Your browser doesn't support javascript.
loading
Radial scan of the molecular electrostatic potential of RNA double helices: an application to the enzyme-tRNA recognition.
Marín, Ray M; Agudelo, William A; Daza C, Edgar E.
Afiliação
  • Marín RM; Grupo de Química Teórica, Universidad Nacional de Colombia and CeiBa, Bogotá DC, Colombia. rmmarinf@unal.edu.co
J Mol Graph Model ; 27(3): 255-65, 2008 Oct.
Article em En | MEDLINE | ID: mdl-18586541
We introduced a method to characterize quantitatively the molecular electrostatic potential (MEP) of the minor and major grooves of base pairs located at nucleic acid double helices. By means of a radial MEP scan, we obtained a n-tuple of potential values corresponding to each groove, which can be analyzed by plotting the MEP values as a function of the angle in the radial scan. We studied base pairs of two different tRNAs, relevant in the recognition process with their cognate aminoacyl tRNA synthetases (aaRSs), in order to correlate their electrostatic behavior with the corresponding aminoacylation activity. We analyzed the first three base pairs of the Escherichia coli tRNA(Ala) acceptor stem, finding several cases where the MEP profiles obtained from the plots are in agreement with the reported aminoacylation activities. Additionally, a non-hierarchical clustering performed over the MEP n-tuples resulted in meaningful classifications that correlate with the activity and with the predicted stereochemistry of the reaction. We also studied the first two base pairs of the E. coli tRNA(Thr) acceptor stem but constraining the analysis to the angle intervals that seem relevant for the binding sites of the enzyme. These intervals were deduced from the ThrRS-tRNA(Thr) complex crystal structure. In this case, we also found a good agreement between the MEP profiles and the activity, supporting the idea that the tRNA identity elements function is to allow an optimal electrostatic complementarity between the aminoacyl-tRNA synthetase and the tRNA.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: RNA de Transferência / Eletricidade Estática / Aminoacil-tRNA Sintetases / Conformação de Ácido Nucleico Tipo de estudo: Prognostic_studies Idioma: En Revista: J Mol Graph Model Assunto da revista: BIOLOGIA MOLECULAR Ano de publicação: 2008 Tipo de documento: Article País de afiliação: Colômbia País de publicação: Estados Unidos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: RNA de Transferência / Eletricidade Estática / Aminoacil-tRNA Sintetases / Conformação de Ácido Nucleico Tipo de estudo: Prognostic_studies Idioma: En Revista: J Mol Graph Model Assunto da revista: BIOLOGIA MOLECULAR Ano de publicação: 2008 Tipo de documento: Article País de afiliação: Colômbia País de publicação: Estados Unidos