Bacteriorhodopsin chromophores

Figure 4 illustrates the kind of information that can be obtained with time-resolved resonance Raman spectroscopy by presenting picosecond resonance Raman spectra of the bacteriorhodopsin chromophore. The data have been used to determine the structure of the J and K intermediates as well as to provide information about an intermediate between K and L. ... 

For two-photon memories, a number of media types and reading mechanisms have been used (165). Generally, media comprise two photon-absorbing chromophores dissolved within a soHd polymer matrix. Suitable reversible photochromic dyes are, for example, spiropyrans. Although photochromic materials often suffer from photobleaching, as well as from instability leading to self-erasure, new materials and host environments are under development (172). Bacteriorhodopsin (BR) also has been proposed as a two-photon memory material. 

FIGURE 10.22 The reaction cycle of bacteriorhodopsin. The intermediate states are indicated by letters, with subscripts to indicate the absorption maxima of the states. Also indicated for each state is the configuration of the retinal chromophore (all-tram or 13-cas) and the protonation state of the Schiff base (C=N or C=N H). 

The CP MAS NMR spectroscopy has been also extensively used for studies of proteins containing retinylidene chromophore like proteorhodopsin or bacteriorhodopsin. Bacteriorhodopsin is a protein component of purple membrane of Halobacterium salinarium.71 7 This protein contains 248 amino acids residues, forming a 7-helix bundle and a retinal chromophore covalently bound to Lys-216 via a Schiff base linkage. It is a light-driven proton pump that translocates protons from the inside to the outside of the cell. After photoisomerization of retinal, the reaction cycle is described by several intermediate states (J, K, L, M, N, O). Between L and M intermediate states, a proton transfer takes place from the protonated Schiff base to the anionic Asp85 at the central part of the protein. In the M and/or N intermediate states, the global conformational changes of the protein backbone take place. 

Fig. 5.4. Structure of the bacteriorhodopsin from Halobacterium halobium. Ribbon diagram of bacteriorhodopsin and retinal as a ball-and-stick model. Bacteriorhodopsin crosses the membrane with seven a-helices that are arranged in a bundle form with the chromophore retinal bound in the interior. According to Kimura et al. (1997), with per-...

Some results. Rapid kinetic methods have revealed that enzymes often combine with substrates extremely quickly,60 with values of k] in Eq. 9-14 falling in the range of 106 to 108 M 1 s . Helix-coil transitions of polypeptides have relaxation times of about 10-8 s, but renaturation of a denatured protein may be much slower. The first detectable structural change in the vitamin A-based chromophore of the light-operated proton pump bacteriorhodopsin occurs in - 5 x 10 8 s, while a proton is pumped through the membrane in... 

UC Chemical Shift-Conformation Relationship in the Chromophores of Rhodopsin and Bacteriorhodopsin... 

The chromophores of rhodopsin and bacteriorhodopsin are 11 -cis- and all-trans-retinal Schiff bases, respectively. Upon binding to the proteins, their unsaturated carbons show anomalous 13C chemical shifts compared with those of corresponding model compounds. This indicates the occurrence of interactions between the chromophore and its surrounding protein matrix. Ab inito shielding calculation reveals that the major part of such anomalous shifts originates in the conformational change of the chromophore. 

The dynamics of proton binding to the extra cellular and the cytoplasmic surfaces of the purple membranes were measured by the pH jump methods [125], The purple membranes selectively labeled by fluorescein Lys-129 of bacteri-orhodopsin were pulsed by protons released in the aqueous bulk from excited pyranine and the reaction of the protons with the indicators was measured. Kinetic analysis of the data implied that the two faces of the membrane differ in then-buffer capacities and in their rates of interaction with bulk protons. The extracellular surfaces of the purple membrane contains one anionic proton binding site per protein molecule with pA" 5.1. This site is within a Coulomb cage radius from Lys-129. The cytoplasmic surface of the purple membrane bears four to five pro-tonable moieties that, due to close proximity, function as a common proton binding site. The reaction of the proton with this cluster is at a very fast rate (3 X 1010 M-1 sec ). The proximity between the elements is sufficiently high that even in 100 mM NaCl, they still function as a cluster. Extraction of the chromophore retinal from the protein has a marked effect on the carboxylates of the cytoplasmic surface, and two to three of them assume positions that almost bar their reaction with bulk protons. Quantitative evaluation of the dynamics of proton transfer from photoactivated bacteriorhodopsin to the bulk has been done by using numerical... 

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