Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains

We present multiple native and denaturation simulations of the B and E domains of the three-helix bundle protein A, totaling 60 ns. The C-terminal helix (H3) consistently denatures later than either of the other two helices and contains residual helical structure in the denatured state. These results are consistent with experiments suggesting that the isolated H3 fragment is more stable than H1 and H2 and that H3 forms early in folding. Interestingly, the denatured state of the B domain is much more compact than that of the E domain. This sequence-dependent effect on the dimensions of the denatured state and the lack of correlation with structure suggest that the radius of gyration can be a misleading reaction coordinate for unfolding/folding. Various unfolding and refolding events are observed in the denaturation simulations. In some cases, the transitions are facilitated through interactions with other portions of the protein—contact-assisted helix formation. In the native simulations, the E domain is very stable: after 6 ns, the Cα root-mean-square deviation from the starting structure is less than 1.4 Å. In contrast, the native state of the B domain deviates more and its inter-helical angles fluctuate. In apparent contrast, we note that the B domain is thermodynamically more stable than the E domain. The simulations suggest that the increased stability of the B domain may be due to heightened mobility, and therefore entropy, in the native state and decreased mobility/entropy in the more compact denatured state.

Histone deacetylase inhibitor selectively induces p21WAF1 expression and gene-associated histone acetylation

Histone deacetylases (HDACs) catalyze the removal of acetyl groups on the amino-terminal lysine residues of core nucleosomal histones. This activity is associated generally with transcriptional repression. We have reported previously that inhibition of HDAC activity by hydroxamic acid-based hybrid polar compounds, such as suberoylanilide hydroxamic acid (SAHA), induces differentiation and/or apoptosis of transformed cells in vitro and inhibits tumor growth in vivo. SAHA is a potentially new therapeutic approach to cancer treatment and is in Phase I clinical trials. In several tumor cell lines examined, HDAC inhibitors alter the expression of less than 1% of expressed genes, including the cell cycle kinase inhibitor p21WAF1. In T24 bladder carcinoma cells, SAHA induces up to a 9-fold increase in p21WAF1 mRNA and protein, which is, at least in part, because of an increase in the rate of transcription of the gene. SAHA causes an accumulation of acetylated histones H3 and H4 in total cellular chromatin by 2 h, which is maintained through 24 h of culture. An increase in the accumulation of acetylated H3 and H4 was detected throughout the p21WAF1 promoter and the structural gene after culture with SAHA. The level of histone acetylation did not change in chromatin associated with the actin and p27 genes, and their mRNA expression was not altered during culture of T24 cells with SAHA. Thus, the present findings indicate that the induction of p21WAF1 by SAHA is regulated, at least in part, by the degree of acetylation of the gene-associated histones and that this induced increase in acetylation is gene selective.

Syntaxin 1A inhibits CFTR chloride channels by means of domain-specific protein–protein interactions

Previously we showed that the functional activity of the epithelial chloride channel that is encoded by the cystic fibrosis gene (CFTR) is reciprocally modulated by two components of the vesicle fusion machinery, syntaxin 1A and Munc-18. Here we report that syntaxin 1A inhibits CFTR chloride channels by means of direct and domain-specific protein–protein interactions. Syntaxin 1A stoichiometrically binds to the N-terminal cytoplasmic tail of CFTR, and this binding is blocked by Munc-18. The modulation of CFTR currents by syntaxin 1A is eliminated either by deletion of this tail or by injecting this tail as a blocking peptide into coexpressing Xenopus oocytes. The CFTR binding site on syntaxin 1A maps to the third predicted helical domain (H3) of this membrane protein. Moreover, CFTR Cl− currents are effectively inhibited by a minimal syntaxin 1A construct (i.e., the membrane-anchored H3 domain) that cannot fully substitute for wild-type syntaxin 1A in membrane fusion reactions. We also show that syntaxin 1A binds to and inhibits the activities of disease-associated mutants of CFTR, and that the chloride current activity of recombinant ΔF508 CFTR (i.e., the most common cystic fibrosis mutant) can be potentiated by disrupting its interaction with syntaxin 1A in cultured epithelial cells. Our results provide evidence for a direct physical interaction between CFTR and syntaxin 1A that limits the functional activities of normal and disease-associated forms of this chloride channel.

A strategy for the identification of proteins targeted by thioredoxin

Thioredoxins are 12-kDa proteins functional in the regulation of cellular processes throughout the animal, plant, and microbial kingdoms. Growing evidence with seeds suggests that an h-type of thioredoxin, reduced by NADPH via NADP-thioredoxin reductase, reduces disulfide bonds of target proteins and thereby acts as a wakeup call in germination. A better understanding of the role of thioredoxin in seeds as well as other systems could be achieved if more were known about the target proteins. To this end, we have devised a strategy for the comprehensive identification of proteins targeted by thioredoxin. Tissue extracts incubated with reduced thioredoxin are treated with a fluorescent probe (monobromobimane) to label sulfhydryl groups. The newly labeled proteins are isolated by conventional two-dimensional electrophoresis: (i) nonreducing/reducing or (ii) isoelectric focusing/reducing SDS/PAGE. The isolated proteins are identified by amino acid sequencing. Each electrophoresis system offers an advantage: the first method reveals the specificity of thioredoxin in the reduction of intramolecular vs. intermolecular disulfide bonds, whereas the second method improves the separation of the labeled proteins. By application of both methods to peanut seed extracts, we isolated at least 20 thioredoxin targets and identified 5—three allergens (Ara h2, Ara h3, and Ara h6) and two proteins not known to occur in peanut (desiccation-related and seed maturation protein). These findings open the door to the identification of proteins targeted by thioredoxin in a wide range of systems, thereby enhancing our understanding of its function and extending its technological and medical applications.

Adventitious Root Growth and Cell-Cycle Induction in Deepwater Rice1

Deepwater rice (Oryza sativa) is adapted to survive conditions of severe flooding over extended periods of time. During such periods adventitious roots develop to provide water, nutrients, and anchorage. In the present study the growth of adventitious roots was induced by treatment with ethylene but not auxin, cytokinin, or gibberellin. Root elongation was enhanced between 8 and 10 h after submergence. The population of cells in the S phase and expression of the S-phase-specific histone H3 gene increased within 4 to 6 h. Within 6 to 8 h the G2-phase population increased. Cell-cycle activation was accompanied by sequential induction of a cdc2-activating kinase homolog, R2, of two cdc2 genes, cdc2Os-1 and cdc2Os-2, and of three cyclin genes, cycA1;3, cycB2;1, and cycB2;2, but only induction of the R2 gene expression preceded the induction of the S phase, possibly contributing to cell-cycle regulation in the G1 phase. Both cdc2 genes were expressed at slightly higher levels during DNA replication. Transcripts of the A-type cyclin accumulated during the S and G2 phases, and transcripts of the B-type cyclins accumulated during the G2 phase. Cyclin expression was induced at all nodes with a similar time course, suggesting that ethylene acts systemically and that root primordia respond to ethylene at an early developmental stage.

Selective association of the methyl-CpG binding protein MBD2 with the silent p14/p16 locus in human neoplasia

DNA methylation of tumor suppressor genes is a common feature of human cancer. The cyclin-dependent kinase inhibitor gene p16/Ink4A is hypermethylated in a wide range of malignant tissues and the p14/ARF gene located 20 kb upstream on chromosome 9p21 is also methylated in carcinomas. p14/ARF (ARF, alternative reading frame) does not inhibit the activities of cyclins or cyclin-dependent kinase complexes; however, the importance of the two gene products in the etiology of cancer resides in their involvement in two major cell cycle regulatory pathways: p53 and the retinoblastoma protein, Rb, respectively. Distinct first exons driven from separate promoters are spliced onto the common exons 2 and 3 and the resulting proteins are translated in different reading frames. Both genes are expressed in normal cells but can be alternatively or coordinately silenced when their CpG islands are hypermethylated. Herein, we examined the presence of methyl-CpG binding proteins associated with aberrantly methylated promoters, the distribution of acetylated histones H3 and H4 by chromatin immunoprecipitation assays, and the effect of chemical treatment with 5-aza-2′-deoxycytidine (5aza-dC) and trichostatin A on gene induction in colon cell lines by quantitative reverse transcriptase–PCR. We observed that the methyl-CpG binding protein MBD2 is targeted to methylated regulatory regions and excludes the acetylated histones H3 and H4, resulting in a localized inactive chromatin configuration. When methylated, the genes can be induced by 5aza-dC but the combined action of 5aza-dC and trichostatin A results in robust gene expression. Thus, methyl-CpG binding proteins and histone deacetylases appear to cooperate in vivo, with a dominant effect of DNA methylation toward histone acetylation, and repress expression of tumor suppressor genes hypermethylated in cancers.

CDP/cut is the DNA-binding subunit of histone gene transcription factor HiNF-D: a mechanism for gene regulation at the G1/S phase cell cycle transition point independent of transcription factor E2F.

Transcription of the genes for the human histone proteins H4, H3, H2A, H2B, and H1 is activated at the G1/S phase transition of the cell cycle. We have previously shown that the promoter complex HiNF-D, which interacts with cell cycle control elements in multiple histone genes, contains the key cell cycle factors cyclin A, CDC2, and a retinoblastoma (pRB) protein-related protein. However, an intrinsic DNA-binding subunit for HiNF-D was not identified. Many genes that are up-regulated at the G1/S phase boundary are controlled by E2F, a transcription factor that associates with cyclin-, cyclin-dependent kinase-, and pRB-related proteins. Using gel-shift immunoassays, DNase I protection, and oligonucleotide competition analyses, we show that the homeodomain protein CDP/cut, not E2F, is the DNA-binding subunit of the HiNF-D complex. The HiNF-D (CDP/cut) complex with the H4 promoter is immunoreactive with antibodies against CDP/cut and pRB but not p107, whereas the CDP/cut complex with a nonhistone promoter (gp91-phox) reacts only with CDP and p107 antibodies. Thus, CDP/cut complexes at different gene promoters can associate with distinct pRB-related proteins. Transient coexpression assays show that CDP/cut modulates H4 promoter activity via the HiNF-D-binding site. Hence, DNA replication-dependent histone H4 genes are regulated by an E2F-independent mechanism involving a complex of CDP/cut with cyclin A/CDC2/ RB-related proteins.

Inverse agonism of histamine H2 antagonist accounts for upregulation of spontaneously active histamine H2 receptors.

Histamine H2 receptors transfected in Chinese hamster ovary (CHO) cells are time- and dose-dependently upregulated upon exposure to the H2 antagonists cimetidine and ranitidine. This effect appears to be H2 receptor-mediated as no change in receptor density was observed after H1 or H3 antagonist treatment or after incubation with the structural analogue of cimetidine, VUF 8299, which has no H2 antagonistic effects. By using transfected CHO cells expressing different densities of wild-type H2 receptors or an uncoupled H2Leu124Ala receptor, the histamine H2 receptor was found to display considerable agonist-independent H2 receptor activity. Cimetidine and ranitidine, which both induce H2 receptor upregulation, actually functioned as inverse agonists in those cell lines displaying spontaneous agonist-independent H2 receptor activity. Burimamide, on the other hand, was shown to act as a neutral antagonist and did as expected not induce H2 receptor upregulation after long-term exposure. The displayed inverse agonism of H2 antagonists appears to be a mechanistic basis for the observed H2 antagonist-induced H2 receptor upregulation in transfected CHO cells. These observations shed new light on the pharmacological classification of the H2 antagonists and may offer a plausible explanation for the observed development of tolerance after prolonged clinical use.

A compositional map of human chromosome band Xq28.

The molar fractions of guanine plus cytosine (GC) in DNA were determined for 36 yeast artificial chromosomes (YACs) which almost completely cover human chromosome band Xq28, a terminal reverse band, corresponding to about 8 Mb of DNA. This allowed the construction of the most complete compositional map to date of a chromosomal band; three regions were observed: (i) a proximal 3.5-Mb region formed by GC-poor L and GC-rich H1 isochores; (ii) a middle 2,2-Mb region essentially formed by a GC-rich H2 isochore and a very GC-rich H3 isochore separated by a GC-poor L isochore, YACs from this region being characterized by a striking compositional heterogeneity and instability; and (iii) a distal 1.3-Mb region exclusively formed by GC-poor L isochores. Gene and CpG island concentrations increased with the GC levels of the isochores, as expected. Xq28 exemplifies a subset of reverse bands which are different from the two other subsets, namely from telomeric bands, which are characterized by specific cytogenetic properties and by the predominance of H2 and H3 isochores, and from the majority of reverse bands, which do not contain H2 and H3 isochores.

Crystal structure of the complex of a catalytic antibody Fab fragment with a transition state analog: structural similarities in esterase-like catalytic antibodies.

The x-ray structure of the complex of a catalytic antibody Fab fragment with a phosphonate transition-state analog has been determined. The antibody (CNJ206) catalyzes the hydrolysis of p-nitrophenyl esters with significant rate enhancement and substrate specificity. Comparison of this structure with that of the uncomplexed Fab fragment suggests hapten-induced conformational changes: the shape of the combining site changes from a shallow groove in the uncomplexed Fab to a deep pocket where the hapten is buried. Three hydrogen-bond donors appear to stabilize the charged phosphonate group of the hapten: two NH groups of the heavy (H) chain complementarity-determining region 3 (H3 CDR) polypeptide chain and the side-chain of histidine-H35 in the H chain (His-H35) in the H1 CDR. The combining site shows striking structural similarities to that of antibody 17E8, which also has esterase activity. Both catalytic antibody ("abzyme") structures suggest that oxyanion stabilization plays a significant role in their rate acceleration. Additional catalytic groups that improve efficiency are not necessarily induced by the eliciting hapten; these groups may occur because of the variability in the combining sites of different monoclonal antibodies that bind to the same hapten.

Evolutionary conservation of human TATA-binding-polypeptide-associated factors TAFII31 and TAFII80 and interactions of TAFII80 with other TAFs and with general transcription factors.

Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription. To investigate protein-protein interactions involved in TFIID assembly and in TAF-mediated activator functions, we have cloned and expressed cDNAs encoding human TAFII80 and TAFII31. Coimmunoprecipitation assays showed that TAFII80 interacted with TAFII250, TAFII31, TAFII20, and TBP, but not with TAFII55. Similar assays showed that TAFII80 interacted with TFIIE alpha and with TFIIF alpha (RAP74) but not with TFIIB, TFIIE beta, or TFIIF beta (RAP30). Further studies with TAFII80 mutations revealed three distinct interaction domains which fall within regions conserved in human TAFII80, Drosophila TAFII60, and yeast TAFII60. The N terminus of TAFII80 (residues 1-100) interacts with both TAFII31 and TAFII20, while two C-terminal regions are involved, respectively, in interactions with TAFII250 and TFIIF alpha (RAP74) (residues 203-276) and with TBP and TFIIE alpha (residues 377-505). The interactions between TAFII80 and general factors TFIIE alpha and TFIIF alpha (RAP74) could be important for recruitment of GTFs during activator-dependent transcription. Because TAFs 80, 31, and 20 show sequence similarities to histones H4, H3, and H2B, as well as some parallel interactions, this subset of TAFs may form a related core structure within TFIID.

Variabilidade populacional em manguezais: análises moleculares e morfológicas em caranguejos Brachyura (Crustacea: Decapoda)

A análise da estruturação populacional de espécies codistribuídas permite a comparação de padrões de estruturação, fornecendo informações acerca dos fatores que influenciam a diferenciação em espécies pertencentes ao mesmo ecossistema. Este projeto teve como objetivo principal analisar a variabilidade intraespecífica em caranguejos habitantes de manguezais, codistribuídos ao longo do Oceano Atlântico Ocidental, por meio de ferramentas moleculares e morfológicas, visando testar a hipótese de elevada estruturação populacional em manguezais. Para este fim, cinco espécies foram utilizadas como modelo (Aratus pisonii, Goniopsis cruentata, Sesarma rectum, Uca thayeri e Ucides cordatus) e avaliadas por meio de marcadores mitocondriais COI e 16S e nuclear H3 e análises morfológicas comparativas e de morfometria. Os dados moleculares revelaram dois padrões, indicando elevada estruturação populacional para as espécies A. pisonii e U. thayeri e ausência de estruturação para G. cruentata, S. rectum e U. cordatus. Os dados morfológicos, no entanto, não acompanham esses padrões, já que não foram encontradas diferenças morfológicas ou morfométricas associadas aos grupos evidenciados pelas análises moleculares. A ausência de fluxo gênico entre regiões para algumas espécies deve-se, muito provavelmente, à existência de fatores que não se limitam ao isolamento por distância, mas também devido a diferenças na duração do estágio larval e a diferenças bruscas em alguns fatores abióticos, como a salinidade, por exemplo, que, associados às diferentes características do desenvolvimento larval de cada espécie, culminam na existência de estruturas populacionais diferentes. Além disso, os padrões de diferenciação genética observados concordam com os cenários biogeográficos propostos para o Atlântico Ocidental, no qual mudanças e flutuações geológicas, climáticas e oceanográficas, resultantes do fechamento do Istmo do Panamá e de ciclos glaciais na América do Norte, promoveram divergência genética.

Complexação de guaiacol com ß-ciclodextrina para tratamento de alveolite seca: avaliação in vitro e in vivo

A alveolite seca (AS) é uma das complicações pós-operatórias mais comuns e sintomáticas na odontologia, porém, até o momento não há um protocolo de tratamento definido. O composto fenólico guaiacol (Gu) é um dos materiais utilizados para revestimento intra-alveolar devido às suas propriedades analgésicas, antioxidantes e antimicrobianas. Contudo, sua desvantagem é a dificuldade de manipulação decorrente da sua baixa estabilidade, alta volatilidade e sensibilidade à oxidação. Para melhorar suas propriedades e aumentar sua aplicabilidade clínica, um complexo de inclusão de Gu com ß-ciclodextrina (ßcd) foi desenvolvido. A formação do complexo supramolecular de Gu:ßcd foi caracterizada mediante a ressonância magnética nuclear (RMN), nos experimentos de 1H e 2D ROESY. A atividade antibacteriana do Gu e Gu:ßcd frente a Escherichia coli, Staphylococcus aureus, Streptococcus mitis, Streptococcus mutans, Streptococcus sanguis e Aggregatibacter actinomycetemcomitans foi analisada pelo método da microdiluição e sua citotoxicidade em osteoblastos de calvária de rato, foi estudado com o ensaio do MTT. O processo de reparo alveolar induzido pelo Gu:ßcd foi avaliado histologicamente após tratamento de alveolite seca em molares inferiores de ratos. A RMN mostrou correlações espaciais entre os hidrogênios internos (H3 e H5) da ßcd e os hidrogênios aromáticos, H(a) e H(b) do Gu, confirmando a formação do complexo. A complexação do Gu na ßcd potencializou seu efeito antibacteriano e reduziu sua citotoxicidade em osteoblastos. O estudo in vivo evidenciou a ocorrência de ossificação no ápice alveolar dos ratos tratados com Gu:ßcd, no 7o dia. No 14o dia, as trabéculas ósseas ocuparam também o terço médio do alvéolo e no 21o dia, todo o alvéolo se encontrava preenchido por osso neoformado. Estes resultados foram similares ao controle negativo e superiores ao controle positivo (Alvogyl®). Os benefícios obtidos pela inclusão do Gu na ßcd foram demonstrados pela melhora das propriedades biológicas do Gu in vitro e o adequado reparo alveolar in vivo.

Comportamento em desgaste por erosão cavitação, erosão - corrosão e em ensaios de microesclerometria linear instrumentada de um aço inoxidável martensítico AISI 410 nitretado a plasma em baixa temperatura, utilizando a tecnologia de tela ativa.

Amostras de um aço inoxidável martensítico AISI 410 temperado e revenido foram nitretadas a plasma em baixa temperatura usando o tratamento de nitretação plasma DC e a nitretação a plasma com tela ativa. Ambos os tratamentos foram realizados a 400 °C, utilizando mistura gasosa de 75 % de nitrogênio e 25 % de hidrogênio durante 20 horas e 400 Pa de pressão. As amostras de aço AISI 410 temperado e revenido foram caracterizadas antes e depois dos tratamentos termoquímicos, usando as técnicas de microscopia óptica, microscopia eletrônica de varredura, medidas de microdureza, difração de raios X e medidas de teor de nitrogênio em função da distância à superfície por espectrometria WDSX de raios X. A resistência à erosão por cavitação do aço AISI 410 nitretado DC e com tela ativa foi avaliada segundo a norma ASTM G32 (1998). Os ensaios de erosão, de erosão - corrosão e de esclerometria linear instrumentada segundo norma ASTM C1624 (2005) somente foram realizados no aço AISI 410 nitretado com tela ativa. Ensaios de nanoindentação instrumentada forma utilizados para medir a dureza (H) e o módulo de elasticidade reduzido (E*) e calcular as relações H/E* e H3/E*2 e a recuperação elástica (We), utilizando o método proposto por Oliver e Pharr. Ambos os tratamentos produziram camadas nitretadas de espessura homogênea constituídas por martensita expandida supersaturada em nitrogênio e nitretos de ferro com durezas superiores a 1200 HV, porém, a nitretação DC produziu maior quantidade de nitretos de ferro do que o tratamento de tela ativa. Os resultados de erosão por cavitação do aço nitretado DC mostraram que a precipitação de nitretos de ferro é prejudicial para a resistência à cavitação já que reduziu drasticamente o período de incubação e aumentou a taxa de perda de massa nos estágios iniciais do ensaio; entretanto, depois da remoção desses nitretos de ferro, a camada nitretada formada somente por martensita expandida resistiu bem ao dano por cavitação. Já no caso do aço nitretado com tela ativa, a resistência à erosão por cavitação aumentou 27 vezes quando comparada com o aço AISI 410 sem nitretar, fato atribuído à pequena fração volumétrica e ao menor tamanho dos nitretos de ferro presente na camada nitretada, às maiores relações H/E* e H3/E*2 e à alta recuperação elástica da martensita expandida. A remoção de massa ocorreu, principalmente, pela formação de crateras e de destacamento de material da superfície dos grãos por fratura frágil sem evidente deformação plástica. As perdas de massa acumulada mostradas pelo aço nitretado foram menores do que aquelas do aço AISI 410 nos ensaios de erosão e de erosão corrosão. O aço nitretado apresentou uma diminuição nas taxas de desgaste em ambos os ensaios de aproximadamente 50 % quando comparadas com o aço AISI 410. O mecanismo de remoção de material foi predominantemente dúctil, mesmo com o grande aumento na dureza. Os resultados de esclerometria linear instrumentada mostraram que a formação de martensita expandida possibilitou uma diminuição considerável do coeficiente de atrito em relação ao observado no caso do aço AISI 410 sem nitretar. O valor de carga crítica de falha foi de 14 N. O mecanismo de falha operante no aço nitretado foi trincamento por tensão.

Effectiveness of influenza vaccination programme in preventing hospital admissions, Valencia, 2014/15 early results

Preliminary results for the 2014/15 season indicate low to null effect of vaccination against influenza A(H3N2)-related disease. As of week 5 2015, there have been 1,136 hospital admissions, 210 were due to influenza and 98% of subtype A strains were H3. Adjusted influenza vaccine effectiveness was 33% (range: 6–53%) overall and 40% (range: 13% to 59%) in those 65 years and older. Vaccination reduced by 44% (28–68%) the probability of admission with influenza.