Active site dynamics in the lead-dependent ribozyme

Conformational dynamics are an important property of ribozymes and other RN A molecules but then is currently only limited information on the relations hip between dynamics and RNA function. A recent structural study of the lea d-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 thi s work, microsecond-to-millisecond dynamics of the leadzyme are probed by a nalysis of the power dependence of C-13 NMR relaxation times in the rotatin g frame (T-1 rho). These results revealed a wide range of conformational dy namics for various residues in the leadzyme. For residue A25 in the active site, the power dependence of TI, yielded an exchange lifetime similar to t hat previously measured by line-shape analysis, and provides an important c alibration of this T-1 rho methodology for probing the dynamics of macromol ecules. Strong evidence was also found for a previously suggested dynamic n etwork of hydrogen bonds stabilizing the GAAA tetraloop motif. Within the a ctive site of the leadzyme, internal motions are observed on a wide variety of time scales, suggesting a complex landscape of accessible states, and p otential correlations between observed motions and catalytic function are d iscussed. These results demonstrate that the power dependence of C-13 T-1 r ho relaxation times provides a valuable method for probing dynamics in nucl eic acids.