Experimental analyses of the chemical dynamics of ribozyme catalysis

Abstract

Most ribozymes in Nature catalyze alcoholysis or hydrolysis of RNA phosphodiester bonds. Studies of the corresponding non-enzymatic reactions reveal a complex mechanistic landscape allowing for a variety of transition states and both concerted and stepwise mechanisms. High-resolution structures, incisive biochemical studies and computer simulations are providing glimpses into how ribozyme catalyzed reactions traverse this landscape. However, direct experimental tests of mechanistic detail at the chemical level are not easily achieved. Kinetic isotope effects (KIEs) probe directly the differences in the vibrational 'environment' of the atoms undergoing chemical transformation on going from the ground state to the transition state. Thus, KIEs can in principle provide direct information about transition state bonding and so may be instrumental in evaluating possible transition states for ribozyme catalyzed reactions. Understanding charge distribution in the transition state may help resolve how rate acceleration is accomplished and perhaps the similarities and differences in how RNA and protein active sites operate. Several barriers to successful application of KIE analysis to ribozymes have recently been overcome, and new chemical details are beginning to emerge.