Here we consider the possibility to characterize the signal complexity of electroencephalograms using calculation of largest Lyapunov exponent explicitly from time series. This would help in detection of seizures, understanding and modeling epileptic activity. Baseline activity and spike-wave discharges (SWDs) were considered as regimes. Three channels relevant for absence epilepsy were studied: the parietal cortex, the ventroposterial medial nucleus of thalamus, and the reticular thalamic nucleus. Experimental data and two types of models were investigated. The result show that SWDs often treated as more or less regular oscillations are characterized by large positive Lyapunov exponent, not very different from the value obtained for baseline activity. The mesoscale network model of epilepsy is mostly able to reproduce this phenomenon, including absolute values. The more simple neuron mass model exhibits Lyapunov exponent during SWDs twice smaller than in baseline.

<abstract> <p>This paper reports the analysis of the intramolecular OH stretching band obtained by Fourier Transform Infrared (FTIR) spectroscopy measurements. In order to characterize the effect of montmorillonite on the properties of Bovine Serum Albumin (BSA) the two-state model is adopted for the analysis of the OH stretching band. We assume that the OH stretching can be divided into two different states of inter-molecular bonding. The results of this experimental work confirm that the montmorillonite leads to a stabilization of the BSA structure. Also, the analysis of the spectra temperature dependence shows a montmorillonite-induced higher thermal stability of the BSA in respect to pristine BSA. Thus, this paper highlights the effectiveness of montmorillonite as thermal bio-protector. A FTIR analysis was carried out to investigate the interaction of Montmorillonite with BSA. Two different approaches, i.e. Spectral Distance and Wavelet analyses, constitute two effective and innovative approaches for the characterization of the thermal properties of pristine BSA and of BSA in the presence of Montmorillonite. The results allowed us to consider as BSA in the presence of Montmorillonite has a lower spectral sensitivity when the temperature changes and, therefore, the role of Montmorillonite as a thermal bio-protector is motivated.</p> </abstract>

The interplay between lipids and embedded proteins in plasma membrane is complex. Membrane proteins affect the stretching or disorder of lipid chains, transbilayer movement and lateral organization of lipids, thus influencing biological processes such as fusion or fission. Membrane lipids can regulate some protein functions by modulating their structure and organization. Cholesterol is a lipid of cell membranes that has been intensively investigated and found to be associated with some membrane proteins and to play an important role in diseases. Human calcitonin (hCt), an amyloid-forming peptide, is a small peptide hormone. The oligomerization and fibrillation processes of hCt can be modulated by different factors such as pH, solvent, peptide concentration, and chaperones. In this work, we investigated the role of cholesterol in hCt incorporation and channel formation in planar lipid membranes made up of palmitoyl-oleoyl-phosphatidylcholine in which no channel activity had been found. The results obtained in this study indicate that cholesterol promotes hCt incorporation and channel formation in planar lipid membranes, suggesting a possible role of sterol as a lipid target for hCt.

The constant increase of computational power has made feasible to investigate the folding mechanism of small proteins using molecular dynamics (MD). Metal-binding proteins (metalloproteins) are usually complicated to model, largely due to the presence of the metal cofactor. Thus, the study of metal-coupled folding is still challenging. In this work, we addressed the folding process of Pyrococcus furiosus rubredoxin (PfRd), a 53-residue protein binding a single iron ion, using different MD methods. Starting from an extended conformation of the polypeptide chain where we preserved the coordination of the metal ion, a classical MD simulation and an extensive accelerated MD run were performed to reconstruct the folding process of the metal-bound protein. For comparison, we simulated also the dynamics of folded PfRd devoid of the metal cofactor (apo-form), starting from the folded structure. For these MD trajectories, we computed various structural and biochemical properties. In addition, we took advantage of available experimental data to quantify the degree to which our simulations sampled conformations close to the native folded state. We observed that the compaction of the hydrophobic core is the main feature driving the folding of the structure. However, we could not reach a fully folded conformation within our trajectories, because of the incomplete removal of the solvent from the core. Altogether, the various MD simulations, including that of the folded apo-form of the protein, suggest that an improvement in the accuracy of the protein force-field is still needed.

Protein-DNA interactions are pivotal for many essential biological processes. Atomic force microscopy (AFM) imaging of protein-DNA systems involved in DNA target site search, identification, and processing by proteins has contributed invaluable information to our understanding of the underlying mechanisms. The single molecule 3D resolution of AFM enables us to uncover stoichiometries and conformational properties of protein-DNA complexes. Its molecular resolution places AFM at the interface between the atomic resolution achievable by crystallography and the comparably poor (typically > hundred nanometers) spatial resolution of optical microscopy. Furthermore, the transient character of protein interactions with nonspecific DNA sites, for example during their target site search renders these complexes difficult to resolve by standard ensemble methods. Here, we review current applications and capabilities of as well as novel advances in AFM imaging in protein-DNA interaction studies.

Cell movement is a complex phenomenon that is fundamental to many physiological and disease processes. It has been the subject of study for more than 200 years, and yet we still do not fully understand this process. Cell movement consists of four steps; protrusion and adhesion formation at the front followed by contractile force generation and detachment at the rear. Much is known about the molecular mechanisms underlying these steps however, it is not clear how they are integrated at the cellular level. Part of the problem is the incorporation of a vast amount of molecular and biophysical data into a basic working model of motility. A promising solution to this problem is the combined approach of mathematical modeling and experimentation, using the fish epithelial keratocyte as a model system. The goal of this review is to illustrate, using examples, how the reciprocity between experimentation and modeling can provide new insights into the mechanism of cell motility. Several modeling approaches are described including: conceptual models, “bottom-up” models based on molecular dynamics, and “top-down” models that consider cell shape and movement. The Graded Radial Extension (GRE) model forms the basis of a several mathematical models, from a simpler 1D model that links actin filament dynamics to cell shape, to more complex 2D and 3D simulations of keratocyte movement. Together these models suggest that cell movement emerges from the mechanical interaction between different sub-processes of motility, namely, the treadmilling actin meshwork, the plasma membrane, adhesion turnover and contractile force generation. In addition, the feedback regulation between these sub-processes is important for the robust, self-organizing nature of movement.

A mutant of cutinase-like enzyme from Saccharomonospora viridis AHK190, Cut190_S226P/R228S, designated as Cut190*, possesses high-thermal stability and has high polyethylene terephthalate (PET)-degrading activity. The functional characterizations of PET-degrading enzymes are generally conducted using accessible substrates such as poly(butylene succinate-co-adipate) (PBSA) and p-nitrophenyl butyrate (pNPB), even though their structures are different from that of PET. Bis(2-hydroxyethyl) terephthalate (BHET) is a component of PET, and the structure is similar to that of PET compared to PBSA and pNPB. Therefore, the analysis using BHET as the substrate is important to evaluate effective PET degradation. In this study, we analyzed the enzymatic activity of Cut190* using BHET under various conditions including Ca2+ concentration and pressure. Although terephthalate was supposed to be the final product, the intermediate product, mono(2-hydroxyethyl) terephthalate (MHET), was the only product generated, possibly due to the low binding affinity of MHET. The Cut190* activity towards BHET was observed even in the absence of Ca2+ and increased with increasing Ca2+ concentration, which is similar to its activity towards pNPB, but different from its activity towards PBSA. The difference can be attributed to the size of substrates. We also analyzed the activities of Cut190* and another high-activity mutant, Cut190*Q138A/D250C-E296C, under high pressures up to 400 MPa. BHET was non-enzymatically hydrolyzed under high pressure at 37 ℃. Enzyme activities were maintained under high pressures, and degradation of BHET in the presence of enzyme was higher than that in the absence of enzyme. Furthermore, the structural analysis of Cut190* under high pressure using Fourier transform infrared spectroscopy showed that most of the enzyme molecules were populated in the native structure below 400 MPa. These results indicate that BHET can contribute to the effective functional analysis of PET-degrading enzyme, and the combination of enzyme and pressure can lead to eco-friendly PET degradation.

Cell surface receptors are involved in numerous important biological processes including embryogenesis, tissue differentiation, and cellular homeostasis. Among them, mechanosensitive ion channels play an essential role in cellular functions of every cell including neurons, cardiomyocytes, and osteocytes. Here, we discuss types, roles, structures, and biophysical factors that affect the functions of mechanosensitive ion channels.

The research of the interaction between bacteria-surface has great importance for titanium biomedical applications once microorganisms offer risks because promoting implant loss. Therefore, study bacterial adhesion and colonization on titanium is interesting because are principal factors infections pathogeny on biomaterials. In this study, commercial grade II titanium was submitted to nitriding treatment to plasma at 2.2 mbar, using gas mixtures of 80% hydrogen (H2) and 20% nitrogen (N2) during 1 hour and 3 hour. The surfaces were physically and chemically characterized. In order to evaluate bacterial response, the surfaces were exposed to <em>Pseudomonas aeruginosa</em>. The titanium surface modified in nitriding plasma, although exposes a higher roughness as compared with untreated samples, exhibited lower bacterial growth. The nitrided sample for 3 hour exhibited the higher amount of TiN phase and the higher concentration of atomic nitrogen on surface and lower bacterial adhered count. These results were confirmed by scanning electron microscopy. Based on these results can be said to the thermochemical treatment of plasma nitriding on titanium samples results a significant reduction of adherence of <em>Pseudomonas aeruginosa</em>. It was found that the Ti surface nitrided offers significant reduction of bacterial adherence which prevent biofilm formation and offersing lower risk of infection and implant remotion.

Lipid vesicles, or liposomes have been widely studied both as a model for cell membranes and for applications such as drug delivery. As a rule, their aqueous environment (in vitro or in vivo) contains various degradation agents, ranging from free radicals to acids and enzymes. This paper investigates the degradation of lipid vesicles as a function of environmental conditions using 3d Monte-Carlo simulations. The time-scale for bilayer degradation is found to be independent of the liposome size, but highly sensitive to the concentration of degradation molecules in solution and to the rate of the degradation reaction.