Ab initio study of the reaction mechanism of ribonuclease A with cytidyl-3 prime ,5 prime -adenosine. I. Geometry optimization of cytidyl-3 prime ,5 prime -adenosine

摘要

As a first part of the ab initio study of the reaction mechanism of ribonuclease A with cytidyl-3 prime ,5 prime -adenosine, the geometry of the cytidyl-3 prime ,5 prime -adenosine substrate has been optimized using the Hartree-Fock method. Eleven different starting structures of cytidyl-3 prime ,5 prime -adenosine have been studied. To guarantee a proper alignment with the active site of the ribonuclease A enzyme, a part of the substrate was fixed during the geometry optimization. The geometry and intramolecular interactions of the refined conformations have been evaluated and two possible prototype structures have been proposed. One of these prototypes is more in accordance with the results of a molecular dynamics simulation and is therefore presented as a model for the geometry of cytidyl-3 prime ,5 prime -adenosine in the initial step of the reaction with ribonuclease A.