Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: Simulations using a novel multipoint steered molecular dynamics approach

Thyroid hormone receptors (TR) are hormone-dependent transcription regulators that play a major role in human health, development, and metabolic functions. The thyroid hormone resistance syndrome, diabetes, obesity, and some types of cancer are just a few examples of important diseases that are related to TR malfunctioning, particularly impaired hormone binding. Ligand binding to and dissociation from the receptor ultimately control gene transcription and, thus, detailed knowledge of binding and release mechanisms are fundamental for the comprehension of the receptor`s biological function and development of pharmaceuticals. In this work, we present the first computational study of ligand entry into the ligand binding domain (LBD) of a nuclear receptor. We report molecular dynamics simulations of ligand binding to TRs using a generalization of the steered molecular dynamics technique designed to perform single-molecule pulling simulations along arbitrarily nonlinear driving pathways. We show that only gentle protein movements and conformational adaptations are required for ligand entry into the LBDs and that the magnitude of the forces applied to assist ligand binding are of the order of the forces involved in ligand dissociation. Our simulations suggest an alternative view for the mechanisms ligand binding and dissociation of ligands from nuclear receptors in which ligands can simply diffuse through the protein surface to reach proper positioning within the binding pocket. The proposed picture indicates that the large-amplitude protein motions suggested by the apo- and holo-RXR alpha crystallographic structures are not required, reconciling conformational changes of LBDs required for ligand entry with other nuclear receptors apo-structures that resemble the ligand-bound LBDs.

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)

Structural modeling of high-affinity thyroid receptor-ligand complexes

Understanding the molecular basis of the binding modes of natural and synthetic ligands to nuclear receptors is fundamental to our comprehension of the activation mechanism of this important class of hormone regulated transcription factors and to the development of new ligands. Thyroid hormone receptors (TR) are particularly important targets for pharmaceuticals development because TRs are associated with the regulation of metabolic rates, body weight, and circulating levels of cholesterol and triglycerides in humans. While several high-affinity ligands are known, structural information is only partially available. In this work we obtain structural models of several TR-ligand complexes with unknown structure by docking high affinity ligands to the receptors` ligand binding domain with subsequent relaxation by molecular dynamics simulations. The binding modes of these ligands are discussed providing novel insights into the development of TR ligands. The experimental binding free energies are reasonably well-reproduced from the proposed models using a simple linear interaction energy free-energy calculation scheme.

Recognition by the Thyroid Hormone Receptor of Canonical DNA Response Elements

To shed more light on the molecular requirements for recognition of thyroid response elements (TRES) by thyroid receptors (TRs), we compared the specific aspects of DNA TRE recognition by different TR constructs. Using fluorescence anisotropy, we performed a detailed and hierarchical study of TR-TRE binding. This wits done by comparing the binding affinities of three different TR constructs for four different TRE DNA elements, including palindromic sequences and direct repeats (F2, PAL, DR-1, and DR-4) as well as their interactions with nonspecific DNA sequences. The effect of MgCl(2) on suppressing of nonselective DNA binding to TR was also investigated. Furthermore, we determined the dissociation constants of the hTR beta DBD (DNA binding domain) and hTR beta DBD-LBD (DNA binding and ligand binding domains) for specific TRES. We found that a minimum DNA recognition peptide derived from DBD (H1TR) is sufficient for recognition and interaction with TREs, whereas scrambled DNA sequences were unrecognized. Additionally, we determined that the TR DBD binds to F2, PAL, and DR-4 with high affinity and similar K(d) values. The TR DBD-LBD recognizes all the tested TRES but binds preferentially to F2, with even higher affinity. Finally, our results demonstrate the important role played by LBDs in modulating TR-DNA binding.

On the Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors

The ligand binding domain (LBD) of nuclear hormone receptors adopts a very compact, mostly alpha-helical structure that binds specific ligands with very high affinity. We use circular dichroism spectroscopy and high-temperature molecular dynamics Simulations to investigate unfolding of the LBDs of thyroid hormone receptors (TRs). A molecular description of the denaturation mechanisms is obtained by molecular dynamics Simulations of the TR alpha and TR beta LBDs in the absence and in the presence of the natural ligand Triac. The Simulations Show that the thermal unfolding of the LBD starts with the loss of native contacts and secondary Structure elements, while the Structure remains essentially compact, resembling a molten globule state. This differs From most protein denaturation simulations reported to date and suggests that the folding mechanism may start with the hydrophobic collapse of the TR LBDs. Our results reveal that the stabilities of the LBDs of the TR alpha and TR beta Subtypes are affected to different degrees by the binding of the isoform selective ligand Triac and that ligand binding confers protection against thermal denaturation and unfolding in a subtype specific manner. Our Simulations indicate two mechanisms by which the ligand stabilizes the LBD: (1) by enhancing the interactions between H8 and H 11, and the interaction of the region between H I and the Omega-loop with the core of the LBD, and (2) by shielding the hydrophobic H6 from hydration.

Gaining ligand selectivity in thyroid hormone receptors via entropy

Nuclear receptors are important targets for pharmaceuticals, but similarities between family members cause difficulties in obtaining highly selective compounds. Synthetic ligands that are selective for thyroid hormone (TH) receptor beta (TR beta) vs. TR alpha reduce cholesterol and fat without effects on heart rate; thus, it is important to understand TR beta-selective binding. Binding of 3 selective ligands (GC-1, KB141, and GC-24) is characterized at the atomic level; preferential binding depends on a nonconserved residue (Asn-331 beta) in the TR beta ligand-binding cavity (LBC), and GC-24 gains extra selectivity from insertion of a bulky side group into an extension of the LBC that only opens up with this ligand. Here we report that the natural TH 3,5,3`-triodothyroacetic acid (Triac) exhibits a previously unrecognized mechanism of TR beta selectivity. TR x-ray structures reveal better fit of ligand with the TR alpha LBC. The TR beta LBC, however, expands relative to TR alpha in the presence of Triac (549 angstrom(3) vs. 461 angstrom(3)), and molecular dynamics simulations reveal that water occupies the extra space. Increased solvation compensates for weaker interactions of ligand with TR beta and permits greater flexibility of the Triac carboxylate group in TR beta than in TR alpha. We propose that this effect results in lower entropic restraint and decreases free energy of interactions between Triac and TR beta, explaining subtype-selective binding. Similar effects could potentially be exploited in nuclear receptor drug design.

Quartz recrystallization regimes, c-axis texture transitions and fluid inclusion reequilibration in a prograde greenschist to amphibolite facies mylonite zone (Ribeira Shear Zone, SE Brazil)

The crystal-plastic behavior of quartz mylonites from the Ribeira Shear Zone (SE Brazil), a major strike-slip structure that was active during a prograde metamorphic phase related to the Neoproterozoic Brasiliano-Pan African Orogeny, was investigated using a multi-method approach. Geothermobarometry results indicate deformational conditions ranging from similar to 300 to similar to 630 degrees C and 500-700 MPa. A strong correlation between mapped metamorphic zones and a dominance of different dynamic recrystallization mechanisms of quartz occurs within the mylonite zone. Bulging recrystallization (BLG) dominates within the chlorite zone between 300 and 410 degrees C, subgrain rotation recrystallization (SGR) operates within the biotite zone from 410 to 520 degrees C, and grain boundary migration recrystallization (GBM) dominates in the garnet zone above 520 degrees C. The development of quartz c-axis textures is mainly governed by temperature and dynamic recrystallization mechanisms. Textures from BLG zone mylonites are characterized by maxima around Z; SGR zone mylonites display single girdles or asymmetric type I crossed girdles; and GBM zone mylonites comprise maxima around Y and intermediate between X and Z. The scarcity or absence of water-bearing fluid inclusions in quartz mylonites from the SGR and GBM zones, which are dominated by carbonic inclusions, suggests water-deficient conditions, whereas BLG zone mylonites are dominated by water-bearing inclusions. This evidence indicates that water was available in the protoliths but has been eliminated with increasing deformation and deformation temperature. No effect of the water content variation on the quartz microstructural and recrystallized grain size evolution was detected, and little influence on c-axis texture development was observed. Most of the fluid inclusion densities were reequilibrated during the shear zone exhumation history, recording a decompression in the range of 300-500 MPa, while microstructural reequilibration effects related to the prograde metamorphism are largely preserved. Fluid inclusion microstructures and densities from two SGR zone samples preserved evidence for a near isothermal compression within the interior of the Ribeira Shear Zone during the prograde metamorphism. (C) 2009 Elsevier B.V. All rights reserved.

Metabolic oxidative stress elicited by the copper(II) complex [Cu(isaepy)(2)] triggers apoptosis in SH-SY5Y cells through the induction of the AMP-activated protein kinase/p38(MAPK)/p53 signalling axis: evidence for a combined use with 3-bromopyruvate in neuroblastoma treatment

We have demonstrated previously that the complex bis[(2-oxindol-3-ylimino)-2-(2-aminoethyl)pyridine-N,N`]copper(II), named [Cu(isaepy)(2)], induces AMPK (AMP-activated protein kinase)-dependent/p53-mediated apoptosis in tumour cells by targeting mitochondria. In the present study, we found that p38(MAPK) (p38 mitogen-activated protein kinase) is the molecular link in the phosphorylation cascade connecting AMPK to p53. Transfection of SH-SY5Y cells with a dominant-negative mutant of AMPK resulted in a decrease in apoptosis and a significant reduction in phospho-active p38(MAPK) and p53. Similarly, reverse genetics of p38(MAPK) yielded a reduction in p53 and a decrease in the extent of apoptosis, confirming an exclusive hierarchy of activation that proceeds via AMPK/p38(MAPK)/p53. Fuel supplies counteracted [Cu(isaepy)(2)]-induced apoptosis and AMPK/p38(MAPK)/p53 activation, with glucose being the most effective, suggesting a role for energetic imbalance in [Cu(isaepy)(2)] toxicity. Co-administration of 3BrPA (3-bromopyruvate), a well-known inhibitor of glycolysis, and succinate dehydrogenase, enhanced apoptosis and AMPK/p38(MAPK)/p53 signalling pathway activation. Under these conditions, no toxic effect was observed in SOD (superoxide dismutase)-overexpressing SH-SY5Y cells or in PCNs (primary cortical neurons), which are, conversely, sensitized to the combined treatment with [Cu(isaepy)(2)] and 3BrPA only if grown in low-glucose medium or incubated with the glucose-6-phosphate dehydrogenase inhibitor dehydroepiandrosterone. Overall, the results suggest that NADPH deriving from the pentose phosphate pathway contributes to PCN resistance to [Cu(isaepy)(2)] toxicity and propose its employment in combination with 3BrPA as possible tool for cancer treatment.

Investigating the Effects of Mifepristone (RU486) in the Behavioral, Hormonal and Central Responses to Acute Stress

Depression is associated with glucocorticoid hypersecretion, due to dysfunction of the hypothalamo-pituitary-adrenocorticol axis (HPA-axis). Because excess glucocorticoids are associated with depressive-like features in humans, glucocorticoid receptor antagonists are currently being tested for antidepressant efficacy in clinical trials. In the current study the hypothesis that mifepristone (RU486), a glucocorticoid receptor antagonist, would decrease the neuroendocrine and central HPA-axis responses to an acute stressor and attentuate depressive like behavior in an animal model of behavioral helplessness (forced swim test) was tested. Adult male rats were treated with 10 mglkg RU486 (subcutaneous) for five days and then exposed to a IO-minute forced swim test (FST), conducted in Plexiglas cylinders. FST sessions were videotaped for later analysis of behavioral immobility. Plasma ACTH and corticosterone CORT were measured at 15min and 90min after FST cessation. Animals were perfused and brains were collected for immunocytochemical assessment of c-Fos expression in the medial prefrontal cortex (mPFC), a brain region implicated in both depression and central control of the HPA axis. RU486 significantly decreased peak ACTH and CORT concentrations following FST exposure. In addition, glucocorticoid negative feedback was at1enuated in RU486-treated animals exposed to the FST. Exposure to FST alone induced c-FOS expression in the mPFC, as measured by the number of c-Fos positive neurons. Treatment with RU486 significantly increased the number of rnPFC c-Fos positive cell following FST exposure. The behavioral data obtained from FST paradigm, demonstrated that RU486 decreased immobility in the FST illustrating the potential efficacy of this drug as an antidepressant. Collectively these data suggest that RU486 dampens HPA-axis responses to stress, possibly by enhancing the excitability of stress-inhibitory neurons in the mPFC. This is particularly exciting, given the fact that this neural region is associated with decreased neural activity during depression in humans.

Biological indicators of stress in pacu (Piaractus mesopotamicus) after capture

Os efeitos da captura (perseguição, contenção em puçá e exposição aérea) no perfil sanguíneo do cortisol, glicose, cloreto, sódio, potássio, cálcio e na osmolaridade, hematócrito, hemoglobina, número de células vermelhas (CV) e volume corpuscular médio (VCM) foram investigados no pacu (Piaractus mesopotamicus). Um total de 132 peixes (49,7 ± 11,7 g) foi submetido à captura com 3 ou 5 minutos de exposição aérea. Nove peixes de cada tratamento foram amostrados 5, 15, 30, 60 minutos e 24 horas depois e outros nove peixes foram amostrados antes da captura e considerados controle. A captura resultou em aumento do cortisol e glicose no sangue 30 e 5 minutos depois da captura, respectivamente, independente do tempo de exposição aérea. Ambos os indicadores recuperaram os valores controle em 24 horas. Nos dois grupos de peixes, o cloreto plasmático diminuiu 60 minutos após captura e não recuperou os valores controle, enquanto o sódio sérico aumentou entre 15 e 30 minutos recuperando a condição controle em 24 horas. Não houve alteração significativa nos valores de potássio, cálcio, osmolaridade ou no hematócrito, hemoglobina, CV e VCM como consequência da captura. Os estressores sequenciais aplicados no pacu durante a captura ativaram o eixo cérebro-pituitária-interrenal (respostas do cortisol e glicose), mas a ativação do eixo cérebro-sistema simpático-células cromafins foi aparentemente moderada (respostas iônicas e hematológicas).

Dietary L-tryptophan alters aggression in juvenile matrinxa Brycon amazonicus

This study evaluated the effect of dietary supplementation with -tryptophan (L-TRP), a serotonin precursor, on the aggressiveness of juvenile matrinx . Fish were kept in individual aquaria for 7 days receiving the diets: D1 (control: 0.47% of TRP), D2 (0.94% of TRP), D3 (1.88% of TRP), and D4 (3.76% of TRP). After this, they were grouped with an intruder fish to establish a resident-intruder relationship during periods of 20 min. Blood cortisol, glucose, chloride, sodium and calcium; hemoglobin, hematocrit, red blood cell count and volume; liver glycogen and lipids were measured. Territoriality had significant effect on the aggressiveness of matrinx (the residents were more aggressive than intruders, < 0.001) and tryptophan significantly affected their behavior. Fish fed with the D2 diet presented a longer latency until the first attack ( = 0.0069) and bit the intruder fewer times ( = 0.0136) during the period of observation, compared to the control group. The frequency of bites and chases after the first attack was not affected by the dietary supplementation of TRP. Physiological variables were not significantly affected by the diet, except for a moderate increase in cortisol level in fish fed with D2 diet after the fight, indicating slight activation of the hypothalamus-pituitary-interrenal axis. The results show that juvenile matrinx have aggressive and territorial behavior and that a diet containing 9.4 g TRP kg(-1) alter their aggressiveness, without affecting the stress-related physiological parameters.

Variação periódica da triiodotironina (T3) plasmática e sua ação na reprodução induzida do matrinxã, Brycon cephalus (Günther, 1869) em cativeiro

O matrinxã, Brycon cephalus, espécie nativa oriunda da Bacia Amazônica, apresenta características adequadas para a piscicultura. Entretanto, trata-se de peixe reofílico, sendo necessário manejo adequado para induzir à reprodução. O objetivo deste trabalho foi caracterizar o perfil da triiodotironina (T3) plasmática no matrinxã, durante 16 meses (outubro/97 a janeiro/99), relacionando-o com a maturação sexual, além de testar a ação do T3 associado ao extrato pituitário de carpa na reprodução induzida da espécie. O experimento foi conduzido no Centro Nacional de Pesquisa de Peixes Tropicais - CEPTA, Pirassununga, SP, e no Departamento de Morfologia e Fisiologia Animal, da Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal - UNESP. Foram amostrados, mensalmente, 8 a 12 peixes, de ambos os sexos, totalizando 173 animais, de onde retirou-se sangue para dosagem do T3 plasmático. As gônadas foram removidas para análise histológica com identificação do sexo e determinação do estádio de maturação. Analisaram-se testículos e ovários de 161 peixes em corte transversal, tendo predominado machos (63,35%) e o estádio sexual imaturo entre ambos. A concentração plasmática de T3 foi maior de dezembro a janeiro, para machos e fêmeas, coincidindo com o período de maior atividade reprodutiva da espécie e maiores temperaturas da água. em janeiro/99, reprodutores de matrinxã foram induzidos com extrato de pituitária de carpa (EPC) associado à administração de T3 (20 mg/kg em 0,1 mL de suspensão oleosa). Os resultados sugeriram que o T3 atuou sinergicamente à gonadotropina do extrato hipofisário e que o tratamento agudo de triiodotironina com o EPC pode estimular o eixo hipotálamo-hipófise-ovário. O tempo de eclosão das larvas provenientes das fêmeas tratadas com o T3 foi menor e o crescimento inicial e a sobrevivência dessas larvas, maiores.

Thyroid status, but not insulin status, affects expression of avian uncoupling protein mRNA in chicken

The aim of this study was to investigate the hormonal regulation of the avian homolog of mammalian uncoupling protein (avUCP) by studying the impact of thyroid hormones and insulin on avUCP mRNA expression in chickens (Gallus gallus). For 3 wk, chicks received either a standard diet (control group), or a standard diet supplemented with triiodothyronine (T-3; T3 group) or with the thyroid gland inhibitor methimazole (MMI group). A fourth group received injections of the deiodinase inhibitor iopanoic acid (IOP group). During the 4th wk of age, all animals received two daily injections of either human insulin or saline solution. The results indicate a twofold overexpression of avUCP mRNA in gastrocnemius muscle of T3 birds and a clear downregulation (-74%) in MMI chickens compared with control chickens. Insulin injections had no significant effect on avUCP mRNA expression in chickens. This study describes for the first time induction of avUCP mRNA expression by the thermogenic hormone T3 in chickens and supports a possible involvement of avUCP in avian thermogenesis.

Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer

A detailed genome mapping analysis of 213,636 expressed sequence tags (EST) derived from nontumor and tumor tissues of the oral cavity, larynx, pharynx, and thyroid was done. Transcripts matching known human genes were identified; potential new splice variants were flagged and subjected to manual curation, pointing to 788 putatively new alternative splicing isoforms, the majority (75%) being insertion events. A subset of 34 new splicing isoforms (5% of 788 events) was selected and 23 (68%) were confirmed by reverse transcription-PCR and DNA sequencing. Putative new genes were revealed, including six transcripts mapped to well-studied chromosomes such as 22, as well as transcripts that mapped to 253 intergenic regions. In addition, 2,251 noncoding intronic RNAs, eventually involved in transcriptional regulation, were found. A set of 250 candidate markers for loss of heterozygosis or gene amplification was selected by identifying transcripts that mapped to genomic regions previously known to be frequently amplified or deleted in head, neck, and thyroid tumors. Three of these markers were evaluated by quantitative reverse transcription-PCR in an independent set of individual samples. Along with detailed clinical data about tumor origin, the information reported here is now publicly available on a dedicated Web site as a resource for further biological investigation. This first in silico reconstruction of the head, neck, and thyroid transcriptomes points to a wealth of new candidate markers that can be used for future studies on the molecular basis of these tumors. Similar analysis is warranted for a number of other tumors for which large EST data sets are available.

Repeated predictable or unpredictable stress: effects on cocaine-induced locomotion and cyclic AMP-dependent protein kinase activity

Stressful experiences appear to have a strong influence on susceptibility to drug taking behavior. Cross-sensitization between stress and drug-induced locomotor response has been found. Locomotor response to novelty or cocaine (10 mg/kg, i.p.), cyclic AMP-dependent protein kinase (PKA) activity in the nucleus accumbens and basal corticosterone levels were evaluated in male adult rats exposed to acute and chronic predictable or unpredictable stress. Rats exposed to a 14-day predictable stress showed increased locomotor response to novelty and to cocaine, whereas rats exposed to chronic unpredictable stress demonstrated increased cyclic AMP-dependent PKA activity in the nucleus accumbens. Both predictable and unpredictable stress increased basal corticosterone plasma levels. These experiments demonstrated that stress-induced early cocaine sensitization depends on the stress regime and is apparently dissociated from stress-induced changes in cyclic AMP-dependent PKA activity and corticosterone levels. (C) 2002 Elsevier B.V. B.V. All rights reserved.