Si/Al and metal loading effects on the templated synthesis of Ni nanowires in CAN and MOR zeolite frameworks

Zeolites with 1D pore channels, such as cancrinite (CAN) and mordenite (MOR), have the potential to be used as templates in the synthesis of subnanometre metal nanowires. Previous studies show a strong correlation between the location of Al atoms in zeolites and the positioning of the metal atoms inside the zeolite framework. Thus, Metropolis Monte Carlo simulations were used here to study the behaviour of Ni atoms within the CAN- and MOR-type zeolites at different Si/Al ratios and Ni loadings. It was found for both zeolite frameworks that a lower Si/Al ratio favoured energetically the positioning of Ni atoms in the 1D pore channels and that higher loadings of Ni promote the formation of 1D Ni structures. These results suggest that it is possible to use zeolites with the CAN and MOR frameworks and low Si/Al ratio as effective templates for the synthesis of metal nanowires.     

Molecular simulation of zeolite flexibility

We present a transferable force field able to model the structure of zeolites when different cation types are considered. Based on simple functional forms and interactions, it can be easily implemented in most common molecular simulation codes. The optimised force field is validated on structural properties (lattice parameters and Si–O–Al angles) for a large variety of zeolites, including faujasites of different Si/Al ratio and different extra-framework cation types (Li⁺, Na⁺, K⁺, Mg²⁺, Ca²⁺ and Co²⁺). The transferability of the force field was successfully tested on zeolites of different topologies such as FAU, LTA, MFI, FER and TON. The predictive capabilities of the potential were tested on structural deformations of alkaline earth Na, Co-X faujasites with different ion-exchange ratios.     

A comparative study of the adsorption of water and methanol in zeolite BEA: a molecular simulation study

Grand canonical Monte Carlo simulations were carried out to study the equilibrium adsorption concentration of methanol and water in all-silica BEA zeolite and HBEA zeolites with different Si/Al ratios over a wide range of temperatures and loadings. These zeolites have oval-shaped channels with one side longer than the other. Water sorption into the hydrophobic BEA zeolite had a sharp transition with its sorption going from zero to near full capacity over a very small pressure range. Methanol sorption was much more gradual with respect to pressure. With the addition of hydrophilic sites for the HBEA zeolites by decreasing the Si/Al ratio, adsorption at lower pressures increased significantly for water and methanol. At higher loadings, water and methanol adsorption were found to behave in fundamentally different ways. Water structures in the zeolite channels formed hydrogen-bonded chains while maximising contact with the surfaces on the longer edges of the zeolite channels. Methanol molecules, in contrast, formed very few hydrogen bonds between themselves, with their hydroxyl groups primarily binding with surface of the shorter edge of the zeolite channels and their methyl groups located near the middle of the zeolite channels. The addition of hydrophilic groups in the HBEA zeolites strongly influenced positions of the methanol hydroxyl groups at high loadings, but did not have a significant effect on water structure.     

Molecular interactions of acetylcholinesterase with senile plaques

Acetylcholinesterase (AChE) present in Alzheimer plaques is resistant to low pH, anti-ChE inhibitors and high substrate concentrations in comparison with the free enzyme. Kinetic and pharmacological studies of AChE-amyloid complexes indicate that steric hindrance by the amyloid over the gorge and the peripheral site of AChE is responsible for these effects.     

Specific interactions of alcohols and non‐alcohols with a biologically active boronic acid derivative: a spectroscopic study

The photophysical properties of 4‐fluoro‐2‐methoxyphenyl boronic acid (4FMPBA) are characterized using absorption and fluorescence techniques in series of non‐alcohols and alcohols. The results are analyzed using different solvent polarity functions and Kamlet and Catalan's multiple regression approaches. The excited state dipole moment and change in dipole moment are calculated using both the solvatochromic shift method and Reichardt's microscopic solvent polarity parameter . The ground state dipole moment is evaluated using quantum chemical calculations. It is found that general solute–solvent and hydrogen bond interactions are operative in this system. A red shift of ~ 9 nm in the emission spectra is observed with an increase in the solvent polarity, which depicts π→π^* transitions, as well as the possibility of an intramolecular charge transfer (ICT) character in the emitting singlet state of 4FMPBA. The relative quantum yield, radiative and non‐radiative decay constants are calculated in alkanes and alcohols using the single point method. It is found that the quantum yield of the molecule varies from 16.81% to 50.79% with the change in solvent polarity, indicating the dependence of fluorescence on the solvent environment. Copyright © 2015 John Wiley & Sons, Ltd.     

Molecular simulation of water removal from simple gases with zeolite NaA

Water vapor removal from some simple gases using zeolite NaA was studied by molecular simulation. The equilibrium adsorption properties of H(2)O, CO, H(2), CH(4) and their mixtures in dehydrated zeolite NaA were computed by grand canonical Monte Carlo simulations. The simulations employed Lennard-Jones + Coulomb type effective pair potential models, which are suitable for the reproduction of thermodynamic properties of pure substances. Based on the comparison of the simulation results with experimental data for single-component adsorption at different temperatures and pressures, a modified interaction potential model for the zeolite is proposed. In the adsorption simulations with mixtures presented here, zeolite exhibits extremely high selectivity of water to the investigated weakly polar/non-polar gases demonstrating the excellent dehydration ability of zeolite NaA in engineering applications.     

Probing the interactions of alcohols with biological membranes with the fluorescent probe Prodan.

Prodan [6-propionyl-2-(dimethylamine)naphthalene] is a hydrophobic fluorescent probe which is extremely sensitive to both the polarity and the hydrogen-bond donating capacity of the solvent. In binary mixtures of solvents, the hydrogen-bond donating effect on Prodan fluorescence saturates at relatively low concentrations of protic solvent while the polarity effect is proportional to the mixture's dielectric constant. The fluorescence emission maximum is approximately a linear function of the dielectric constant in both protic and aprotic solvents, and this allows estimation of the dielectric constant in both environments. In phospholipid bilayers and biological membranes, Prodan exhibits two distinct emission peaks: blue (430-445 nm) and green (470-505 nm). Temperature determines the relative intensity of the two peaks, but their wavelengths depend on the type of membrane and appear to reflect a specific membrane environment. In phospholipid vesicles, alcohols reduce the fluorescence intensity of the blue peak and produce a red-shift in the emission maximum of the green peak. Taking the partition coefficients of the alcohols into account, short-chain alcohols are much more effective than longer-chain alcohols in red-shifting the emission maximum of the green peak. Alcohols have similar effects on Prodan fluorescence in liver microsomal and mitochondrial membranes, synaptosomal membranes, and red blood cell plasma membranes. However, in liver organelle membranes the red-shift of the green peak is the dominant effect while in plasma membranes the quenching of the fluorescence of the blue peak is dominant. These effects are observed at low (pharmacological) ethanol concentrations and provide a unique tool for probing the interactions of ethanol with biological membranes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Molecular interactions of human Exo1 with DNA

Human Exo1 is a member of the RAD2 nuclease family with roles in replication, repair and recombination. Despite sharing significant amino acid sequence homology, the RAD2 proteins exhibit disparate nuclease properties and biological functions. In order to identify elements that dictate substrate selectivity within the RAD2 family, we sought to identify residues key to Exo1 nuclease activity and to characterize the molecular details of the human Exo1–DNA interaction. Site-specific mutagenesis studies demonstrate that amino acids D78, D173 and D225 are critical for Exo1 nuclease function. In addition, we show that the chemical nature of the 5′-terminus has a major impact on Exo1 nuclease efficiency, with a 5′-phosphate group stimulating degradation 10-fold and a 5′-biotin inhibiting degradation 10-fold (relative to a 5′-hydroxyl moiety). An abasic lesion located within a substrate DNA strand impedes Exo1 nucleolytic degradation, and a 5′-terminal abasic residue reduces nuclease efficiency 2-fold. Hydroxyl radical footprinting indicates that Exo1 binds predominantly along the minor groove of flap DNA, downstream of the junction. As will be discussed, our results favor the notion that the single-stranded DNA structure is pinched by the helical arch of the protein and not threaded through this key recognition loop. Furthermore, our studies indicate that significant, presumably biologically relevant, differences exist between the active site dynamics of Exo1 and Fen1.     

Molecular and functional interactions of alpha-synuclein with Rab3a

Alpha-synuclein (a-Syn) is a presynaptic protein, the misfolding of which is associated with Parkinson’s disease. Rab GTPases are small guanine nucleotide binding proteins that play key roles in vesicle trafficking and have been associated with a-Syn function and dysfunction. a-Syn is enriched on synaptic vesicles, where it has been reported to interact with GTP-bound Rab3a, a master regulator of synaptic vesicle trafficking. a-Syn is known to bind weakly to Rab8a in solution via a positively charged patch, but the physiological implications of such interactions have not been explored. Here, we investigate direct interactions between a-Syn and Rab3a in solution and on lipid membranes using NMR spectroscopy. We find that the C terminus of a-Syn interacts with Rab3a in a manner similar to its previously reported interaction with Rab8a. While weak in solution, we demonstrate that this interaction becomes stronger when the proteins are bound to a membrane surface. The Rab3a binding site for a-Syn is similar to the surface that contacts the Rab3a effector rabphilin-3A, which modulates the enzymatic activity of Rab3a. Accordingly, we show that a-Syn inhibits GTP hydrolysis by Rab3a and that inhibition is more potent on the membrane surface, suggesting that their interaction may be functionally relevant. Finally, we show that phosphorylation of a-Syn residue Ser 129, a modification associated with Parkinson’s disease pathology, enhances its interactions with Rab3a and increases its ability to inhibit Rab3a GTP hydrolysis. These results represent the first observation of a functional role for synuclein-Rab interactions and for a-Syn Ser 129 phosphorylation.     

Protein-hydrocarbon interactions. Interactions of various proteins with decane in the presence of alcohols

1. Solutions of proteins were subjected to gentle agitation in the presence of small quantities of decane containing different alcohols. 2. Some of the protein was lost from solution and adsorbed on the surface of the emulsion formed; at the same time some decane was bound to the protein remaining in solution. 3. Comparison of these results with those obtained with pure decane suggests that a mixed film of protein+alcohol is formed on the surface of the emulsion. 4. If the concentration of alcohol in decane is increased the amount of protein adsorbed on the emulsion is decreased. This phenomenon was used to compare the effect of different alcohols in disrupting the hydrophobic interactions between proteins and hydrocarbons.     

Phosphatidyl alcohols: Effect of head group size on domain forming properties and interactions with sterols

In this study, we have examined the membrane properties and sterol interactions of phosphatidyl alcohols varying in the size of the alcohol head group coupled to the sn-3-linked phosphate. Phosphatidyl alcohols of interest were dipalmitoyl derivatives with methanol (DPPMe), ethanol (DPPEt), propanol (DPPPr), or butanol (DPPBu) head groups. The Phosphatidyl alcohols are biologically relevant, because they can be formed in membranes by the phospholipase D reaction in the presence of alcohol. The melting behavior of pure phosphatidyl alcohols and mixtures with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) or cholesterol was assessed using high sensitivity differential scanning calorimetry (DSC). DPPMe had the highest melting temperature (∼ 49 °C), whereas the other phosphatidyl alcohols had similar melting temperatures as DPPC (∼ 40-41 °C). All phosphatidyl alcohols, except DPPMe, also showed good miscibility with DPPC. The effects of cholesterol on the melting behavior and membrane order in multilamellar bilayer vesicles were assessed using steady-state anisotropy of 1,6-diphenyl-1,3,5-hexatriene (DPH) and DSC. The ordering effect of cholesterol in the fluid phase was lower for all phosphatidyl alcohols as compared to DPPC and decreased with increasing head group size. The formation of ordered domains containing the phosphatidyl alcohols in complex bilayer membranes was determined using fluorescence quenching of DPH or the sterol analogue cholesta-5,7,(11)-trien-3-beta-ol (CTL). The phosphatidyl alcohols did not appear to form sterol-enriched ordered domains, whereas DPPMe, DPPEt appeared to form ordered domains in the temperature window examined (10-50 °C). The partitioning of CTL into bilayer membranes containing phosphatidyl alcohols was to a small extent increased for DPPMe and DPPEt, but in general, sterol interactions were weak or unfavorable for the phosphatidyl alcohols. Our results show that the biophysical and sterol interacting properties of phosphatidyl alcohols, having identical acyl chain structures, are markedly dependent on the size of the head group.     

Molecular interactions of ribosomal components

Summary Five of the 30S ribosomal proteins from E. coli were tested for their ability to bind to 16S ribosomal RNA. Only one of these, S15, can form a complex with the RNA. Quantitative measurements as well as competition experiments show that the RNA binding site for the attachment of S15 is specific for this protein.These experiments complete our analysis of all 21 of the 30S ribosomal proteins. Five of these have now been shown to form a site-specific complex with 16S RNA. These are S4, S7, S8, S15 and S20. The relationship of these data to the assembly and structure of the ribosome are discussed.     

Molecular mapping of thrombin-receptor interactions

In addition to its procoagulant and anticoagulant roles in the blood coagulation cascade, thrombin works as a signaling molecule when it interacts with the G-protein coupled receptors PAR1, PAR3, and PAR4. We have mapped the thrombin epitopes responsible for these interactions using enzymatic assays and Ala scanning mutagenesis. The epitopes overlap considerably, and are almost identical to those of fibrinogen and fibrin, but a few unanticipated differences are uncovered that help explain the higher (90-fold) specificity of PAR1 relative to PAR3 and PAR4. The most critical residues for the interaction with the PARs are located around the active site where mutations affect recognition in the order PAR4 > PAR3 > PAR1. Other important residues for PAR binding cluster in a small area of exosite I where mutations affect recognition in the order PAR1 > PAR3 > PAR4. Owing to this hierarchy of effects, the mutation W215A selectively compromises PAR4 cleavage, whereas the mutation R67A abrogates the higher specificity of PAR1 relative to PAR3 and PAR4. 3D models of thrombin complexed with PAR1, PAR3, and PAR4 are constructed and account for the perturbations documented by the mutagenesis studies.     

Molecular interactions of ribosomal components

Summary The site-specific complex formed between 16S RNA and the 30S ribosomal protein S4 from Escherichia coli has been degraded with pancreatic ribonuclease. We have recovered the nuclease-resistant RNA from this complex; we call it S4aR. S4aR will bind to S4, but it will not bind to the other 30S proteins that can form site-specific complexes with 16S RNA. The data presented here as well as elsewhere (Schaup et al., 1971b) show that S4aR has a mass of about 150000 daltons and that it is made up of several separate RNA fragments, each of which enters the complex with S4. We conclude that S4 interacts with several separate binding sites on the RNA and that these probably contain a great deal of double stranded structure.     

Molecular interactions of ribosomal components

Summary The formation of a complex between individual 30S ribosomal proteins and 16S ribosomal RNA was studied by three techniques: zone centrifugation, molecular-sieve chromatography and electrophoresis in polyacrylamide gels. Five 30S proteins form a stable complex with the RNA under the conditions used to assemble ribosomes. Specific and nonspecific complex formation can be distinguished by an analysis of the concentration-dependence for complex formation. Similarly, competition experiments between heterologous proteins that bind to RNA can also be used to establish the uniquness of the RNA binding sites for ribosomal proteins. The data show that four of the five proteins bind to unique sites on the RNA. The fifth protein binds nonspecifically to the RNA. In addition, cooperative interactions between several proteins were observed; these enhance the interaction of proteins with the 16S RNA. A partial assembly sequence for the 30S ribosomal subunit is presented.