Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics

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Publikace nespadá pod Lékařskou fakultu, ale pod Středoevropský technologický institut. Oficiální stránka publikace je na webu muni.cz.

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SRIPATHI Kamali N. BANÁŠ Pavel RÉBLOVÁ Kamila ŠPONER Jiří OTYEPKA Michal WALTER Nils G.

Rok publikování 2015
Druh Článek v odborném periodiku
Časopis / Zdroj Physical Chemistry Chemical Physics
Fakulta / Pracoviště MU

Středoevropský technologický institut

Citace
www http://pubs.rsc.org/en/content/articlepdf/2015/cp/c4cp05083e
Doi http://dx.doi.org/10.1039/c4cp05083e
Obor Fyzikální chemie a teoretická chemie
Klíčová slova HEPATITIS-DELTA-VIRUS; SELF-CLEAVING RIBOZYMES; ACID-BASE CATALYSIS; MOLECULAR-DYNAMICS; CONFORMATIONAL SWITCH; CLEAVAGE ACTIVITY; METAL-ION; MECHANISTIC CHARACTERIZATION; CRYSTAL-STRUCTURE; GENOMIC RIBOZYME
Přiložené soubory
Popis The hepatitis delta virus (HDV) is the only known human pathogen whose genome contains a catalytic RNA motif (ribozyme). The overall architecture of the HDV ribozyme is that of a double-nested pseudoknot, with two GU pairs flanking the active site. Although extensive studies have shown that mutation of either wobble results in decreased catalytic activity, little work has focused on linking these mutations to specific structural effects on catalytic fitness. Here we use molecular dynamics simulations based on an activated structure to probe the active site dynamics as a result of wobble pair mutations. In both wild-type and mutant ribozymes, the in-line fitness of the active site (as a measure of catalytic proficiency) strongly depends on the presence of a C75(N3H3+)N1(O5') hydrogen bond, which positions C75 as the general acid for the reaction. Our mutational analyses show that each GU wobble supports catalytically fit conformations in distinct ways; the reverse G25U20 wobble promotes high in-line fitness, high occupancy of the C75(N3H3+)G1(O5') general-acid hydrogen bond and stabilization of the G1U37 wobble, while the G1U37 wobble acts more locally by stabilizing high in-line fitness and the C75(N3H3+)G1(O5') hydrogen bond. We also find that stable type I A-minor and P1.1 hydrogen bonding above and below the active site, respectively, prevent local structural disorder from spreading and disrupting global conformation. Taken together, our results define specific, often redundant architectural roles for several structural motifs of the HDV ribozyme active site, expanding the known roles of these motifs within all HDV-like ribozymes and other structured RNAs.
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