Computer Graphics Modelling and Molecular Dynamics Simulation of the Core of the Self Splicing Intervening Sequence of the T4 NrdB mRNA in the Presence of the Guanosine Cofactor

Abstract

The active site of the self splicing intron in the T4 nrdB RNA has been modelled on a graphics workstation on the basis of the suggested 3D arrangement of the Tetrahymena IVS¹. This structure was then subjected to energy minimization and molecular dynamics simulation to relax tensions. The cofactor guanosine was docked to a proposed² binding site where it was found to fit well.