On the pH dependent behavior of the firefly bioluminescence: protein dynamics and water content in the active pocket

Understanding bioluminescence presents fascinating challenges for fundamental sciences and numerous opportunities for practical applications. As a representative example, the firefly bioluminescent system has been intensively studied in both experimental and computational areas. However, there are still remaining questions regarding especially the detailed protein dynamics and the mechanisms of its color modulation. Here, we report on the pH dependent behavior of the firefly bioluminescence primarily based on molecular dynamics simulations. We find that the overall protein structure is generally resilient to pH variations. As the protein does not exhibit any structural distortions that can affect the emission property, we next focus on the dynamics in the active pocket and its effect on color modulation by adopting different protonation states in the pocket. With this, we observe red-shifted emissions at acidic conditions as consistent with previous studies. Most importantly, we find that a water molecule in the active pocket can mediate flexible motions of neighboring groups, which can subsequently modify the emission properties to a substantial degree. Based on the observations, we propose that the active pocket is in a dry condition during the luminescence process. Our results highlight the importance of understanding the role of the dynamics near the active pocket in modulating bioluminescence.