Protonation bacteriorhodopsin

Feng Zhou, Andreas Windemuth, and Klaus Schulten. Molecular-dynamis study of the proton pump cycle of bacteriorhodopsin. Biochem., 32(9) 2291-2306, 1993. 

Figure 12.S Schematic diagram of the bacteriorhodopsin molecule illustrating the relation between the proton channel and bound retinal in its tram form. A to E are the seven transmembrane helices. Retinal is covalently bound to a lysine residue. The relative positions of two Asp residues, which are important for proton transfer, are also shown. (Adapted from R. Henderson et al.,...

Fi re 12.6 Schematic diagram Illustrating the proton movements in the photocycle of bacteriorhodopsin. The protein adopts two main conformational states, tense (T) and relaxed (R). The T state binds trans-tetinal tightly and the R state binds c/s-retinal. (a) Stmcture of bacteriorhodopsin in the T state with hflus-retinal bound to Lys 216 via a Schiff base, (b) A proton is transferred from the Schiff base to Asp 85 following isomerization of retinal and a conformational change of the protein. 

Lanyi, J.K. Bacteriorhodopsin as a model for proton pumps. Nature 375 461-464, 1995. 

Bacteriorhodopsin contains seven transmembrane a helices Bacteriorhodopsin is a light-driven proton pump... 

ITowever, membrane proteins can also be distributed in nonrandom ways across the surface of a membrane. This can occur for several reasons. Some proteins must interact intimately with certain other proteins, forming multisubunit complexes that perform specific functions in the membrane. A few integral membrane proteins are known to self-associate in the membrane, forming large multimeric clusters. Bacteriorhodopsin, a light-driven proton pump protein, forms such clusters, known as purple patches, in the membranes of Halobacterium halobium (Eigure 9.9). The bacteriorhodopsin protein in these purple patches forms highly ordered, two-dimensional crystals. 

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). 

When Mitchell first described his chemiosmotic hypothesis in 1961, little evidence existed to support it, and it was met with considerable skepticism by the scientific community. Eventually, however, considerable evidence accumulated to support this model. It is now clear that the electron transport chain generates a proton gradient, and careful measurements have shown that ATP is synthesized when a pH gradient is applied to mitochondria that cannot carry out electron transport. Even more relevant is a simple but crucial experiment reported in 1974 by Efraim Racker and Walther Stoeckenius, which provided specific confirmation of the Mitchell hypothesis. In this experiment, the bovine mitochondrial ATP synthasereconstituted in simple lipid vesicles with bac-teriorhodopsin, a light-driven proton pump from Halobaeterium halobium. As shown in Eigure 21.28, upon illumination, bacteriorhodopsin pumped protons... 

It is interesting to compare the thermal-treatment effect on the secondary structure of two proteins, namely, bacteriorhodopsin (BR) and photosynthetic reaction centers from Rhodopseudomonas viridis (RC). The investigation was done for three types of samples for each object-solution, LB film, and self-assembled film. Both proteins are membrane ones and are objects of numerous studies, for they play a key role in photosynthesis, providing a light-induced charge transfer through membranes—electrons in the case of RC and protons in the case of BR. 

FIGURE 2.3 The three main families of mammalian G-protein-coupled 7TM receptors in mammals. No obvious sequence identity is found between the rhodopsin-like family A, the glucagon/VIP/calcitonin family B, and the metabotropic glutamate/chemosensor family C of G-protein-coupled 7TM receptors, with the exception of the disulfide bridge between the top of TM-III and the middle of extracellular loop-2 (see Figure 2.2). Similarly, no apparent sequence identity exists among members of these three families and, for example the 7TM bitter taste receptors, the V1R pheromone receptors, and the 7TM frizzled proteins, which all are either known or believed to be G-protein-coupled receptors. Bacteriorhodopsins, which are not G-protein-coupled proteins but proton pumps, are totally different in respect to amino-acid sequence but have a seven-helical bundle arranged rather similarly to that for the G-protein-coupled receptors. 

Figure 2-3. Protonated Schiff-base of retinal (PSBR) and computational models used in ONIOM QM QM calculations (left). Electrostatic effects of the surrounding protein on excitation energies in bacteriorhodopsin evaluated using TD-B3LYP Amber right). (Adapted from Vreven and Morokuma [37] (Copyright American Institute of Physics) and Vreven et al. [38], Reprinted with permission.)...

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. 

Dynamic nuclear polarisation (DNP) enhanced 15N CP MAS NMR has been exploited by Mark-Jurkauskas et al.79 in the studies of intermediates of the bacteriorhodopsin photocycle. The data for L intermediate were similar to those found for 13-ds,15-anti retylidene chloride, while those for K intermediate were similar to those of acid blue bacteriorhodopsin in which the Schiff base counterion was neutralised (Table 3). The 15N chemical shifts observed have shown that for bacteriorhodopsin, the Schiff base in K intermediate state loses contact with its counterion and establishes a new one in L intermediate state. The proton energy stored at the beginning in the electrostatic modes has been transformed to torsional modes. The transfer of energy is facilitated by the reduction of bond order alternation in the polyene chain when the counterion interaction is initially broken and is driven by the attraction of the Schiff base to a new counterion. 3D CP MAS experiments of NCOCX, NCACX, CONCA and CAN(CO)CA types have been used in studies of proteorhodopsin.71... 

Roux, B. Nina, M. Pomes, R. Smith, J., Thermodynamic stability of water molecules in the Bacteriorhodopsin proton channel a molecular dynamics and free energy perturbation study, Biophys. J. 1996, 71, 670-681... 

In this paper, we will describe one of examples, where artificial archaeal glycolipids are applied to the construction of nano-devices containing energy-conversion membrane proteins, by employing the phytanyl-chained glycolipid we have recently developed, i.e., l,3-di-o-phytanyl-2-o- ((3-D-maltotriosyl) glycerol (Mab (Phyt)2, Fig. 1) [16,17] and natural proton pump, bacteriorhodopsin (BR) derived from purple membranes of the extremely halophilic archaeon Halobacterium salinarium S9 [18],... 

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]).

Proton gradients can be built up in various ways. A very unusual type is represented by bacteriorhodopsin (1), a light-driven proton pump that various bacteria use to produce energy. As with rhodopsin in the eye, the light-sensitive component used here is covalently bound retinal (see p. 358). In photosynthesis (see p. 130), reduced plastoquinone (QH2) transports protons, as well as electrons, through the membrane (Q cycle, 2). The formation of the proton gradient by the respiratory chain is also coupled to redox processes (see p. 140). In complex III, a Q,cycle is responsible for proton translocation (not shown). In cytochrome c oxidase (complex IV, 3), trans-... 

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