Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations.

Amyloid fibril formation is an intrinsic property of short peptides, non-disease proteins, and proteins associated with neurodegenerative diseases. Aggregates of the Aß and tau proteins, the α-synuclein protein, and the prion protein are observed in the brain of Alzheimer's, Parkinson's, and prion disease patients, respectively. Due to the transient short-range and long-range interactions of all species and their high aggregation propensities, the conformational ensemble of these devastating proteins, the exception being for the monomeric prion protein, remains elusive by standard structural biology methods in bulk solution and in lipid membranes. To overcome these limitations, an increasing number of simulations using different sampling methods and protein models have been performed. In this chapter, we first review our main contributions to the field of amyloid protein simulations aimed at understanding the early aggregation steps of short linear amyloid peptides, the conformational ensemble of the Aß40/42 dimers in bulk solution, and the stability of Aß aggregates in lipid membrane models. Then we focus on our studies on the interactions of amyloid peptides/inhibitors to prevent aggregation, and long amyloid sequences, including new results on a monomeric tau construct.

Bulk nanobubbles: Production and investigation of their formation/stability mechanism.

Nanobubbles (ΝΒs) have attracted concentrated scientific attention due to their unique physicochemical properties and large number of potential applications. In this study, a novel nanobubble generator with low energy demand, operating continuously, is presented. Air and oxygen bulk nanobubbles (NBs@air and NBs@O2) with narrow size distribution and outstanding stability were prepared in water solution. The bulk NBs' behavior was evaluated taking into consideration the hydrodynamic diameter and ζ-potential as a function of processing time, gas type, pH value and NaCl concentration. According to the results the optimum processing time was 30 min, whereas the effect of water salinity was stronger in NBs@O2 than NBs@air. In order to investigate further the NBs properties, Electron Paramagnetic Resonance (EPR) spectroscopy was applied for quantitative analysis of free radicals following the spin trapping methodology. The mechanism of bulk NBs' generation and their extremely long-time stability can be attributed mainly to the hydrogen bonding interactions. The formation of a diffusion layer, by absorption of OH- due to electrostatic interaction, contributing to negative surface charge, whereas the interaction of ions with the surface hydroxylic groups provide the equilibrium between the protonation and deprotonation of water and finally the formation of a stable interface layer. A remarkable highlight of this work is the long-time stability of generated bulk NBs which is up to three months.

Contribution analysis of methane production from food waste in bulk solution and on bio-electrode in a bio-electrochemical anaerobic digestion reactor.

Quantitative evaluation of methane production either in bulk sludge or biofilm on electrodes was performed in a bio-electrochemical anaerobic digestion (BEAD) reactor with a lower electrode surface area/reactor working volume (A/V) ratio (7.0 m2/m3). Methane production by electrochemical reaction was also evaluated in the BEAD reactor with a biofilm-free electrode under the same conditions as in other experimental sets. The contributions of bulk sludge, biofilms on the electrodes, and electrochemical reactions in the BEAD reactor, on methane production, were 70.2%, 29.8%, and 0%, respectively. The principal methane-producing reactions occurred in the bulk sludge facilitated by H2-dependent methylotrophic and hydrogenotrophic methanogens. Hydrogenotrophic methanogenesis was also the main methane-producing reaction in the biofilms attached to the bio-electrodes. Quantitative analysis of methane production (29.8%) in the biofilm revealed that bio-electrochemical processes involving H2 and direct bio-electrochemical methane production contributed 8.7% and less than 0.1%, respectively. Interestingly, biochemical processes (21.1%) contributed the most to the overall production of methane in the biofilm. Bulk sludge contributed more to methane production than the biofilm, but the methane production per unit mass of volatile solid on the electrodes was about 1.6-times higher than that of bulk sludge. Methane was not produced in the BEAD reactor with biofilm-free electrodes. Therefore, formation and maintenance of biofilms on the electrodes are essential for improved methane production in BEAD reactors.

Electroactive microorganisms in bulk solution contribute significantly to methane production in bioelectrochemical anaerobic reactor.

The role of anaerobic microorganisms suspended in the bulk solution on methane production was investigated in a bioelectrochemical anaerobic reactor with the electrode polarized at 0.5 V. The electron transfer from substrate to methane and hydrogen were 25% and 7.5%, respectively, in the absence of the anaerobic microorganisms in the bulk solution. As the anaerobic microorganisms increased to 4400 mg/L, the electrons transferred to methane increased to 83.3% but decreased to 0.3% in hydrogen. The electroactive microorganisms (EAM), including exoelectrogens and electrotrophs, enriched in the bulk solution that confirmed by the redox peaks in the cyclic voltammogram was proportional to the anaerobic microorganism. The methane yield based on COD removal was dependent on the anaerobic microorganisms in the bulk solution rather than on the bioelectrode surface. The EAM suspended in the bulk solution are enriched by the polarized electrode, and significantly improve methane production in bioelectrochemical anaerobic reactor.

Different Stability of DNA Origami Nanostructure between on Interface and in Bulk Solution.

DNA origami possesses a promising prospect in the fields including cancer therapy, enhancing catalytic activity, controllable nanorobot, etc. However, all the brilliant performances are based on its structural integrity, which is a big challenge for this technology. In this paper, we investigated the effects of interface on the stability of DNA origami and found that with treatments like heating, pH fluctuation, reducing ionic strength, the origami on interface always showed better stability than that in bulk solution because of the restriction imposed by the bond between solid surface and origami. Our results have great potential to inspire researchers to develop a complex that can provide origami an interface to strengthen its stability.

Counting ions and other nucleophiles at surfaces by chemical trapping.

The interfaces of membranes and other aggregates are determined by the polarity, electrical charge, molecular volume, degrees of motional freedom and packing density of the head groups of the amphiphiles. These properties also determine the type of bound ion (ion selectivity) and its local density, i.e. concentration defined by choosing an appropriate volume element at the aggregate interface. Bulk and local ion concentrations can differ by orders of magnitude. The relationships between ion (or other compound) concentrations in the bulk solvent and in the interface are complex but, in some cases, well established. As the local ion concentration, rather than that in the bulk, controls a variety of properties of membranes, micelles, vesicles and other objects of theoretical and applied interests, measurement of local (interfacial, bound) ion concentrations is of relevance for understanding and characterizing such aggregates. Many experimental methods for estimating ion distributions between the bulk solution and the interface provide indirect estimates because they are based on concentration-dependent properties, rather than concentration measurements. Dediazoniation, i.e. the loss of N2, of a substituted diazophenyl derivative provides a tool for determining the number of nucleophiles (including neutral or negatively charged ions) surrounding the diazophenyl derivative prior to the dediazoniation event. This reaction, defined as chemical trapping, and the appropriate reference points obtained in bulk solution allow direct measurements of local concentrations of a variety of nucleophiles at the surface of membranes and other aggregates. Here we review our contributions of our research group to the use, and understanding, of this method and applications of chemical trapping to the description of local concentrations of ions and other nucleophiles in micelles, reverse micelles, vesicles and solvent mixtures. Among other results, we have shown that interfacial water determines micellar shape, zwitterionic vesicle-forming amphiphiles display ion selectivity and urea does not accumulate at micellar interfaces. We have also shown that reaction products can be predicted from the composition of the initial state, even in non-ideal solvent mixtures, supporting the usefulness of chemical trapping as a method to determine local concentrations. In addition, we have analysed the mechanism of dediazoniation, both on theoretical and experimental basis, and concluded that the formation of a free phenyl cation is not a necessary part of the reaction pathway.

Direct electrochemistry and intramolecular electron transfer of ascorbate oxidase confined on L-cysteine self-assembled gold electrode.

A direct electrochemistry and intramolecular electron transfer of multicopper oxidases are of a great importance for the fabrication of these enzyme-based bioelectrochemical-devices. Ascorbate oxidase from Acremonium sp. (ASOM) has been successfully immobilized via a chemisorptive interaction on the l-cysteine self-assembled monolayer modified gold electrode (cys-SAM/AuE). Thermodynamics and kinetics of adsorption of ASOM on the cys-SAM/AuE were studied using cyclic voltammetry. A well-defined redox wave centered at 166±3mV (vs. Ag│AgCl│KCl(sat.)) was observed in 5.0mM phosphate buffer solution (pH7.0) at the fabricated ASOM electrode, abbreviated as ASOM/cys-SAM/AuE, confirming a direct electrochemistry, i.e., a direct electron transfer (DET) between ASOM and cys-SAM/AuE. The direct electrochemistry of ASOM was further confirmed by taking into account the chemical oxidation of ascorbic acid (AA) by O2 via an intramolecular electron transfer in the ASOM as well as the electrocatalytic oxidation of AA at the ASOM/cys-SAM/AuE. Thermodynamics and kinetics of the adsorption of ASOM on the cys-SAM/AuE have been elaborated along with its direct electron transfer at the modified electrodes on the basis of its intramolecular electron transfer and electrocatalytic activity towards ascorbic acid oxidation and O2 reduction. ASOM saturated surface area was obtained as 2.41×10(-11)molcm(-2) with the apparent adsorption coefficient of 1.63×10(6)Lmol(-1). The ASOM confined on the cys-SAM/AuE possesses its essential enzymatic function.