Essential mechanistic principles of proteins, such as the lock-and-key principle in substrate binding, were identified over the last few decades. The CRC 1078 had set itself the goal of introducing a new principle in the understanding of protein mechanisms of action: The control and coordination of complex protein function by protonation dynamics. Spatio-temporal fluctuations of these functionally relevant hydrogen-bonded networks result from proton movements on different time and length scales - from femtoseconds to seconds and from less than 0.1 nm to more than 10 nm. The experimental studies of the CRC 1078 were combined with theory and simulations to achieve a deeper understanding of the proton-dependent mechanisms in the selected protein families. Different facets of protonation dynamics were investigated in two proteins central to biological energy conversion: Oxygen reduction coupled to proton pumping by cytochrome c oxidase and water oxidation catalyzed by photosystem II, respectively. While electron transfer in these proteins can be slowed down or even prevented by major structural changes, light-induced conformational changes play a crucial role in the mechanism of both phytochromes and channelrhodopsins as well as in pH-controlled proton channels. The functionality of the latter was compared with that of the pH-gated viroporins. These structural changes are often associated with or driven by proton movements. The development and adaptation of various experimental and theoretical methods to the requirements of specific protein systems was an essential aspect of research in the CRC 1078. These included the incorporation of non-canonical amino acids into proteins, time-resolved serial femtosecond X-ray crystallography, nuclear magnetic resonance spectroscopy at high magnetic fields, time-resolved electronic and vibrational spectroscopy over a large dynamic range as well as multiscale modeling approaches from quantum mechanics, molecular dynamics simulation and their hybrids. The application of such advanced techniques was challenging, as most of the proteins are integral membrane proteins. Finally, the CRC 1078 achieved its original goal of gaining a comprehensive understanding of protonation dynamics as an important element of the functional mechanisms of five selected protein families and, thus, understanding this process as a generic principle of protein function.
