VISUALIZING ALLOSTERY IN THE GENE-REGULATORY LYSINE RIBOSWITCH

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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. Riboswitches are recently described RNA domains that directly bind to cellular metabolites and control gene expression in cis in bacteria and eukaryotes. Due to their role in cellular homeostasis and their potential as antibacterial drug targets, structural studies of riboswitches are of immediate interest. Crystal structures of several types of riboswitches bound to their cognate metabolites have been reported. However, the mechanism of riboswitch function is not well understood due to the lack of structural information regarding the metabolite-free conformation. The goal of this proposal is to probe the solution structure of the metabolite-free conformation and the metabolite-bound conformation of four riboswitches by SAXS: the thiamine pyrophosphate (TPP), flavin mononucleotide (FMN), glycine (Gly), and lysine (Lys) riboswitches. Previous studies of the glycine riboswitch have demonstrated the utility of SAXS studies (Lipfert et al, JMB, 2007) to investigate the global size and shape of these RNA aptamers. The conformational change induced upon binding metabolite is expected to be on the order of 5 - 20 Angstroms and is well suited for experimentation at the APS. Performing SAXS studies on both the metabolite-free and metabolite-bound conformations will provide insight into the global structural changes involved in the gene-regulatory response of riboswitches. Obtaining Rg and P(r) plots for these conformations will allow us to model the RNA before and after the gene-regulatory switching event. These studies will complement concurrent structure determination of the metabolite bound conformation by X-ray crystallography, providing a detailed structural explanation of riboswitch function.