Understanding the catalytic function of ribozymes will require information about the dynamics of the molecule. The lead-dependent ribozyme, or leadzyme, has several features that make it an excellent choice for examining this question. The leadzyme's core contains bases which are experiencing conformational dynamics of a variety of time- scales. Using 13C relaxation experiments in conjunction with Lipari- Szabo formalism, a simple model of the motions of bases within the leadzyme will be developed. The recent development of methods for measuring 1H-13C, 1H-15N, and 1H-1H dipolar couplings will be used with a variation. Instead of using bicelles that align in the magnetic field to induce partial alignment of the leadzyme, the filamentous phage Pf1 will be used to induce partial alignment of the leadzyme. Pf1 has been shown to align in a magnetic field and preliminary work in the Pardi lab indicates Pf1 readily aligns oligonucleotides. The 1H-13C dipolar couplings from the leadzyme's core will provide new angular restraints that will be used for structural refinement of the core residues. The combination of a model for the motions of the bases within the core and a refined model of the core will provide insight into the role of conformational dynamics in the leadzyme's activity. This may also lead to a clearer picture of the general role of conformational dynamics in ribozyme function.
