional barrier at the channel exit acting as a molecular counter. To identify permeation, we compare the molecule residence time in the native channel with one that is chemically modified at the exit. We use the well‐studied outer membrane channel from E. coli, OmpF. Position 181, which is below the constriction region, was subsequently mutated into cysteine (E181C) in an otherwise cysteine‐free system, then functionalized by covalent binding with one of the two blockers MTSES or GLT. We measured the passage of model peptides, mono‐, tri‐, hepta‐arginine and of norfloxacin, as an example for antibiotic permeation.     

Structure-based prediction of the conductance properties of ion channels

The HOLE procedure allows the prediction of the absolute conductance of an ion channel model from its structure. The original prediction method uses an empirically corrected Ohmic method. It is most successful, with predictions being reliable to within a factor of two. A new modification of the procedure is presented in which the self-diffusion coefficients of water molecules from molecular dynamics simulation are used to replace the empirical correction factor. A "prediction" of the conductance for the porin OmpF by the new method is made and shown to be very close to the experimental value. HOLE also allows the prediction of the effect that the addition of non-electrolyte polymers will have on channel conductance. The method has great potential to yield structural information from data provided by single channel recordings but needs further validation by making measurements on channels of known structure. Preliminary results are given of single channel records establishing the effects of non-electrolytes on the conductance of gramicidin D channels. As an example of the potential uses of the procedure application is made to examine the oligomerization of alpha-toxin (alpha-hemolysin) channels. A model for the alpha-toxin hexamer, based on the crystal structure for the heptamer, is generated using molecular mechanics methods. The compatibility of the structures with single channel conductance data is assessed using HOLE.     

Carbene Footprinting Reveals Binding Interfaces of a Multimeric Membrane‐Spanning Protein

Mapping the interaction sites between membrane‐spanning proteins is a key challenge in structural biology. In this study a carbene‐footprinting approach was developed and applied to identify the interfacial sites of a trimeric, integral membrane protein, OmpF, solubilised in micelles. The diazirine‐based footprinting probe is effectively sequestered by, and incorporated into, the micelles, thus leading to efficient labelling of the membrane‐spanning regions of the protein upon irradiation at 349 nm. Areas associated with protein–protein interactions between the trimer subunits remained unlabelled, thus revealing their location.     

Interaction of cephalosporins with outer membrane channels of Escherichia coli. Revealing binding by fluorescence quenching and ion conductance fluctuations

Outer membrane channels in gram-negative bacteria are implicated in the influx of the latest generation of cephalosporins. We have measured the interaction strengths of ceftriaxone, cefpirome and ceftazidime in the two most abundant outer membrane porins of Escherichia coli, OmpF and OmpC, by both ion current fluctuations through single protein channels and fluorescence quenching. Statistical analysis of individual antibiotic entry events in membrane-incorporated porins yielded the kinetic rates and the equilibrium binding constant of each antibiotic-porin pair. Affinity constants were independently obtained by measuring the static quenching of inherent tryptophan fluorescence in the porins in the presence of the antibiotics. Through an empirical inner filter effect correction we have succeeded in measuring the chemical interaction of these strongly absorbing antibiotics, and obtained a qualitative agreement with conductance measurements. The interaction of all three antibiotics is smaller for OmpC than OmpF, and in the case of each porin the interaction strength series ceftriaxone > cefpirome > ceftazidime is maintained.     

Detergent-associated solution conformations of helical and beta-barrel membrane proteins

Membrane proteins present major challenges for structural biology. In particular, the production of suitable crystals for high-resolution structural determination continues to be a significant roadblock for developing an atomic-level understanding of these vital cellular systems. The use of detergents for extracting membrane proteins from the native membrane for either crystallization or reconstitution into model lipid membranes for further study is assumed to leave the protein with the proper fold with a belt of detergent encompassing the membrane-spanning segments of the structure. Small-angle X-ray scattering was used to probe the detergent-associated solution conformations of three membrane proteins, namely bacteriorhodopsin (BR), the Ste2p G-protein coupled receptor from Saccharomyces cerevisiae, and the Escherichia coli porin OmpF. The results demonstrate that, contrary to the traditional model of a detergent-associated membrane protein, the helical proteins BR and Ste2p are not in the expected, compact conformation and associated with detergent micelles, while the beta-barrel OmpF is indeed embedded in a disk-like micelle in a properly folded state. The comparison provided by the BR and Ste2p, both members of the 7TM family of helical membrane proteins, further suggests that the interhelical interactions between the transmembrane helices of the two proteins differ, such that BR, like other rhodopsins, can properly refold to crystallize, while Ste2p continues to prove resistant to crystallization from an initially detergent-associated state.     

Alteration in the electrophoretic mobility of OmpC due to variations in the ammonium persulfate concentration in sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

Studies on Salmonella typhi and Salmonella typhimurium outer membrane proteins have shown that the relative position of OmpC porin in sodium dodecyl sulfate.polyacrylamide gel electrophoresis undergoes an important shift when the concentration of ammonium persulfate in the running gel is increased from 6 to 12 mM. The apparent molecular mass at these concentrations was estimated to be 34 and 40 kDa, respectively. Under similar electrophoretic conditions the apparent molecular mass estimated for OmpF was 37.6 and 38.2 kDa. Therefore, OmpC moves from a leading position to a position behind OmpF. For Escherichia coli OmpC the shift observed is less pronounced than that occurring in Salmonellae.     

Cover Picture: On the Function and Structure of Synthetically Modified Porins (Angew. Chem. Int. Ed. 26/2009)

Synthetic Modulators are introduced into the trimeric porin OmpF by protein semisynthesis/click chemistry or by S‐alkylation, as U. Koert, L.‐O. Essen et al. report in their Communication on page 4853 ff. The choice of synthetic modulator and the type of covalent attachment significantly affect the blockage efficiency. A model for the functional properties is postulated on the basis of an X‐ray structure analysis of a crown ether/OmpF hybrid.

     

Rinse and evaporation coating of poly(methyl methacrylate) microchip for separation of sodium dodecyl sulfate-protein complex

We developed a novel channel wall coating on a poly(methyl methacrylate) (PMMA) microchip using methylcellulose (MC) as a coating reagent to suppress electroosmotic flow (EOF) following the strong analytes adsorption via hydrophobic interaction with channel walls of PMMA. Our coating was obtained by first rinsing channel walls with MC-containing aqueous solution followed by evaporation. The coating made the hydrophilic channel wall lowering EOF by two orders of magnitude (1.2 x 10(-5)cm(2)V(-1)s(-1)) as well as reducing the hydrophobic adsorption. On the coated channel walls, we successfully separated sodium dodecyl sulfate-protein complexes with high reproducibility and efficiency using dextran as a lower viscosity protein separation medium.     

Specific binding of adamantane drugs and direction of their polar amines in the pore of the influenza M2 transmembrane domain in lipid bilayers and dodecylphosphocholine micelles determined by NMR spectroscopy

The transmembrane domain of the influenza M2 protein (M2TM) forms a tetrameric proton channel important for the virus lifecycle. The proton-channel activity is inhibited by amine-containing adamantyl drugs amantadine and rimantadine, which have been shown to bind specifically to the pore of M2TM near Ser31. However, whether the polar amine points to the N- or C-terminus of the channel has not yet been determined. Elucidating the polar group direction will shed light on the mechanism by which drug binding inhibits this proton channel and will facilitate rational design of new inhibitors. In this study, we determine the polar amine direction using M2TM reconstituted in lipid bilayers as well as dodecylphosphocholine (DPC) micelles. (13)C-(2)H rotational-echo double-resonance NMR experiments of (13)C-labeled M2TM and methyl-deuterated rimantadine in lipid bilayers showed that the polar amine pointed to the C-terminus of the channel, with the methyl group close to Gly34. Solution NMR experiments of M2TM in DPC micelles indicate that drug binding causes significant chemical shift perturbations of the protein that are very similar to those seen for M2TM and M2(18-60) bound to lipid bilayers. Specific (2)H-labeling of the drugs permitted the assignment of drug-protein cross peaks, which indicate that amantadine and rimantadine bind to the pore in the same fashion as for bilayer-bound M2TM. These results strongly suggest that adamantyl inhibition of M2TM is achieved not only by direct physical occlusion of the channel, but also by perturbing the equilibrium constant of the proton-sensing residue His37. The reproduction of the pharmacologically relevant specific pore-binding site in DPC micelles, which was not observed with a different detergent, DHPC, underscores the significant influence of the detergent environment on the functional structure of this membrane protein.