Following the proton: My journey through bioenergetics

As devised by Peter Mitchell's chemiosmosis, protons are actively translocated across a biological membrane, creating the proton motive force, which stores free energy in the form of an electrochemical gradient. Here, protons (H⁺ ions) are not merely participants but the core mediators of energy transduction: they store energy as a gradient, transfer it across membranes, and release it in a controlled manner to drive essential biological processes like ATP synthesis. Proton transfer occurs on different timescales and distances - from femtoseconds to seconds and from less than 1 Å to 10 nm. Protonation dynamics can tune and control the redox potentials and pK_a values of individual residues or catalytically active groups, drive and respond to the conformational changes of proteins and the water clusters associated with them. As a personal reflection, I will showcase examples of membrane proteins - particularly microbial rhodopsins and cytochrome c oxidase - as platforms to dissect proton transfer with high spatial and temporal resolution. A central aspect of my work has been the development and application of time-resolved and surface-enhanced infrared spectroscopy to monitor protein structural dynamics in real time. We have extended these approaches to channelrhodopsins and other optogenetic tools (the flavoproteins LOV, BLUF, and CRY), elucidating how light-activated conformational changes drive functionality. This work connects fundamental bioenergetics with applications in neuroscience. By integrating spectroscopy, structural biology, and theoretical approaches, we seek to establish a comprehensive framework that links protein dynamics to function, with implications for bioenergetics, photobiology, and the design of light-driven biomolecular systems.