Active site dynamics in the lead-dependent ribozyme

Conformational dynamics are an important property of ribozymes and other RNA molecules but then is currently only limited information on the relationship between dynamics and RNA function. A recent structural study of the lead-dependent ribozyme, known as the leadzyme, showed significant dynamics at the active site and indicated that a structural rearrangement is required for the reaction to proceed from the ground to the transition state. In this work, microsecond-to-millisecond dynamics of the leadzyme are probed by analysis of the power dependence of C-13 NMR relaxation times in the rotating frame (T-1 rho). These results revealed a wide range of conformational dynamics for various residues in the leadzyme. For residue A25 in the active site, the power dependence of TI, yielded an exchange lifetime similar to that previously measured by line-shape analysis, and provides an important calibration of this T-1 rho methodology for probing the dynamics of macromolecules. Strong evidence was also found for a previously suggested dynamic network of hydrogen bonds stabilizing the GAAA tetraloop motif. Within the active site of the leadzyme, internal motions are observed on a wide variety of time scales, suggesting a complex landscape of accessible states, and potential correlations between observed motions and catalytic function are discussed. These results demonstrate that the power dependence of C-13 T-1 rho relaxation times provides a valuable method for probing dynamics in nucleic acids.