A 1.2 NS MOLECULAR-DYNAMICS SIMULATION OF THE RIBONUCLEASE T-1-3'-GUANOSINE MONOPHOSPHATE COMPLEX

In this study a molecular dynamics simulation of ribonuclease T-1 in c omplex with its product 3'GMP has been performed for a time span of 1. 2 ns. By increasing the simulation time, the dynamic properties of the protein could be analyzed in more detail. Water has been included in an 18 Angstrom radius sphere around the active site. We find that in t his system 600 ps of simulation is needed before a stable conformation is reached as measured by the RMS (root mean square) difference from the starting structure, which was adapted from the crystallographic st ructure of ribonuclease T-1 (RNT1)-2'GMP. The increased length of the simulation gives new opportunities to study the behavior of protein mo tion. Several parameters such as the temperature factors and correlati on functions change noticeably during the simulation. A possible mecha nism for the diffusion of guanine from or to the active site was detec ted. This involves a two-step procedure, in which Tyr45 first opens th e binding pocket, whereupon the phosphate rearranges its contacts with the catalytic residues. The motion of Tyr45 is different from what ha s been proposed from the structure of nucleotide-free RNT1. The bindin g site closes again during the simulation. We suggest that this mechan ism is used to remove the product after catalysis, but not necessarily for the association of the substrate. These rearrangements are much s lower than could have been detected in a shorter simulation.