Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation.
J Phys Chem B
; 115(25): 8346-57, 2011 Jun 30.
Article
in En
| MEDLINE
| ID: mdl-21644800
ABSTRACT
The crystal structure of the precleaved form of the hepatitis delta virus (HDV) ribozyme reveals two Gâ¢U wobbles near the active site a rare reverse Gâ¢U wobble involving a syn G base, and a standard Gâ¢U wobble at the cleavage site. The catalytic mechanism for this ribozyme has been proposed to involve a Mg(2+) ion bound to the reverse Gâ¢U wobble, as well as a protonated C75 base. We carried out molecular dynamics simulations to analyze metal ion interaction with the reverse and standard Gâ¢U wobbles and to investigate the impact of C75 protonation on the structure and motions of the ribozyme. We identified two types of Mg(2+) ions associated with the ribozyme, chelated and diffuse, at the reverse and standard Gâ¢U wobbles, respectively, which appear to contribute to catalysis and stability, respectively. These two metal ion sites exhibit relatively independent behavior. Protonation of C75 was observed to locally organize the active site in a manner that facilitates the catalytic mechanism, in which C75(+) acts as a general acid and Mg(2+) as a Lewis acid. The simulations also indicated that the overall structure and thermal motions of the ribozyme are not significantly influenced by the catalytic Mg(2+) interaction or C75 protonation. This analysis suggests that the reaction pathway of the ribozyme is dominated by small local motions at the active site rather than large-scale global conformational changes. These results are consistent with a wealth of experimental data.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Hepatitis Delta Virus
/
RNA, Catalytic
/
Magnesium
Language:
En
Journal:
J Phys Chem B
Journal subject:
QUIMICA
Year:
2011
Document type:
Article
Affiliation country:
United States