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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Postdoctoral Individual National Research Service Award (F32)
Project #
1F32GM020064-01
Application #
2865270
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Project Start
1999-05-01
Project End
Budget Start
1999-05-01
Budget End
2000-04-30
Support Year
1
Fiscal Year
1999
Total Cost
Indirect Cost
Name
University of Colorado at Boulder
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
City
Boulder
State
CO
Country
United States
Zip Code
80309