Hydrogen/deuterium exchange mass spectrometry for characterizing phosphoenolpyruvate-induced structural transitions in Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.1)

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

Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1)

The 1.7 angstrom resolution crystal structure of recombinant family G/11 beta-1,4-xylanase (rXynA) from Bacillus subtilis 1A1 shows a jellyroll fold in which two curved P-sheets form the active-site and substrate-binding cleft. The onset of thermal denaturation of rXynA occurs at 328 K, in excellent agreement with the optimum catalytic temperature. Molecular dynamics simulations at temperatures of 298-328 K demonstrate that below the optimum temperature the thumb loop and palm domain adopt a closed conformation. However, at 328 K these two domains separate facilitating substrate access to the active-site pocket, thereby accounting for the optimum catalytic temperature of the rXynA. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Water regulation of actinomycin-D binding to DNA: the interplay among drug affinity, DNA long-range conformation, and hydration

Actiaomycin-D (actD) binds to natural DNA at two different classes of binding sites, weak and strong. The affinity for these sites is highly dependent on DNA se(sequence and solution conditions, and the interaction appears to be purely entropic driven Although the entropic character of this reaction has been attributed to the release of water molecules upon drug to DNA complex formation, the mechanism by which hydration regulates actD binding and discrimination between different classes of binding sites on natural DNA is still unknown. In this work, we investigate the role of hydration on this reaction using the osmotic stress method. We skew that the decrease of solution water activity, due to the addition of sucrose, glycerol ethylene glycol, and betaine, favors drug binding to the strong binding sites on DNA by increasing both the apparent binding affinity Delta G, and the number of DNA base pairs apparently occupied by the bound drug n(bp/actD). These binding parameters vary linearly with the logarithm of the molar fraction of water in solution log(X-w), which indicates the contribution of water binding to the energetic of the reaction. It is demonstrated that the hydration change measured upon binding increases proportionally to the apparent size of the binding site n(bp/uctD). This indicates that n(bp/actD) measured from the Scatchard plod is a measure of the size of the DNA molecule changing conformation due to ligand binding. We also find that the contribution of DNA deformation, gauged by n(bp/act) to the total free energy of binding Delta G, is given by Delta G = Delta G(local) + n(bp/actD) x delta G(DNA), where Delta G(local), = -8020 +/- 51 cal/mol of actD bound and delta G(DNa) = -24.1 +/- 1.7cal/mol of base pair at 25 degrees C. We interpret Delta G(local), as the energetic contribution due to the direct interactions of actD with the actual tetranucleotide binding site, and it n(bp/actB) X delta G(DNA) as that due to change inconformation, induced by binding, of it n(bp/actD) DNA base pairs flanking the local site. This interpretation is supported by the agreement found between the value of delta G(DNA) and the torsional free energy change measured independently. We conclude suggesting an allosteric model for ligand binding to DNA, such that the increase in binding affinity is achieved by increasing the relaxation of the unfavorable free energy of binding storage at the local site through a larger number of DNA base pairs. The new aspect on this model is that the size of the complex is not fixed but determined by solutions conditions, such as water activity, which modulate the energetic barrier to change helix conformation. These results may suggest that long-range allosteric transitions of duplex DNA are involved in the inhibition of RNA synthesis by actD, and more generally, in the regulation of transcription. (C) 2000 John Wiley & Sons, Inc.

Investigation of DMSO-Induced Conformational Transitions in Human Serum Albumin Using Two-Dimensional Raman Optical Activity Spectroscopy

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

Genetic associations of sexual precocity with growth traits and visual scores of conformation, finishing, and muscling in Nelore cattle

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

Genetic associations of conformation, finishing precocity and muscling visual scores with mature weight in Nelore cattle

Were estimate (co)variance and genetic associations between conformation, finishing precocity and muscling visual scores measured at weaning (SCW, SFW and SMW, respectively) and yearling (SCY. SFY and SMY, respectively) with mature weight (MW) in Nelore cows, in order to predict the possible changes that inclusion of visual scores in beef cattle selection indices would bring to female mature weight. The data set contained records of 36,757 females, born between 1993 and 2006, belonging to the Jacarezinho cattle raising farm. (Co)variance components were estimated by bivariate animal models using Bayesian inference method through Gibbs sampling, assuming a linear model for MW and a nonlinear (threshold) model for conformation, finishing precocity and muscling visual scores. The first 10,000 rounds were considered as the burn-in period and discarded. The posterior means of direct heritability distributions were: 0.16 +/- 0.02 (SCW); 0.20 +/- 0.02 (SFW); 0.19 +/- 0.02 (SMW); 0.24 +/- 0.02 (SCY); 0.31 +/- 0.02 (SFY); 0.32 +/- 0.02 (SMY) and 0.46 +/- 0.04 (MW). Estimates of genetic correlations between visual scores and MW were positive and moderate, ranging from 0.27 +/- 0.06 to 0.36 +/- 0.04. Visual scores and MW should respond favorably to direct selection. Mature weight can be used in Nelore breeding programs designed to monitor the cows' size. Selection of animals with higher conformation, finishing precocity and muscling scores, especially at yearling, should promote an increase in cows' mature weight. (c) 2010 Elsevier B.V. All rights reserved.

Indirect optical transitions from carriers trapped on the delta doping and on the parabolic quantum well

In this work, doped AlGaAs/GaAs parabolic quantum wells (PQW) with different well widths (from 1000 angstrom up to 3000 angstrom) were investigated by means of photoluminescence (PL) measurements. In order to achieve the 2DEG inside the PQW Si delta doping is placed at both side of the well. We have observed that the thickness of this space layer plays a major rule on the characteristics of the 2DEG. It has to be thicker enough to prevent any diffusions of Si to the well and thin enough to allow electrons migration inside the well. From PL measurement, we have observed beside the intra well transitions, indirect transitions involving still trapped electron on the delta doping and holes inside the PQW. For the thinness sample, we have measured a well defined PL peak at low energy side of the GaAs bulk emission. With the increasing of the well thickness this peak intensity decreases and for the thickest sample it almost disappears. Our theoretical calculation indicated that carriers (electron and holes) are more placed at the center of the PQW. In this way, when the well thickness increases the distance between electrons on the delta doping and holes on the well also increases, it decreases the probability of occurrence of these indirect optical transitions. (C) 2012 Published by Elsevier B.V. Selection and/or peer-review under responsibility of Universidade Federal de Juiz de Fora, Brazil.

High-energy transitions of shallow magnetodonors in a GaAs/Al0.3Ga0.7As multiple quantum well

The high-energy states of a shallow donor in a GaAs/Ga0.7Al0.3As multiple-quantum-well structure subjected to a magnetic field in the growth direction are studied both theoretically and experimentally. Effects due to higher confinement subbands as well as due to the electron-phonon interaction are investigated. We show that most of the peaks in the infrared photoconductivity spectrum are due to direct transitions from the ground state to the m = +/-1 magnetodonor states associated with the first subband, but transitions to the m = +/-1 states of the third subband are also apparent. The remaining photoconductivity peaks are explained by phonon-assisted impurity transitions.

Structural phase transitions of PbZr0.52Ti0.48O3 ceramic: An infrared spectroscopy study

The recent discovery of a ferroelectric monoclinic phase in the PbZr1-xTixO3 (PZT) system attained the attention of several researchers due to the possibility of understanding the relationships between structural features and piezoelectric properties. The nature of the monoclinic phase in some PZT compositions remains controversial and unclear. In this work, structural phase transitions of PbZr0.52Ti0.48O3 ceramic were investigated by infrared spectroscopy as a function of temperature. Studies were centered on nu(1)-stretching modes and corresponding half width Wi as a function of temperature. The occurrence of the anomalies in the infrared spectra as a function of temperature suggests the following monoclinic ( LT) -> monoclinic ( HT) -> tetragonal phase transition were observed at 183 K and at 263 K.

Modeling the dielectric response of lanthanum modified lead zirconate titanate ferroelectric ceramics-an approach to the phase transitions in relaxor ferroelectrics

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

Implant-retained thumb prosthesis with anti-rotational attachment for a geriatric patient

This report presents the use of a dental implant with an anti-rotational attachment for the retention of a thumb prosthesis. A retention system was manufactured with an attachment (UCLA) screwed into the implant with a two-bar system that was cast in metallic silver palladium. A substructure made from heat-cured acrylic resin was joined to the retention system by clips to join the thumb to the finger (bar clip) in the cast with implant rejoinder. The silicone material, Silastic-MDX 44210, was used to achieve function and aesthetics. Following osseointegration, no skin problems were observed. Whilst the implant-retained digital prosthesis presented some motor limitations, it allowed the patient to return to entertainment and achieve social conviviality.

Orthodontic treatment of a midline diastema related to mesiodens and thumb-sucking habit

OBJETIVO: A associação de mesiodens com hábito de sucção digital como fatores etiológicos de diastemas medianos é uma situação clínica incomum e, quando presente, provoca um comprometimento estético e funcional. O objetivo desse trabalho é descrever o caso clínico de um paciente, aos 9 anos de idade, com mordida aberta anterior e um diastema mediano de 9 mm. DESCRIÇÃO do CASO: Após o diagnóstico ortodôntico, a conduta terapêutica foi a exodontia do mesiodens e instalação de uma grade palatina fixa para controle do hábito de sucção digital. em seguida, bráquetes ortodônticos foram colados nos incisivos centrais superiores e o diastema foi fechado possibilitando a irrupção espontânea dos incisivos laterais. Quando adequados níveis de trespasse vertical e horizontal entre os incisivos foi alcançado e o hábito removido, o tratamento foi finalizado. CONCLUSÃO: É importante ressaltar que com o objetivo de alcançar resultados estéticos e funcionais satisfatórios, minimizando sequelas ao desenvolvimento da oclusão deve-se realizar o diagnóstico precoce e intervenção imediata dos diastemas medianos patológicos.

Influence of Quaternary Conformation on the Biological Activities of the Asp49-phospholipases A(2)s from Snake Venoms

One of the main components of snake venoms are the Asp49-phospholipases A(2), also known as svPLA(2)s. The study of these toxins is a matter of great scientific interest due to their wide variety of biological effects. In this work we present strong evidences found in literature and other aspects which strengthen the importance of quaternary assembly for understanding the activities and molecular evolution of svPLA(2)s.

A micelle nucleation model for the interaction of dodecyl sulphate with Lys49-phospholipases A(2)

Bothropstoxin-I (BthTx-I) is a Lys49-PLA(2) from the venom of Bothrops jararacussu that lacks detectable catalytic activity, yet causes rapid Ca2+-independent membrane damage. With the aim of understanding the interaction between BthTx-I and amphiphilic molecules, we have studied the interaction of sodium dodecyl sulphate (SDS) with the protein. Circular dichroism and attenuated total reflection Fourier-transform infrared spectra of BthTx-I reveal changes in the alpha-helical organization of the protein at an SDS/BthTx-I molar ratio of 20-25. At SDS/BthTx-I ratios of 40-45 the alpha-helices return to a native-like conformation, although fluorescence emission anisotropy measurements of 2-amino-N-hexadecyl-benzamide (AHBA) demonstrate that the total SDS is below the critical micelle concentration when this transition occurs. These results may be interpreted as the result of SDS accumulation by the BthTx-I homodimer and the formation of a pre-micelle SDS/BthTx-I complex, which may subsequently be released from the protein surface as a free micelle. Similar changes in the alpha-helical organization of BthTx-I were observed in the presence of dipalmitoylphosphatidylcholine liposomes, suggesting that protein structure transitions coupled to organization changes of bound amphiphiles may play a role in the Ca2+-independent membrane damage by Lys49-PLA(2)s. (c) 2006 Elsevier B.V. All rights reserved.