Chromophore isomerization

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. 

Bacteriorhodopsin (bR) is a transmembrane protein located in the cell membrane of purple bacteria and contains in its ground state an all-trans retinal chromophore that absorbs at 570 nm. After illumination, the chromophore isomerizes, and a proton is pumped in five consecutive steps from the cytoplasm to the extracellular side of the membrane. The resulting pH gradient is then used to synthesize ATP. In the first proton-transfer step, the proton located at the retinal chromophore Schiff base is transferred to a nearby aspartate residue (Figure 14-6). Our studies on this first proton-transfer step in bacteriorhodopsin (bR) after photoisomerization [90,91,92]... 

The evidence favoring a trans 13-cis chromophore isomerization in BRt should be considered in light of recent photoinduced... 

The isomerization models discussed above differ from that described by Warshel, where J625 and PBAT are partially isomer-ized chromophores (90°) and their decay to Kfc g and BAT, respectively, is described by a motion on a potential surface involving both protein relaxation (proton translocation) and additional chromophore isomerization. This model implies that in K ig and BAT, proton translocation has taken place in the opsin, but it is not discriminative concerning whether a chromophore isomerization has taken place at this stage. 

Balashov SP, Imasheva ES, Govindjee R, Ebrey TG. Titration of aspartate-85 in bacteriorhodopsin what it says about chromophore isomerization and proton release. Biophys. J. 1996 70 473 81. 

The first picosecond study on a biological molecule was centered on the kinetics of the primary intermediate, bathorhodopsin during the visual transduction process. Low-temperature experiments had established the presence of an intermediate species referred to as bathorhodopsin, which seemed to be quite stable at low temperatures, 77 K and 7 K. However, because of its ultrafast formation time constant at room temperature, it could not be measured before the development of picosecond spectroscopy. It was established however that the first intermediate bathorhodopsin decayed, at room temperature, into a second intermediate lumirhodopsin then to two other species called metarhodopsin I and metarhodopsin II. Eventually, at some point, the chromophore isomerizes. " The intermediate at which the isomerization occurs is not known or at least unequivocally agreed upon. The recent picosecond... 

Balashov, S. P, Imasheva, E. S., Govindjee, R., Ebrey, T. G. (1996). Titration of aspartate-85 in bacteriorhodopsin what it says about chromophore isomerization and proton release. Biophysical Journal, 70, 473 81. http //dx.doi.org/10.1016/S0006-3495(96)79591-7. Becker, W. G., Bard, A. J. (1983). Photoluminescence and photoindnced oxygen adsorption of colloidal zinc sulfide dispersions. The Journal of Physical Chemistry, 87,4888-4893. Bico, J., Thiele, U., Quere, D. (2002). Wetting of textured surfaces. Colloids and Surfaces A Physicochemical Engineering Aspects, 206, 41—46. 

When rhodopsin absorbs a photon of light, the 11-c/s-retinal chromophore isomerizes to the all-transform, causing... 

Infrared spectroscopic studies of macromolecules became increasingly powerful with the development of Fourier transform techniques [44, 47, 48, 59-67]. (See Chap. 1 for a description of an FTIR spectrometer.) FTIR measurements can be used to probe changes in the bonding or interactions of individual amino acid side chains in proteins. Bacteriorhodopsin provides an illustration. When bacterio-rhodopsin is illuminated, its protonated retinylidine Schiff base chromophore isomerizes and then transfers a proton to a group in the protein. FTIR measurements showed the formation of an absorption band at 1,763 cm in addition to a set of absorption changes attributable to the chromophore [63, 68]. In bacteriorhodopsin that was enriched in [4- C]-aspartic acid the band appeared at 1,720 cm and an additional shift to 1,712 cm was obtained when the sovent was replaced by D2O. These observations indicated that the band reflected C=0 stretching of a protonated aspartic acid, leading to identification of a particular aspartic acid residue as the H" acceptor for deprotonation of the chromophore. 

Shown in Figure 135.3 are the main classes of residues for which mutants have been made that show altered photocycle kinetics. There are two classes of mutants that were shown to lengthen the O state. First, the O state can be lengthened by inhibiting chromophore isomerization from 13-cis to aU-frans. 

This was accomplished in the Val-49 and Leu-93 mutants, shown in Figure 135.3(B), Group 3. However, these mutants are not optimal for use in BR-based three-dimensional memories, because the O —> P transition requires all-trans to 9-cis photochemistry.Thus, mutants that inhibit chromophore isomerization to all-tra s wiU decrease the probability of entry into the branched photocycle. 

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