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)

The Hilbert space of the Chern-Simons theory on a cylinder: a loop quantum gravity approach

As a laboratory for loop quantum gravity, we consider the canonical quantization of the three-dimensional Chern-Simons theory on a noncompact space with the topology of a cylinder. Working within the loop quantization formalism, we define at the quantum level the constraints appearing in the canonical approach and completely solve them, thus constructing a gauge and diffeomorphism invariant physical Hilbert space for the theory. This space turns out to be infinite dimensional, but separable.

POLYNOMIAL AND GROUP IDENTITIES IN ALTERNATIVE LOOP ALGEBRAS

We investigate polynomial identities on an alternative loop algebra and group identities on its (Moufang) unit loop. An alternative loop ring always satisfies a polynomial identity, whereas whether or not a unit loop satisfies a group identity depends on factors such as characteristic and centrality of certain kinds of idempotents.

The smallest simple Moufang loop

We study the simple Moufang loop GLL(F(2)) and give a complete description of its lattice of subloops. (C) 2008 Elsevier Inc. All rights reserved.

Some classes of semisimple group (and loop) algebras over finite fields

We determine the structure of the semisimple group algebra of certain groups over the rationals and over those finite fields where the Wedderburn decompositions have the least number of simple components We apply our work to obtain similar information about the loop algebras of mdecomposable RA loops and to produce negative answers to the isomorphism problem over various fields (C) 2010 Elsevier Inc All rights reserved

Superoxide radical protects liposome-contained cytochrome c against oxidative damage promoted by peroxynitrite and free radicals

The effects of nitrosative species on cyt c structure and peroxidase activity were investigated here in the presence of O(2)(center dot-) and anionic and zwitterionic vesicles. Nitrosative species were generated by 3-morpholinesydnonymine (SIN1) decomposition, using cyt c heme iron and/or molecular oxygen as electron acceptor. Far-and near-UV CD spectra of SIN1-treated cyt c revealed respectively a slight decrease of a-helix content (from 39 to 34%) and changes in the tryptophan structure accompanied by increased fluorescence. The Soret CD spectra displayed a significant decrease of the positive signal at 403 nm. EPR spectra revealed the presence of a low-spin cyt c form (S = 1/2) with g(1) = 2.736, g(2) = 2.465, and g(3) = 2.058 after incubation with SIN1. These data suggest that the concomitant presence of NO(center dot) and O(2)(center dot-) generated from dissolved oxygen, in a system containing cyt c and liposomes, promotes chemical and conformational modi. cations in cyt c, resulting in a hypothetical bis-histidine hexacoordinated heme iron. We also show that, paradoxically, O(2)(center dot-) prevents not only membrane lipoperoxidation by peroxide-derived radicals but also oxidation of cyt c itself due to the ability of O(2)(center dot-) to reduce heme iron. Finally, lipoperoxidation measurements showed that, although it is a more efficient peroxidase, SIN1-treated cyt c is not more effective than native cyt c in promoting damage to anionic liposomes in the presence of tert-ButylOOH, probably due to loss of affinity with negatively charged lipids. (C) 2009 Elsevier Inc. All rights reserved.

Accumulation of (5 ` S)-8,5 `-cyclo-2 `-deoxyadenosine in organs of Cockayne syndrome complementation group B gene knockout mice

Cockayne syndrome (CS) is a human genetic disorder characterized by sensitivity to UV radiation, neurodegeneration, premature aging among other phenotypes. CS complementation group B (CS-B) gene (csb) encodes the CSB protein (CSB) that is involved in base excision repair of a number of oxidatively induced lesions in genomic DNA in vivo. We hypothesized that CSB may also play a role in cellular repair of the DNA helix-distorting tandem lesion (5`S)-8,5`-cyclo-2`-deoxyadenosine (S-cdA). Among many DNA lesions. S-cdA is unique in that it represents a concomitant damage to both the sugar and base moieties of the same nucleoside. Because of the presence of the C8-C5` covalent bond, S-cdA is repaired by nucleotide excision repair unlike most of other oxidatively induced lesions in DNA, which are subject to base excision repair. To test our hypothesis, we isolated genomic DNA from brain, kidney and liver of wild type and csb knockout (csb(-/-)) mice. Animals were not exposed to any exogenous oxidative stress before the experiment. DNA samples were analysed by liquid chromatography/mass spectrometry with isotope-dilution. Statistically greater background levels of S-cdA were observed in all three organs of csb(-/-) mice than in those of wild type mice. These results suggest the in vivo accumulation of S-cdA in genomic DNA due to lack of its repair in csb(-/-) mice. Thus, this study provides, for the first time, the evidence that CSB plays a role in the repair of the DNA helix-distorting tandem lesion S-cdA. Accumulation of unrepaired S-cdA in vivo may contribute to the pathology associated with CS. Published by Elsevier B.V.

DMSO-Induced Denaturation of Hen Egg White Lysozyme

We report on the size, shape, structure, and interactions of lysozyme in the ternary system lysozyme/DMSO/water at low protein concentrations. Three structural regimes have been identified, which we term the ""folded"" (0 < phi(DMSO) < 0.7), ""unfolded"" (0.7 <= phi(DMSO) < 0.9), and ""partially collapsed"" (0.9 <= phi(DMSO) < 1.0) regime. Lysozyme resides in a folded conformation with an average radius of gyration of 1.3 +/- 0.1 nm for phi(DMSO) < 0.7 and unfolds (average R(g) of 2.4 +/- 0.1 nm) above phi(DMSO) > 0.7. This drastic change in the protein`s size coincides with a loss of the characteristic tertiary structure. It is preceded by a compaction of the local environment of the tryptophan residues and accompanied by a large increase in the protein`s overall flexibility. In terms of secondary structure, there is a gradual loss of alpha-helix and concomitant increase of beta-sheet structural elements toward phi(DMSO) = 0.7, while an increase in phi(DMSO) at even higher DMSO volume fractions reduces the presence of both a-helix and beta-sheet secondary structural elements. Protein-protein interactions remain overall repulsive for all values of phi(DMSO) An attempt is made to relate these structural changes to the three most important physical mechanisms that underlie them: the DMSO/water microstructure is strongly dependent on the DMSO volume fraction, DMSO acts as a strong H-bond acceptor, and DMSO is a bad solvent for the protein backbone and a number of relatively polar side groups, but a good solvent for relatively apolar side groups, such as tryptophan.

Oxindole-Schiff base copper(II) complexes interactions with human serum albumin: Spectroscopic, oxidative damage, and computational studies

CD and EPR were used to characterize interactions of oxindole-Schiff base copper(II) complexes with human serum albumin (HSA). These imine ligands form very stable complexes with copper, and can efficiently compete for this metal ion towards the specific N-terminal binding site of the protein, consisting of the amino acid sequence Asp-Ala-His. Relative stability constants for the corresponding complexes were estimated from CD data, using the protein as competitive ligand, with values of log K(CuL) in the range 15.7-18.1, very close to that of [Cu(HSA)] itself, with log K(CuHSA) 16.2. Some of the complexes are also able to interfere in the a-helix structure of the protein, while others seem not to affect it. EPR spectra corroborate those results, indicating at least two different metal species in solution, depending on the imine ligand. Oxidative damage to the protein after incubation with these copper(II) complexes, particularly in the presence of hydrogen peroxide, was monitored by carbonyl groups formation, and was observed to be more severe when conformational features of the protein were modified. Complementary EPR spin-trapping data indicated significant formation of hydroxyl and carbon centered radicals, consistent with an oxidative mechanism. Theoretical calculations at density functional theory (DFT) level were employed to evaluate Cu(II)-L binding energies, L -> Cu(II) donation, and Cu(II) -> L back-donation, by considering the Schiff bases and the N-terminal site of HSA as ligands. These results complement previous studies on cytotoxicity, nuclease and pro-apoptotic properties of this kind of copper(II) complexes, providing additional information about their possibilities of transport and disposition in blood plasma. (C) 2009 Elsevier Inc. All rights reserved.

W-dalaprojektet - Vinnande partnerskap mellan näringsliv och högskola

Samverkan mellan företag, stat, kommuner, landsting o.s.v. och högskolor representerar tillsammans den plattform vilken ofta benämns som Triple Helix. Denna typ av samverkan utgår från antagandet att de inblandade aktörerna kan få belöningar som överstiger de bidrag som de själva sätter in. En sådan samverkan antas också ge företag och den region de befinner sig i konkurrensfördelar och möjligheter att växa och utvecklas. Syftet med Wdalaprojektet, som startade våren 2005 och som skulle avslutas i och med utgången av 2006, var att bygga upp en sådan varaktig samverkan. Den frågan som är i fokus är hur framgångsrikt W-dalaprojektet varit i dessa avseenden? Den här studien försöker:a) beskriva hur projektet initierats och implementeratsb) värdera i vilken utsträckning projektets mål har uppnåtts samtc) identifiera och värdera funktionaliteten hos den samverkansmodellsom använtsErfarenheterna från projektet kan sammanfattas i sex punkter för vad som kan antas vara väsentligt för en långsiktig samverkan att fungera.1. Det behövs fora för kontinuerliga möten och en formaliserad organisation2. ”Kontaktpunkter” för att koordinera samarbetet spelar en viktig roll3. Högskolans ”leveransförmåga” måste förbättras4. ”Kulturkrockar” och en bristande ömsesidig tilltro5. Förmågan att definiera behov av samverkan behöver förbättras6. Långsiktig hållbar ekonomi

Projektet W-Dala Plus - metodutveckling i samverkan mellannäringsliv och högskola

Projektet W-dala Plus - metodutveckling i samverkan mellan näringsliv och högskola är en fortsättning på det s.k. W-dalaprojektet (W-Dala – vinnande partnerskap mellan näringsliv och högskola) som startade våren 2005 och som, något försenat, avslutades under våren 2007. Syftet med det inledande projektet var att bygga upp en varaktig och innovativ samverkan mellan regionens näringsliv, den offentliga sektorns organisationer ochden högre utbildningen, för att skapa en ”triple helix-anda”. Sådan samverkan kan ske både formaliserat och genom att informella nätverk byggs upp. Denna samverkan avsågs att ”kunna bli självbärande genom att företagarna själva betalar för sitt behov av fortbildning och uppdragsforskning” (Projektplanen, W-Dala). Syftet var också att det arbete som inleddes skulle kunna öka företagens konkurrenskraft och därmed bidratill regional tillväxt.Syftet med studien är att belysa, tolka och analysera hur W-Dalaprojektet vidareutvecklats genom att projektet W-Dala Plus - metodutveckling i samverkan mellan näringsliv och högskola genomförts samt vilka erfarenheter som är möjliga att dra från detta. Resultatet kan i sin tur ge indikationer mot vilka områden fortsatta insatser kan vara lämpliga att riktas.

Análise ultraestrutural da glândula corpo dorsal do caracol pulmonado Megalobulimus abbreviatus Becquaert 1948

O corpo dorsal (CD) é uma glândula endócrina presente junto aos gânglios cerebrais de todos os moluscos pulmonados (sinapomorfia) e, em Megalobulimus abbreviatus, o CD estende-se até o complexo de gânglios subesofageais. Tem sido atribuído o papel de produtor de hormônio gonadotrópico feminino para os pulmonados mais estudados (Helix pomatia, Helix aspersa e Lymnaea stagnalis). Em trabalho anterior foram descritos o aspecto histológico de glândula esteroidogênica e as variações citológicas sazonais do CD de Megalobulimus; o período de maior atividade sintética glandular coincide com o período de maior atividade reprodutiva. Um dos objetivos desse trabalho é identificar ultra-estruturalmente a presença e o tipo de terminações nervosas junto às células do CD, nas diferentes porções desta glândula, parte supraesofageal, junto aos gânglios cerebrais (GC) e subesofageal, junto aos gânglios pleurais (PL). Nesse estudo também pretende-se investigar a imunorreatividade ao neuropeptídeo FMRFamida no CD, supondo que este peptídeo, existente em grande quantidade em numerosos neurônios cerebrais, possa estar envolvido no controle inibitório destes gânglios sobre a atividade sintética glandular. Para o trabalho, diferentes regiões do CD (Fig. 2) foram fixadas em diferentes meses (5 animais/estação) em paraformaldeído 2% e glutaraldeído 1%, diluídos em tampão fosfato 0,1M, pH 7,4 (para imunoistoquímica, a fixação foi em paraformaldeído 4% e glutaraldeído 0,1%); pós-fixados em OsO4 1% diluído em TF; desidratado em álcool e acetona e incluído em resina Durcupan. As secções ultrafinas foram analisadas no Centro de Microscopia Eletrônica da UFRGS (microscópio eletrônico de transmissão JEOL JEM1200ExII). Para a imunoistoquímica, antes da pós-fixação com OsO4, os cortes (vibrátomo, 100 µm) foram processados para imunoistoquímica ao anticorpo anti-FMRFamida (Chemicon, 1:900) pelo procedimento peroxidase-anti-peroxidase. O CD se estende dos GC aos PL, acompanhando os conetivos cérebro-pleurais. Tanto na região subesofageal como supraesofageal, as células do CD de Megalobulimus abbreviatus estão inervadas por terminações axonais que fazem estreito contato com as células secretoras, semelhantes a sinapses “en passant”, contendo grânulos eletrodensos. Na porção dorsal à comissura cerebral são encontrados pequenos feixes de axônios, indicando que a inervação do CD provém da comissura cerebral. As terminações axonais encontradas no CD mostram algumas terminações axonais imunnorreativas a FMRFamida, sugerindo a participação deste neuropeptídeo no controle do CD. As células do CD apresentam características evidentes de tecido esteroidogênico.