Exploring fast proton transfer events associated with lateral proton diffusion on the surface of membranes

Kinetic Diagram Analysis: A Python Library for Calculating Steady-State Observables of Kinetic Systems Analytically

Kinetic diagrams are commonly used to represent biochemical systems in order to study phenomena such as free energy transduction and ion selectivity. While numerical methods are commonly used to analyze such kinetic networks, the diagram method by King, Altman and Hill makes it possible to construct exact algebraic expressions for steady-state observables in terms of the rate constants of the kinetic diagram. However, manually obtaining these expressions becomes infeasible for models of even modest complexity as the number of the required intermediate diagrams grows with the factorial of the number of states in the diagram. We developed Kinetic Diagram Analysis (KDA), a Python library that programmatically generates the relevant diagrams and expressions from a user-defined kinetic diagram. KDA outputs symbolic expressions for state probabilities and cycle fluxes at steady-state that can be symbolically manipulated and evaluated to quantify macroscopic system observables. We demonstrate the KDA approach for examples drawn from the biophysics of active secondary transmembrane transporters. For a generic 6-state antiporter model, we show how the introduction of a single leakage transition reduces transport efficiency by quantifying substrate turnover. We apply KDA to a real-world example, the 8-state free exchange model of the small multidrug resistance transporter EmrE of Hussey et al (J General Physiology 152 (2020), e201912437), where a change in transporter phenotype is achieved by biasing two different subsets of kinetic rates: alternating access and substrate unbinding rates. KDA is made available as open source software under the GNU General Public License version 3.

Poly(2-Oxazoline) Amphiphilicity Tunes the Excited-State Proton Transfer of Pyrenol-Based Polyphotoacids

The ability of light to change the properties of light-responsive polymers opens avenues for targeted release of cargo with a high degree of spatial and temporal control. Recently, we established photoacid polymers as light-switchable macromolecular amphiphiles. In these systems, light-induced excited-state proton transfer (ESPT) causes changes in amphilicity. However, as the intermolecular process itself critically depends on the local environment of the photoacid unit within the polymer, the overall amphiphilicity directly influences ESPT. Thus, understanding the impact of the local environment on the photophysics of photoacidic side chains is key to material design. In this contribution we address both thermodynamic and kinetic aspects of ESPT in oxazoline-based amphiphilic polymers with pyrenol-based photoacid side chains. We will compare the effect of polymer design, i. e. statistical and block arrangements, i. e. in poly[(2-ethyl-2-oxazoline)-co-(1-(6/8-hydroxyperene)sulphonylaziridine)] and poly(2-ethyl-2-oxazoline)-block-poly[(2-ethyl-2-oxazoline)-co-(2-(3-(6-hydroxypyrene)sulphonamide)propyl-2-oxazoline), on the intermolecular proton transfer reaction by combining steady-state and time-resolved absorption and emission spectroscopy. ESPT appears more prominent in the statistical copolymer compared to a block copolymer with overall similar pyrenol loading. We hypothesize that the difference is due to different local chain arrangements adopted by the polymers in the two cases.

Controlling the Collision Type and Frequency of Single Pt Nanoparticles at Chemically Modified Gold Electrodes

Studying the electrochemical response of single nanoparticles at an electrode surface gives insight into the dynamic and stochastic processes that occur at the electrode interface. Herein, we investigated single platinum nanoparticle collision dynamics and type (elastic vs inelastic) at gold electrode surfaces modified with self-assembled monolayers (SAMs) of varying terminal chemistries. Collision events are measured via the faradaic current from catalytic reactions at the Pt surface. By changing the terminal, solution-facing group of a thiolate monolayer, we observed the effect of hydrophobicity at the solution-electrode interface on single-particle collisions by employing either a hydrophobic -CH3 terminal group (1-hexanethiol), a hydrophilic -OH terminal group (6-mercaptohexanol), or an equimolar mixture of the two. Changes in the terminal group lead to alterations in collision-induced current magnitude, collisional frequency, and the distinct shape of the collision event current transient. The effects of the terminal group of the SAM were probed by measuring quantitative differences in the events monitored through both the hydrogen evolution reaction (HER) and hydrazine oxidation. In both cases, a platinum nanoparticle (PtNP) favors adsorption to bare and hydrophilic surfaces but demonstrates elastic collision behavior when it collides with a hydrophobic surface. In the case of a mixed monolayer, distinct characteristics of hydrophobic and hydrophilic surfaces are observed. We report how single nanoparticle collisions can reveal nanoscale surface heterogeneity and can be used to manipulate the nature of single-particle interactions on an electrode surface by functionalized self-assembled monolayers.

Proton transfer and regulation across chemical interfaces by small-molecule assemblies

We report on measurements and control of proton gradient across interfaces of water and dichloroethane. Such interfaces are interesting as mimics of biological membranes. We use impedance spectroscopy to quantify interfacial proton gradient and identify proton transfer modes. We quantify proton movement using reciprocal of time constant (τ-1 ) acquired from electrochemical impedance modeling. We show that proton gradient across interfaces of water/dichloroethane and τ-1 correlate with the aqueous phase pH, changing from ca. 1 s-1 at pH 1 to 0.2 s-1 at pH 7. τ-1 changes in the presence of proton shuttling fat-soluble molecules. Dinitrophenol acts as a pH activated proton coupler which is active at around neutral pH and inert at pH <4. However, quinone type cofactors change the interfacial proton transport when activated by redox reactions with ferrocene type molecules, such as decamethyl ferrocence (DMFc). Quinone type cofactors show distinct features in their impedance response assigned to a proton coupled electron transfer (PCET) process, different from the uncoupled proton transfer activity of dinitrophenol. The observed PCET reaction significantly changes τ-1 . We use τ-1 as a proton transport descriptor. In particular, CoQ10 -DMFc shows a τ-1 of 3.5 s-1 at pH 7, indicating how small-molecule assemblies change proton availability.

Solid-State Molecular Protonics Devices of Solid-Supported Biological Membranes Reveal the Mechanism of Long-Range Lateral Proton Transport

Lateral proton transport (PT) on the surface of biological membranes is a fundamental biochemical process in the bioenergetics of living cells, but a lack of available experimental techniques has resulted in a limited understanding of its mechanism. Here, we present a molecular protonics experimental approach to investigate lateral PT across membranes by measuring long-range (70 μm) lateral proton conduction via a few layers of lipid bilayers in a solid-state-like environment, i.e., without having bulk water surrounding the membrane. This configuration enables us to focus on lateral proton conduction across the surface of the membrane while decoupling it from bulk water. Hence, by controlling the relative humidity of the environment, we can directly explore the role of water in the lateral PT process. We show that proton conduction is dependent on the number of water molecules and their structure and on membrane composition, where we explore the role of the headgroup, the tail saturation, the membrane phase, and membrane fluidity. The measured PT as a function of temperature shows an inverse temperature dependency, which we explain by the desorption and adsorption of water molecules into the solid membrane platform. We explain our findings by discussing the role of percolating hydrogen bonding within the membrane structure in a Grotthuss-like mechanism.

A New Theory about Interfacial Proton Diffusion Revisited: The Commonly Accepted Laws of Electrostatics and Diffusion Prevail

The high propensity of protons to stay at interfaces has attracted much attention over the decades. It enables long-range interfacial proton diffusion without relying on titratable residues or electrostatic attraction. As a result, various phenomena manifest themselves, ranging from spillover in material sciences to local proton circuits between proton pumps and ATP synthases in bioenergetics. In an attempt to replace all existing theoretical and experimental insight into the origin of protons' preference for interfaces, TELP, the "Transmembrane Electrostatically-Localized Protons" hypothesis, has been proposed. The TELP hypothesis envisions static H+ and OH- layers on opposite sides of interfaces that are up to 75 µm thick. Yet, the separation at which the electrostatic interaction between two elementary charges is comparable in magnitude to the thermal energy is more than two orders of magnitude smaller and, as a result, the H+ and OH- layers cannot mutually stabilize each other, rendering proton accumulation at the interface energetically unfavorable. We show that (i) the law of electroneutrality, (ii) Fick's law of diffusion, and (iii) Coulomb's law prevail. Using them does not hinder but helps to interpret previously published experimental results, and also helps us understand the high entropy release barrier enabling long-range proton diffusion along the membrane surface.

Effect of salt addition on a triblock copolymer-zwitterionic surfactant assembly: insight from excited-state proton transfer

Copolymer-surfactant assemblies are frequently utilized across various fields, from medicine to nanotechnology. Understanding the organization of the mixed assemblies in a saline environment will further expand their application horizons, especially under physiological conditions. Excited-state proton transfer (ESPT) can provide insight into the hydration nature and organization of the non-toxic assembly of a triblock copolymer F127 (poly-(ethylene oxide)101 (PEO101)-poly(propylene oxide)56 (PPO56)-PEO101)) and a zwitterionic sulfobetaine surfactant N-dodecyl-N,N-dimethyl-3-ammoniopropane sulfonate (SB12). Here, we present a comprehensive investigation of the compactness and hydration nature of the F127-SB12 mixed assemblies at different salt concentrations using the ESPT of 8-hydroxy pyrene-1,3,6-trisulfonate (HPTS). In the absence of salts, gradual SB12 addition to a premicellar (0.4 mM) or a post-micellar (4 mM) F127 solution leads to an anomalous modulation of the protonated and deprotonated emission bands. The emission intensity ratio (protonated/deprotonated) first increases to a maximum at a particular SB12 concentration (6 mM and 35 mM for the premicellar and post-micellar F127 assemblies, respectively), and then the ratio decreases with a further increase in the surfactant concentration. Since the intensity ratio is an indicator of the retardation of the ESPT process, the mixed micellar configuration displaying a maximum intensity ratio represents the most compact and least hydrated state. Salt addition to this configuration lowers the intensity ratio, signifying an enhanced ESPT process. Dynamic light scattering (DLS) results indicate that the size of the mixed assembly remains almost unaltered with the addition of salts. Thus, salinity enhances the ESPT process inside the F127-SB12 mixed assemblies without significantly altering the hydrodynamic radius.

Diffusion coefficients and MSD measurements on curved membranes and porous media

We study some geometric aspects that influence the transport properties of particles that diffuse on curved surfaces. We compare different approaches to surface diffusion based on the Laplace-Beltrami operator adapted to predict concentration along entire membranes, confined subdomains along surfaces, or within porous media. Our goal is to summarize, firstly, how diffusion in these systems results in different types of diffusion coefficients and mean square displacement measurements, and secondly, how these two factors are affected by the concavity of the surface, the shape of the possible barriers or obstacles that form the available domains, the sinuosity, tortuosity, and constrictions of the trajectories and even how the observation plane affects the measurements of the diffusion. In addition to presenting a critical and organized comparison between different notions of MSD, in this review, we test the correspondence between theoretical predictions and numerical simulations by performing finite element simulations and illustrate some situations where diffusion theory can be applied. We briefly reviewed computational schemes for understanding surface diffusion and finally, discussed how this work contributes to understanding the role of surface diffusion transport properties in porous media and their relationship to other transport processes.

Proton Migration on Top of Charged Membranes

Proton relay between interfacial water molecules allows rapid two-dimensional diffusion. An energy barrier, ΔGr‡, opposes proton-surface-to-bulk release. The ΔGr‡-regulating mechanism thus far has remained unknown. Here, we explored the effect interfacial charges have on ΔGr‡'s enthalpic and entropic constituents, ΔGH‡ and ΔGS‡, respectively. A light flash illuminating a micrometer-sized membrane patch of a free-standing planar lipid bilayer released protons from an adsorbed hydrophobic caged compound. A lipid-anchored pH-sensitive dye reported protons' arrival at a distant membrane patch. Introducing net-negative charges to the bilayer doubled ΔGH‡, while positive net charges decreased ΔGH‡. The accompanying variations in ΔGS‡ compensated for the ΔGH‡ modifications so that ΔGr‡ was nearly constant. The increase in the entropic component of the barrier is most likely due to the lower number and strength of hydrogen bonds known to be formed by positively charged residues as compared to negatively charged moieties. The resulting high ΔGr‡ ensured interfacial proton diffusion for all measured membranes. The observation indicates that the variation in membrane surface charge alone is a poor regulator of proton traffic along the membrane surface.

Exploring cationic polyelectrolyte-micelle interaction via excited-state proton transfer. Signatures of probe transfer

Excited-state proton transfer (ESPT) is a sensitive tool for the delicate monitoring of structural reorganization, hydration level, and confinement within surfactant and polymer assemblies. Here, we investigate the interaction of a cationic polyelectrolyte, poly(diallyl dimethylammonium chloride) (PDADMAC), with micelles of differently charged surfactants using 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS) as an ESPT probe. We used three surfactants: anionic sodium dodecyl sulfate (SDS), cationic dodecyl trimethylammonium bromide (DTAB), and zwitterionic N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (SB12), possessing the same alkyl (dodecyl) chain but varying headgroup charges. The fluorescence of HPTS residing initially within the micellar medium modulates differently in the presence of PDADMAC. For the anionic SDS and cationic DTAB micelles, the emission spectrum of HPTS does not alter significantly; however, for SB12 micelles, the emission spectrum undergoes a strong modulation upon adding the polyelectrolyte. The emission intensities quench strongly at a low concentration of PDADMAC but recover at a higher concentration. The emission intensity ratio of the two emission bands also changes significantly, implying strong modulation of the ESPT process with varying PDADMAC concentrations. The time-resolved area normalized emission spectra (TRANES) disclose single isoemissive points in the SB12 micelle at low and high concentrations of PDADMAC but two different isoemissive points (one characteristic of the SB12 micelle at 500 nm and another characteristic of the PDADMAC interface at 480 nm) in the mixed assembly at an intermediate concentration. Detailed analysis suggests that the polyelectrolyte can enforce the transfer of the anionic probe HPTS from the zwitterionic micelle to the PDADMAC assembly above a specific PDADMAC concentration. The transfer of the molecular probe between two assemblies resembles a drug sequestration event, and the study reveals necessary emission signatures.

Recent Development of Moisture-Enabled-Electric Nanogenerators

Power generation by converting energy from the ambient environment has been considered a promising strategy for developing decentralized electrification systems to complement the electricity supply for daily use. Wet gases, such as water evaporation or moisture in the atmosphere, can be utilized as a tremendous source of electricity by emerging power generation devices, that is, moisture-enabled-electric nanogenerators (MEENGs). As a promising technology, MEENGs provided a novel manner to generate electricity by harvesting energy from moisture, originating from the interactions between water molecules and hydrophilic functional groups. Though the remarkable progress of MEENGs has been achieved, a systematic review in this specific area is urgently needed to summarize previous works and provide sharp points to further develop low-cost and high-performing MEENGs through overcoming current limitations. Herein, the working mechanisms of MEENGs reported so far are comprehensively compared. Subsequently, a systematic summary of the materials selection and fabrication methods for currently reported MEENG construction is presented. Then, the improvement strategies and development directions of MEENG are provided. At last, the demonstrations of the applications assembled with MEENGs are extracted. This work aims to pave the way for the further MEENGs to break through the performance limitations and promote the popularization of future micron electronic self-powered equipment.

Conduction Mechanism in Graphene Oxide Membranes with Varied Water Content: From Proton Hopping Dominant to Ion Diffusion Dominant

Proton conductors, particularly hydrated solid membranes, have various applications in sensors, fuel cells, and cellular biological systems. Unraveling the intrinsic proton transfer mechanism is critical for establishing the foundation of proton conduction. Two scenarios on electrical conduction, the Grotthuss and the vehicle mechanisms, have been reported by experiments and simulations. But separating and quantifying the contributions of these two components from experiments is difficult. Here, we present the conductive behavior of a two-dimensional layered proton conductor, graphene oxide membrane (GOM), and find that proton hopping is dominant at low water content, while ion diffusion prevails with increasing water content. This change in the conduction mechanism is attributable to the layers of water molecules in GOM nanosheets. The overall conductivity is greatly improved by forming one layer of water molecules. It reaches the maximum with two layers of water molecules, resulting from creating a complete hydrogen-bond network within GOM. When more than two layers of water molecules enter the GOM nanosheets, inducing the breakage of the ordered lamellar structure, protons spread in both in-plane and out-of-plane directions inside the GOM. Our results validate the existence of two conduction mechanisms and show their distinct contributions to the overall conductivity. Furthermore, these findings provide an optimization strategy for the design of realizing the fast proton transfer in materials with water participation.

The Dual Use of the Pyranine (HPTS) Fluorescent Probe: A Ground-State pH Indicator and an Excited-State Proton Transfer Probe

Molecular fluorescent probes are an essential experimental tool in many fields, ranging from biology to chemistry and materials science, to study the localization and other environmental properties surrounding the fluorescent probe. Thousands of different molecular fluorescent probes can be grouped into different families according to their photophysical properties. This Account focuses on a unique class of fluorescent probes that distinguishes itself from all other probes. This class is termed photoacids, which are molecules exhibiting a change in their acid-base transition between the ground and excited states, resulting in a large change in their pKa values between these two states, which is thermodynamically described using the Förster cycle. While there are many different photoacids, we focus only on pyranine, which is the most used photoacid, with pKa values of ∼7.4 and ∼0.4 for its ground and excited states, respectively. Such a difference between the pKa values is the basis for the dual use of the pyranine fluorescent probe. Furthermore, the protonated and deprotonated states of pyranine absorb and emit at different wavelengths, making it easy to focus on a specific state. Pyranine has been used for decades as a fluorescent pH indicator for physiological pH values, which is based on its acid-base equilibrium in the ground state. While the unique excited-state proton transfer (ESPT) properties of photoacids have been explored for more than a half-century, it is only recently that photoacids and especially pyranine have been used as fluorescent probes for the local environment of the probe, especially the hydration layer surrounding it and related proton diffusion properties. Such use of photoacids is based on their capability for ESPT from the photoacid to a nearby proton acceptor, which is usually, but not necessarily, water. In this Account, we detail the photophysical properties of pyranine, distinguishing between the processes in the ground state and the ones in the excited state. We further review the different utilization of pyranine for probing different properties of the environment. Our main perspective is on the emerging use of the ESPT process for deciphering the hydration layer around the probe and other parameters related to proton diffusion taking place while the molecule is in the excited state, focusing primarily on bio-related materials. Special attention is given to how to perform the experiments and, most importantly, how to interpret their results. We also briefly discuss the breadth of possibilities in making pyranine derivatives and the use of pyranine for controlling dynamic reactions.

Using Proton Geminate Recombination as a Probe of Proton Migration on Biological Membranes

Proton migration on biological membranes plays a major role in cellular respiration and photosynthesis, but it is not yet fully understood. Here we show that proton dissociation kinetics and related geminate recombination can be used as a probe of such proton migration mechanisms. We develop a simple model for the process and apply it to analyze the results obtained using a photo-induced proton release probe (chemically modified photoacid) tethered to phosphatidylcholine membranes. In our theoretical model, we apply approximate treatment for the diffusional cloud of the geminate proton around the dissociated photoacid and consider arbitrary dimension of the system, 1 < d < 3. We observe that in d > 2, there is a kinetic phase transition between an exponential and a power-law kinetic phases. The existence of an exponential decay phase at the beginning of the proton dissociation is a signature of d > 2 systems. In most other cases, the exponential decay phase is not present, and the kinetics follows a diffusional power-law P(t) ∼ t^-d/2 that develops after a short initiation time. Specifically, in a 1D case, which corresponds to the desorption of a proton from the surface, the dissociation occurs by the slow power-law ∼1/t and explains the abnormally slow desorption rate reported recently in experiments.

Proton diffusion and hydrolysis enzymatic reaction in 100 nm scale biomimetic nanochannels

Liquids in 10-100 nm spaces are expected to play an important role in biological systems. However, the liquid properties and their influence on biological activity have been obscured due to the difficulty in nanoscale measurements, either in vivo or in vitro. In this study, an in vitro analytical platform for biological systems is established. The nanochannels were modified with lipid bilayers, thereby serving as a model for biological confinement, e.g., the intercellular or intracellular space. As a representative property, the proton diffusion coefficient was measured by a nanofluidic circuit using fluorescein as a pH probe. It was verified that proton conduction was enhanced for channel widths less than 330 nm. A proton-related enzymatic reaction, the hydrolysis reaction, was also investigated, and a large confinement effect was observed.

Dehydrated UiO-66(SH)2 : The Zr-O Cluster and Its Photocatalytic Role Mimicking the Biological Nitrogen Fixation

This work reports the dehydrated Zr-based MOF UiO-66(SH)₂ as a visible-light-driven photocatalyst to mimic the biological N₂ fixation process. The ¹⁵ N₂ and other control experiments demonstrated that the new photocatalyst is highly efficient in converting N₂ to ammonia. In-situ TGA, XPS, and EXAFS as well as first-principles simulations were used to demonstrate the role of the thermal treatment and the changes of the local structures around Zr due to the dehydration. It was shown that the dehydration opened a gate for the entry of N₂ molecules into the [Zr₆ O₆ ] cluster where the strong N≡N bond was broken stepwise by μ-N-Zr type interactions driven by the photoelectrons aided by the protonation. This mechanism was discussed in comparison with the Lowe-Thorneley mechanism proposed for the MoFe nitrogenase, and with emphasis on the [Zr₆ O₆ ] cluster effect and the leading role of photoelectrons over the protonation. The results shed new light on understanding the catalytic mechanism of biological N₂ fixation and open a new way to fix N₂ under mild conditions.

Surface Protolysis and Its Kinetics Impact the Electrical Double Layer

Surface conductivity in the electrical double layer (EDL) is known to be affected by proton hopping and diffusion at solid-liquid interfaces. Yet, the role of surface protolysis and its kinetics on the thermodynamic and transport properties of the EDL are usually ignored as physical models consider static surfaces. Here, using a novel molecular dynamics method mimicking surface protolysis, we unveil the impact of such chemical events on the system's response. Protolysis is found to strongly affect the EDL and electrokinetic aspects with major changes in ζ potential and electro-osmotic flow.

Light-Modulated Cationic and Anionic Transport across Protein Biopolymers*

Light is a convenient source of energy and the heart of light-harvesting natural systems and devices. Here, we show light-modulation of both the chemical nature and ionic charge carrier concentration within a protein-based biopolymer that was covalently functionalized with photoacids or photobases. We explore the capability of the biopolymer-tethered photoacids and photobases to undergo excited-state proton transfer and capture, respectively. Electrical measurements show that both the photoacid- and photobase-functionalized biopolymers exhibit an impressive light-modulated increase in ionic conductivity. Whereas cationic protons are the charge carriers for the photoacid-functionalized biopolymer, water-derived anionic hydroxides are the suggested charge carriers for the photobase-functionalized biopolymer. Our work introduces a versatile toolbox to photomodulate both protons and hydroxides as charge carriers in polymers, which can be of interest for a variety of applications.

Addressing Particle Compositional Heterogeneities in Super-Resolution-Enhanced Live-Cell Ratiometric pH Sensing with Ultrasmall Fluorescent Core-Shell Aluminosilicate Nanoparticles

The interrogation of metabolic parameters like pH in live-cell experiments using optical super-resolution microscopy (SRM) remains challenging. This is due to a paucity of appropriate metabolic probes enabling live-cell SRM-based sensing. Here we introduce ultrasmall fluorescent core-shell aluminosilicate nanoparticle sensors (FAM-ATTO647N aC' dots) that covalently encapsulate a reference dye (ATTO647N) in the core and a pH-sensing moiety (FAM) in the shell. Only the reference dye exhibits optical blinking enabling live-cell stochastic optical reconstruction microscopy (STORM). Using data from cells incubated for 60 minutes with FAM-ATTO647N aC' dots, pixelated information from total internal reflection fluorescence (TIRF) microscopy-based ratiometric sensing can be combined with that from STORM-based localizations via the blinking reference dye in order to enhance the resolution of ratiometric pH sensor maps beyond the optical diffraction limit. A nearest-neighbor interpolation methodology is developed to quantitatively address particle compositional heterogeneity as determined by separate single-particle fluorescence imaging methods. When combined with STORM-based estimates of the number of particles per vesicle, vesicle size, and vesicular motion as a whole, this analysis provides detailed live-cell spatial and functional information, paving the way to a comprehensive mapping and understanding of the spatiotemporal evolution of nanoparticle processing by cells important, e.g. for applications in nanomedicine.

Phenolic compounds alter the ion permeability of phospholipid bilayers via specific lipid interactions

This study aims to understand the role of specific phenolic-lipid interactions in the membrane-altering properties of phenolic compounds. We combine tethered lipid bilayer (tBLM) electrical impedance spectroscopy (EIS) with all-atom molecular dynamics (MD) simulations to study the membrane interactions of six phenolic compounds: caffeic acid methyl ester, caffeic acid, 3,4 dihydroxybenzoic acid, chlorogenic acid, syringic acid and p-coumaric acid. tBLM/EIS experiments showed that caffeic acid methyl ester, caffeic acid and 3,4 dihydroxybenzoic acid significantly increase the permeability of phospholipid bilayers to Na⁺ ions. In contrast, chlorogenic acid, syringic acid and p-coumaric acid showed no effect. Experiments with lipids lacking the phosphate group show a significant decrease in the membrane-altering effects indicating that specific phenolic-lipid interactions are critical in altering ion permeability. MD simulations confirm that compounds that alter ion permeability form stable interactions with the phosphate oxygen. In contrast, inactive phenolic compounds are superficially bound to the membrane surface and primarily interact with interfacial water. Our combined results show that compounds with similar structures can have very different effects on ion permeability in membranes. These effects are governed by specific interactions at the water-lipid interface and show no correlation with lipophilicity. Furthermore, none of the compounds alter the overall structure of the phospholipid bilayer as determined by area per lipid and order parameters. Based on data from this study and previous findings, we propose that phenolic compounds can alter membrane ion permeability by causing local changes in lipid packing that subsequently reduce the energy barrier for ion-induced pores.

Anomalous interfacial dynamics of single proton charges in binary aqueous solutions

Our understanding of the dynamics of charge transfer between solid surfaces and liquid electrolytes has been hampered by the difficulties in obtaining interface, charge, and solvent-specific information at both high spatial and temporal resolution. Here, we measure at the single charge scale the dynamics of protons at the interface between an hBN crystal and binary mixtures of water and organic amphiphilic solvents (alcohols and acetone), evidencing a marked influence of solvation on interfacial dynamics. Applying single-molecule localization microscopy to emissive crystal defects, we observe correlated activation between adjacent ionizable surface defects, mediated by the transport of single excess protons along the solid/liquid interface. Solvent content has a nontrivial effect on interfacial dynamics, leading at intermediate water fraction to an increased surface diffusivity, as well as an increased affinity of the proton charges to the solid surface. Our measurements evidence the notable role of solvation on interfacial proton charge transport.

pH dependent electrical properties of the inner- and outer- leaflets of biomimetic cell membranes

Composition and asymmetry of lipid membranes provide a means for regulation of trans-membrane permeability of ions and small molecules. The pH dependence of these processes plays an important role in the functioning and survival of cells. In this work, we study the pH dependence of membrane electrical resistance and capacitance using electrochemical impedance spectroscopy (EIS), surface plasmon resonance (SPR) and neutron reflectometry (NR) measurements of biomimetic tethered bilayer lipid membranes (tBLMs). tBLMs were prepared with single-component phospholipid compositions, as well as mixtures of phospholipids (phosphatidylcholine, phosphatidylserine, phosphatidylethanolamine, sphingomyelin and cholesterol) that mimic the inner- and outer- leaflets of plasma cell membranes. We found that all studied tBLMs have a resistance maximum at pHs near the pK_as of the phospholipids. SPR and NR indicated that surface concentration of phospholipids and the thickness of the hydrophobic part of the membrane did not change versus pH. We postulate that these maxima are the result of protonation of the phosphate oxygen of the phospholipids and that hydronium ions play a major role in the conductance at pHs < pK_as while sodium ions play the major role at pHs > pK_as. An additional sharp resistance maximum of the PE tBLMs found at pH 5.9 and most likely represents the phosphatidylethanolamine's isoelectric point. The data show the key roles of the characteristic parts of phospholipid molecules: terminal group (choline, carboxyl, amine), phosphate, glycerol and ester oxygens on the permeability and selectivity of ions through the membrane. The interactions between these groups lead to significant differences in the electrical properties of biomimetic models of inner- and outer- leaflets of the plasma cell membranes.

Water at charged interfaces

The ubiquity of aqueous solutions in contact with charged surfaces and the realization that the molecular-level details of water-surface interactions often determine interfacial functions and properties relevant in many natural processes have led to intensive research. Even so, many open questions remain regarding the molecular picture of the interfacial organization and preferential alignment of water molecules, as well as the structure of water molecules and ion distributions at different charged interfaces. While water, solutes and charge are present in each of these systems, the substrate can range from living tissues to metals. This diversity in substrates has led to different communities considering each of these types of aqueous interface. In this Review, by considering water in contact with metals, oxides and biomembranes, we show the essential similarity of these disparate systems. While in each case the classical mean-field theories can explain many macroscopic and mesoscopic observations, it soon becomes apparent that such theories fail to explain phenomena for which molecular properties are relevant, such as interfacial chemical conversion. We highlight the current knowledge and limitations in our understanding and end with a view towards future opportunities in the field.

Architecture of bacterial respiratory chains

Bacteria power their energy metabolism using membrane-bound respiratory enzymes that capture chemical energy and transduce it by pumping protons or Na⁺ ions across their cell membranes. Recent breakthroughs in molecular bioenergetics have elucidated the architecture and function of many bacterial respiratory enzymes, although key mechanistic principles remain debated. In this Review, we present an overview of the structure, function and bioenergetic principles of modular bacterial respiratory chains and discuss their differences from the eukaryotic counterparts. We also discuss bacterial supercomplexes, which provide central energy transduction systems in several bacteria, including important pathogens, and which could open up possible avenues for treatment of disease.

A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation

Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.

Phonon-mediated lipid raft formation in biological membranes

Short-wavelength collective molecular motions, also known as phonons, have recently attracted much interest in revealing dynamic properties of biological membranes through the use of neutron and X-ray scattering, infrared and Raman spectroscopies, and molecular dynamics simulations. Experimentally detecting unique vibrational patterns such as, shear phonon excitations, viscoelastic crossovers, transverse acoustic phonon gaps, and continuous and truncated optical phonon modes in cellular membranes, to name a few, has proven non-trivial. Here, we review recent advances in liquid thermodynamics that have resulted in the development of the phonon theory of liquids. The theory has important predictions regarding the shear vibrational spectra of fluids, namely the emergence of viscoelastic crossovers and transverse acoustic phonon gaps. Furthermore, we show that these vibrational patterns are common in soft (non-crystalline) materials, including, but not limited to liquids, colloids, liquid crystals (mesogens), block copolymers, and biological membranes. The existence of viscoelastic crossovers and acoustic phonon gaps define the self-diffusion properties of cellular membranes and provide a molecular picture of the transient nature of lipid rafts (Bolmatov et al., 2020). Importantly, the timescales (picoseconds) for the formation and dissolution of transient lipid rafts match the lifetime of the formation and breakdown of interfacial water hydrogen bonds. Apart from acoustic propagating phonon modes, biological membranes can also support more energetic non-propagating optical phonon excitations, also known as standing waves or breathing modes. Importantly, optical phonons can be truncated due to the existence of finite size nanodomains made up of strongly correlated lipid-cholesterol molecular pairs. These strongly coupled molecular pairs can serve as nucleation centers for the formation of stable rafts at larger length scales, due to correlations of spontaneous fluctuations (Onsager's regression hypothesis). Finally and importantly, molecular level viscoelastic crossovers, acoustic phonon gaps, and continuous and truncated optical phonon modes may offer insights as to how lipid-lipid and lipid-protein interactions enable biological function.

Environmental and Endogenous Acids Can Trigger Allergic-Type Airway Reactions

Inflammatory allergic and nonallergic respiratory disorders are spreading worldwide and often coexist. The root cause is not clear. This review demonstrates that, from a biochemical point of view, it is ascribable to protons (H+) released into cells by exogenous and endogenous acids. The hypothesis of acids as the common cause stems from two considerations: (a) it has long been known that exogenous acids present in air pollutants can induce the irritation of epithelial surfaces, particularly the airways, inflammation, and bronchospasm; (b) according to recent articles, endogenous acids, generated in cells by phospholipases, play a key role in the biochemical mechanisms of initiation and progression of allergic-type reactions. Therefore, the intracellular acidification and consequent Ca2+ increase, induced by protons generated by either acid pollutants or endogenous phospholipases, may constitute the basic mechanism of the multimorbidity of these disorders, and environmental acidity may contribute to their spread.

The archaeal-bacterial lipid divide, could a distinct lateral proton route hold the answer?

The archaea-bacteria lipid divide is one of the big evolutionary enigmas concerning these two domains of life. In short, bacterial membranes are made of fatty-acid esters whereas archaeal ones contain isoprenoid ethers, though at present we do not have a good understanding on why they evolved differently. The lateral proton transfer mode of energy transduction in membranes posits that protons utilize the solvation layer of the membrane interface as the main route between proton pumps and ATPases, avoiding dissipation of energy to the bulk phase. In this article I present the hypothesis on a proton-transport route through the ester groups of bacterial phospholipids as an explanation for the evolutionary divergence seen between bacteria and archaea. REVIEWERS: This article was reviewed by Uri Gophna (Editorial Board member) and Víctor Sojo.

Phyllotaxis Turns Over a New Leaf-A New Hypothesis

Phyllotaxis describes the periodic arrangement of plant organs most conspicuously floral. Oscillators generally underlie periodic phenomena. A hypothetical algorithm generates phyllotaxis regulated by the Hechtian growth oscillator of the stem apical meristem (SAM) protoderm. The oscillator integrates biochemical and mechanical force that regulate morphogenetic gradients of three ionic species, auxin, protons and Ca2+. Hechtian adhesion between cell wall and plasma membrane transduces wall stress that opens Ca2+ channels and reorients auxin efflux "PIN" proteins; they control the auxin-activated proton pump that dissociates Ca2+ bound by periplasmic arabinogalactan proteins (AGP-Ca2+) hence the source of cytosolic Ca2+ waves that activate exocytosis of wall precursors, AGPs and PIN proteins essential for morphogenesis. This novel approach identifies the critical determinants of an algorithm that generates phyllotaxis spiral and Fibonaccian symmetry: these determinants in order of their relative contribution are: (1) size of the apical meristem and the AGP-Ca2+ capacitor; (2) proton pump activity; (3) auxin efflux proteins; (4) Ca2+ channel activity; (5) Hechtian adhesion that mediates the cell wall stress vector. Arguably, AGPs and the AGP-Ca2+ capacitor plays a decisive role in phyllotaxis periodicity and its evolutionary origins.

Exploring the inner environment of protein hydrogels with fluorescence spectroscopy towards understanding their drug delivery capabilities

Time-resolved fluorescence have used to explore the inner surface and solvation dynamics within protein hydrogels assisting in rationalizing their drug binding and release capabilities.

Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules

Permeability (P_m) across biological membranes is of fundamental importance and a key factor in drug absorption, distribution, and development. Although the majority of drugs will be charged at some point during oral delivery, our understanding of membrane permeation by charged species is limited. The canonical model assumes that only neutral molecules partition into and passively permeate across membranes, but there is mounting evidence that these processes are also facile for certain charged species. However, it is unknown whether such ionizable permeants dynamically neutralize at the membrane surface or permeate in their charged form. To probe protonation-coupled permeation in atomic detail, we herein apply continuous constant-pH molecular dynamics along with free energy sampling to study the permeation of a weak base propranolol (PPL), and evaluate the impact of including dynamic protonation on P_m. The simulations reveal that PPL dynamically neutralizes at the lipid-tail interface, which dramatically influences the permeation free energy landscape and explains why the conventional model overestimates the assigned intrinsic permeability. We demonstrate how fixed-charge-state simulations can account for this effect, and propose a revised model that better describes pH-coupled partitioning and permeation. Our results demonstrate how dynamic changes in protonation state may play a critical role in the permeation of ionizable molecules, including pharmaceuticals and drug-like molecules, thus requiring a revision of the standard picture.

Competing for the same space: protons and alkali ions at the interface of phospholipid bilayers

Maintaining gradients of solvated protons and alkali metal ions such as Na⁺ and K⁺ across membranes is critical for cellular function. Over the last few decades, both the interactions of protons and alkali metal ions with phospholipid membranes have been studied extensively and the reported interactions of these ions with phospholipid headgroups are very similar, yet few studies have investigated the potential interdependence between proton and alkali metal ion binding at the water-lipid interface. In this short review, we discuss the similarities between the proton-membrane and alkali ion-membrane interactions. Such interactions include cation attraction to the phosphate and carbonyl oxygens of the phospholipid headgroups that form strong lipid-ion and lipid-ion-water complexes. We also propose potential mechanisms that may modulate the affinities of these cationic species to the water-phospholipid interfacial oxygen moieties. This review aims to highlight the potential interdependence between protons and alkali metal ions at the membrane surface and encourage a more nuanced understanding of the complex nature of these biologically relevant processes.

Biomimetic Polyelectrolytes Based on Polymer Nanosheet Films and Their Proton Conduction Mechanism

We report a biomimetic polyelectrolyte based on amphiphilic polymer nanosheet multilayer films. Copolymers of poly( N-dodecylacrylamide- co-vinylphosphonic acid) [p(DDA/VPA)] form a uniform monolayer at the air-water interface. By depositing such monolayers onto solid substrates using the Langmuir-Blodgett (LB) method, multilayer lamellae films with a structure similar to a bilayer membrane were fabricated. The proton conductivity at the hydrophilic interlayer of the lamellar multilayer films was studied by impedance spectroscopy under temperature- and humidity-controlled conditions. At 60 °C and 98% relative humidity (RH), the conductivity increased with increasing mole fraction of VPA ( n) up to 3.2 × 10^-2 S cm^-1 for n = 0.41. For a film with n = 0.45, the conductivity decreased to 2.2 × 10^-2 S cm^-1 despite the increase of proton sources. The reason for this decrease was evaluated by studying the effect of the distance between the VPAs ( l_VPA) on the proton conductivity as well as their activation energy. We propose that for n = 0.41, l_VPA is the optimal distance not only to form an efficient two-dimensional (2D) hydrogen bonding network but also to reorient water and VPA. For n = 0.45, on the other hand, the l_VPA was too close for a reorientation. Therefore, we concluded that there should be an optimal distance to obtain high proton conductivity at the hydrophilic interlayer of such multilayer films.

Understanding the effect of nanoconfinement on the structure of water hydrogen bond networks

Dynamic hydrogen bond trails in water confined between two phospholipid membranes traced by the information flow model.