18.06.24 - Peter Hamm

Universal Behavior in the Nonequilibrium Response of Photoactive Proteins

Over the last decade, we have performed time-resolved experiments on a wide set of photoactive proteins, both artificially photo-switchable proteins (i.e., various PDZ domains [1-3] and MCL‑1/peptide complexes [4]), as well as naturally photo-switchable proteins (i.e., cyanobacteriochrome Slr1393-g3 [5,6] and TePixJ [7]). All these proteins have in common that they are relatively small, compact and rigid single domain proteins, but in terms of details of their structure, the embedded chromophore and their biological function they are in part very different. In either case, the embedded chromophore photo-isomerizes after electronic excitation, which is an ultrafast (i.e., femtosecond to a few picosecond) photochemical process. The essentially instantaneous conformational change initially perturbs the structure of the immediate protein environment of the chromophore. This local perturbation then “propagates” over the entire protein in a cascade of events, which spread over a wide range timescales from picosecond to milliseconds. Our spectroscopic method to study this phenomenon is transient (pump-probe) IR spectroscopy, in which an ultrafast visible or near-UV laser pulse excites the chromophore, and a properly delayed IR pulse probes the response of the protein at a later time. Experimental concepts have been developed that allow us to cover all relevant timescales from picoseconds to potentially seconds in one and the same experimental run [8]. In addition, we extract “lifetime spectra” from the experimental data, based on exponential fitting together with a maximum entropy method in order to identify kinetic processes [5]. Interestingly and very universally for all studied proteins [1-7], the “dynamical content” reveals discrete timescales, which are distributed roughly equidistantly on a logarithmic time-axis with about 0.8 lifetime-peaks/decade. All-atom molecular dynamics simulations can reproduce the effect for a given protein in a semi-quantitative manner [2]. However, the universal character of the response calls for more generic models, and ideas in that direction will be discussed.            

[1] B. Buchli, S. A. Waldauer, R. Walser, M. Donten, R. Pfister, N. Blöchliger, S. Steiner, A. Caflisch, O. Zerbe and P. Hamm, Proc. Natl. Acad. Sci. USA, 2013, 110, 11725

[2] O. Bozovic, C. Zanobini, A. Gulzar, B. Jankovic, D. Buhrke, M. Post, S.Wolf, G. Stock and P. Hamm, Proc. Natl. Acad. Sci. USA, 2020, 117, 26031

[3] O. Bozovic, J. Ruf, C. Zanobini, B. Jankovic, D. Buhrke, P. J. M. Johnson, and P. Hamm, J. Phys. Chem. Lett., 2021, 12, 4262

[4] P. J. Heckmeier, J. Ruf, D. Buhrke, B. G. Jankovic, and P. Hamm, J. Mol. Biol., 2022, 434, 167499

[5] D. Buhrke, K. Oppelt, P. J. Heckmeier, R. Fernández-Terán, and P. Hamm, J. Chem. Phys., 2020, 153, 245101

[6] D. Buhrke, Y. Lahav, A. Rao, J. Ruf, I. Schapiro and P. Hamm, J. Am. Chem. Soc. 2023, 145, 15766

[7] J. Ruf, Flavia Bindschedler and D. Buhrke, Phys. Chem. Chem. Phys., 2023, 25, 6016

[8] J. Helbing and P.Hamm, J. Phys. Chem. A, 2023 127, 6347