Tryptophanyl fluorescence lifetime distribution of hyperthermophilic β-glycosidase from molecular dynamics simulation: A comparison with the experimental data

Abstract

A molecular dynamics simulation approach has been utilized to understand the unusual fluorescence emission decay observed for β-glycosidase from the hyperthermophilic bacterium Solfolobus sulfataricus (Sβgly), a tetrameric enzyme containing 17 tryptophanyl residues for each subunit. The tryptophanyl emission decay of Sβgly results from a bimodal distribution of fluorescence lifetimes with a short-lived component centered at 2.5 ns and a long-lived one at 7.4 ns (Bismuto E, Nucci R, Rossi M, Irace G, 1999, Proteins 27:71–79). From the examination of the trajectories of the side chains capable of causing intramolecular quenching for each tryptophan microenvironment and using a modified Stern–Volmer model for the emission quenching processes, we calculated the fluorescence lifetime for each tryptophanyl residue of Sβgly at two different temperatures, i.e., 300 and 365 K. The highest temperature was chosen because in this condition Sβlgy evidences a maximum in its catalytic activity and is stable for a very long time. The calculated lifetime distributions overlap those experimentally determined. Moreover, the majority of trytptophanyl residues having longer lifetimes correspond to those originally identified by inspection of the crystallographic structure. The tryptophanyl lifetimes appear to be a complex function of several variables, such as microenvironment viscosity, solvent accessibility, the chemical structure of quencher side chains, and side-chain dynamics. The lifetime calculation by MD simulation can be used to validate a predicted structure by comparing the theoretical data with the experimental fluorescence decay results.