Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange

Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T(3)) or antagonist (NH(3)). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, C-terminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T(3), but not NH(3), increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T(3) but not NH(3.) We present data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes. (Molecular Endocrinology 25: 15-31, 2011)

Structure, Dynamics, and RNA Interaction Analysis of the Human SBDS Protein

Shwachman-Bodian-Diamond syndrome is an autosomal recessive genetic syndrome with pleiotropic phenotypes, including pancreatic deficiencies, bone marrow dysfunctions with increased risk of myelodysplasia or leukemia, and skeletal abnormalities. This syndrome has been associated with mutations in the SBDS gene, which encodes a conserved protein showing orthologs in Archaea and eukaryotes. The Shwachman-Bodian-Diamond syndrome pleiotropic phenotypes may be an indication of different cell type requirements for a fully functional SBDS protein. RNA-binding activity has been predicted for archaeal and yeast SBDS orthologs, with the latter also being implicated in ribosome biogenesis. However, full-length SBDS orthologs function in a species-specific manner, indicating that the knowledge obtained from model systems may be of limited use in understanding major unresolved issues regarding SBDS function, namely, the effect of mutations in human SBDS on its biochemical function and the specificity of RNA interaction. We determined the solution structure and backbone dynamics of the human SBDS protein and describe its RNA binding site using NMR spectroscopy. Similarly to the crystal structures of Archaea, the overall structure of human SBDS comprises three well-folded domains. However, significant conformational exchange was observed in NMR dynamics experiments for the flexible linker between the N-terminal domain and the central domain, and these experiments also reflect the relative motions of the domains. RNA titrations monitored by heteronuclear correlation experiments and chemical shift mapping analysis identified a classic RNA binding site at the N-terminal FYSH (fungal, Yhr087wp, Shwachman) domain that concentrates most of the mutations described for the human SBDS. (C) 2010 Elsevier Ltd. All rights reserved.

On the open-circuit interaction between methanol and oxidized platinum electrodes

In the present work, results of the interaction between methanol and oxidized platinum surfaces as studied via transients of open-circuit potentials are presented. The surface oxidation before the exposure to interaction with 0.5 M methanol was performed at different polarization times at 1.4 V vs reversible hydrogen electrode (RHE). In spite of the small changes in the initial oxide content, the increase of the pre-polarization time induces a considerable increase of the time needed for the oxide consumption during its interaction with methanol. The influence of the identity of the chemisorbing anion on the transients was also investigated in the following media: 0.1 M HClO4, 0.5 M H2SO4, and 0.5 M H2SO4 + 0.1 mM Cl-. It was observed that the transient time increases with the energy of anion chemisorption and, more importantly, without a change in the shape of the transient, meaning that free platinum sites are available at the topmost layer all over the transient and not only in the potential region of small oxide `coverage`. The impact of the pre-polarization time and the effect of anion chemisorption on the transients are rationalized in terms of the presence of surface and subsurface oxygen driven by place exchange.

The origin of the molecular interaction between amino acids and gold nanoparticles: A theoretical and experimental investigation

This study describes the synthesis of novel biological hybrid materials, where 3D structures were obtained using gold nanoparticles (AuNps) and methionine (Met) in a one-step procedure in aqueous media. The type of nanostructure can be controlled by tuning the intermolecular interactions between Met and AuNp, which strongly depends on the pH used for the synthesis. Computational simulation using the density-functional theory (DFT) showed that the AuNp - Met 3D structures are formed upon reorientation of Met molecules so that the backbone amine groups interact via H-bonds. These findings were experimentally confirmed using FTIR and UV-vis spectroscopy. Crown Copyright (C) 2008 Published by Elsevier B. V. All rights reserved.

Debt composition and exchange rate balance sheet effects in Brazil: A firm level analysis

In this paper we study the interaction between macroeconomic environment and firms’ balance sheet effects in Brazil during the 1990’s. We start by assessing the influence of macroeconomic conditions on firms’ debt composition in Brazil. We found that larger firms tend to change debt currency composition more in response to a change in the exchange rate risk than small firms. We then proceed to investigate if and how exchange rate balance sheet effects affected the firms’ investment decisions. We test directly the exchange rate balance sheet effect on investment. Contrary to earlier findings (Bleakley and Cowan, 2002), we found that firms more indebted in foreign currency tend to invest less when there is an exchange rate devaluation. We tried different controls for the competitiveness effect. First, we control directly for the effect of the exchange rate on exports and imported inputs. We then pursue an alternative investigation strategy, inspired by the credit channel literature. According to this perspective, Tobin’s q can provide an adequate control for the competitiveness effect on investment. Our results provide supporting evidence for imperfect capital markets, and for a negative exchange rate balance sheet effect in Brazil. The results concerning the exchange rate balance sheet effect on investment are statistically significant and robust across the different specifications. We tested the results across different periods, classified according to the macroeconomic environment. Our findings suggest that the negative exchange rate balance sheet effect we found in the whole sample is due to the floating exchange rate period. We also found that exchange rate devaluations have important negative impact on both cash flows and sales of indebted firms. Furthermore, the impact of exchange rate variations is asymmetric, and the significant effect detected when no asymmetry is imposed is engendered by exchange rate devaluations.

Gas exchange rates, plant height, yield components, and productivity of upland rice as affected by plant regulators

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

Ultraviolet-B and water stress effects on growth, gas exchange and oxidative stress in sunflower plants

The effects and interaction of drought and UV-B radiation were studied in sunflower plants (Helianthus annuus L. var. Catissol-01), growing in a greenhouse under natural photoperiod conditions. The plants received approximately 1.7 W m(-2) (controls) or 8.6 W m(-2) (+UV-B) of UV-B radiation for 7 h per day. The UV-B and water stress treatments started 18 days after sowing. After a period of 12 days of stress, half of the water-stressed plants (including both UV-B irradiated or non-irradiated) were rehydrated. Both drought and UV-B radiation treatments resulted in lower shoot dry matter per plant, but there was no significant interaction between the two treatments. Water stress and UV-B radiation reduced photosynthesis, stomatal conductance and transpiration. However, the amplitude of the effects of both stressors was dependent on the interactions. This resulted in alleviation of the negative effect of drought on photosynthesis and transpiration by UV-B radiation as the water stress intensified. Intercelluar CO(2) concentration was initially reduced in all treatments compared to control plants but it increased with time. Photosynthetic pigments were not affected by UV-B radiation. Water stress reduced photosynthetic pigments only under high UV-B radiation. The decrease was more accentuated for chlorophyll a than for chlorophyll b. As a measure for the maximum efficiency of photosystem II in darkness F (v)/F (m) was used, which was not affected by drought stress but initially reduced by UV-B radiation. Independent of water supply, UV-B radiation increased the activity of pirogalol peroxidase and did not increase the level of malondialdehyde. on the other hand, water stress did not alter the activity of pirogalol peroxidase and caused membrane damage as assessed by lipid peroxidation. The application of UV-B radiation together with drought seemed to have a protective effect by lowering the intensity of lipid peroxidation caused by water stress. The content of proline was not affected by UV-B radiation but was increased by water stress under both low and high UV-B radiation. After 24 h of rehydration, most of the parameters analyzed recovered to the same level as the unstressed plants.

Monitoring the positioning of short polycationic peptides in model lipid bilayers by combining hydrogen/deuterium exchange and electrospray ionization mass spectrometry

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

Gas exchange and ventilation during dormancy in the tegu lizard Tupinambis merianae

The tegu lizard Tupinambis merianae exhibits an episodic ventilatory pattern when dormant at 17 degrees C but a uniform ventilatory pattern when dormant at 25 degrees C. At 17 degrees C, ventilatory episodes were composed of 1-22 breaths interspaced by non-ventilatory periods lasting 1.8-26min, Dormancy at the higher body temperature was accompanied by higher rates of O-2 consumption and ventilation. The increase in ventilation was due only to increases in breathing frequency with no change observed in tidal volume. The air convection requirement for O-2 did not differ at the two body temperatures. The respiratory quotient was 0.8 at 17 degrees C and 1.0 at 25 degrees C. We found no consistent relationship between expired gas composition and the start/end of the ventilatory period during episodic breathing at 17 degrees C. However, following non-ventilatory periods of increasing duration, there was an increase in the pulmonary O-2 extraction that was not coupled to an equivalent increase in elimination of CO2 from the lungs. None of the changes in the variables studied could alone explain the initiation/termination of episodic ventilation in the tegus, suggesting that breathing episodes are shaped by a complex interaction between many variables. The estimated oxidative cost of breathing in dormant tegus at 17 degrees C was equivalent to 52.3% of the total metabolic rate, indicating that breathing is the most costly activity during dormancy.

Recursive renormalization of the singlet one-pion-exchange plus point-like interactions

The subtracted kernel approach is shown to be a powerful method to be implemented recursively in scattering equations with regular plus point-like interactions. The advantages of the method allows one to recursively renormalize the potentials, with higher derivatives of the Dirac-delta, improving previous results. The applicability of the method is verified in the calculation of the 1 So nucleon-nucleon phase-shifts, when considering a potential with one-pion-exchange plus a contact interaction and its derivatives. The S-1(0) renormalization parameters are fitted to the data. The method can in principle be extended to any derivative order of the contact interaction, to higher partial waves and to coupled channels. (c) 2005 Elsevier B.V. All rights reserved.

Rho-nucleon tensor coupling and charge-exchange resonances

The Gamow-Teller resonance in Pb-208 is discussed in the context of a self-consistent RPA, based on the relativistic mean field theory. We inquire on the possibility of substituting the phenomenological Landau-Migdal force by a microscopic nucleon-nucleon interaction, generated from the rho-nucleon tensor coupling. The effect of this coupling turns out to be very small when the short range correlations are not taken into account, but too large when these correlations are simulated by the simple extraction of the contact terms from the resulting nucleon-nucleon interaction. (C) 2000 Elsevier B.V. B.V. All rights reserved.

Renormalizing the NN interaction with multiple subtractions

The aim of this work is to show how to renormalize the nucleon-nucleon interaction at next-to-next-to-leading order using a. systematic subtractive renormalization approach with multiple subtractions. As an example, we calculate the phase shifts for the partial waves with total angular momentum J = 2. The intermediate driving terms at each recursive step as well as the renormalized T-matrix are also shown. We conclude that our method is reliable for singular potentials such as the two-pion exchange and derivative contact interactions.

Positronium interaction and its Bose-Einstein condensation

We present the actual state of affairs and future perspectives in the study of a quantum system of a collection of positronium (Ps) atoms. The interaction of a Ps atom with other atoms and molecules and specially with another Ps atom is described in some detail as Ps-Ps interaction should play a crucial role in the dynamics of an assembly of Ps atoms. Using a simple model-exchange potential, we could describe the available experimental results of Ps scattering reasonably well. The present scenario of the observation of Ps2 molecule, Ps Bose-Einstein condensate (BEC) and the annihilation laser from a Ps BEC is presented. Possibilities of a Ps BEC formation via laser cooling of Ps atoms and via Ps formation in cavities are considered and difficulties with each procedure discussed (C) 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Subtractive renormalization of one-pion-exchange and contact interactions

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

Polystyrene-type resin used for peptide synthesis: application for anion-exchange and affinity chromatography

This paper deals with an unusual application for a copolymer of styrene-1 % divinylbenzene bearing high amount of aminomethyl groups for anion-exchange and affinity chromatography. The so-called aminomethyl resin (AMR), to date only employed for peptide synthesis, swelled appreciably in water and was used successfully to purify negatively charged peptides. By correlating swelling degree of beads with pH of the media, it was possible to estimate that the AMR amino group pK(a) is approximately 5.5. In addition, the synthesized acetyl-(NANP)(3)-AMR succeeded in the affinity interaction with large antibody molecules related to malaria transmission and raised previously against this dodecapeptide sequence. (C) 2004 Elsevier B.V. All rights reserved.