RESUMO
Unbinding pathways of retinoic acid (RA) bound to retinoic acid receptor (RAR) have been explored by the random expulsion molecular dynamics (REMD) method. Our results show that RA may exit the binding site of RAR through flexible regions close to the H1-H3 loop and beta-sheets, without displacing H12 from its agonist position. This result may explain kinetic differences between agonist and antagonist ligands observed for other nuclear receptors. The extended and flexible structure of RA initiated a methodological study in a simplified two-dimensional model system. The REMD force should in general be distributed to all atoms of the ligand to obtain the most unbiased results, but for a ligand which is tightly bound in the binding pocket through a strong electrostatic interaction, application of the REMD force on a single atom is preferred.
Assuntos
Modelos Químicos , Modelos Moleculares , Receptores do Ácido Retinoico/química , Receptores do Ácido Retinoico/ultraestrutura , Tretinoína/química , Sítios de Ligação , Simulação por Computador , Cinética , Modelos Estatísticos , Ligação Proteica , Conformação Proteica , Mapeamento de Interação de Proteínas/métodos , Distribuição AleatóriaRESUMO
RXR, a member of the superfamily of nuclear hormone receptors, regulates gene transcription in response to 9-cis-retinoic acid. We previously showed that, among nuclear receptors, RXR is unique in that it self-associates into homotetramers, and that these tetramers dissociate rapidly upon ligation. Here, we report that binding of RXR tetramers to DNA containing two RXR response elements results in a dramatic DNA-looping. RXR can thus juxtapose distant DNA sequences, enabling transcriptional regulation by far-upstream factors. We show that RXR functions as a DNA architectural factor and that, while this activity is regulated by 9-cis-retinoic acid, it is distinct from and independent of the receptor's intrinsic transcriptional activity. The data establish RXR as the first identified architectural factor whose activity is regulated by a small ligand, and demonstrate a novel mechanism of transcriptional regulation by retinoids.
Assuntos
DNA/química , Regulação da Expressão Gênica , Conformação de Ácido Nucleico , Estrutura Quaternária de Proteína , Receptores do Ácido Retinoico/química , Fatores de Transcrição/química , Transcrição Gênica , Animais , Sequência de Bases , Células COS , Chlorocebus aethiops , DNA/metabolismo , DNA/ultraestrutura , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Substâncias Macromoleculares , Dados de Sequência Molecular , Peso Molecular , Receptores do Ácido Retinoico/metabolismo , Receptores do Ácido Retinoico/ultraestrutura , Sequências Reguladoras de Ácido Nucleico , Receptores X de Retinoides , Retinoides/metabolismo , Fatores de Transcrição/metabolismo , Fatores de Transcrição/ultraestruturaRESUMO
The article discusses the principal structure of nuclear receptors. The structure and function of retinoid receptors, their main ligands and inhibitors are analysed. Data (experimental and clinical) concerning the immunotropic antineoplastic and cardiovascular activity of the main retinoids are given.
