Fast Photochemistry of Prototypical Phytochromes—A Species vs. Subunit Specific Comparison

Abstract

Phytochromes are multi-domain red light photosensor proteins, which convert red light photons to biological activity utilizing the multitude of structural and chemical reactions. The steady increase in structural information obtained from various bacteriophytochromes has increased understanding about the functional mechanism of the photochemical processes of the phytochromes. Furthermore, a number of spectroscopic studies have revealed kinetic information about the light-induced reactions. The spectroscopic changes are, however, challenging to connect with the structural changes of the chromophore and the protein environment, as the excited state properties of the chromophores are very sensitive to the small structural and chemical changes of their environment. In this article, we concentrate on the results of ultra-fast spectroscopic experiments which reveal information about the important initial steps of the photoreactions of the phytochromes. We survey the excited state properties obtained during the last few decades. The differences in kinetics between different research laboratories are traditionally related to the differences of the studied species. However, we notice that the variation in the excited state properties depends on the subunit composition of the protein as well. This observation illustrates a feedback mechanism from the other domains to the chromophore. We propose that two feedback routes exist in phytochromes between the chromophore and the remotely located effector domain. The well-known connection between the subunits is the so-called tongue region, which changes its secondary structure while changing the light-activated state of the system. The other feedback route which we suggest is less obvious, it is made up of several water molecules ranging from the dimer interface to the vicinity of the chromophore, allowing even proton transfer reactions nearby the chromophore.

MAS NMR on a Red/Far-Red Photochromic Cyanobacteriochrome All2699 from Nostoc

“…Such signal splitting is not confined to this ring but also seen in several regions of the chromophore, such as C15 associated with the C – D methine bridge, the B -ring propionate (C8 1 , C8 2 , and C8 3 ) and also C17 and C18 1 H of ring D . This observation further supports the notion that both native phytochromes and CBCRs in their Pr dark states are heterogeneous population mixtures that can be distinguished structurally [4,6,18,35,44,45,46,47], biologically [48,49], spectrally [50,51,52,53,54,55] and photochemically [56,57,58,59,60,61]. The apparent A -ring signal splitting is inherently linked to the heterogeneous attachment of the chromophore to C138 and the variable packing of ring A .…”

Photochemistry and transient intermediates in a bacteriophytochrome photocycle revealed by multiscale simulations

“…Finally, we note that our estimated timescales for the photochemical process are significantly shorter than what seen in transient absorption measurements, which for the PSM of DrBph phytochrome report an excited-state lifetime of about 170 ps 63 , attributed to a concomitant reorganization of the hydrogen-bonding network in the chromophore binding pocket. On the other hand, in support of our results, the more recent femtosecond X-ray crystallography study 45 has detected a twist of the D-ring already after a delay time of 1 ps after photoexcitation.…”

“…According to the literature and to our previous MD simulations 36,48,[60][61][62][63][64][65][66][67] , the Pr state is conformationally heterogeneous. In order to capture such heterogeneity, the initial nuclear ensemble of the system was prepared via three ground-state QM/MM MD simulations (R1-R3 in the following) performed on the model system (Fig.…”

“…To conclude, there is not yet consensus about the excited state lifetime of phytochromes, as it has been shown to strongly depend on the type of construct (i.e., chromophore binding domain, photosensory module or full-length system) 63,77 . Moreover, a more complex excited state decay with multi-exponential kinetics has been seen in some bacterial phytochromes 60,63,64,73,78 .…”

Coordination of the biliverdin D-ring in bacteriophytochromes

“…Comparing the lifetimes obtained from global analysis is difficult, because they depend on the amplitudes of the corresponding spectra and the number of components used for the fits. 74 Therefore, we have calculated average lifetimes. For this, we have calculated the amplitudes of the corresponding decay-associated spectra (DADS) of each component over the detected spectral range (Table SI 1 and Fig.…”