Molecular dynamics of tryptophan in ribonuclease-T1. I. Simulation strategies and fluorescence anisotropy decay

Abstract

Molecular dynamics simulations of Ribonuclease-T1 (RNAse-T1) were performed using x-ray crystal coordinates for the enzyme and various simulation strategies. From each of the simulations, a predicted fluorescence anisotropy decay for the single-tryptophan residue was derived and compared with experimental values for the limiting anisotropy of this protein. Simulations conducted in vacuo demonstrated large displacements among some of the residues adjacent to the tryptophan side chain. As a consequence, the ring system rotates relatively unhindered through an angle far in excess of that implied by experimental data. In contrast, the explicit simulation of solvent within a stochastic boundary led to excellent agreement between simulation and experiment. In the case of RNAse-T1, the experimentally-determined limiting anisotropy is useful as a criterion of simulation accuracy in the vicinity of the tryptophan side chain.