Bacteriorhodopsin ground state

Fig. 2. A tentative scheme of the bacteriorhodopsin pump. bR indicates the bacteriorhodopsin ground state, and L, M, N(P) and O indicate the corresponding intermediates of the photocycle. NHs, =N2 and =NH represent the protonated Schiff base of the idUtrans retinal residue, the deprotonated and the protonated Schiff bases of 13-cw retinal residues, respectively. -COOH and -COO are the protonated and the deprotonated Asp-96 carboxylic group, respectively. The outward hydrophilic H -conducting pathway (the proton well) is shaded. (From Skulachev[35].)...

So far we have exclusively discussed time-resolved absorption spectroscopy with visible femtosecond pulses. It has become recently feasible to perfomi time-resolved spectroscopy with femtosecond IR pulses. Flochstrasser and co-workers [M, 150. 151. 152. 153. 154. 155. 156 and 157] have worked out methods to employ IR pulses to monitor chemical reactions following electronic excitation by visible pump pulses these methods were applied in work on the light-initiated charge-transfer reactions that occur in the photosynthetic reaction centre [156. 157] and on the excited-state isomerization of tlie retinal pigment in bacteriorhodopsin [155]. Walker and co-workers [158] have recently used femtosecond IR spectroscopy to study vibrational dynamics associated with intramolecular charge transfer these studies are complementary to those perfomied by Barbara and co-workers [159. 160], in which ground-state RISRS wavepackets were monitored using a dynamic-absorption technique with visible pulses. 

Fig. 11.16 The pulse sequence used to monitor the evolution of carboncarbon double-quantum coherence over a single rotor period in the presence of the proton-carbon heteronuclear dipolar coupling (a). The evolution of the double-quantum coherence between the Cl 4 and Cl 5 carbons in the retinal of bacteriorhodopsin in the ground state (b). The observed evolution is consistent with a C14-C15 torsion angle of 164° (reproduced with permission from Ref. [172]).

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 ground state of bacteriorhodopsin, also called the initial, light-adapted, BR, or resting state, refers to the protein with a relatively... 

Various models for the mechanism of proton translocation by bacteriorhodopsin have been postulated. The essential features of these models are in the ground state the Q-ring of the aW-trans retinal group is tightly bound in a hydrophobic pocket... 

Figure 16.5 Bacteriorhodopsin photocycle. Absorption of a photon leaves, after a few ps, the protein in a ground state K with a distorted geometry. Further reversible conformational changes lead to the L state, which initiates the proton transfer sequence.

At the molecular level, it is the light-induced trans-to-cis isomerization of the chromophore retinal that drives the vectorial proton transport. A detailed understanding of the molecular events leading to proton transport was greatly enhanced by elucidation of the crystal structures of ground-state bacteriorhodopsin and several intermediates of the photocycle. The detailed picture is gradually emerging but is still in a state of flux. Periodic reviews were provided by Lanyi. - ... 

Over the years, several nomenclatures for the photocycle intermediates were introduced. As the photocycle models become more complex, so does the nomenclature. Unfortunately, there is not a single nomenclature that is able to handle all the new intermediates being discovered. Also, not aU intermediates are related to color changes of the chromophore. All the different nomenclatures contain the above-mentioned three basic photocycle species and can, therefore, be compared using these three species as a reference. Initially, the ground, red-shifted, and blue-shifted states were called P, and /j. In 1995, the names pG, pR, and pB were introduced by Hoff et aU Yet another nomenclature was introduced in 1996, in which these species were called PYP, PYP, and PYPjj, based upon the photocycle nomenclature of bacteriorhodopsin. The nomenclatures are made even more complicated by the use of additional subscripts that state a specific property of the species (e.g., the absorption maximum). Such a property... 

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