Yellow proteins

The binding model, suggested by Brian Matthews, is shown schematically in (a) with connected circles for the Ca positions, (b) A schematic diagram of the Cro dimer with different colors for the two subunits, (c) A schematic space-filling model of the dimer of Cro bound to a bent B-DNA molecule. The sugar-phosphate backbone of DNA is orange, and the bases ate yellow. Protein atoms are colored red, blue, green, and white, [(a) Adapted from D. Ohlendorf et al., /. Mol. Evol. 19 109-114, 1983. (c) Courtesy of Brian Matthews.]... 

Riboflavin was first isolated from whey in 1879 by Blyth, and the structure was determined by Kuhn and coworkers in 1933. For the structure determination, this group isolated 30 mg of pure riboflavin from the whites of about 10,000 eggs. The discovery of the actions of riboflavin in biological systems arose from the work of Otto Warburg in Germany and Hugo Theorell in Sweden, both of whom identified yellow substances bound to a yeast enzyme involved in the oxidation of pyridine nucleotides. Theorell showed that riboflavin 5 -phosphate was the source of the yellow color in this old yellow enzyme. By 1938, Warburg had identified FAD, the second common form of riboflavin, as the coenzyme in D-amino acid oxidase, another yellow protein. Riboflavin deficiencies are not at all common. Humans require only about 2 mg per day, and the vitamin is prevalent in many foods. This vitamin... 

Cho, K. W., Colepicolo, P., and Hastings, J. W. (1989). Autoinduction and aldehyde chain-length effects on the bioluminescent emission from the yellow protein associated with luciferase in Vibrio fischeri strain Y-lb. Photochetn. Photobiol. 50 671-677. 

Renal 1.9 3.9 (yellow protein in tubule lumen eosinophilic droplets in cells of proximal convoluted tubules increased kidney weights) 23.4 M (proteinuria) ... 

As shown by the calculations of bacteriorhodopsin (Section 2.3.2.1), ONIOM is an excellent tool for excited-state reactions in biology. The important rhodopsin system has been studied both by TD-B3LYP Amber [80] and CASSCF Amber [81]. Another example of the combination of CASSCF with Amber for the surrounding protein can be found for the yellow protein [82],... 

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]. 

The attention of biochemists was first attracted to flavins as a result of their color and fluorescence. The study of spectral properties of flavins (Fig. 15-8) has been of importance in understanding these coenzymes. The biochemical role of the flavin coenzymes was first recognized through studies of the "old yellow enzyme"144 145 which was shown by Theorell to contain riboflavin 5 -phosphate. By 1938, FAD was recognized as the coenzyme of a different yellow protein, D-amino acid oxidase of kidney tissue. Like the pyridine nucleotides, the new flavin coenzymes were reduced by dithionite to nearly colorless dihydro forms (Figs. 15-7 and 15-8) revealing the chemical basis for their function as hydrogen carriers. 

A yellow protein, isolated from yeast, was found to have the remarkable property of being decolorized by the reducing system of glucose 6-phosphate plus the protein and coferment from red blood cells. 

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. 

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