Study of conformational changes in biliverdin within a domain of the bacteriophytochrome
Résumé
Phytochromes are a large family of photoreceptor proteins composed of three domains : PAS (Per-ARNT-Sim), GAF (cGMP-phosphodiesterase/adenylate cyclase/FhIA) et PHY (phytochrome specific). The GAF domain binds a linear tetrapyrrole chromophore via a cysteine residue. The chromophore biliverdin, a bile pigment derived from the breakdown of the heme, is present in various organisms. Biliverdin plays a role as a chromophore, absorbing and emitting light in a specific range, making it important in the study of light-sensitive proteins and their applications in biotechnology and medicine. In this research, we aim to construct the energy profile that connects two protein structures including biliverdin in two distinct conformations. This analysis is important for understanding the molecular mechanisms behind conformational changes in phytochromes. For that, we performed umbrella sampling simulations, which is a molecular dynamics simulation that allows us to map out energy barriers between different states. The energy profile provides us information on the feasibility of the conformational transition, revealing key factors that govern this process. Additionally, molecular dynamics simulations allow us to analyze the trajectories of the protein over time, offering a detailed view of how interactions between the protein and biliverdin stabilize one conformation over another. By identifying the driving process behind these transitions, we can better understand how phytochromes function and the way for future applications in designing light-sensitive biomolecular tools.