RESUMO
Lipid-linked oligosaccharides (LLOs) play an important role in the N-glycosylation pathway as the donor substrate of oligosaccharyltransferases (OSTs), which are responsible for the en bloc transfer of glycan chains onto a nascent polypeptide. The lipid component of LLO in both eukarya and archaea consists of a dolichol, and an undecaprenol in prokarya, whereas the number of isoprene units may change between species. Given the potential relevance of LLOs and their related enzymes to diverse biotechnological applications, obtaining reliable LLO models from distinct domains of life could support further studies on complex formation and their processing by OSTs, as well as protein engineering on such systems. In this work, molecular modeling techniques, such as quantum mechanics calculations, molecular dynamics simulations, and metadynamics were employed to study eukaryotic (Glc3-Man9-GlcNAc2-PP-Dolichol), bacterial (Glc1-GalNAc5-Bac1-PP-Undecaprenol), and archaeal (Glc1-Man1-Gal1-Man1-Glc1-Gal1-Glc1-P-Dolichol) LLOs in membrane bilayers. Microsecond molecular dynamics simulations and metadynamics calculations of LLOs revealed that glycan chains are more prone to interact with the membrane lipid head groups, while the PP linkages are positioned at the lipid phosphate head groups level. The dynamics of isoprenoid chains embedded within the bilayer are described, and membrane dynamics and related properties are also investigated. Overall, there are similarities regarding the structure and dynamics of the eukaryotic, the bacterial, and the archaeal LLOs in bilayers, which can support the comprehension of their association with OSTs. These data may support future studies on the transferring mechanism of the oligosaccharide chain to an acceptor protein.
Assuntos
Metabolismo dos Lipídeos , Modelos Moleculares , Oligossacarídeos/química , Oligossacarídeos/metabolismo , Configuração de Carboidratos , Membrana Celular/metabolismo , GlicosilaçãoRESUMO
Chalcones and flavonoids constitute a large family of plant secondary metabolites that have been explored as a potential source of novel pharmaceutical products. While the simulation of these compounds by molecular dynamics (MD) can be a valuable strategy to assess their conformational properties and so further develop their role in drug discovery, there are no set of force field parameters specifically designed and experimentally validated for their conformational description in condensed phase. So the current work developed a new parameter set for MD simulations of these compounds' main scaffolds under GROMOS force field. We employed a protocol adjusting the atomic charges and torsional parameters to the respective quantum mechanical derived dipole moments and dihedrals rotational profiles, respectively. Experimental properties of organic liquids were used as references to the calculated values to validate the parameters. Additionally, metadynamics simulations were performed to evaluate the conformational space of complex chalcones and flavonoids, while NOE contacts during simulations were measured and compared to experimental data. Accordingly, the employed protocol allowed us to obtain force field parameters that reproduce well the target data and may be expected to contribute in more accurate computational studies on the biological/therapeutical role of such molecules.
RESUMO
Antithrombin (AT) is a serpin that inhibits mainly thrombin and fXa after being activated by binding to glycosaminoglycans as heparin and heparan sulfate. Upon binding, the native AT conformation, relatively inactive as a protease inhibitor, is converted to an activated form. Recently, a new compound, named TMI, was discovered in our group with nanomolar affinity to antithrombin, and shown to be able to induce a partial activation of antithrombin. As TMI represents an original scaffold for structural optimizations aiming the development of new antithrombotic drugs, the present work demonstrated, through a series of molecular dynamics simulations, that TMI is able to modulate AT reactive center loop flexibility similarly to what is observed to heparin, as well as exposing AT P1 residue, Arg393. These results represent the first atomic level indication of AT conformational activation by TMI, and may offer a predictive basis for future studies aiming TMI structural optimization.
Assuntos
Antitrombinas/química , Ativadores de Enzimas/química , Fibrinolíticos/química , Heparina/química , Heparitina Sulfato/química , Fosfatos de Inositol/química , Regulação Alostérica , Antitrombinas/metabolismo , Sítios de Ligação , Desenho de Fármacos , Ativadores de Enzimas/metabolismo , Fator Xa/química , Fibrinolíticos/metabolismo , Heparina/metabolismo , Heparitina Sulfato/metabolismo , Humanos , Fosfatos de Inositol/metabolismo , Cinética , Simulação de Dinâmica Molecular , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Termodinâmica , Trombina/químicaRESUMO
PURPOSE: To collect the semantic association norms of 96 Brazilian Portuguese words for further application in the formulation of a speech recognition test using sentences with controlled word predictability. METHODS: Study participants were 67 volunteers aged 18 to 27 years. A semantic association task with word class delimitation was used. RESULTS: The mean sizes of the total and meaning sets were larger in the second recall to both verb and noun classes. The prevalent semantic association strength in the first recall was strong to the first word and moderate to the second word. In the second recall, the prevalent semantic association strength was moderate to both the first and second words. Significant negative correlation was observed between association strength and total and meaning set sizes. CONCLUSION: The semantic association norms of 96 Brazilian Portuguese words were collected as proposed and resulted in semantic associates for each target word in the verb and noun classes that were used in a speech recognition assessment considering sentences with controlled word predictability.
Assuntos
Semântica , Testes de Discriminação da Fala/instrumentação , Adulto , Brasil , Feminino , Humanos , Idioma , Masculino , Vocabulário , Adulto JovemRESUMO
RESUMO Objetivo coletar normas de associação semântica de 96 palavras do português brasileiro e aplicá-las, posteriormente, na elaboração de um teste de reconhecimento de fala com frases com controle da previsibilidade da palavra. Método participaram 67 voluntários com idades entre 18 e 27 anos. Foi aplicada uma tarefa de associação semântica com delimitação de classe de palavras. Resultados o tamanho médio do conjunto total e do significativo foi maior para a segunda evocação para as classes de verbos e substantivos. A força de associação semântica que prevaleceu na primeira recordação foi forte para a primeira e média para a segunda palavra. Na segunda recordação, a força de associação com maior prevalência foi média para a primeira e para a segunda palavra. Foi observada correlação negativa significativa entre a força de associação e os tamanhos total e significativo do conjunto. Conclusão Normas de associação semântica de 96 palavras do português brasileiro foram coletadas conforme proposto e resultaram em palavras associadas semanticamente para cada alvo nas categorias de verbo e substantivo, as quais foram utilizadas em um teste de reconhecimento de fala com frases considerando a previsibilidade da palavra.
ABSTRACT Purpose To collect the semantic association norms of 96 Brazilian Portuguese words for further application in the formulation of a speech recognition test using sentences with controlled word predictability. Methods Study participants were 67 volunteers aged 18 to 27 years. A semantic association task with word class delimitation was used. Results The mean sizes of the total and meaning sets were larger in the second recall to both verb and noun classes. The prevalent semantic association strength in the first recall was strong to the first word and moderate to the second word. In the second recall, the prevalent semantic association strength was moderate to both the first and second words. Significant negative correlation was observed between association strength and total and meaning set sizes. Conclusion The semantic association norms of 96 Brazilian Portuguese words were collected as proposed and resulted in semantic associates for each target word in the verb and noun classes that were used in a speech recognition assessment considering sentences with controlled word predictability.
Assuntos
Humanos , Masculino , Feminino , Adulto , Adulto Jovem , Semântica , Testes de Discriminação da Fala/instrumentação , Vocabulário , Brasil , IdiomaRESUMO
The last step of the bacterial N-glycosylation pathway involves PglB, an oligosaccharyltransferase, which is responsible for the en bloc transfer of a fully assembled oligosaccharide chain to a protein possessing the extended motif D/E-X-N-X-S/T. Recently, this molecule had its full structure elucidated, enabling the description of its domains and the proposition of a catalytic mechanism. By employing molecular dynamics simulations, we were able to evaluate structural aspects of PglB, suggesting prevalent motions that may bring insights into the mechanism of the glycosylated peptide detachment. Additionally, we identified transient states at the catalytic site, in which the previously described carboxamide twisting mechanism was observed. Aided by quantum mechanics calculations for each different conformational states of the catalytic site, we determined the presence of an octahedral metal coordination, along with the presence of one water molecule at the catalytic site.
Assuntos
Proteínas de Bactérias/química , Domínio Catalítico , Hexosiltransferases/química , Magnésio/farmacologia , Proteínas de Membrana/química , Simulação de Dinâmica Molecular , Motivos de Aminoácidos , Sequência de Aminoácidos , Proteínas de Bactérias/metabolismo , Campylobacter/enzimologia , Hexosiltransferases/metabolismo , Magnésio/química , Proteínas de Membrana/metabolismo , Dados de Sequência Molecular , Ligação ProteicaRESUMO
Ipecac alkaloids are secondary metabolites produced in the medicinal plant Psychotria ipecacuanha. Emetine is the main alkaloid of ipecac and one of the active compounds in syrup of Ipecac with emetic property. Here we evaluated emetine's potential as an antiviral agent against Human Immunodeficiency Virus. We performed in vitro Reverse Transcriptase (RT) Assay and Natural Endogenous Reverse Transcriptase Activity Assay (NERT) to evaluate HIV RT inhibition. Emetine molecular docking on HIV-1 RT was also analyzed. Phenotypic assays were performed in non-lymphocytic and in Peripheral Blood Mononuclear Cells (PBMC) with HIV-1 wild-type and HIV-harboring RT-resistant mutation to Nucleoside Reverse Transcriptase Inhibitors (M184V). Our results showed that HIV-1 RT was blocked in the presence of emetine in both models: in vitro reactions with isolated HIV-1 RT and intravirion, measured by NERT. Emetine revealed a strong potential of inhibiting HIV-1 replication in both cellular models, reaching 80% of reduction in HIV-1 infection, with low cytotoxic effect. Emetine also blocked HIV-1 infection of RT M184V mutant. These results suggest that emetine is able to penetrate in intact HIV particles, and bind and block reverse transcription reaction, suggesting that it can be used as anti-HIV microbicide. Taken together, our findings provide additional pharmacological information on the potential therapeutic effects of emetine.
Assuntos
Alcaloides/administração & dosagem , Emetina/administração & dosagem , Infecções por HIV/tratamento farmacológico , Transcriptase Reversa do HIV/antagonistas & inibidores , HIV-1/efeitos dos fármacos , Alcaloides/química , Fármacos Anti-HIV/administração & dosagem , Fármacos Anti-HIV/química , Emetina/química , Infecções por HIV/enzimologia , Infecções por HIV/virologia , Transcriptase Reversa do HIV/química , HIV-1/patogenicidade , Humanos , Leucócitos Mononucleares/efeitos dos fármacos , Leucócitos Mononucleares/virologia , Mutação , Inibidores da Transcriptase Reversa/administração & dosagem , Inibidores da Transcriptase Reversa/química , Replicação Viral/efeitos dos fármacosRESUMO
The aerial parts of Ipomoea batatas are described herein to produce four new resin glycosides, designated as ipomotaosides A, B, C, and D. Ipomotaoside A was found to present inhibitory activity on both cyclooxygenases. However, the conformational elucidation of these molecules may be difficult due to their high flexibility. In this context, the current work presents a conformational characterization of ipomotaosides A-D in aqueous and nonaqueous solvents. The employed protocol includes metadynamics evaluation and unrestrained molecular dynamics simulations (MD). The obtained data provided structural models for the ipomotaosides in good agreement with previous ROESY distances measured in pyridine. Accordingly, the most abundant conformation of ipomotaoside A in solution was employed in flexible docking studies, providing a structural basis for the compound's inhibition of COX enzymes. The so-obtained complex supports resin glycosides' role as original scaffolds for future studies, aiming at structural optimization and development of potential new anti-inflammatory agents.
Assuntos
Ciclo-Oxigenase 1/química , Ciclo-Oxigenase 2/química , Inibidores de Ciclo-Oxigenase/química , Glicosídeos/química , Ipomoea batatas/química , Configuração de Carboidratos , Sequência de Carboidratos , Espectroscopia de Ressonância Magnética , Simulação de Dinâmica Molecular , Extratos Vegetais/química , Ligação Proteica , Resinas Vegetais/químicaRESUMO
PURPOSE: To describe the judgement of the concreteness of a set of 162 Brazilian Portuguese words, prior to the elaboration of a speech recognition test, as well as to verify the influence of variables such as the frequency of occurrence of the words and age and undergraduate program year of the participants on the concreteness ratings. METHODS: Fifty undergraduate Speech-Language Pathology and Audiology students from a public university rated the concreteness of a set of 162 words using a seven-point scale where the lowest concreteness degree was represented by number one and the highest by number seven. Participants were free to choose any number in the scale. RESULTS: The results showed a tri-modal distribution of values, suggesting the classification of three categories, according to the concreteness rating. The low concreteness category ranged from 1.76 to 3.45; the medium concreteness category, from 3.46 to 4.95; and the high concreteness rating, from 4.96 to 6.70. Positive correlation was found between the concreteness rating and the coefficient of variation, whereby the higher the rating attributed to a word, the lesser variation in the responses. No significant correlation was found between concreteness ratings and the frequency of occurrence of words. The influence of age and undergraduate year was significant for some correlations. CONCLUSION: Results showed three concreteness categories, and suggest that concreteness can be considered an independent attribute of words, since their frequency of occurrence, as well as participants' age and undergraduate program year did not influence the ratings attributed. The words classified in the high concreteness category were subsequently used for the elaboration of a speech recognition test.
Assuntos
Julgamento , Semântica , Patologia da Fala e Linguagem , Estudantes de Ciências da Saúde , Vocabulário , Brasil , Feminino , Humanos , Masculino , Adulto JovemRESUMO
OBJETIVO: Descrever o julgamento de concretude de um conjunto de 162 palavras da Língua Portuguesa, visando a elaboração de um teste de reconhecimento de fala, bem como verificar a influência de variáveis como frequência de ocorrência das palavras, idade e série do curso de graduação dos participantes neste julgamento. MÉTODOS: Cinquenta estudantes universitários de um curso de Fonoaudiologia de uma universidade pública julgaram 162 palavras quanto à concretude, por meio de uma escala de sete pontos, sendo o menor grau de concretude representado pelo número um e o grau de concretude máximo, representado pelo número sete. Foi permitido ao sujeito escolher qualquer ponto da escala. RESULTADOS: Os resultados mostraram uma distribuição tri-modal, sugerindo que as palavras fossem classificadas em três categorias quanto ao grau de concretude. A faixa de julgamento das palavras de baixa concretude variou de 1,76 a 3,45, as de média concretude, na faixa de 3,46 a 4,95 e as de alta concretude, de 4,96 e até 6,70. Houve correlação positiva entre o grau de concretude das palavras e o coeficiente de variação de forma que, quanto maior a nota atribuída para a palavra, menor foi a variação de respostas. Não ocorreu correlação significativa entre a frequência de ocorrência das palavras e o julgamento de concretude. A influência da idade e da série do curso de graduação no julgamento foi significativa para algumas correlações. CONCLUSÃO: Os resultados revelaram três categorias quanto ao grau de concretude e sugerem que a concretude pode ser considerada um atributo independente das palavras, uma vez que a frequência de ocorrência das palavras, bem como a idade e a série do curso de graduação dos participantes não influenciou o julgamento de concretude. As palavras categorizadas com alto grau de concretude foram utilizadas em etapas posteriores da elaboração de um teste de reconhecimento de fala.
PURPOSE: To describe the judgement of the concreteness of a set of 162 Brazilian Portuguese words, prior to the elaboration of a speech recognition test, as well as to verify the influence of variables such as the frequency of occurrence of the words and age and undergraduate program year of the participants on the concreteness ratings. METHODS: Fifty undergraduate Speech-Language Pathology and Audiology students from a public university rated the concreteness of a set of 162 words using a seven-point scale where the lowest concreteness degree was represented by number one and the highest by number seven. Participants were free to choose any number in the scale. RESULTS: The results showed a tri-modal distribution of values, suggesting the classification of three categories, according to the concreteness rating. The low concreteness category ranged from 1.76 to 3.45; the medium concreteness category, from 3.46 to 4.95; and the high concreteness rating, from 4.96 to 6.70. Positive correlation was found between the concreteness rating and the coefficient of variation, whereby the higher the rating attributed to a word, the lesser variation in the responses. No significant correlation was found between concreteness ratings and the frequency of occurrence of words. The influence of age and undergraduate year was significant for some correlations. CONCLUSION: Results showed three concreteness categories, and suggest that concreteness can be considered an independent attribute of words, since their frequency of occurrence, as well as participants' age and undergraduate program year did not influence the ratings attributed. The words classified in the high concreteness category were subsequently used for the elaboration of a speech recognition test.