Molecular dynamics simulation of photoinduced intramolecular signaling in proteins

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The propagation of energetic and conformational changes in a protein, in other words, energytransfer and intramolecular signaling, plays a vital role in biomolecular function. Femtosecondtime-resolved infrared experiments on photoswitchable proteins provide a new and promising wayto study these processes, the microscopic mechanisms of which are only little understood. To facilitatethe interpretations of ongoing experiments on the villin headpiece, the WW domain, and thePDZ2 domain, we will perform extensive molecular dynamics (MD) simulations. Using nonequilibriumMD techniques, we will identify the time scales, efficiency, and pathways of the vibrationalenergy flow in these model proteins. Intramolecular allosteric interactions or intramolecular signalingwill be studied by employing an azobenzene photoswitch, which has the potential to switchbetween the ligand-bound and ligand-free state of the PDZ2 domain. Extensive MD simulationsof the photoinduced conformational change and intramolecular signaling will be conducted thatallow us to observe the functioning of the protein in real time. Moreover, we will calculate transientinfrared spectra to facilitate the direct comparison to experiment.