Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations

Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 angstrom resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis, for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting beta-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge-charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.

Optimal-state-dependent rules, credibility, and inflationary inertia

This paper examines the output losses caused by disinflation and the role of credibility in a model where pricing mIes are optimal and individual prices are rigid. Individual nominal rigidity is modeled as resulting from menu costs. The interaction between optimal pricing mIes and credibility is essential in determining the inflationary inertia. A continued period of high inflation generates an asymmetric distribution of price deviations, with more prices that are substantially lower than their desired leveIs than prices that are substantially higher than the optimal ones. When disinflation is not credible, inflationary inertia is engendered by this asymmetry: idiosyncratic shocks trigger more upward than downward adjustments. A perfect1y credible disinflation causes an immediate change of pricing rules which, by rendering the price deviation distribution less asymmetric, practically annihilates inflationary inertia. An implication of our model is that stabilization may be sucessful even when credibility is low, provided that it is preceded by a mechanism of price alignment. We also develop an analytical framework for analyzing imperfect credibility cases.

Simulations under Ideal and Nonideal Conditions for Characterization of a Passive Doppler Geographical Location System Using Extension of Data Reception Network

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structure of acetone and dimethyl sulfoxide from Monte Carlo simulations and MM2 calculations

The structure of acetone and dimethyl sulfoxide in the liquid phase is investigated using Monte Carlo simulations and MM2 calculations. The principal site - site correlations and degree of structure in both liquids have been investigated. The results showed that dimethyl sulfoxide is more structured than acetone. At short distances the dipoles of neighboring molecules are found to be in antiparallel configurations, but further apart the molecules tend to be aligned predominantly as head to tail. In both liquids there is evidence of strong methyl - oxygen interaction, important to the structure of the liquids. The contacts suggest weak hydrogen bonds between methyl hydrogen and oxygen.

NOISE and ULTRAVIOLET DIVERGENCES IN SIMULATIONS of GINZBURG-LANDAU-LANGEVIN TYPE of EQUATIONS

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Evaluating and classifying contaminated areas based on loss functions using annealing simulations

This paper presents a methodology based on geostatistical theory for quantifying the risks associated with heavy-metal contamination in the harbor area of Santana, Amapa State, Northern Brazil. In this area there were activities related to the commercialization of manganese ore from Serra do Navio. Manganese and arsenic concentrations at unsampled sites were estimated by postprocessing results from stochastic annealing simulations; the simulations were used to test different criteria for optimization, including average, median, and quantiles. For classifying areas as contaminated or uncontaminated, estimated quantiles based on functions of asymmetric loss showed better results than did estimates based on symmetric loss, such as the average or the median. The use of specific loss functions in the decision-making process can reduce the costs of remediation and health maintenance. The highest global health costs were observed for manganese. (c) 2008 Elsevier B.V. All rights reserved

Relation between quality and rheological properties of lactic beverages

The physicochemical (pH, fat and total solids content), sensory (appearance, consistency and taste), and rheological characteristics of five different commercial brands of lactic beverages were determined. Rheological measurements were obtained at 5 degreesC and 25 degreesC using a Brookfield rheometer. The experimental data were described by the power law and Herschel-Bulkley models. The ANOVA of the results were conducted using an incomplete block design, and using Tukey test. Samples showed a significant difference (P less than or equal to 0.05%) for fat content and pH. There was a significant difference in total solids content only among Nestle (A), Batavo (C), and Parmalat (D) samples. Sensory evaluation showed more global acceptability for Nestle; however, Nestle and Vigor (E) lactic beverages obtained better results for appearance than for consistency and taste. Batavo obtained the best score for taste. All test samples exhibited non-Newtonian behavior, with thixotropy. Upward curves showed pseudoplastic behavior, while downward curves showed dilatant behavior with the exception of the Nestle sample, at 25 degreesC. Lactic beverages from all brands analyzed showed similar rheological behavior. (C) 2001 Elsevier B.V. Ltd. All rights reserved.

Coil to extended coil transition in polygalacturonic acid: Conductometric titration and monte carlo simulations

The conformational transition from coil to extended coil for polygalacturonic acid has been studied by conductometric titrations and Monte Carlo simulations. The results of conductometric titrations at different polymer concentrations have been analyzed using the model proposed by Manning,1 which describes the conductivity of polyelectrolitic solutions. This experimental approach provides the transport factor and the average distance between charged groups at different degrees of ionization (α). The mean distances between charged groups have been compared with the values obtained by Monte Carlo simulations. In these simulations the polymer chain is modeled as a self-avoiding random walk in a cubic lattice. The monomers interact through the unscreened Coulombic potential. The ratio between the end-to-end distance and the number of ionized beads provides the average distance between charged monomers. The experimental and theoretical values are in good agreement for the whole range of ionization degrees accessed by conductometric titrations. These results suggest that the electrostatic interactions seem to be the major contribution for the coil to extended coil conformational change. The small deviations for α ≤ 0.5 suggests that the stiffness of the chain, associated with local interactions, becomes increasingly significant as the fraction of charged groups is decreased. © 2000 American Chemical Society.

A study of the effect of overshooting deep convection on the water content of the TTL and lower stratosphere from Cloud Resolving Model simulations

Simulations of overshooting, tropical deep convection using a Cloud Resolving Model with bulk microphysics are presented in order to examine the effect on the water content of the TTL (Tropical Tropopause Layer) and lower stratosphere. This case study is a subproject of the HIBISCUS (Impact of tropical convection on the upper troposphere and lower stratosphere at global scale) campaign, which took place in Bauru, Brazil (22° S, 49° W), from the end of January to early March 2004. Comparisons between 2-D and 3-D simulations suggest that the use of 3-D dynamics is vital in order to capture the mixing between the overshoot and the stratospheric air, which caused evaporation of ice and resulted in an overall moistening of the lower stratosphere. In contrast, a dehydrating effect was predicted by the 2-D simulation due to the extra time, allowed by the lack of mixing, for the ice transported to the region to precipitate out of the overshoot air. Three different strengths of convection are simulated in 3-D by applying successively lower heating rates (used to initiate the convection) in the boundary layer. Moistening is produced in all cases, indicating that convective vigour is not a factor in whether moistening or dehydration is produced by clouds that penetrate the tropopause, since the weakest case only just did so. An estimate of the moistening effect of these clouds on an air parcel traversing a convective region is made based on the domain mean simulated moistening and the frequency of convective events observed by the IPMet (Instituto de Pesquisas Meteorológicas, Universidade Estadual Paulista) radar (S-band type at 2.8 Ghz) to have the same 10 dBZ echo top height as those simulated. These suggest a fairly significant mean moistening of 0.26, 0.13 and 0.05 ppmv in the strongest, medium and weakest cases, respectively, for heights between 16 and 17 km. Since the cold point and WMO (World Meteorological Organization) tropopause in this region lies at ∼ 15.9 km, this is likely to represent direct stratospheric moistening. Much more moistening is predicted for the 15-16 km height range with increases of 0.85-2.8 ppmv predicted. However, it would be required that this air is lofted through the tropopause via the Brewer Dobson circulation in order for it to have a stratospheric effect. Whether this is likely is uncertain and, in addition, the dehydration of air as it passes through the cold trap and the number of times that trajectories sample convective regions needs to be taken into account to gauge the overall stratospheric effect. Nevertheless, the results suggest a potentially significant role for convection in determining the stratospheric water content. Sensitivity tests exploring the impact of increased aerosol numbers in the boundary layer suggest that a corresponding rise in cloud droplet numbers at cloud base would increase the number concentrations of the ice crystals transported to the TTL, which had the effect of reducing the fall speeds of the ice and causing a ∼13% rise in the mean vapour increase in both the 15-16 and 16-17 km height ranges, respectively, when compared to the control case. Increases in the total water were much larger, being 34% and 132% higher for the same height ranges, but it is unclear whether the extra ice will be able to evaporate before precipitating from the region. These results suggest a possible impact of natural and anthropogenic aerosols on how convective clouds affect stratospheric moisture levels.

Mathematical analysis and simulations involving chemotherapy and surgery on large human tumours under a suitable cell-kill functional response

Dosage and frequency of treatment schedules are important for successful chemotherapy. However, in this work we argue that cell-kill response and tumoral growth should not be seen as separate and therefore are essential in a mathematical cancer model. This paper presents a mathematical model for sequencing of cancer chemotherapy and surgery. Our purpose is to investigate treatments for large human tumours considering a suitable cell-kill dynamics. We use some biological and pharmacological data in a numerical approach, where drug administration occurs in cycles (periodic infusion) and surgery is performed instantaneously. Moreover, we also present an analysis of stability for a chemotherapeutic model with continuous drug administration. According to Norton & Simon [22], our results indicate that chemotherapy is less eficient in treating tumours that have reached a plateau level of growing and that a combination with surgical treatment can provide better outcomes.

Espaçamentos dendríticos primários da liga Sn-5%Pb solidificada direcionalmente em um sistema horizontal

Este trabalho desenvolve um estudo teórico-experimental sobre a correlação entre parâmetros térmicos e os espaçamentos dendríticos primários da liga Sn-5%Pb solidificada direcionalmente em um sistema horizontal sob condições transientes de extração de calor. Os perfis de temperatura foram medidos em diferentes posições do lingote e os dados obtidos foram armazenados automaticamente. São apresentados resultados para o coeficiente de transferência de calor na interface metal/molde o qual foi calculado a partir de uma análise comparativa entre os perfis térmicos experimentais e valores teóricos fornecidos por um modelo numérico. Um método teórico-experimental é aplicado para determinar as velocidades de deslocamento da isoterma liquidus e as taxas de resfriamento. Os resultados teóricos e experimentais levantados apresentaram boa concordância. Um estudo comparativo é realizado entre os dados encontrados neste trabalho e aqueles apresentados na literatura para os espaçamentos dendríticos primários da liga investigada quando solidificada direcionalmente nos sistemas verticais ascendente e descendente, sob as mesmas condições assumidas neste trabalho. A análise das microestruturas indica que os espaçamentos dendríticos primários são bastante influenciados pelos parâmetros térmicos de solidificação.

Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The NINJA-2 project: detecting and characterizing gravitational waveforms modelled using numerical binary black hole simulations

The Numerical INJection Analysis (NINJA) project is a collaborative effort between members of the numerical relativity and gravitational-wave (GW) astrophysics communities. The purpose of NINJA is to study the ability to detect GWs emitted from merging binary black holes (BBH) and recover their parameters with next-generation GW observatories. We report here on the results of the second NINJA project, NINJA-2, which employs 60 complete BBH hybrid waveforms consisting of a numerical portion modelling the late inspiral, merger, and ringdown stitched to a post-Newtonian portion modelling the early inspiral. In a 'blind injection challenge' similar to that conducted in recent Laser Interferometer Gravitational Wave Observatory (LIGO) and Virgo science runs, we added seven hybrid waveforms to two months of data recoloured to predictions of Advanced LIGO (aLIGO) and Advanced Virgo (AdV) sensitivity curves during their first observing runs. The resulting data was analysed by GW detection algorithms and 6 of the waveforms were recovered with false alarm rates smaller than 1 in a thousand years. Parameter-estimation algorithms were run on each of these waveforms to explore the ability to constrain the masses, component angular momenta and sky position of these waveforms. We find that the strong degeneracy between the mass ratio and the BHs' angular momenta will make it difficult to precisely estimate these parameters with aLIGO and AdV. We also perform a large-scale Monte Carlo study to assess the ability to recover each of the 60 hybrid waveforms with early aLIGO and AdV sensitivity curves. Our results predict that early aLIGO and AdV will have a volume-weighted average sensitive distance of 300 Mpc (1 Gpc) for 10M circle dot + 10M circle dot (50M circle dot + 50M circle dot) BBH coalescences. We demonstrate that neglecting the component angular momenta in the waveform models used in matched-filtering will result in a reduction in sensitivity for systems with large component angular momenta. This reduction is estimated to be up to similar to 15% for 50M circle dot + 50M circle dot BBH coalescences with almost maximal angular momenta aligned with the orbit when using early aLIGO and AdV sensitivity curves.