Activity of Single Insect Olfactory Receptors Triggered by Airborne Compounds Recorded in Self-Assembled Tethered Lipid Bilayer Nanoarchitectures

Membrane proteins are among the most difficult to study as they are embedded in the cellular membrane, a complex and fragile environment with limited experimental accessibility. To study membrane proteins outside of these environments, model systems are required that replicate the fundamental properties of the cellular membrane without its complexity. We show here a self-assembled lipid bilayer nanoarchitecture on a solid support that is stable for several days at room temperature and allows the measurement of insect olfactory receptors at the single-channel level. Using an odorant binding protein, we capture airborne ligands and transfer them to an olfactory receptor from Drosophila melanogaster (OR22a) complex embedded in the lipid membrane, reproducing the complete olfaction process in which a ligand is captured from air and transported across an aqueous reservoir by an odorant binding protein and finally triggers a ligand-gated ion channel embedded in a lipid bilayer, providing direct evidence for ligand capture and olfactory receptor triggering facilitated by odorant binding proteins. This model system presents a significantly more user-friendly and robust platform to exploit the extraordinary sensitivity of insect olfaction for biosensing. At the same time, the platform offers a new opportunity for label-free studies of the olfactory signaling pathways of insects, which still have many unanswered questions.

Molecular dynamics simulations of the dielectric constants of salt-free and salt-doped polar solvents

We develop a Stockmayer fluid model that accounts for the dielectric responses of polar solvents (water, MeOH, EtOH, acetone, 1-propanol, DMSO, and DMF) and NaCl solutions. These solvent molecules are represented by Lennard-Jones (LJ) spheres with permanent dipole moments and the ions by charged LJ spheres. The simulated dielectric constants of these liquids are comparable to experimental values, including the substantial decrease in the dielectric constant of water upon the addition of NaCl. Moreover, the simulations predict an increase in the dielectric constant when considering the influence of ion translations in addition to the orientation of permanent dipoles.

Biphasic concentration patterns in ionic transport under nanoconfinement revealed in steady-state and time-dependent properties

Ion permeation across nanoscopic structures differs considerably from microfluidics because of strong steric constraints, transformed solvent properties, and charge-regulation effects revealed mostly in diluted solutions. However, little is known about nanofluidics in moderately concentrated solutions, which are critically important for industrial applications and living systems. Here, we show that nanoconfinement triggers general biphasic concentration patterns in a myriad of ion transport properties by using two contrasting systems: a biological ion channel and a much larger synthetic nanopore. Our findings show a low-concentration regime ruled by classical Debye screening and another one where ion-ion correlations and enhanced ion-surface interactions contribute differently to each electrophysiological property. Thus, different quantities (e.g., conductance vs noise) measured under the same conditions may appear contradictory because they belong to different concentration regimes. In addition, non-linear effects that are barely visible in bulk conductivity only in extremely concentrated solutions become apparent in nanochannels around physiological conditions.

Design and directed evolution of noncanonical β-stereoselective metalloglycosidases

Metallohydrolases are ubiquitous in nearly all subclasses of hydrolases, utilizing metal elements to activate a water molecule and facilitate its subsequent dissociation of diverse chemical bonds. However, such a catalytic role of metal ions is rarely found with glycosidases that hydrolyze the glycosidic bonds in sugars. Herein, we design metalloglycosidases by constructing a hydrolytically active Zn-binding site within a barrel-shaped outer membrane protein OmpF. Structure- and mechanism-based redesign and directed evolution have led to the emergence of Zn-dependent glycosidases with catalytic proficiency of 2.8 × 10⁹ and high β-stereoselectivity. Biochemical characterizations suggest that the Zn-binding site constitutes a key catalytic motif along with at least one adjacent acidic residue. This work demonstrates that unprecedented metalloenzymes can be tailor-made, expanding the scope of inorganic reactivities in proteinaceous environments, resetting the structural and functional diversity of metalloenzymes, and providing the potential molecular basis of unidentified metallohydrolases and novel whole-cell biocatalysts.

Blocker Effect on Diffusion Resistance of a Membrane Channel: Dependence on the Blocker Geometry

Being motivated by recent progress in nanopore sensing, we develop a theory of the effect of large analytes, or blockers, trapped within the nanopore confines, on diffusion flow of small solutes. The focus is on the nanopore diffusion resistance which is the ratio of the solute concentration difference in the reservoirs connected by the nanopore to the solute flux driven by this difference. Analytical expressions for the diffusion resistance are derived for a cylindrically symmetric blocker whose axis coincides with the axis of a cylindrical nanopore in two limiting cases where the blocker radius changes either smoothly or abruptly. Comparison of our theoretical predictions with the results obtained from Brownian dynamics simulations shows good agreement between the two.

Computational Insights into the Role of External and Local Electric Fields in Macrocyclic Chemical and Biological Systems

The investigation of the role of the electric field in systems of widespread interest employing computational techniques is an emerging area of research. The outcome of applying an oriented external electric field (OEEF) on the geometric and electronic properties of the chemically unique π-conjugated cyclic carbon ring compounds has been explored with density functional theory (DFT). Distinct changes in the structural and electronic features of such ring compounds are observed upon the application of OEEFs. Importantly, the calculations indicate that a mixed aliphatic-aromatic conjugated ring converts from a singlet to a triplet after the application of an OEEF, suggesting potential applications in optoelectronics for such molecules, without the need for photochemically induced change in the spin state. Furthermore, the influence of built-in local electric fields (LEFs) present in naturally occurring macrocyclic systems such as valinomycin has also been explored. Static and ab initio molecular dynamics (AIMD) calculations indicate that LEFs are the primary driving factor in determining the energetically favoured position of counter anions such as chloride (Cl^- ) in the potassium (K⁺ ) and sodium (Na⁺ ) coordinated valinomycin macrocycle structures: they exist inside the cage in the case of K⁺ sequestration by valinomycin and outside for Na⁺ . This divergence has been proposed to be the determining factor for the selectivity of the valinomycin macrocycle for binding a K⁺ cation over Na⁺ .

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.

Bicarbonate permeation through anion channels: its role in health and disease

Many anion channels, frequently referred as Cl^- channels, are permeable to different anions in addition to Cl^-. As the second-most abundant anion in the human body, HCO₃^- permeation via anion channels has many important physiological roles. In addition to its classical role as an intracellular pH regulator, HCO₃^- also controls the activity and stability of dissolved proteins in bodily fluids such as saliva, pancreatic juice, intestinal fluid, and airway surface liquid. Moreover, HCO₃^- permeation through these channels affects membrane potentials that are the driving forces for transmembrane transport of solutes and water in epithelia and affect neuronal excitability in nervous tissue. Consequently, aberrant HCO₃^- transport via anion channels causes a number of human diseases in respiratory, gastrointestinal, genitourinary, and neuronal systems. Notably, recent studies have shown that the HCO₃^- permeabilities of several anion channels are not fixed and can be altered by cellular stimuli, findings which may have both physiological and pathophysiological significance. In this review, we summarize recent progress in understanding the molecular mechanisms and the physiological roles of HCO₃^- permeation through anion channels. We hope that the present discussions can stimulate further research into this very important topic, which will provide the basis for human disorders associated with aberrant HCO₃^- transport.

Effect of a post-translational modification mimic on protein translocation through a nanopore

Post-translational modifications (PTMs) of proteins are recognized as crucial components of cell signaling pathways through modulating folding, altering stability, changing interactions with ligands, and, therefore, serving multiple regulatory functions. PTMs occur as covalent modifications of the protein's amino acid side chains or the length and composition of their termini. Here we study the functional consequences of PTMs for α-synuclein (αSyn) interactions with the nanopore of the voltage-dependent anion channel (VDAC) of the outer mitochondrial membrane. PTMs were mimicked by a divalent Alexa Fluor 488 sidechain attached separately at two positions on the αSyn C-terminus. Using single-channel reconstitution into planar lipid membranes, we find that such modifications change interactions drastically in both efficiency of VDAC inhibition by αSyn and its translocation through the VDAC nanopore. Analysis of the on/off kinetics in terms of an interaction "quasipotential" allows the positions of the C-terminal modifications to be determined with an accuracy of about three residues. Moreover, our results uncover a previously unobserved mechanism by which cytosolic proteins control β-barrel channels and thus a new regulatory function for PTMs.

Mapping Intrachannel Diffusive Dynamics of Interacting Molecules onto a Two-Site Model: Crossover in Flux Concentration Dependence

This study focuses on how interactions of solute molecules affect the concentration dependence of their flux through narrow membrane channels. It is assumed that the molecules cannot bypass each other because of their hard-core repulsion. In addition, other short- and long-range solute-solute interactions are included into consideration. These interactions make it impossible to develop an analytical theory for the flux in the framework of a diffusion model of solute dynamics in the channel. To overcome this difficulty, we course-grain the diffusion model by mapping it onto a two-site one, where the rate constants describing the solute dynamics are expressed in terms of the parameters of the initial diffusion model. This allows us (i) to find an analytical solution for the flux as a function of the solute concentration and (ii) to characterize the solute-solute interactions by two dimensionless parameters. Such a characterization proves to be very informative as it results in a clear classification of the effects of the solute-solute interactions on the concentration dependence of the flux. Unexpectedly, this dependence can be nonmonotonic, exhibiting a sharp maximum in a certain parameter range. We hypothesize that such a behavior may constitute an element of a regulatory mechanism, wherein maximal flux reports on the optimal solute concentration in the bulk near the channel entrance.

Variation of the Fermi level and the electrostatic force of a metallic nanoparticle upon colliding with an electrode

When a metallic nanoparticle (NP) comes in close contact with an electrode, its Fermi level equilibrates with that of the electrode if their separation is less than the cut-off distance for electron tunnelling. In the absence of chemical reactions in solution, the charge on the metallic nanoparticle is constant outside this range before or after the collision. However, the double layer capacitances of both the electrode and the NP are influenced by each other, varying as the function of distance. Because the charge on the nanoparticle is constant, the outer potential of the metallic NP and hence its Fermi level varies as the capacitance changes. This effect is more pronounced for small particles (<10 nm) in diluted supporting electrolyte solutions, especially if the metallic nanoparticle and the electrode have different potentials of zero charge. Nanoparticles were found to be more electrochemically active in the vicinity of the electrode. For example, the outer potential of a positively-polarized 2 nm radius NP was predicted to decrease by 35 mV or 100 mV (depending on the electrostatic model used to describe the electric double layer), when the NP moved from an electrode at 1 V (vs. its pzc) to the bulk. The force between the equilibrated NP and the electrode is always repulsive when they have the same pzc. Otherwise there can be an attraction even when the NP and the electrode carry charges of the same sign, due to the redistibution of surface charge density at both the NP and electrode surface.

Macroscopic electric field inside water-filled biological nanopores

Multi-drug resistance bacteria are a challenging problem of contemporary medicine. This is particularly critical for Gram-negative bacteria, where antibiotics are hindered by the outer membrane to reach internal targets. Here more polar antibiotics make use of nanometric water-filled channels to permeate inside. We present in this work a computational all-atom approach, using water as a probe, for the calculation of the macroscopic electric field inside water-filled channels. The method allows one to compare not only different systems but also the same system under different conditions, such as pH and ion concentration. This provides a detailed picture of electrostatics in biological nanopores shedding more light on how the charged residues of proteins determine the electric field inside, and also how medium can tune it. These details are central to unveil the filtering mechanism behind the permeation of small polar molecules through nanometric water-filled channels.

Contact Potentials, Fermi Level Equilibration, and Surface Charging

This article focuses on contact electrification from thermodynamic equilibration of the electrochemical potential of the electrons of two conductors upon contact. The contact potential difference generated in bimetallic macro- and nanosystems, the Fermi level after the contact, and the amount and location of the charge transferred from one metal to the other are discussed. The three geometries considered are spheres in contact, Janus particles, and core-shell particles. In addition, the force between the two spheres in contact with each other is calculated and is found to be attractive. A simple electrostatic model for calculating charge distribution and potential profiles in both vacuum and an aqueous electrolyte solution is described. Immersion of these bimetallic systems into an electrolyte solution leads to the formation of an electric double layer at the metal-electrolyte interface. This Fermi level equilibration and the associated charge transfer can at least partly explain experimentally observed different electrocatalytic, catalytic, and optical properties of multimetallic nanosystems in comparison to systems composed of pure metals. For example, the shifts in the surface plasmon resonance peaks in bimetallic core-shell particles seem to result at least partly from contact charging.

Pore dilatation increases the bicarbonate permeability of CFTR, ANO1 and glycine receptor anion channels

KEY POINTS

Cellular stimuli can modulate the ion selectivity of some anion channels, such as CFTR, ANO1 and the glycine receptor (GlyR), by changing pore size. Ion selectivity of CFTR, ANO1 and GlyR is critically affected by the electric permittivity and diameter of the channel pore. Pore size change affects the energy barriers of ion dehydration as well as that of size-exclusion of anion permeation. Pore dilatation increases the bicarbonate permeability (P HC O3/ Cl ) of CFTR, ANO1 and GlyR. Dynamic change in P HC O3/ Cl may mediate many physiological and pathological processes.

ABSTRACT

Chloride (Cl(-) ) and bicarbonate (HCO3 (-) ) are two major anions and their permeation through anion channels plays essential roles in our body. However, the mechanism of ion selection by the anion channels is largely unknown. Here, we provide evidence that pore dilatation increases the bicarbonate permeability (P HC O3/ Cl ) of anion channels by reducing energy barriers of size-exclusion and ion dehydration of HCO3 (-) permeation. Molecular, physiological and computational analyses of major anion channels, such as cystic fibrosis transmembrane conductance regulator (CFTR), anoctamin-1(ANO1/TMEM16A) and the glycine receptor (GlyR), revealed that the ion selectivity of anion channels is basically determined by the electric permittivity and diameter of the pore. Importantly, cellular stimuli dynamically modulate the anion selectivity of CFTR and ANO1 by changing the pore size. In addition, pore dilatation by a mutation in the pore-lining region alters the anion selectivity of GlyR. Changes in pore size affected not only the energy barriers of size exclusion but that of ion dehydration by altering the electric permittivity of water-filled cavity in the pore. The dynamic increase in P HC O3/ Cl by pore dilatation may have many physiological and pathophysiological implications ranging from epithelial HCO3 (-) secretion to neuronal excitation.

Selectivity of Protein Ion Channels and the Role of Buried Charges. Analytical Solutions, Numerical Calculations, and MD Simulations

The preference of large protein ion channels for cations or anions is mainly determined by the electrostatic interactions of mobile ions with charged residues of the protein. Here we discuss the widely spread paradigm that the charges determining the channel selectivity are only those that can be considered solvent-accessible because of their location near the permeation pathways of ions and water molecules. Theoretical predictions for the electric potential and average ion densities inside the pore are presented using several approaches of increasing resolution: from analytical and numerical solutions of electrostatic equations in a model channel up to all-atom molecular dynamics simulations and continuum electrostatic calculations performed in a particular biological channel, the bacterial porin OmpF. The results highlight the role of protein dieletric properties and the importance of the initial choice of the residue ionization states in the understanding of the molecular basis of large channel selectivity irrespective of the level of resolution of the computational approach used.

Journey of poly-nucleotides through OmpF porin

OmpF is an abundant porin in many bacteria which attracts attention as a promising biological nanopore for DNA sequencing. We study the interactions of OmpF with pentameric poly-nucleotides (poly-Ns) in silico. The poly-N molecule is forced to translocate through the lumen of OmpF. Subsequently, the structural and dynamical effects of translocation steps on protein and poly-N molecules are explored in detail. The external loops of OmpF are introduced as the main region for discrimination of poly-Ns based on their organic bases. Structural network analyses of OmpF in the presence or absence of poly-Ns characterize special residues in the structural network of porin. These residues pave the way for engineering OmpF protein. The poly-N-specific pattern of OmpF's local conductance is detected in the current study. Computing the potential of mean force for translocation steps, we define the energetic barrier ahead of poly-N to move through OmpF's lumen. We suggest that fast translocation of the examined poly-N molecules through OmpF seems unattainable by small external driving forces. Our computational results suggest some abilities for OmpF porin like OmpF's potential for being used in poly-N sequencing.

Dielectric constant of liquids confined in the extended nanospace measured by a streaming potential method

Understanding liquid structure and the electrical properties of liquids confined in extended nanospaces (10-1000 nm) is important for nanofluidics and nanochemistry. To understand these liquid properties requires determination of the dielectric constant of liquids confined in extended nanospaces. A novel dielectric constant measurement method has thus been developed for extended nanospaces using a streaming potential method. We focused on the nonsteady-state streaming potential in extended nanospaces and successfully measured the dielectric constant of liquids within them without the use of probe molecules. The dielectric constant of water was determined to be significantly reduced by about 3 times compared to that of the bulk. This result contributes key information toward further understanding of the chemistry and fluidics in extended nanospaces.

Cationic PAMAM dendrimers as pore-blocking binary toxin inhibitors

Dendrimers are unique highly branched macromolecules with numerous groundbreaking biomedical applications under development. Here we identified poly(amido amine) (PAMAM) dendrimers as novel blockers for the pore-forming B components of the binary anthrax toxin (PA63) and Clostridium botulinum C2 toxin (C2IIa). These pores are essential for delivery of the enzymatic A components of the internalized toxins from endosomes into the cytosol of target cells. We demonstrate that at low μM concentrations cationic PAMAM dendrimers block PA63 and C2IIa to inhibit channel-mediated transport of the A components, thereby protecting HeLa and Vero cells from intoxication. By channel reconstitution and high-resolution current recording, we show that the PAMAM dendrimers obstruct transmembrane PA63 and C2IIa pores in planar lipid bilayers at nM concentrations. These findings suggest a new potential role for the PAMAM dendrimers as effective polyvalent channel-blocking inhibitors, which can protect human target cells from intoxication with binary toxins from pathogenic bacteria.

Membrane potential generated by ion adsorption

It has been widely acknowledged that the Goldman-Hodgkin-Katz (GHK) equation fully explains membrane potential behavior. The fundamental facet of the GHK equation lies in its consideration of permeability of membrane to ions, when the membrane serves as a separator for separating two electrolytic solutions. The GHK equation describes that: variation of membrane permeability to ion in accordance with ion species results in the variation of the membrane potential. However, nonzero potential was observed even across the impermeable membrane (or separator) separating two electrolytic solutions. It gave rise to a question concerning the validity of the GHK equation for explaining the membrane potential generation. In this work, an alternative theory was proposed. It is the adsorption theory. The adsorption theory attributes the membrane potential generation to the ion adsorption onto the membrane (or separator) surface not to the ion passage through the membrane (or separator). The computationally obtained potential behavior based on the adsorption theory was in good agreement with the experimentally observed potential whether the membrane (or separator) was permeable to ions or not. It was strongly speculated that the membrane potential origin could lie primarily in the ion adsorption on the membrane (or separator) rather than the membrane permeability to ions. It might be necessary to reconsider the origin of membrane potential which has been so far believed explicable by the GHK equation.

Electrostatic interactions drive the nonsteric directional block of OmpF channel by La3+

Ion channels regulate the transport of molecules and the electric signal transduction in living cells by means of complex and even highly sophisticated mechanisms. We focus here on the crucial role that polyvalent ions, well-known modulators of many biological nanosystems, play in ion channel function. In particular, we show that trace amounts of lanthanum are able to block the bacterial porin OmpF, a large biological pore of Escherichia coli wide enough to exchange antibiotics and other larger molecules. The underlying mechanism has a strong directional character: it is sensitive to the sign of the applied voltage and to the side of the blocker addition. We explore these channel features by combining planar lipid bilayer electrophysiology at the single channel level, site-directed mutagenesis, and inductively coupled plasma mass spectrometry (ICP-MS). In contrast to other well-described channel blockers, which seem to occlude the narrower part of the pore, we envisage a nonsteric mechanism based on electrostatic interactions.

Electromagnetic fields (UHF) increase voltage sensitivity of membrane ion channels; possible indication of cell phone effect on living cells

The effects of ultra high frequency (UHF) nonionizing electromagnetic fields (EMF) on the channel activities of nanopore forming protein, OmpF porin, were investigated. The voltage clamp technique was used to study the single channel activity of the pore in an artificial bilayer in the presence and absence of the electromagnetic fields at 910 to 990 MHz in real time. Channel activity patterns were used to address the effect of EMF on the dynamic, arrangement and dielectric properties of water molecules, as well as on the hydration state and arrangements of side chains lining the channel barrel. Based on the varied voltage sensitivity of the channel at different temperatures in the presence and absence of EMF, the amount of energy transferred to nano-environments of accessible groups was estimated to address the possible thermal effects of EMF. Our results show that the effects of EMF on channel activities are frequency dependent, with a maximum effect at 930 MHz. The frequency of channel gating and the voltage sensitivity is increased when the channel is exposed to EMF, while its conductance remains unchanged at all frequencies applied. We have not identified any changes in the capacitance and permeability of membrane in the presence of EMF. The effect of the EMF irradiated by cell phones is measured by Specific Absorption Rate (SAR) in artificial model of human head, Phantom. Thus, current approach applied to biological molecules and electrolytes might be considered as complement to evaluate safety of irradiating sources on biological matter at molecular level.

Effects of electrical polarization on the opening rate constant of a voltage-gated ion channel

Ion channel gating kinetics can be described using Kramers' diffusion theory of reaction rates between several closed and open states, where transition rates between states depend exponentially on the membrane potential V. It has been suggested that transition rates have a more complex dependence on V at voltage extremes, but this has never been quantified. We measured the rate constant of the last closed to open transition in a voltage-gated ion channel and show that it does not depend exponentially on membrane potential at values of V greater than ≈150 mV. To explain this behavior, we estimate the effects of electrical polarization of the water contained in crevices within the channel protein, using an electrostatic model of the approximate three-dimensional geometry and the nonlinear effects of charges on the polarization of water.

Kinetics and thermodynamics of binding reactions as exemplified by anthrax toxin channel blockage with a cationic cyclodextrin derivative

The thermodynamics of binding reactions is usually studied in the framework of the linear van't Hoff analysis of the temperature dependence of the equilibrium constant. The logarithm of the equilibrium constant is plotted versus inverse temperature to discriminate between two terms: an enthalpic contribution that is linear in the inverse temperature, and a temperature-independent entropic contribution. When we apply this approach to a particular case-blockage of the anthrax PA(63) channel by a multicharged cyclodextrin derivative-we obtain a nearly linear behavior with a slope that is characterized by enthalpy of about 1 kcal/mol. In contrast, from blocker partitioning between the channel and the bulk, we estimate the depth of the potential well for the blocker in the channel to be at least 8 kcal/mol. To understand this apparent discrepancy, we use a simple model of particle interaction with the channel and show that this significant difference between the two estimates is due to the temperature dependence of the physical forces between the blocker and the channel. In particular, we demonstrate that if the major component of blocker-channel interaction is van der Waals interactions and/or Coulomb forces in water, the van't Hoff enthalpy of the binding reaction may be close to zero or even negative, including cases of relatively strong binding. The results are quite general and, therefore, of importance for studies of enzymatic reactions, rational drug design, small-molecule binding to proteins, protein-protein interactions, and protein folding, among others.

Redefining electrical double layer thickness in narrow confinements: effect of solvent polarization

In this paper we delineate the consequences of field-dependent solvent polarization in the electric double layer (EDL) electrostatic potential distribution, and the effective EDL thickness in narrow nanofluidic confinements with thick (or overlapping) EDLs. The EDL, formed at the interface between a charged substrate and an electrolyte solution, induces a large electric field spanning across few nanometer distances from the interface. As a result, a polar solvent like water gets polarized, making its relative permittivity a function of the EDL electric field. This affects the overall EDL electrostatic potential distribution and most importantly, leads to a significant reduction of the effective EDL thickness, with the extent of the reduction being dictated by the value of field independent EDL thickness, strength of the solvent polarization, and the substrate-liquid interfacial electrostatic potential. Such a finding will necessitate redefining the classical EDL thickness, which will be of overwhelming significance in nanofluidic transport.

Insights on the permeability of wide protein channels: measurement and interpretation of ion selectivity

Ion channels are hollow proteins that have evolved to exhibit discrimination between charged solutes. This property, known as ion selectivity is critical for several biological functions. By using the bacterial porin OmpF as a model system of wide protein channels, we demonstrate that significant insights can be gained when selectivity measurements are combined with electrodiffusion continuum models and simulations based on the atomic structure. A correct interpretation of the mechanisms ruling the many sources of channel discrimination is a first, indispensable step for the understanding of the controlled movement of ions into or out of cells characteristic of many physiological processes. We conclude that the scattered information gathered from several independent approaches should be appropriately merged to provide a unified and coherent picture of the channel selectivity.

Critical assessment of OmpF channel selectivity: merging information from different experimental protocols

The ion selectivity of a channel can be quantified in several ways by using different experimental protocols. A wide, mesoscopic channel, the OmpF porin of the outer membrane of E. coli, serves as a case study for comparing and analysing several measures of the channel cation-anion permeability in chlorides of alkali metals (LiCl, NaCl, KCl, CsCl). We show how different insights can be gained and integrated to rationalize the global image of channel selectivity. To this end, reversal potential, channel conductance and bi-ionic potential (two different salts with a common anion on each side of the channel but with the same concentration) experiments are discussed in light of an electrodiffusion model based on the Poisson-Nernst-Planck formalism. Measurements and calculations based on the atomic crystal structure of the channel show that each protocol displays a particular balance between the different sources of selectivity.

High electric field effects on gigahertz dielectric properties of water measured with microwave microfluidic devices

Silicon microstrip line devices with 260 nm planar microfluidic channels are fabricated and used to investigate water dielectric saturation effects. Microwave scattering parameter measurements are conducted from 1 to 16 GHz under different uniform dc electric fields. When the applied dc field is increased to approximately 1 MV/cm, the measured transmission coefficient S(21) is increased up to 18 dB, which indicates a large change in water dielectric properties. Extracted water permittivity (epsilon=epsilon'+jepsilon") shows that epsilon' and epsilon" are changed up to 70% and 50%, respectively.

Overcharging below the nanoscale: multivalent cations reverse the ion selectivity of a biological channel

We report charge inversion within a nanoscopic biological protein ion channel in salts of multivalent ions. The presence of positive divalent and trivalent counterions reverses the cationic selectivity of the OmpF channel, a general diffusion porin located in the outer membrane of E. coli. We discuss the conditions under which charge inversion can be inferred from the change in sign of the measured quantity, the channel zero current potential. By comparing experimental results in protein channels whose charge has been modified after site-directed mutagenesis, the predictions of current theories of charge inversion are critically examined. It is emphasized that charge inversion does not necessarily increase with the bare surface charge density of the interface and that even this concept of surface charge density may become meaningless in some biological ion channels. Thus, any theory based on electrostatic correlations or chemical binding should explicitly take into account the particular structure of the charged interface.

Protein structure and ionic selectivity in calcium channels: selectivity filter size, not shape, matters

Calcium channels have highly charged selectivity filters (4 COO(-) groups) that attract cations in to balance this charge and minimize free energy, forcing the cations (Na(+) and Ca(2+)) to compete for space in the filter. A reduced model was developed to better understand the mechanism of ion selectivity in calcium channels. The charge/space competition (CSC) mechanism implies that Ca(2+) is more efficient in balancing the charge of the filter because it provides twice the charge as Na(+) while occupying the same space. The CSC mechanism further implies that the main determinant of Ca(2+) versus Na(+) selectivity is the density of charged particles in the selectivity filter, i.e., the volume of the filter (after fixing the number of charged groups in the filter). In this paper we test this hypothesis by changing filter length and/or radius (shape) of the cylindrical selectivity filter of our reduced model. We show that varying volume and shape together has substantially stronger effects than varying shape alone with volume fixed. Our simulations show the importance of depletion zones of ions in determining channel conductance calculated with the integrated Nernst-Planck equation. We show that confining the protein side chains with soft or hard walls does not influence selectivity.

Determination of the charge profile in the KcsA selectivity filter using ab initio calculations and molecular dynamics simulations

The charge profile of K+ and Na+ ions moving in a single file across the filter of the KcsA channel is determined using both molecular dynamics simulations and ab initio calculations. We show a strong correlation between the charge variation and the ion location resulting in a saw-tooth profile, which provides additional information on the influence of charge transfer on the permeation and selectivity of the channel.