Photoactivity, yellow protein

Anderson, S., S. Crosson, and K. Moffat (2004). Short hydrogen bonds in photoactive yellow protein. Acta Crystallogr 60 1008-1016. 

Kort, R., K. J. Hellingwerf, and R. B. G. Ravelli (2004). Initial events in the photocycle of photoactive yellow protein. J Biol Chem 279 26417-26424. 

Ihee, H., Rajagopal, S., Srajer, V., Pahl, R., Schmidt, M., Schotte, R, Anfinrud, P. A., Wulff, M., and Moffat, K. 2005. Visualizing chromophore isomerization in photoactive yellow protein from nanoseconds to seconds by time-resolved crystallography. Pmc. Natl. Acad. Set, USA 102 7145-50. 

There are many systems of different complexity ranging from diatomics to biomolecules (the sodium dimer, oxazine dye molecules, the reaction center of purple bacteria, the photoactive yellow protein, etc.) for which coherent oscillatory responses have been observed in the time and frequency gated (TFG) spontaneous emission (SE) spectra (see, e.g., [1] and references therein). In most cases, these oscillations are characterized by a single well-defined vibrational frequency, It is therefore logical to anticipate that a single optically active mode is responsible for these features, so that the description in terms of few-electronic-states-single-vibrational-mode system Hamiltonian may be appropriate. 

Femtosecond visible pump - midinfrared probe setup for the study of protein dynamics. Isomerization in Photoactive Yellow Protein... 

Ultrafast photoreaction dynamics in protein nanospaces (PNS) as revealed by fs fluorescence dynamics studies on photoactive yellow protein (PYP) and related systems... 

Isomerization process in the native and denatured photoactive yellow protein probed by subpicosecond absorption spectroscopy... 

The Photoactive Yellow Protein (PYP) is the blue-light photoreceptor that presumably mediates negative phototaxis of the purple bacterium Halorhodospira halophila [1]. Its chromophore is the deprotonated trans-p-coumaric acid covalently linked, via a thioester bond, to the unique cystein residue of the protein. Like for rhodopsins, the trans to cis isomerization of the chromophore was shown to be the first overall step of the PYP photocycle, but the reaction path that leads to the formation of the cis isomer is not clear yet (for review see [2]). From time-resolved spectroscopy measurements on native PYP in solution, it came out that the excited-state deactivation involves a series of fast events on the subpicosecond and picosecond timescales correlated to the chromophore reconfiguration [3-7]. On the other hand, chromophore H-bonding to the nearest amino acids was shown to play a key role in the trans excited state decay kinetics [3,8]. In an attempt to evaluate further the role of the mesoscopic environment in the photophysics of PYP, we made a comparative study of the native and denatured PYP. The excited-state relaxation path and kinetics were monitored by subpicosecond time-resolved absorption and gain spectroscopy. 

The Photoactive Yellow Protein (PYP) is thought to be the photoreceptor responsible for the negative phototaxis of the bacterium Halorhodospira halophila [1]. Its chromophore, the deprotonated 4-hydroxycinnamic (or p-coumaric) acid, is covalently linked to the side chain of the Cys69 residue by a thioester bond. Trans-cis photoisomerization of the chromophore was proved to occur during the early steps of the PYP photocycle. Nevertheless, the reaction pathway leading to the cis isomer is still discussed (for a review, see ref. [2]). Time-resolved spectroscopy showed that it involves subpicosecond and picosecond components [3-7], some of which could correspond to a flipping motion of the chromophore carbonyl group [8,9]. 

Figure 6.3 Three snapshots of MD and Car—Parrinello molecular dynamics simulations of the photoactive yellow protein, showing the entire protein (left), the pocket containing the chromophore (middle), and the chromophore itself (right). Thanks to Dr. Elske Leenders and Dr. Evert Jan Meijer for the simulation snapshots.

Hybrid multiscale models enable us to focus on the relevant part of a system. For example, Leenders et al. studied the proton transfer process in the photoactive yellow protein (Figure 6.3) [9], They used Car-Parrinello molecular dynamics [10], a QM method for dynamics simulations, to describe the chromophore and its hydrogen-bonded network in the protein pocket (middle and right-hand circles). This was combined with a traditional MD force field of 28 600 atoms, simulating the entire protein in water (left-hand circle). 

To begin to elucidate such issues and to create a theoretical framework for them, we have focused [4-9] on a model of a protonated Schiff base (PSB) in a nonequilibrium dielectric continuum solvent. A key feature for the Sj-Sq Cl in PSBs such as retinal which plays a key role in the chromophore s cis-trans isomerization is that a charge transfer is involved, implying a strong electrostatic coupling to a polar and polarizable environment. In particular, there is translocation of a positive charge [92], discussed further below. Charge transfer also characterizes the earliest events in the photoactive yellow protein photocycle, for example [93],... 

T. Rocha-Rinza, K. Sneskov, O. Christiansen, U. Ryde, J. Kongsted, Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein, Phys. Chem. Chem. Phys. 13 (2011) 1585. 

Structure of the Photointermediate of Photoactive Yellow Protein and the Propagation Mechanism of Structural Change... 

Abstract. A recently developed new method to monitor reaction kinetics of intermolecular interaction is reviewed. This method is based on the measurement of the time-dependent diffusion coefficient using the pulsed-laser-induced transient grating technique. Using this method, conformation change, transient association, and transient dissociation on reactions are successfully detected. The principle and some applications to studies on changes in the intermolecular interactions of photosensor proteins (e.g., photoactive yellow protein, phototropins, AppA) in the time domain are described. In particular, unique features of this time-dependent diffusion coefficient method are discussed. 

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