Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy

Abstract

The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un-and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.

Critical assessment of the FeC and CO bond strength in carboxymyoglobin: a QM/MM local vibrational mode study

“…These small molecular ligands play a key role in many biological processes via transferring signals for conformational changes of the Mb protein, resulting in diverse enzymatic activity [5]. One has monitored the interaction between the small ligands coordinated to the iron of the heme group and the active site pocket of Mb by vibrational spectroscopy, in particular by resonance Raman techniques [6] and timeresolved resonance Raman spectroscopy [7]. CO has been considered a useful vibrational spectroscopy probe because the CO absorption band can easily be identified in the spectrum.…”

Light- and temperature-dependent dynamics of chromophore and protein structural changes in bathy phytochrome Agp2

“…Spectroscopic measurements. Photoconversion of the sample was achieved by irradiation the Pfr (Pr) state at 785 nm (660 nm) using a light-emitting diode, providing a photon flux of ∼2 × 1021 (3 × 10 20 ) photons per m 2 per sec. To establish a pure Pfr state as a starting point for the experiments, the sample was irradiated with 660 nm for 120 s at ambient temperature.…”

Machine learning for electronically excited states of molecules

“…Besides the electronic excitations that take place in molecules after light excitation, ML models have successfully entered research fields, which focus on other types of excitations as well. Those are for example vibrational or rotational excitations giving rise to Raman spectra or Infrared spectra, 43,109,[200][201][202][203][204] nuclear magnetic resonance, 205 or magnetism, 206,207 which we will also not consider in this review.…”