Simulating electrostatic effects on electronic transitions in proteins

Abstract

Biopolymer fluorescence in biology and biochemistry is increasingly used for characterising equilibrium, dynamics and imaging. This is typically done by monitoring wavelength and intensity changes without necessarily knowing what causes such changes in detail. Simulations have been at the core of the considerable recent progress in improving the microscopic understanding of wavelength and quenching of fluorescence intensity in biopolymers. This review focuses on one of the most used intrinsic probes for protein behaviour, tryptophan (Trp), which is arguably now one of the best understood probes of internal structure and dynamics for proteins – despite its reputation to the contrary. In this review, we highlight selected classical molecular dynamics in combination with quantum mechanics simulations from our group and others during the past 20 years that support this view. The work includes simulations of time-dependent wavelength shifts in solvents and proteins, fluorescence-quenching rates, dielectric compensation by water, heterogeneity of quenching rates and applications to protein folding.