Development of a multiscale strategy for the modeling of photoreceptors: A focus on phytochromes

Light-induced processes in proteins play a pivotal role in a variety of essential biological functions, encompassing vision, energy production through photosynthesis, and the regulation of biological rhythms. Photoreceptors are composed of a sensory domain housing the light-absorbing chromophore. This domain is responsible for detecting light and transmitting the signal to effector modules. Upon the absorption of photons, structural changes in the chromophore propagate initially to the binding pocket and subsequently throughout the entire protein, ultimately activating the biological function. This Ph.D. thesis aims to develop a multiscale strategy for tracking the entire sequence of events, beginning with the initial electronic excitation in the embedded chromophore up to the large structural changes in the protein. To reach this goal, I have combined nonadiabatic QM/MM MD simulations with fully classical (MM) MD and enhanced sampling techniques.