On the pH dependence of protein stability

This paper treats the free energy contribution of ionizable groups to protein stability. A method is presented for the calculation of the pH dependence of the denaturation free energy of a protein, which yields results that can be compared directly to experiment. The first step in the treatment is the determination of the average charges of all the ionizable groups in both the folded and unfolded protein. An expression due to Tanford then relates the pH dependence of the unfolding free energy to the difference in net charge between the two states. In order to determine absolute rather than relative unfolding free energies, it is necessary to calculate the total contribution of ionizable groups to protein stability at some reference pH. This is accomplished through a statistical mechanical treatment similar to the one used previously in the calculation of pKas. The treatment itself is rigorous but it suffers from uncertainties in the pKa calculations. Nevertheless, the overall shape of experimentally observed plots of denaturation free energy as a function of pH are reasonably well reproduced by the calculations. A number of general conclusions that arise from the analysis are: (1) knowledge of titration curves and/or effective pKa values of ionizable groups in proteins is sufficient to calculate the pH dependence of the denaturation free energy with respect to some reference pH value. However, in order to calculate the absolute contribution of ionizable groups to protein stability, it is necessary to also know the intrinsic pKa of each group. This is defined as the pKa of a group in a hypothetical state of the protein where all other groups are neutral. (2) Due to desolvation effects, ionizable groups destabilize proteins, although the effect is strongly dependent on pH. There are however, strongly stabilizing pairwise Coulombic interactions on the surface of proteins. (3) Plots of stability versus pH should not be interpreted in terms of a group whose pKa corresponds to the titration midpoint, but rather to a group with different pKas (that correspond approximately to the titration end points) in each state. (4) Any residual structure in the GuHCl-denatured state of proteins appears to have little effect on the pH dependence of stability. (5) pH-dependent unfolding, for example to the "molten globule" state, appears due to individual groups with anomalous pKas whose locations on the protein surface may determine the nature of the unfolded state.     

Raman spectra and structural analysis in ZrOxNy thin films

Raman spectroscopy has been used as a local probe to characterize the structural evolution of magnetron-sputtered decorative zirconium oxynitride ZrO_xN_y films which result from an increase of reactive gas flow in the deposition. The lines shapes, the frequency position and widths of the Raman bands show a systematic change as a function of the reactive gas flow (a mixture of both oxygen and nitrogen). The as-deposited zirconium nitride film presents a Raman spectrum with the typical broadened bands, due to the disorder induced by N vacancies. The recorded Raman spectrum of the zirconium oxide film is typical of the monoclinic phase of ZrO₂, which is revealed also by X-ray diffraction. Raman spectra of zirconium oxynitride thin films present changes, which are found to be closely related with the oxygen content in films and the subsequent structural changes.     

Time and space for segmenting personal photo sets

Multimedia Tools and Applications - A personal collection of photos shows large variability in the depicted items, making difficult a fully automated solution to cope with sensory and semantic...     

Lyapunov-based switched extremum seeking for photovoltaic power maximization

This paper presents a practical variation of extremum seeking (ES) that guarantees asymptotic convergence through a Lyapunov-based switching scheme (Lyap-ES). Traditional ES methods enter a limit cycle around the optimum. Lyap-ES converges to the optimum by exponentially decaying the perturbation signal once the system enters a neighborhood around the extremum. As a case study, we consider maximum power point tracking (MPPT) for photovoltaics. Simulation results demonstrate how Lyap-ES is self-optimizing in the presence of varying environmental conditions and produces greater energy conversion efficiencies than traditional MPPT methods. Experimentally measured environmental data is applied to investigate performance under realistic operating scenarios.     

Sugarcane Serine Peptidase Inhibitors,Serine Peptidases,and Clp Protease System Subunits Associated with Sugarcane Borer (Diatraea saccharalis) Herbivory and Wounding

Sugarcane’s (Saccharum spp.) response to Diatraea saccharalis (F.) (Lepidoptera: (Crambidae) herbivory was investigated using a macroarray spotted with 248 sugarcane Expressed Sequence Tags (ESTs) encoding serine peptidase inhibitors, serine peptidases. and Clp protease system subunits. Our results showed that after nine hours of herbivory, 13 sugarcane genes were upregulated and nine were downregulated. Among the upregulated genes, nine were similar to serine peptidase inhibitors and four were similar to Bowman-Birk Inhibitors (BBIs). Phylogenetic analysis revealed that these sequences belong to a phylogenetic group of sugarcane BBIs that are potentially involved in plant defense against insect predation. The remaining four upregulated genes included serine peptidases and one homolog to the Arabidopsis AAA+ chaperone subunit ClpD, which is a member of the Clp protease system. Among the downregulated genes, five were homologous to serine peptidases and four were homologous to Arabidopsis Clp subunits (three homologous to Clp AAA+ chaperones and one to a ClpP-related ClpR subunit). Although the roles of serine peptidase inhibitors in plant defenses against herbivory have been extensively investigated, the roles of plant serine peptidases and the Clp protease system represent a new and underexplored field of study. The up- and downregulated D. saccharalis genes presented in this study may be candidate genes for the further investigation of the sugarcane response to herbivory.     

Application of polysaccharide hydrogels in adsorption and controlled‐extended release of fertilizers processes

This article studied the applicability of poly(acrylamide) and methylcellulose (PAAm‐MC) hydrogels as potential delivery vehicle for the controlled‐extended release of ammonium sulfate (NH₄)₂SO₄ and potassium phosphate (KH₂PO₄) fertilizers. PAAm‐MC hydrogels with different acrylamide (AAm) and MC concentrations were prepared by a free radical polymerization method. The adsorption and desorption kinetics of fertilizers were determined using conductivity measurements based on previously built analytical curve. The addition of MC in the PAAm chains increased the quantities of (NH₄)₂SO₄ and KH₂PO₄ loaded and extended the time and quantities of fertilizers released. Coherently, both loading and releasing processes were strongly influenced by hydrophilic properties of hydrogels (AAm/MC mass proportion). The best sorption (124.0 mg KH₂PO₄/g hydrogel and 58.0 mg (NH₄)₂SO₄/g hydrogel) and desorption (54.9 mg KH₂PO₄/g hydrogel and 49.5 mg (NH₄)₂SO₄/g hydrogel) properties were observed for 6.0% AAm–1.0% MC hydrogels (AAm/MC mass proportion equal 6), indicating that these hydrogels are potentially viable to be used in controlled‐extended release of fertilizers systems. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012     

FAME Production and Fatty Acid Profiles from Moist Chlorella sp. and Nannochloropsis oculata Biomass

In the present study, we investigated the production of fatty acid methyl esters (FAME) from moist Chlorella sp. and Nannochloropsis oculata biomass using a hydrolysis–esterification process. Additionally, we evaluated for the first time the fatty acid profile before and after this process. Hydrolysis of the lipid fraction was performed on a moist biomass in the presence of differing amounts of an acid catalyst in both 50 and 100 % w/w water relative to the biomass. The esterification of the crude extracts of the free fatty acids (FFA) was then investigated. The experiments show that in the presence of 50 % w/w water relative to the biomass, the hydrolysis–esterification process results in higher FFA and FAME yields. The analysis of the fatty ester profiles did not reveal any degradation of the FFA from the microalgae biomass under the hydrolysis–esterification conditions. The results were compared with both extraction–transesterification and direct transesterification processes using dry biomass. The extraction–transesterification and hydrolysis–esterification processes resulted in similar FAME yields and similar profiles of the fatty esters from dry and moist biomass materials, respectively.     

Application of Cohesive Zone Modeling to Composite Bonded Repairs

Cohesive zone models can play an important role in the definition of repair strategies. These models allow the prediction of damage initiation and propagation. They are based on a softening relationship between stresses and relative displacements between crack faces, thus simulating a gradual degradation of material properties. Typically, stress-based and energetic fracture mechanics criteria are used to simulate damage initiation and growth, respectively. Those elements are placed at the planes where damage is prone to occur which, in the case of bonded repairs, is usually easy to identify a priori. Taking this into consideration, cohesive mixed-mode damage models based on interface finite elements were used with the objective of optimizing the repair efficiency. The determination of the cohesive pure mode softening laws is a key aspect of these models, and the direct method is the most accurate process to do it. The models were validated and applied to two different cases involving repairs. Several geometrical aspects influencing the single-strap repair strength were analyzed as well as the evolution of the maximum load and alteration of damage mechanism as a function of the angle used in scarf joints. It was verified that CZM are able to predict with accuracy the damage mechanisms and strength of composite bonded repairs, thus constituting a powerful tool in its design.     

Approximation of the inverse of the Hodge matrix via sparsity pattern

The solution of electromagnetic wave propagation problems in time domain using an explicit method requires the inversion of Hodge matrices. This paper proposes an approximation to obtain a sparse inverse via the sparsity pattern of the original matrix. It is also shown the application of the algorithm Cuthill–McKee on Hodge matrices in order to reduce their bandwidth and thus speed up the method of recursive sparsification. Copyright © 2014 John Wiley & Sons, Ltd.