The folding of knotted proteins: insights from lattice simulations

We carry out systematic Monte Carlo simulations of Go lattice proteins to investigate and compare the folding processes of two model proteins whose native structures differ from each other due to the presence of a trefoil knot located near the terminus of one of the protein chains. We show that the folding time of the knotted fold is larger than that of the unknotted protein and that this difference in folding time is particularly striking in the temperature region below the optimal folding temperature. Both proteins display similar folding transition temperatures, which is indicative of similar thermal stabilities. By using the folding probability reaction coordinate as an estimator of folding progression we have found out that the formation of the knot is mainly a late folding event in our shallow knot system.

Biodegradation rate constants in different NF/UF fractions of cork processing wastewaters

Cork processing wastewater is an aqueous complex mixture of organic compounds that have been extracted from cork planks during the boiling process. These compounds, such as polysaccharides and polyphenols, have different biodegradability rates, which depend not only on the natureof the compound but also on the size of the compound. The aim of this study is to determine the biochemical oxygen demands (BOD) and biodegradationrate constants (k) for different cork wastewater fractions with different organic matter characteristics. These wastewater fractions were obtained using membrane separation processes, namely nanofiltration (NF) and ultrafiltration (UF). The nanofiltration and ultrafiltration membranes molecular weight cut-offs (MWCO) ranged from 0.125 to 91 kDa. The results obtained showed that the biodegradation rate constant for the cork processing wastewater was around 0.3 d(-1) and the k values for the permeates varied between 0.27-0.72 d(-1), being the lower values observed for permeates generated by the membranes with higher MWCO and the higher values observed for the permeates generated by the membranes with lower MWCO. These higher k values indicate that the biodegradable organic matter that is permeated by the membranes with tighter MWCO is more readily biodegradated.

Three-dimensional patchy lattice model for empty fluids

The phase diagram of a simple model with two patches of type A and ten patches of type B (2A10B) on the face centred cubic lattice has been calculated by simulations and theory. Assuming that there is no interaction between the B patches the behavior of the system can be described in terms of the ratio of the AB and AA interactions, r. Our results show that, similarly to what happens for related off-lattice and two-dimensional lattice models, the liquid-vapor phase equilibria exhibit reentrant behavior for some values of the interaction parameters. However, for the model studied here the liquid-vapor phase equilibria occur for values of r lower than 1/3, a threshold value which was previously thought to be universal for 2AnB models. In addition, the theory predicts that below r = 1/3 (and above a new condensation threshold which is < 1/3) the reentrant liquid-vapor equilibria are so extreme that it exhibits a closed loop with a lower critical point, a very unusual behavior in single-component systems. An order-disorder transition is also observed at higher densities than the liquid-vapor equilibria, which shows that the liquid-vapor reentrancy occurs in an equilibrium region of the phase diagram. These findings may have implications in the understanding of the condensation of dipolar hard spheres given the analogy between that system and the 2AnB models considered here. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4771591]

Three-dimensial patchy lattice model: Ring formation and phase separation

We investigate the structural and thermodynamic properties of a model of particles with 2 patches of type A and 10 patches of type B. Particles are placed on the sites of a face centered cubic lattice with the patches oriented along the nearest neighbor directions. The competition between the self- assembly of chains, rings, and networks on the phase diagram is investigated by carrying out a systematic investigation of this class of models, using an extension ofWertheim's theory for associating fluids and Monte Carlo numerical simulations. We varied the ratio r epsilon(AB)/epsilon(AA) of the interaction between patches A and B, epsilon(AB), and between A patches, epsilon(AA) (epsilon(BB) is set to theta) as well as the relative position of the A patches, i.e., the angle. between the (lattice) directions of the A patches. We found that both r and theta (60 degrees, 90 degrees, or 120 degrees) have a profound effect on the phase diagram. In the empty fluid regime (r < 1/2) the phase diagram is reentrant with a closed miscibility loop. The region around the lower critical point exhibits unusual structural and thermodynamic behavior determined by the presence of relatively short rings. The agreement between the results of theory and simulation is excellent for theta = 120 degrees but deteriorates as. decreases, revealing the need for new theoretical approaches to describe the structure and thermodynamics of systems dominated by small rings. (C) 2014 AIP Publishing LLC.

Three-Dimensional patchy lattice model for empty fluids

The phase diagram of a simple model with two patches of type A and ten patches of type B (2A10B) on the face centred cubic lattice has been calculated by simulations and theory. Assuming that there is no interaction between the B patches the behavior of the system can be described in terms of the ratio of the AB and AA interactions, r. Our results show that, similarly to what happens for related off-lattice and two-dimensional lattice models, the liquid-vapor phase equilibria exhibit reentrant behavior for some values of the interaction parameters. However, for the model studied here the liquid-vapor phase equilibria occur for values of r lower than 1/3, a threshold value which was previously thought to be universal for 2AnB models. In addition, the theory predicts that below r = 1/3 (and above a new condensation threshold which is < 1/3) the reentrant liquid-vapor equilibria are so extreme that it exhibits a closed loop with a lower critical point, a very unusual behavior in single-component systems. An order-disorder transition is also observed at higher densities than the liquid-vapor equilibria, which shows that the liquid-vapor reentrancy occurs in an equilibrium region of the phase diagram. These findings may have implications in the understanding of the condensation of dipolar hard spheres given the analogy between that system and the 2AnB models considered here.

The condensation and ordering of models of empty liquids

We consider a simple model consisting of particles with four bonding sites ("patches"), two of type A and two of type B, on the square lattice, and investigate its global phase behavior by simulations and theory. We set the interaction between B patches to zero and calculate the phase diagram as the ratio between the AB and the AA interactions, epsilon(AB)*, varies. In line with previous work, on three-dimensional off-lattice models, we show that the liquid-vapor phase diagram exhibits a re-entrant or "pinched" shape for the same range of epsilon(AB)*, suggesting that the ratio of the energy scales - and the corresponding empty fluid regime - is independent of the dimensionality of the system and of the lattice structure. In addition, the model exhibits an order-disorder transition that is ferromagnetic in the re-entrant regime. The use of low-dimensional lattice models allows the simulation of sufficiently large systems to establish the nature of the liquid-vapor critical points and to describe the structure of the liquid phase in the empty fluid regime, where the size of the "voids" increases as the temperature decreases. We have found that the liquid-vapor critical point is in the 2D Ising universality class, with a scaling region that decreases rapidly as the temperature decreases. The results of simulations and theoretical analysis suggest that the line of order-disorder transitions intersects the condensation line at a multi-critical point at zero temperature and density, for patchy particle models with a re-entrant, empty fluid, regime. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3657406]

Bioconversion of D-glucose into D-glucosone by immobilized glucose 2-oxidase from Coriolus versicolorat moderate pressures

The immobilized glucose 2-oxidase (pyranose oxidase, pyranose:oxygen-2-oxidoreductase, EC 1.1.3.10) from Coriolus versicolor was used to convert D-glucose into D-glucosone at moderate pressures, up to 150 bar, with compressed air in a modified commercial batch reactor. Several parameters affecting biocatalysis at moderate pressures were investigated as follows: pressure, different forms of immobilized biocatalysts, glucose concentration, pH, temperature and the presence of catalase. Glucose 2-oxidase (GOX2) was purified by immobilized metal affinity chromatography on epoxy-activated Sepharose 6B-IDA-Cu(II) column at pH 6.0. Purified enzyme and catalase were immobilized into a polyethersulfone (PES) membrane in the presence of glutaraldehyde and gelatin. Enhancement of the bioconversion of D-glucose was done by the pressure since an increase in the pressure with compressed air increases the conversion rates. The optimum temperature and pH for bioconversion of D-glucose were found to be 62 degrees C and pH 6.0, respectively and the activation energy (E(a)) was 28.01 kJ mol(-1). The apparent kinetic constants (V(max)' K(m)', K(cat)' and K(cat)/K(m)') for this bioconversion were 2.27 U mg(-1) protein, 11.15 mM, 8.33 s(-1) and 747.38 s(-1) M(-1), respectively. The immobilized biomass of C. versicolor as well as crude extract containing GOX2 activity were also useful for bioconversion of D-glucose at 65 bar with a yield of 69.9 +/- 3.8% and 91.3 +/- 1.2%, respectively. The immobilized enzyme was apparently stable for several months without any significant loss of enzyme activity. On the other hand, this immobilized enzyme was also stable at moderate pressures, since such pressures did not affect significantly the enzyme activity. (C) 2010 Elsevier Ltd. All rights reserved.

Boron-doped nanocrystalline silicon thin films for solar cells

This article reports on the structural, electronic, and optical properties of boron-doped hydrogenated nanocrystalline silicon (nc-Si: H) thin films. The films were deposited by plasma-enhanced chemical vapour deposition (PECVD) at a substrate temperature of 150 degrees C. Crystalline volume fraction and dark conductivity of the films were determined as a function of trimethylboron-to-silane flow ratio. Optical constants of doped and undoped nc-Si: H were obtained from transmission and reflection spectra. By employing p(+) nc-Si: H as a window layer combined with a p' a-SiC buffer layer, a-Si: H-based p-p'-i-n solar cells on ZnO:Al-coated glass substrates were fabricated. Device characteristics were obtained from current-voltage and spectral-response measurements. (C) 2011 Elsevier B. V. All rights reserved.

Communication: The criticality of self-assembled rigid rods on triangular lattices

The criticality of self-assembled rigid rods on triangular lattices is investigated using Monte Carlo simulation. We find a continuous transition between an ordered phase, where the rods are oriented along one of the three (equivalent) lattice directions, and a disordered one. We conclude that equilibrium polydispersity of the rod lengths does not affect the critical behavior, as we found that the criticality is the same as that of monodisperse rodson the same lattice, in contrast with the results of recently published work on similar models. (C) 2011 American Institute of Physics. [doi:10.1063/1.3556665]

Trends in properties of para-substituted 3-(phenylhydrazo)pentane-2,4-diones

Trends between the Hammett's sigma(p) and related normal sigma(n)(p), inductive sigma(I), resonance sigma(R), negative sigma(-)(p) and positive sigma(+)(p) polar conjugation and Taft's sigma(o)(p) substituent constants and the N-H center dot center dot center dot O distance, delta(N-H) NMR chemical shift, oxidation potential (E-p/2(ox), measured in this study by cyclic voltammetry (CV)) and thermodynamic parameters (pK, Delta G(0), Delta H-0 and Delta S-0) of the dissociation process of unsubstituted 3-(phenylhydrazo)pentane-2,4-dione (HL1) and its para-substituted chloro (HL2), carboxy (HL3), fluoro (HL4) and nitro (HL5) derivatives were recognized. The best fits were found for sigma(p) and/or sigma(-)(p) in the cases of d(N center dot center dot center dot O), delta(N-H) and E-p/2(ox), showing the importance of resonance and conjugation effects in such properties, whereas for the above thermodynamic properties the inductive effects (sigma(I)) are dominant. HL2 exists in the hydrazo form in DMSO solution and in the solid state and contains an intramolecular H-bond with the N center dot center dot center dot O distance of 2.588(3)angstrom. It was also established that the dissociation process of HL1-5 is non-spontaneous, endothermic and entropically unfavourable, and that the increase in the inductive effect (sigma(I)) of para-substitutents (-H < -Cl < -COOH < -F < -NO2) leads to the corresponding growth of the N center dot center dot center dot O distance and decrease of the pK and of the changes of Gibbs free energy, of enthalpy and of entropy for the HL1-5 acid dissociation process. The electrochemical behaviour of HL1-5 was interpreted using theoretical calculations at the DFT/HF hybrid level, namely in terms of HOMO and LUMO compositions, and of reactivities induced by anodic and cathodic electron-transfers. Copyright (C) 2010 John Wiley & Sons, Ltd.

Unified min-max and interlacing theorems for linear operators

There exist striking analogies in the behaviour of eigenvalues of Hermitian compact operators, singular values of compact operators and invariant factors of homomorphisms of modules over principal ideal domains, namely diagonalization theorems, interlacing inequalities and Courant-Fischer type formulae. Carlson and Sa [D. Carlson and E.M. Sa, Generalized minimax and interlacing inequalities, Linear Multilinear Algebra 15 (1984) pp. 77-103.] introduced an abstract structure, the s-space, where they proved unified versions of these theorems in the finite-dimensional case. We show that this unification can be done using modular lattices with Goldie dimension, which have a natural structure of s-space in the finite-dimensional case, and extend the unification to the countable-dimensional case.

Production of hydroxamic acids by immobilized Pseudomonas aeruginosa cells Kinetic analysis in reverse micelles

Intact cells from Pseudomonas aeruginosa strain L10 containing amidase were used as biocatalysts both free and immobilized in a reverse micellar system. The apparent kinetic constants for the transamidation reaction in hydroxamic acids synthesis, were determined using substrates such as aliphatic, amino acid and aromatic amides and esters, in both media. In reverse micelles, K-m values decreased 2-7 fold relatively to the free biocatalyst using as substrates acetamide, acrylamide, propionamide and glycinamide ethyl ester. We have concluded that overall the affinity of the biocatalyst to each substrate increases when reactions are performed in the reversed micellar system as opposed to the buffer system. The immobilized biocatalyst in general, exhibits higher stability and faster rates of reactions at lower substrates concentration relatively to the free form, which is advantageous. Additionally, the immobilization revealed to be suitable for obtaining the highest yields of hydroxamic acids derivatives, in some cases higher than 80%. (C) 2013 Elsevier B.V. All rights reserved.

Formation of oriented nickel aggregates in rutile single crystals by Ni implantation

The magnetic and electrical properties of Ni implanted single crystalline TiO2 rutile were studied for nominal implanted fluences between 0.5 x 10(17) cm(-2) and 2.0 x 10(17) cm(-2) with 150 keV energy, corresponding to maximum atomic concentrations between 9 at% and 27 at% at 65 nm depth, in order to study the formation of metallic oriented aggregates. The results indicate that the as implanted crystals exhibit superparamagnetic behavior for the two higher fluences, which is attributed to the formation of nanosized nickel clusters with an average size related with the implanted concentration, while only paramagnetic behavior is observed for the lowest fluence. Annealing at 1073 K induces the aggregation of the implanted nickel and enhances the magnetization in all samples. The associated anisotropic behavior indicates preferred orientations of the nickel aggregates in the rutile lattice consistent with Rutherford backscattering spectrometry-channelling results. Electrical conductivity displays anisotropic behavior but no magnetoresistive effects were detected. (C) 2013 Elsevier B.V. All rights reserved.

Hydrogen peroxide sensing, signaling and regulation of transcription factors

The regulatory mechanisms by which hydrogen peroxide (H2O2) modulates the activity of transcription factors in bacteria (OxyR and PerR), lower eukaryotes (Yap1, Maf1, Hsf1 and Msn2/4) and mammalian cells (AP-1, NRF2, CREB, HSF1, HIF-1, TP53, NF-κB, NOTCH, SP1 and SCREB-1) are reviewed. The complexity of regulatory networks increases throughout the phylogenetic tree, reaching a high level of complexity in mammalians. Multiple H2O2 sensors and pathways are triggered converging in the regulation of transcription factors at several levels: (1) synthesis of the transcription factor by upregulating transcription or increasing both mRNA stability and translation; (ii) stability of the transcription factor by decreasing its association with the ubiquitin E3 ligase complex or by inhibiting this complex; (iii) cytoplasm-nuclear traffic by exposing/masking nuclear localization signals, or by releasing the transcription factor from partners or from membrane anchors; and, (iv) DNA binding and nuclear transactivation by modulating transcription factor affinity towards DNA, co-activators or repressors, and by targeting specific regions of chromatin to activate individual genes. We also discuss how H2O2 biological specificity results from diverse thiol protein sensors, with different reactivity of their sulfhydryl groups towards H2O2, being activated by different concentrations and times of exposure to H2O2. The specific regulation of local H2O2 concentrations is also crucial and results from H2O2 localized production and removal controlled by signals. Finally, we formulate equations to extract from typical experiments quantitative data concerning H2O2 reactivity with sensor molecules. Rate constants of 140 M-1s−1 and ≥ 1.3 × 103 M-1s−1 were estimated, respectively, for the reaction of H2O2 with KEAP1 and with an unknown target that mediates NRF2 protein synthesis. In conclusion, the multitude of H2O2 targets and mechanisms provides an opportunity for highly specific effects on gene regulation that depend on the cell type and on signals received from the cellular microenvironment.

Microscopic Theory of Anchoring Transitions at the Surfaces of Pure Liquid-Crystals and their Mixtures .1. The Fowler Approximation

We have generalized earlier work on anchoring of nematic liquid crystals by Sullivan, and Sluckin and Poniewierski, in order to study transitions which may occur in binary mixtures of nematic liquid crystals as a function of composition. Microscopic expressions have been obtained for the anchoring energy of (i) a liquid crystal in contact with a solid aligning surface; (ii) a liquid crystal in contact with an immiscible isotropic medium; (iii) a liquid crystal mixture in contact with a solid aligning surface. For (iii), possible phase diagrams of anchoring angle versus dopant concentration have been calculated using a simple liquid crystal model. These exhibit some interesting features including re-entrant conical anchoring, for what are believed to be realistic values of the molecular parameters. A way of relaxing the most drastic approximation implicit in the above approach is also briefly discussed.