Abstract
The hepatitis delta virus (HDV) is the only known human pathogen to contain a catalytic RNA motif (ribozyme) in its genome. The native structure of the HDV ribozyme consists of five helices (P1 - P4 and P1.1), which come together to form a double-nested pseudoknot. Within this complicated ribozyme are several landmarks of structural importance, and alterations of these landmarks often lead to decreased ribozymal activity. We have used extended explicit solvent molecular dynamics simulations to investigate structural dynamics of HDV ribozyme. We plan on including effects of base protonation and base substitutions, using the available X-ray structures and their modifications as the starting structures. Specific attention has been paid to nucleotides in the catalytic pocket and the flexible L3 region. We have in detail investigated the effect of the force field choice on the ribozyme structural dynamics, by comparing several simulation force field variants, including our recent reparametrization of the chi profile of the Cornell et al (AMBER) force field.
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