Field-induced reorganization of the neural membrane lipid bilayer: a proposed role in the regulation of ion-channel dynamics

We present a computational model demonstrating that an electric field propagating in the plane of the neural membrane during transmembrane ion movement creates lateral concentration gradients of the lipids. Due to this field-induced reorganization, ethenes of the lipid chains become aligned and polarized. This finding is interpreted within the context of molecular studies of protein folding in biological membranes. We propose that electrostatic interactions between membrane dipoles and charged amino acid residues of the unfolded ion-channel protein regulate protein-folding kinetics (channel closing). These electrostatic interactions thus regulate electrical signaling in neurons.     

Neural membrane microdomains as computational systems: Toward molecular modeling in the study of neural disease

Several studies indicate that the lipid biological membrane contains discrete regions known as rafts or microdomains. These structures range in size from approximately 50 to 70nm to nearly a mum and play important roles in cell signaling. In the neuron, computational models suggest that transiently polarized microdomain ethenes may regulate ion-channel dynamics and control impulse propagation. Thus the microdomain is nominated as the fundamental unit of nervous system signaling. Based on this model, the article proposes a first-approximation design for a supported-membrane device which would mimic microdomain properties. The basic architecture would consist of an electrically addressable biotemplated nanowire crossing an artificial membrane corralled in a vertical carbon nanofiber barrier. Advantages and disadvantages of model components are discussed at length. It is proposed that artificial devices of this type would be medically useful in simulating membrane states correlated with neural disease. This possibility is examined with reference to the A-current potassium channel, implicated in epilepsy.     

Dynamics of electron transfer pathways in cytochrome C oxidase

Cytochrome c oxidase mediates the final step of electron transfer reactions in the respiratory chain, catalyzing the transfer between cytochrome c and the molecular oxygen and concomitantly pumping protons across the inner mitochondrial membrane. We investigate the electron transfer reactions in cytochrome c oxidase, particularly the control of the effective electronic coupling by the nuclear thermal motion. The effective coupling is calculated using the Green's function technique with an extended Huckel level electronic Hamiltonian, combined with all-atom molecular dynamics of the protein in a native (membrane and solvent) environment. The effective coupling between Cu(A) and heme a is found to be dominated by the pathway that starts from His(B204). The coupling between heme a and heme a(3) is dominated by a through-space jump between the two heme rings rather than by covalent pathways. In the both steps, the effective electronic coupling is robust to the thermal nuclear vibrations, thereby providing fast and efficient electron transfer.     

Managing methanogens and homoacetogens to promote reductive dechlorination of trichloroethene with direct delivery of H2 in a membrane biofilm reactor

A study with H(2)-based membrane biofilm reactors (MBfRs) was undertaken to examine the effectiveness of direct H(2) delivery in ex-situ reductive dechlorination of chlorinated ethenes. Trichloroethene (TCE) could be reductively dechlorinated to ethene with up to 95% efficiency as long as the pH-increase effects of methanogens and homoacetogens were managed and dechlorinators were selected for during start-up by creating H(2) limitation. Based on quantitative PCR, the dominant bacterial groups in the biofilm at the end of reactor operation were Dehalococcoides, Geobacter, and homoacetogens. Pyrosequencing confirmed the dominance of the dechlorinators and identified Acetobacterium as the key homoacetogen. Homoacetogens outcompeted methanogens for bicarbonate, based on the effluent concentration of acetate, by suppressing methanogens during batch start-up. This was corroborated by the methanogenesis functional gene mcrA, which was 1-2 orders of magnitude lower than the FTHFS functional gene for homoacetogens. Imaging of the MBfR fibers using scanning electron microscopy showed a distinct Dehalococcoides-like morphology in the fiber biofilm. These results support that direct addition of H(2) can allow for efficient and complete reductive dechlorination, and they shed light into how H(2)-fed biofilms, when operated to manage methanogenic and homoacetogenic activity, can be used for ex-situ bioremediation of chlorinated ethenes.     

地下水脱卤过程中的微生物种间代谢互作：提高原位氯代烯烃厌氧脱氯效能的有效途径

有机卤呼吸细菌(organohalide-respiring bacteria, OHRB)在氯代烯烃污染地下水的原位生物修复中扮演着关键性的角色,提高其丰度及活性对氯代烯烃的完全去除具有重要意义。在实际环境中,有机卤呼吸细菌往往与多种微生物共存,微生物种间代谢互作现象十分普遍,有机污染物的完全无害化往往需要通过微生物菌群的协同代谢作用来实现。因此,本文围绕微生物种间代谢互作进行综述,对目前获得的脱氯微生物菌种资源及脱氯机理进行了回顾,重点阐述了专性OHRB、非专性OHRB和非OHRB的种间代谢互作行为及机制,并提出以种间代谢互作为指导进行合成微生物群落的构建来有效提高氯代烯烃厌氧生物降解效率,为实现环境氯代烯烃类有机污染物的快速、彻底无害化提供理论指导。     

A Transparent Planar Concentrator Using Aggregates of gem‐Pyrene Ethenes

The luminescence properties of pyrene ethenes, both as monomer and aggregate species, are found to depend on the regioisomer structure. Systematic shifts in absorption, emission, and excitation spectra of the gem‐pyrene ethenes, both in solution and in rigid polymer hosts, are consistent with weakly interacting H‐aggregate formation. This aggregation leads to excimer‐like emission with Stokes shifts greater than 1 eV. Planar concentrators fabricated from gem‐pyrene diphenylethenes show comparable performance to previously reported inorganic phosphors. The UV absorption and emission properties of the planar concentrator devices exhibit potential for transparent solar concentrators or visible–blind photodetector applications. This is the first demonstration of exploiting the unusual photophysics of molecular aggregates in planar concentrators.     

Construction and optimisation of a computer model for a bacterial membrane

The main steps in the construction of a computer model for a bacterial membrane are described. The membrane has been built of 72 lipid molecules, 54 of which being 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphatidylethanolamine (POPE) and 18--1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphatidyl-rac-glycerol (POPG) molecules (thus in the proportion of 3:1). The membrane was hydrated with 1955 water molecules (approximately 27 water molecules per lipid). To neutralise the electronic charge (-e) on each POPG molecule, 18 sodium ions (Na+) were added to the membrane close to the POPG phosphate groups. The atomic charges on the POPE and POPG headgroups were obtained from ab initio quantum mechanical restrained electrostatic potential fitting (RESP) (Bayly et al., 1993, J. Phys. Chem. 97, 10269) using the GAMESS program at the 6-31G* level (Schmidt et al., 1993, J. Comput. Chem. 14, 1347). The model constructed in this way provided an initial structure for subsequent molecular dynamics simulation studies intended to elucidate the atomic level interactions responsible for the structure and dynamics of the bacterial membrane.     

Formation and detoxification of reactive intermediates in the metabolism of chlorinated ethenes

Short-chain halogenated aliphatics, such as chlorinated ethenes, constitute a large group of priority pollutants. This paper gives an overview on the chemical and physical properties of chlorinated aliphatics that are critical in determining their toxicological characteristics and recalcitrance to biodegradation. The toxic effects and principle metabolic pathways of halogenated ethenes in mammals are briefly discussed. Furthermore, the bacterial degradation of halogenated compounds is reviewed and it is described how product toxicity may explain why most chlorinated ethenes are only degraded cometabolically under aerobic conditions. The cometabolic degradation of chlorinated ethenes by oxygenase-producing microorganisms has been extensively studied. The physiology and bioremediation potential of methanotrophs has been well characterized and an overview of the available data on these organisms is presented. The sensitivity of methanotrophs to product toxicity is a major limitation for the transformation of chlorinated ethenes by these organisms. Most toxic effects arise from the inability to detoxify the reactive chlorinated epoxyethanes occurring as primary metabolites. Therefore, the last part of this review focuses on the metabolic reactions and enzymes that are involved in the detoxification of epoxides in mammals. A key role is played by glutathione S-transferases. Furthermore, an overview is presented on the current knowledge about bacterial enzymes involved in the metabolism of epoxides. Such enzymes might be useful for detoxifying chlorinated ethene epoxides and an example of a glutathione S-transferase with activity for dichloroepoxyethane is highlighted.     

Chemical reactions and membranes: A macroscopic basis for active transport II. Non-linear aspects

The physical principles that material and charge are conserved provide a basis for the design of a membrane capable of performing active ion transport in which the connection between “metabolic energy” input and the ion transport process itself is electrical rather than material. Molecular interactions between components in this system are irrelevant to its function. A second model built on the same principles performs active ion transport in a statically symmetrical membrane. The basis of its operation is a weakly stable unsymmetrical concentration profile arising from an enzyme-catalyzed reaction occurring within the membrane. The function of this membrane is irreversibly terminated (“killed”) by interference either with intramembrane concentration gradients or with the reactions which maintain them. Hence, any attempt to study this system by breaking it apart destroys the basis of its function. The existence of these models reveals the logical insufficiency of the molecular biologist's approach to understanding the basis of active transport: Neither the experimental techniques for structure determination (disruption, purification, characterization, and reconstitution) nor the fundamental question of that discipline (What is the molecular connection between &*|… ?) of the molecular biologist are applicable to the study or interpretation of these model systems. While the model systems are artificial, they incorporate only widely applicable concepts of physical chemistry and biochemical kinetics. The is no reason for excluding such mechanisms in natural membrane transport systems. If they are present, then more effective strategies of investigation will be required.     

Molecular dynamics simulations of creatine kinase and adenine nucleotide translocase in mitochondrial membrane patch

Interaction between mitochondrial creatine kinase (MtCK) and adenine nucleotide translocase (ANT) can play an important role in determining energy transfer pathways in the cell. Although the functional coupling between MtCK and ANT has been demonstrated, the precise mechanism of the coupling is not clear. To study the details of the coupling, we turned to molecular dynamics simulations. We introduce a new coarse-grained molecular dynamics model of a patch of the mitochondrial inner membrane containing a transmembrane ANT and an MtCK above the membrane. The membrane model consists of three major types of lipids (phosphatidylcholine, phosphatidylethanolamine, and cardiolipin) in a roughly 2:1:1 molar ratio. A thermodynamics-based coarse-grained force field, termed MARTINI, has been used together with the GROMACS molecular dynamics package for all simulated systems in this work. Several physical properties of the system are reproduced by the model and are in agreement with known data. This includes membrane thickness, dimension of the proteins, and diffusion constants. We have studied the binding of MtCK to the membrane and demonstrated the effect of cardiolipin on the stabilization of the binding. In addition, our simulations predict which part of the MtCK protein sequence interacts with the membrane. Taken together, the model has been verified by dynamical and structural data and can be used as the basis for further studies.     

System for dynamic measurements of membrane capacitance in intact epithelial monolayers.

Dynamic measurements of exocytosis have been difficult to perform in intact epithelial monolayers. We have designed a system that estimates with +/-1% accuracy (99% confidence) the total membrane capacitance of monolayers represented by a lumped model. This impedance measurement and analysis system operates through a conventional transepithelial electrophysiology clamp, performing all signal measurements as frequently as every 5 s. Total membrane capacitance (the series combination of apical and basolateral membranes) is the inverse of one of three unique coefficients that describe the monolayer impedance. These coefficients are estimated using a weighted, nonlinear, least-squares algorithm. Using the estimated coefficients, solution ranges for individual membrane parameters are calculated, frequently providing results within +/-20% of true values without additional electrophysiological measurements. We determined the measurement system specifications and statistical significance of estimated parameters using 1) analytical testing with circuit simulation software and equation-generated data; 2) a system noise analysis combined with Monte Carlo simulations; and 3) analog model circuits for calibration of the electronic system and to check equation-generated results. Finally, the time course of capacitance changes associated with purinergically stimulated mucin exocytosis are quantified in monolayers of the colonic goblet cell-like cell line HT29-CI.16E.     

Evolution and development of model membranes for physicochemical and functional studies of the membrane lateral heterogeneity

One of the main questions in the membrane biology is the functional roles of membrane heterogeneity and molecular localization. Although segregation and local enrichment of protein/lipid components (rafts) have been extensively studied, the presence and functions of such membrane domains still remain elusive. Along with biochemical, cell observation, and simulation studies, model membranes are emerging as an important tool for understanding the biological membrane, providing quantitative information on the physicochemical properties of membrane proteins and lipids. Segregation of fluid lipid bilayer into liquid-ordered (Lo) and liquid-disordered (Ld) phases has been studied as a simplified model of raft in model membranes, including giant unilamellar vesicles (GUVs), giant plasma membrane vesicles (GPMVs), and supported lipid bilayers (SLB). Partition coefficients of membrane proteins between Lo and Ld phases were measured to gauze their affinities to lipid rafts (raftophilicity). One important development in model membrane is patterned SLB based on the microfabrication technology. Patterned Lo/Ld phases have been applied to study the partition and function of membrane-bound molecules. Quantitative information of individual molecular species attained by model membranes is critical for elucidating the molecular functions in the complex web of molecular interactions. The present review gives a short account of the model membranes developed for studying the lateral heterogeneity, especially focusing on patterned model membranes on solid substrates.     

Molecular aspects of the interaction between amphotericin B and a phospholipid bilayer: molecular dynamics studies

Amphotericin B (AmB) is a polyene macrolide antibiotic used to treat systemic fungal infections. The molecular mechanism of AmB action is still only partly characterized. AmB interacts with cell-membrane components and forms membrane channels that eventually lead to cell death. The interaction between AmB and the membrane surface can be regarded as the first (presumably crucial) step on the way to channel formation. In this study molecular dynamics simulations were performed for an AmB–lipid bilayer model in order to characterize the molecular aspects of AmB–membrane interactions. The system studied contained a box of 200 dimyristoylphosphatidylcholine (DMPC) molecules, a single AmB molecule placed on the surface of the lipid bilayer and 8,065 water molecules. Two molecular dynamics simulations (NVT ensemble), each lasting 1 ns, were performed for the model studied. Two different programs, CHARMM and NAMD2, were used in order to test simulation conditions. The analysis of MD trajectories brought interesting information concerning interactions between polar groups of AmB and both DMPC and water molecules. Our studies show that AmB preferentially took a vertical position, perpendicular to the membrane surface, with no propensity to enter the membrane. Our finding may suggest that a single AmB molecule entering the membrane is very unlikely.Figure The figure presents the whole structure of the system simulated—starting point. AmB is presented as a space-filling model, DMPC molecules—green sticks, water molecules—red sticks     

A model for continuous enzymatic saccharification of cellulose with simultaneous removal of glucose syrup

Cellulase of Trichoderma viride was concentrated in various molecular cutoff membranes, and flux rates and retention of activity were studied under ultra-filtration conditions. Little or no Cellulase was discharged through the membranes tested. The concentrated (5–8-fold) enzymes were used to saccharify finely ground substrate (Solka Floe) in stirred tank (STR) and membrane reactors (MR). A pressure filtration vessel provided with a membrane for simultaneous removal of low molecular weight products (glucose) from the reacting system (Cellulose-Cellulase) is designated as a membrane reactor. Continuous digestion of dense cellulose suspension in the membrane reactor was achieved. Using PM-30 (Amicon) membrane reasonably high mass flux values (9.7–23.3 gals/ft²—day) were obtained in separating glucose from a digest of 30% cellulose suspension. Abcor membrane (HFA 300) was equally effective and necessitated less care in handling. Nearly 14% glucose concentration has been achieved in less than 50 hrs in STR by digesting a 30% cellulose suspension. Based on experimental data a model system is proposed for the continuous steady state Saccharification of ground substrate in which there is continuous removal of concentrated glucose syrup, and a feedback of enzyme.     

Mechanically mediated electron transfer in model metallo-enzyme interfaces

In this paper, we develop a physical analysis of charge transfer in the model 'metallo-enzyme' complex which consists of a synthetic redox-addressed assembly (a 'reaction center') hybridized with a quantum dot (a gold nanoparticle) and attached via molecular bridge (a spacer) to the electrode. This artificial system allows us to model electronic transduction in experimental redox ezyme-gold nanoparticle hybrid structure recently reported by Xiao et al. [Xiao, Y., Patolsky, F., Katz, E., Hainfeid, J.F., Willner, I., 2003. Science 299, 1877-1881]. We consider a photosensitive spacer that allows us to control the conductivity of the bridge by light. In this paper we will focus on a special type of nanoelectro-mechanical processes in this system and investigate single electronic effects in there.     

Measurement and modeling of multiple substrate oxidation by methanotrophs at 20 degrees C

Earlier experiments have shown that when Methylosinus trichosporium OB3b was grown at 30 degrees C, greater growth and degradation of chlorinated ethenes was observed under particulate methane monooxygenase (pMMO)-expressing conditions than sMMO-expressing conditions. The effect of temperature on the growth and ability of methanotrophs to degrade chlorinated ethenes, however, has not been examined, particularly temperatures more representative of groundwater systems. Thus, experiments were performed at 20 degrees C to examine the effect of mixtures of trichloroethylene, trans-dichloroethylene and vinyl chloride in the presence of methane on the growth and ability of Methylosinus trichosporium OB3b cells to degrade these pollutants. Although the maximal rates of chlorinated ethane degradation were greater by M. trichosporium OB3b expressing sMMO as compared with the same cell expressing pMMO, the growth and ability of sMMO-expressing cells to degrade these cosubstrates was substantially inhibited in their presence as compared with the same cell expressing pMMO. The Delta model developed earlier was found to be useful for predicting the effect of chlorinated ethenes on the growth and ability of M. trichosporium OB3b to degrade these compounds at a growth temperature of 20 degrees C. Finally, it was also discovered that at 20 degrees C, cells expressing pMMO exhibited faster turnover of methane than sMMO-expressing cells, unlike that found earlier at 30 degrees C, suggesting that temperature may exert selective pressure on methanotrophic communities to express sMMO or pMMO.     

Two-terminal electronic circuit neuron model with excitable membrane V-I-t characteristics

Two-terminal electronic circuit neuron model is described. The model has time-variant voltagecurrent characteristics of an excitable membrane. Corresponding equivalent circuit is shown by the use of time-invariant elements as a voltage-controlled oscillator. The design principle of the model is outlined. Two application examples are demonstrated: (1) Simulator of the excitable membrane for the investigation of a voltage-clamp instrument, which works in the low current and low voltage region. (2) Circuit model for an electric organ of a weakly electric fish, Apteronotus.