ATP-dependent active transport simulations based on a phosphatase-channel-kinase membrane structure

Simulations of coupled interactions involving enzymatic reaction diffusion and electrostatic interactions were conducted under a fixed phosphatase-channel-kinase (PCK) topology oriented from the outside to the inside of a charged membrane structure. Depending on the phosphatase and kinase locations, we recently demonstrated that active transport of a phosphorylated substrate may occur via this PCK topology. The present analysis demonstrates that, if in addition to this topology, a phosphatase activity (P(1)) is also present on the inner side of the membrane, but outside the unstirred layer surrounding the inner membrane surface, then active transport of the corresponding unphosphorylated substrate may also occur. Therefore, this PCK membrane topology, which behaves as a specific ATP-dependent transporter, appears as a general topology permitting; first, on its own the active transport of a phosphorylated substrate; second, when associated with a phosphatase acting in the bulk of the receiver compartment, the active transport of the corresponding unphosphorylated substrate, that is, in most cases, the transport of an uncharged substrate. The general mathematical model given permits the active transport of a phosphorylated substrate to be analyzed (in the absence of P(1)), the active transport of an unphosphorylated substrate (in the presence of P(1)), whatever the charge distributions on both sides of the membrane surface and whatever the positions of the membrane-bound phosphatase and the membrane-bound kinase. This general model also takes into account the consumption of ATP occurring into the receiver compartment during the time course of these transport phenomena. A broad analysis of the role played by the main parameters taken into account in the model was conducted to precisely define the physicochemical conditions and the membrane topology needed for the highest active transports within the shortest time.     

Active transport of glycerol-3-phosphate with artificial enzyme membranes: A new kinetic model for active transport processes

An approach to the mechanism which may govern translocation and active transport system is presented. Two artificial enzyme membranes with immobilized kinase and immobilized phosphatase, respectively, were used close together to separate two unequal compartments of a specially designed diffusion cell in order to mimic solute active transport. Experiments were conducted and both translocation and active transport of glycerol-3-phosphate were obtained. The theoretical analysis of this active transport-like phenomenon, which underlines the key role played by the charge distribution on the membrane and the diffusion layers existing close to the membrane-bound enzymes is presented and is in good agreement with the experimental data. Our results mainly demonstrate that under specific conditions, the association of kinase and phosphatase activities on both parts of a porous membrane functions as an enzymic pump which performs active transport. Such results may be of general significance and lead us to suggest that a carrier could be substituted by two catalytic activities bound on both parts of a structure of channel type and catalysing two opposite reactions in diffusion layers.     

Artificial enzymic membrane pump for glucose transport against its chemical gradient

An artificial glucokinase/phosphatase porous membrane separating two unequal compartments of a diffusion cell was used to pump glucose from one compartment against the concentration gradient of the opposite one. Our results mainly demonstrate that, a kinase/phosphatase reactional sequence acting on both parts of a pore structure and necessarily in unstirred layers may pump a neutral solute from one compartment against the concentration gradient of the opposite one without any detectable pollution of the charged intermediary product. The corresponding theoretical analysis, which underlines the key role played by the diffusion layers located on both parts of this bienzymic membrane and the membrane's charge effect, was found in good agreement with the experimental data. This study corroborates well the new kinetic model recently proposed for primary scalar active transport of small hydrophilic molecules involving ATP as the energy supply.     

Enzymatic membranes for the selective transport of neutral molecules by electrophoresis

The active and selective transport of glucose and glycerol was carried out using electrophoresis and artificial enzymatic membranes. These positively charged composite membranes carry, on the face adjacent to the donor compartment of an electrophoresis module, a specific kinase (hexokinase or glycerokinase) and, on the opposite face, an alkaline phosphatase (ALP). Phosphorylation of the neutral substrate (glucose or glycerol) on the donor side by the kinase generates a negatively charged phosphorylated substrate, whose transmembrane migration is promoted by an electric field and by the membrane's positive charge. Dephosphorylation of the phosphorylated substrate by ALP on the opposite face regenerates the neutral substrate, which accumulates in the receiver compartment of the electrophoresis module. Using an electrophoresis module specifically designed for this study, our experiments were carried out enabling glucose and glycerol to be concentrated approximately eight- and twelve-fold, respectively, in 8 h.     

Coupled transport membranes II: : The mechanism of uranium transport with a tertiary amine

This paper describes the parameters controlling the coupled transport of uranium anions through liquid membranes. The membranes consist of a microporous polymeric support with a liquid, tertiary amine complexing agent held within the pores by capillary forces. When this liquid membrane is interposed between two aqueous solutions of unequal ion concentrations, the complexing agent can pick up the anion on one side of the membrane and carry it across the membrane by diffusion in the form of a neutral complex. Ions of opposite charge may be carried in the same direction, or ions of like charge may be carried in the opposite direction. We refer to these two modes of transport as “co-transport” and “counter-transport”, respectively. In the coupled transport of uranium, both co-transport and counter-transport can occur. p]The coupling of the flows of two ions permits one of the ions to be pumped against its concentration gradient. We have demonstrated “uphill diffusion” of uranium against substantial concentration gradients, and at significant rates. A number of factors affect uranium flux, principally the concentrations of uranium and the coupled ion in the aqueous solutions. The base strength of the tertiary amine is also an important parameter.     

Hydrogen‐bonding interactions in the active site of a low molecular weight protein‐tyrosine phosphatase

Molecular dynamics simulation of the Michaelis complex, phospho‐enzyme intermediate, and the wild‐type and C12S mutant have been carried out to examine hydrogen‐bonding interactions in the active site of the bovine low molecular weight protein‐tyrosine phosphatase (BPTP). It was found that the S_γ atom of the nucleophilic residue Cys‐12 is ideally located at a position opposite from the phenylphosphate dianion for an inline nucleophilic substitution reaction. In addition, electrostatic and hydrogen‐bonding interactions from the backbone amide groups of the phosphate‐binding loop strongly stabilize the thiolate anion, making Cys‐12 ionized in the active site. In the phospho‐enzyme intermediate, three water molecules are found to form strong hydrogen bonds with the phosphate group. In addition, another water molecule can be identified to form bridging hydrogen bonds between the phosphate group and Asp‐129, which may act as the nucleophile in the subsequent phosphate hydrolysis reaction, with Asp‐129 serving as a general base. The structural difference at the active site between the wild‐type and C12S mutant has been examined. It was found that the alkoxide anion is significantly shifted toward one side of the phosphate binding loop, away from the optimal position enjoyed by the thiolate anion of the wild‐type enzyme in an S_N2 process. This, coupled with the high pK_a value of an alcoholic residue, makes the C12S mutant catalytically inactive. These molecular dynamics simulations provided details of hydrogen bonding interactions in the active site of BPTP, and a structural basis for further studies using combined quantum mechanical and molecular mechanical potential to model the entire dephosphorylation reaction by BPTP. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1192–1203, 2000     

Classifying substrate specificities of membrane transporters from Arabidopsis thaliana

Membrane transporters catalyze the active transport of molecules across biological barriers such as lipid bilayer membranes. Currently, the experimental annotation of which proteins transport which substrates is far from complete and will likely remain so for much longer. Therefore, it is highly desirable to develop computational methods that may aid in the substrate annotation of putative membrane transport proteins. Here, we measured the similarity of membrane transporters from Arabidopsis thaliana by their amino acid composition, higher sequence order information, amino acid characteristics, or sequence conservation. We considered the substrate classes amino acids, oligopeptides, phosphates, and hexoses. Substrate classification based on the amino acid frequency yielded an accuracy of 75% or higher. Integrating additional information improved the prediction performance to 90% and higher.     

How do P-type ATPases transport ions?

P-type ATPases are a large family of membrane proteins that perform active ion transport across biological membranes. In these proteins, the energy-providing ATP hydrolysis is coupled to ion transport of one or two ion species across the respective membrane. The pump function of the investigated pumps is described by a so-called Post-Albers cycle. Main features of the pumping process are (1) a Ping-Pong mechanism, i.e. both transported ion species are transferred successively and in opposite direction across the membrane, (2) the transport process for each ion species consists of a sequence of reaction steps, which are ion binding, ion occlusion, conformational transition of the protein, successive deocclusion of the ions and release to the other side of the membrane. (3) Recent experimental evidence shows that the ion-binding sites are placed in the transmembrane section of the proteins and that ion movements occur preferentially during the ion binding and release processes. The main features of the mechanism include narrow access channels from both sides, one gate per access channel, and an ion-binding moiety that is adapted specifically to the ions that are transported, and differently in both principal conformations.     

The molecular mechanism of dicarboxylic acid transport in Escherichia coli K 12.

It is the purpose of this communication to review the properties of the dicarboxylic acid transport system in Escherichia coli K 12, in particular the role of various dicarboxylate transport proteins, and the disposition of these components in the cytoplasmic membrane. The dicarboxylate transport system is an active process and is responsible for the uptake of succinate, fumarate, and malate. Membrane vesicles prepared from the EDTA, lysozyme, and osmotic shock treatment take up the dicarboxylic acids in the presence of an electron donor. Genetic analysis of various transport mutants indicates that there is only one dicarboxylic acid transport system present in Escherichia coli K 12, and that at least 3 genes, designated cbt, dct A, and dct B, are involved in this transport system. The products corresponding to the 3 genes are: a periplasmic binding protein (PBP) specified by cbt, and 2 membrane integral proteins, SBP 1 and SBP 2, specified by dct B and dct A, respectively. Components SBP 1 and SBP 2 appear to be exposed on both the inner and outer surfaces of the membrane, and lie in close proximity to each other. The substrate recognition sites of SBP 2 and SBP 1 are exposed on the outer and inner surfaces of the membrane respectively. The data presently available suggest that dicarboxylic acids may be translocated across the membrane via a transport channel. A tentative working model on the mechanism of translocation of dicarboxylic acids across the cell envelope by the periplasmic binding protein, and the 2 membrane carrier proteins is presented.     

Computational Insights into Allosteric Conformational Modulation of P-Glycoprotein by Substrate and Inhibitor Binding

The ATP-binding cassette (ABC) transporter P-glycoprotein (P-gp) is a physiologically essential membrane protein that protects many tissues against xenobiotic molecules, but limits the access of chemotherapeutics into tumor cells, thus contributing to multidrug resistance. The atomic-level mechanism of how substrates and inhibitors differentially affect the ATP hydrolysis by P-gp remains to be elucidated. In this work, atomistic molecular dynamics simulations in an explicit membrane/water environment were performed to explore the effects of substrate and inhibitor binding on the conformational dynamics of P-gp. Distinct differences in conformational changes that mainly occurred in the nucleotide-binding domains (NBDs) were observed from the substrate- and inhibitor-bound simulations. The binding of rhodamine-123 can increase the probability of the formation of an intermediate conformation, in which the NBDs were closer and better aligned, suggesting that substrate binding may prime the transporter for ATP hydrolysis. By contrast, the inhibitor QZ-Leu stabilized NBDs in a much more separated and misaligned conformation, which may result in the deficiency of ATP hydrolysis. The significant differences in conformational modulation of P-gp by substrate and inhibitor binding provided a molecular explanation of how these small molecules exert opposite effects on the ATPase activity. A further structural analysis suggested that the allosteric communication between transmembrane domains (TMDs) and NBDs was primarily mediated by two intracellular coupling helices. Our computational simulations provide not only valuable insights into the transport mechanism of P-gp substrates, but also for the molecular design of P-gp inhibitors.     

Density functional approach to adsorption of simple fluids on surfaces modified with a brush-like chain structure

A density functional theory to describe adsorption of a simple fluid from a gas phase on a surface modified with pre-adsorbed chains is proposed. The chains are bonded to the surface by one of their ends, so they can form a brush-like structure. Two models are investigated. According to the first model all but the terminating segment of a chain can change the configuration during the adsorption of fluid species. The second model assumes that the chains remain "frozen", and the system is considered as a nonuniform quenched-annealed mixture. We apply simple form of interactions to study adsorption phenomena, microscopic structure, and layering transitions. Our principal findings show that new layering phase transitions can occur because of a chemical modification of the substrate under certain conditions, in comparison with nonmodified surfaces. However, opposite trends, that is, smoothing the adsorption isotherms, can also be observed, depending on the surface density of the grafted chains.     

Synthetic catalytic pores

Catalytic activity of a synthetic multifunctional pore is studied in large unilamellar vesicles under conditions where substrate and synthetic catalytic pore (SCP) approach the membrane either from the same side (cis catalysis) or from opposite sides (trans catalysis). A synthetic supramolecular rigid-rod beta-barrel with excellent ion channel characteristics is identified as SCP using 8-acetoxypyrene-1,3,6-trisulfonate (AcPTS) as model substrate. The key finding is that application of supportive membrane potentials increases the initial velocity of AcPTS esterolysis (v0). This results in an increase of Vmax beyond experimental error (+30%), whereas KM increases less significantly. Long-range electrostatic steering by the membrane potential, possibly guiding substrates into the transmembrane catalyst and, more importantly, accelerating product release (foff = 1.3) is discussed as one possible explanation of this global reduction of catalyst saturation. Control experiments show, inter alia, that similarly strong changes do not occur with opposing membrane potentials.     

Photodriven Active Ion Transport Through a Janus Microporous Membrane

Precise control of ion transport is a fundamental characteristic for the sustainability of life. It remains a great challenge to develop practical and high‐performance artificial ion‐transport system that can allow active transport of ions (protons) in an all solid‐state nanoporous material. Herein, we develop a Janus microporous membrane by combining reduced graphene oxide (rGO) and conjugated microporous polymer (CMP) for controllable photodriven ion transport. Upon light illumination, a net ionic current is generated from the CMP to the rGO side of the membrane, indicating that the rGO/CMP Janus membrane can realize photodriven directional and anti‐gradient ion transport. Analogously to the p‐n junction in photovoltaic devices, light is firstly converted into separated charges to trigger a transmembrane potential, which subsequently drives directional ion movement. For the first time, this method enables integration of a photovoltaic effect with an ionic field to drive active ion transport. With the advantages of scaled up production and easy fabrication, the concept of photovoltaic ion transport based on Janus microporous membrane may find wide application in energy storage and conversion, photodriven ion‐sieving, and water treatment.     

Effects of the relative humidity and water droplet on adhesion of a bio-inspired nano-film

Inspired by geckos' adhesion, the effect of water membrane forming due to the environmental humidity, on the adhesion between a bio-inspired nano-film and a substrate is investigated first. The disjoining pressure is considered, which results in an enhancing adhesion between the nano-film and substrate. When the thickness of water membrane increases, water droplets will form and a repulsive capillary force between the nano-film and substrate is produced. The total adhesion force decreases with an increasing volume of water droplets. The two opposite results in the two different models are consistent well with two seemingly inconsistent experimental observations by Huber et al. (2005) [4] and Sun et al. (2005) [5], respectively, and may be significant for the development of artificial biomimetic attachment systems.     

Contributions of the nanovoid structure to the kinetics of moisture transport in epoxy resins

Absorbed moisture can degrade the physical properties of an epoxy resin, jeopardizing the performance of an epoxy‐based component. Although specific water–epoxy interactions are known to be very important in determining transport behavior, the role of network topology is not clear. In this article, a series of epoxies in which the topology is systematically varied (and the polarity held constant) is used to explore how topology influences the kinetics of moisture transport. The topology is quantified via the positron annihilation lifetime spectroscopy technique in terms of the size and volume fraction of electron density heterogeneities 5–6 Å in diameter, a dimension comparable to the 3‐Å kinetic diameter of a water molecule. Surprisingly, the volume fraction of such nanopores does not affect the diffusion coefficient (D) of water in any of the resins studied. For temperatures at and below 35 °C, there is a mild exponential dependence of D on the average nanopore size observed. Otherwise, the kinetics of moisture transport do not appear to depend on the nanopores. However, the initial flux of moisture into the epoxy does appear to correlate with the intrinsic hole volume fraction. That this correlation persists only in the initial stages of absorption is partially understood in terms of the ability of the water to alter the nanopore structure; only in the initial stages of uptake are the nanopores, as quantified in the dry state, relevant to transport. The role of specific epoxy–water interactions are also discussed in terms of transport kinetics. The lack of a correlation between the topology and transport suggests that polar interactions, and not topology, provide the rate‐limiting step of transport. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 776–791, 2000     

Vectorial behavior of a homogeneous artificial bienzyme membrane

Two sequential enzymes (xanthine oxidase and uricase) were immobilized in a homogeneous artificial membrane. The first substrate (xanthine) is a competitive inhibitor for the second enzyme (uricase). The paper deals with experimental and numerical results obtained with such a membrane studied under asymmetrical boundary conditions for the inhibitor (xanthine). Asymmetry at the boundaries gives rise to an asymmetrical function. In this way, a vectorial behavior of the global system is observed; urate concentration is increasing in the second compartment and decreasing in the first one. It is demonstrated that a pseudoactive transport is able to arise from a membrane symmetrical in structure when working under functional asymmetry.     

pH-driven assembly of various supported lipid platforms: a comparative study on silicon oxide and titanium oxide

Supported lipid platforms are versatile cell membrane mimics whose structural properties can be tailored to suit the application of interest. By identifying parameters that control the self-assembly of these platforms, there is potential to develop advanced biomimetic systems that overcome the surface specificity of lipid vesicle interactions under physiological conditions. In this work, we investigated the adsorption kinetics of vesicles onto silicon and titanium oxides as a function of pH. On each substrate, a planar bilayer and a layer of intact vesicles could be self-assembled in a pH-dependent manner, demonstrating the role of surface charge density in the self-assembly process. Under acidic pH conditions where both zwitterionic lipid vesicles and the oxide films possess near-neutral electric surface charges, vesicle rupture could occur, demonstrating that the process is driven by nonelectrostatic interactions. However, we observed that the initial rupturing process is insufficient for propagating bilayer formation. The role of electrostatic interactions for propagating bilayer formation differs for the two substrates; electrostatic attraction between vesicles and the substrate is necessary for complete bilayer formation on titanium oxide but is not necessary on silicon oxide. Conversely, in the high pH regime, repulsive electrostatic interactions can result in the irreversible adsorption of intact vesicles on silicon oxide and even a reversibly adsorbed vesicle layer on titanium oxide. Together, the results show that pH is an effective tool to modulate vesicle-substrate interactions in order to create various self-assembled lipid platforms on hydrophilic substrates.     

A core-shell strategy for constructing a single-molecule junction

Understanding the effects of intermolecular interactions on the charge-transport properties of metal/molecule/metal junctions is an important step towards using individual molecules as building blocks for electronic devices. This work reports a systematic electron-transport investigation on a series of "core-shell"-structured oligo(phenylene ethynylene) (Gn-OPE) molecular wires. By using dendrimers of different generations as insulating "shells", the intermolecular π-π interactions between the OPE "cores" can be precisely controlled in single-component monolayers. Three techniques are used to evaluate the electron-transport properties of the Au/Gn-OPE/Au molecular junctions, including crossed-wire junction, scanning tunneling spectroscopy (STS), and scanning tunneling microscope (STM) break-junction techniques. The STM break-junction measurement reveals that the electron-transport pathways are strongly affected by the size of the side groups. When the side groups are small, electron transport could occur through three pathways, including through single-molecule junctions, double-molecule junctions, and molecular bridges between adjacent molecules formed by aromatic π-π coupling. The dendrimer shells effectively prohibit the π-π coupling effect, but at the same time, very large dendrimer side groups may hinder the formation of Au-S bonds. A first-generation dendrimer acts as an optimal shell that only allows electron transport through the single-molecule junction pathway, and forbids the other undesired pathways. It is demonstrated that the dendrimer-based core-shell strategy allows the single-molecule conductance to be probed in a homogenous monolayer without the influence of intermolecular π-π interactions.     

Application of chemometrically processed thermogravimetric data for identification of baclofen-excipient interactions

Studies are constantly being conducted on the elaboration of efficient methods to confirm the compatibility of active pharmaceutical ingredients (APIs) and excipients, since medicinal products, apart from their APIs, also contain numerous excipients that not only have important functions in pharmaceutical preparations but can also initiate or participate in interactions with drug substances, which eventually lead to a decline in drug quality. With this in mind, research was undertaken to evaluate two of the most often applied pattern recognition methods, hierarchical cluster analysis (HCA) and principal component analysis (PCA), as supporting techniques in the identification of potential physicochemical interactions that may occur during the preformulation of solid dosage forms. The investigation performed with the use of baclofen and selected excipients has shown that with thermogravimetric analysis, HCA and PCA fulfill their role as supporting techniques in the interpretation of the data obtained. Based on these methods, it is possible to detect incompatibilities between baclofen and excipients, and the data obtained concur strongly with the results of differential scanning calorimetry and IR spectrometry analyses.