Atomic-scale characterization of conformational changes in the preQ1 riboswitch aptamer upon ligand binding.
J Mol Graph Model
; 30: 179-85, 2011 Sep.
Article
em En
| MEDLINE
| ID: mdl-21831681
ABSTRACT
Riboswitches are mRNA structural elements that act as intracellular sensors of small-molecule metabolites. By undergoing conformational changes capable of modulating translation or terminating transcription, riboswitches are able to play a role in regulating the concentration of essential metabolites in the cell. Computer-guided fluorescence experiments were carried out to interrogate molecular dynamics and conformational changes in the minimal riboswitch aptamer that binds 7-aminomethyl-7-deazaguanine (preQ1). Our combined experimental results and computational analysis suggest that the preQ1 riboswitch apo form is structured but shows no evidence of a ligand-binding pocket. Simulations of the apo and bound forms indicate a large conformational change is triggered by the breaking of the Watson-Crick base pairing of nucleotides G11 and C31 upon preQ1 removal, followed by collapse of the pocket due to interfering π-stacking. Computational predictions of local aptamer dynamics were validated by fluorescence experiments employing 2-aminopurine substitutions. In-line probing reactions confirmed that fluorophore-labeled riboswitches retain similar higher-order structural features as the unlabeled aptamer upon ligand binding, although their affinity for the ligand is reduced by the introduction of the fluorescent reporter.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Pirimidinonas
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Pirróis
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RNA
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Aptâmeros de Nucleotídeos
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Simulação de Dinâmica Molecular
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Riboswitch
Idioma:
En
Ano de publicação:
2011
Tipo de documento:
Article