SOLUTION SAXS OF A RNA HELICASE AND ITS COMPLEXES WITH RNA

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. DEx(D/H)-box RNA helicases, which are responsible for "chaperoning" RNA structure in many different contexts, are multi-domain proteins that are thought to undergo substantial conformational changes in order to catalyze ATP-dependent unfolding/refolding of target RNAs. Working with a three-domain helicase that binds specific fragments of 23S rRNA with high affinity (namely, the YxiN protein of Bacillus subtilis), we propose to use solution small angle x-ray scattering to delineate the conformational changes this protein undergoes in response to RNA binding and the ATPase cycle that drives the helicase activity. Both fulllength YxiN and subfragments thereof have been expressed and purified, and crystallographic structures of individual domains of YxiN or close homologs have been solved. Structures of individual domains are being incorporated into modeling the solution conformations of the full-length protein and subfragments thereof. SAXS data have been collected which show that in absence of ligands, YxiN and 2-domain fragments thereof behave like "beads on a string", with flexible linkers between domains. We now wish to examine the interactions with RNA, to determine under what conditions binding of RNA condenses the protein into a compact structure that is required for helicase activity.