Poster abstracts

Poster number 45 submitted by Charles Hoogstraten

The utility of NMR relaxation-dispersion data in characterizing invisible states of RNA

Charles G. Hoogstraten (Biochemistry & Molecular Biology, Michigan State University), Samantha L. Alexander (Biochemistry & Molecular Biology, Michigan State University), Alison M. Gjidoda (Biochemistry & Molecular Biology, Michigan State University), Neil A. White (Biochemistry & Molecular Biology, Michigan State University), Patrick O. Ochieng (Biochemistry & Molecular Biology, Michigan State University), Robert Fidis (Biochemistry & Molecular Biology, Michigan State University)

Abstract:
NMR spin-relaxation dispersion measurements have the ability to report on the chemical shift changes between the major structure of a protein or RNA and a lightly-populated “invisible state” that cannot be analyzed via the usual techniques of structural biology. Our group and others have introduced and applied techniques to use uniformly- and specifically-labeled 13C nuclei to detect such invisible states in RNA. In many cases, the question of interest is whether the observed minor conformer is a functionally relevant form or simply an unstructured state. For example, the sampling of a conformation resembling a ligand-bound form can be taken as evidence for a conformational-capture binding mechanism.

In this work, we examine the feasibility of detecting such sampling using NMR. In the docking transition of the hairpin ribozyme, both loops A and B undergo dramatic conformational changes between the free and bound form. We use contemporary chemical-shift calculation algorithms to predict the spectral shifts expected upon the transition of loop A from its free form to a hypothetical “docked-like” conformation. In parallel, we report progress toward the derivation of a reference set of 1H and 13C chemical shifts for nucleotide residues in unstructured RNA regions. Comparison of the predictions of chemical shift changes for loop A unfolding vs. docked-state sampling allows the feasibility of distinguishing these two possibilities using relaxation-dispersion measurements to be assessed.

Keywords: Ribozyme, NMR Spectroscopy, Chemical Shift