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)

Deuterium Equilibrium Time in Saliva of Newborn Infants

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Dynamics of glyphosate-induced conformational changes of Mycobacterium tuberculosis 5-enolpyruvylshikimate-3-phosphate synthase (EC 2.5.1.19) determined by hydrogen-deuterium exchange and electrospray mass spectrometry

The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the reaction between shikimate 3-phosphate and phosphoenolpyruvate to form 5-enolpyruvylshikimate 3-phosphate, an intermediate in the shikimate pathway, which leads to the biosynthesis of aromatic amino acids. EPSPS exists in an open conformation in the absence of substrates and/or inhibitors and in a closed conformation when bound to the substrate and/or inhibitor. In the present report, the H/D exchange properties of EPSPS from Mycobacterium tuberculosis (Mt) were investigated for both enzyme conformations using ESI mass spectrometry and circular dichroism (CD). When the conformational changes identified by H/D exchanges were mapped on the 3-D structure, it was observed that the apoenzyme underwent extensive conformational changes due to glyphosate complexation, characterized by an increase in the content of alpha-helices from 40% to 57%, while the beta-sheet content decreased from 30% to 23%. These results indicate that the enzyme underwent a series of rearrangements of its secondary structure that were accompanied by a large decrease in solvent access to many different regions of the protein. This was attributed to the compaction of 71% of alpha-helices and 57% of beta-sheets as a consequence of glyphosate binding to the enzyme. Apparently, MtEPSPS undergoes a series of inhibitor-induced conformational changes, which seem to have caused synergistic effects in preventing solvent access to the core of molecule, especially in the cleft region. This may be part of the mechanism of inhibition of the enzyme, which is required to prevent the hydration of the substrate binding site and also to induce the cleft closure to avoid entrance of the substrates.

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)

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)

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 (NH3). 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, Cterminal 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 NH3, 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 NH3.Wepresent 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). Copyright © 2011 by The Endocrine Society.

Bioelectrical impedance with different equations versus deuterium oxide dilution method for the inference of body composition in healthy older persons

There is no consensus regarding the accuracy of bioimpedance for the determination of body composition in older persons. This study aimed to compare the assessment of lean body mass of healthy older volunteers obtained by the deuterium dilution method (reference) with those obtained by two frequently used bioelectrical impedance formulas and one formula specifically developed for a Latin-American population. A cross-sectional study. Twenty one volunteers were studied, 12 women, with mean age 72 +/- 6.7 years. Urban community, Ribeiro Preto, Brazil. Fat free mass was determined, simultaneously, by the deuterium dilution method and bioelectrical impedance; results were compared. In bioelectrical impedance, body composition was calculated by the formulas of Deuremberg, Lukaski and Bolonchuck and Valencia et al. Lean body mass of the studied volunteers, as determined by bioelectrical impedance was 37.8 +/- 9.2 kg by the application of the Lukaski e Bolonchuk formula, 37.4 +/- 9.3 kg (Deuremberg) and 43.2 +/- 8.9 kg (Valencia et. al.). The results were significantly correlated to those obtained by the deuterium dilution method (41.6 +/- 9.3 Kg), with r=0.963, 0.932 and 0.971, respectively. Lean body mass obtained by the Valencia formula was the most accurate. In this study, lean body mass of older persons obtained by the bioelectrical impedance method showed good correlation with the values obtained by the deuterium dilution method. The formula of Valencia et al., developed for a Latin-American population, showed the best accuracy.

Investigation of a superthermal ultracold neutron source based on a solid deuterium converter for the TRIGA Mainz reactor

Research in fundamental physics with the free neutron is one of the key tools for testing the Standard Model at low energies. Most prominent goals in this field are the search for a neutron electric dipole moment (EDM) and the measurement of the neutron lifetime. Significant improvements of the experimental performance using ultracold neutrons (UCN) require reduction of both systematic and statistical errors.rnThe development and construction of new UCN sources based on the superthermal concept is therefore an important step for the success of future fundamental physics with ultracold neutrons. rnSignificant enhancement of today available UCN densities strongly correlates with an efficient use of an UCN converter material. The UCN converter here is to be understood as a medium which reduces the velocity of cold neutrons (CN, velocity of about 600 m/s) to the velocity of UCN (velocity of about 6 m/s).rnSeveral big research centers around the world are presently planning or constructing new superthermal UCN sources, which are mainly based on the use of either solid deuterium or superfluid helium as UCN converter.rnThanks to the idea of Yu.Pokotilovsky, there exists the opportunity to build competitive UCN sources also at small research reactors of the TRIGA type. Of course these smaller facilities don't promise high UCN densities of several 1000 UCN/cm³, but they are able to provide densities around 100 UCN/cm³ for experiments.rnIn the context of this thesis, it was possible to demonstrate succesfully the feasibility of a superthermal UCN source at the tangential beamport C of the research reactor TRIGA Mainz. Based on a prototype for the future UCN source at the Forschungs-Neutronenquelle Heinz Maier-Leibnitz (FRMII) in munich, which was planned and built in collaboration with the Technical University of Munich, further investigations and improvements were done and are presented in this thesis. rnIn parallel, a second UCN source for the radial beamport D was designed and built. The comissioning of this new source is foreseen in spring 2010.rnAt beamport D with its higher thermal neutron flux, it should be possible to increase the available UCN densities of 4 UCN/cm³ by minimum one order of magnitude.

Enantioselective synthesis of Equol with Ir-BARF and labelling with deuterium

In this project we researched and optimized an new synthetic route for R-Equol, a molecule that is attracting increasing interest for the medicine because of its phytoestrogenic properties and the chemoprevention of breast cancer. To reach this objective we start, from smaller building blocks, with the synthesis of Daidzein followed by a chemoselective borane reduction to obtain an olefin that will be hydrogenated enantioselectively with a commercial Ir-BARF catalyst. The increasing success of these catalysts even with this genre of substrates has already given good results with different catalysts in both e.e. and yield. For further researches we deuterate the Equol in the aliphatic O-ring and attempt a secondary synthetic route with an hydrogenation using QN-modified Pd.

Radioprotection of cultured cells by preincubation in medium containing deuterium oxide

Pretreatment with deuterium oxide (D2O) has been shown to protect mice against lethal effects of X-rays. In contrast, X-irradiation of cultured mammalian cells in D2O-containing medium has previously been reported to result in increased cell killing. Therefore, the effects of preincubation in medium containing 20% D2O on radiosensitivity were tested, using cells of a heat-sensitive cell-cycle mutant (21-Tb) of the murine mastocytoma P 815-X2. The mutant cells proliferate at 33 degrees C and are arrested in G1 phase in a state of reversible proliferative quiescence at 39.5 degrees C. Prior to irradiation with single X-ray doses of 0-10 Gy, the cells were cultured in normal or D2O-containing medium, either for 96 h at 33 degrees C ('proliferating cells'), or for 72 h at 33 degrees C followed by 24 h at 39.5 degrees C ('arrested cells'). After X-irradiation the cells were resuspended in normal medium, and cell survival was determined by the capacity of cells to form colonies in fibrin gels. Preincubation in medium containing 20% D2O resulted in a radioprotective effect on both proliferating and arrested cells, particularly at the higher X-ray doses. This radioprotection was manifested as a decreased slope of the semilogarithmic survival curves, whereas pretreatment with D2O had no significant effect on postirradiation repair as judged from Dq values. These results support the interpretation that the increase in postirradiation survival may be attributed to incorporation of deuterium into cellular metabolites during the period of preincubation.