Proton pumping mechanism

The electrochemical potential across the membrane drives protons back into the cell through a membrane ATP synthase complex very similar to that of mitochondria and chloroplasts. Thus, when 02 is limited, halobacteria can use light to supplement the ATP synthesized by oxidative phosphorylation. Halobacteria do not evolve 02, nor do they carry out photoreduction of NADP+ their phototransducing machinery is therefore much simpler than that of cyanobacteria or plants. Nevertheless, the proton-pumping mechanism used by this simple protein may prove to be prototypical for the many other, more complex, ion pumps. Bacteriorhodopsin ... 

In these mechanisms, electron transport through the various components of the electron-transport chain leads to structural changes in the proteins of the chain, such that changes in their pKa values (Chap. 3) of ionizable amino acid residues occurs. For example, an increase in the pKa of a residue adjacent to the matrix side of the membrane would lead to proton uptake from the matrix, while a decrease in the pKa of a residue adjacent to the intermembranous side of the membrane could lead to release of a proton. The net effect of these processes is the transfer of protons from the matrix to the intermembranous side of the membrane. However, proton-pump mechanisms do not make strong predictions of the H+/e stoichiometries. 

No, it is inconsistent with this hypothesis, which predicts an H+/e value of 1.0. Such stoichiometries may, however, be explained by proton-pump mechanisms, in which electron transfer is coupled to changes in the pKa values of proteins within Complex I. 

Fig. 4. Proposed functions of the hydroxyfarnesylethyl group of heme A. (A) A possible electron transfer pathway formed by overlapping of rr-electron orbitals in the alkyl chain with that of the pyrrole. (B) A side-on coordination of the terminal double bond to Cub and a coordination of a deprotonated form of the double bond to Fe j. A proposed proton-pumping mechanism including the redox-coupled change in the two coordination states.

Figure 6.6-17 Model of proton pump mechanism of bacteriorhodopsin.

As just discussed, reactions with H2O2 can be used to generate P [46], but recently it has been shown that a species (Fe" +=0 , Cub ) is formed, when the mixed-valence enzyme reacts with H2O2 [59], and this species is not an intermediate in the reaction of the fully or partially reduced oxidase with O2. It may, however, become useful for investigations of the role of Cub in the proton-pump mechanism, since it has this ion reduced. 

Wang, J., El-Sayed, M.A., Time-resolved Eourier transform infrared spectroscopy of the polarizable proton continua and the proton pump mechanism of bacteriorhodopsin, Biophys. J, 2001, 80, 961-971. 

Abresch et aL, 1998] and of the lumen-side domain of cytochrome/[Martinez et al., 1996]. Finally, in cytochrome c oxidase, two independent theoretical studies have predicted the hydration of buried cavities implicated in the uptake of protons [Riistama et al, 1997 Hofacker and Schulten, 1998]. Although these water molecules were not resolved in published crystallographic structures of the P. denitrificans [Iwata et al, 1995] and bovine heart [Tsukihara et al, 1996] enzymes, many of them are well-defined in a new structure of the Rb, sphaeroides enzyme [M. Svensson-Ek, personal communication]. Understanding the molecular properties giving rise to proton transport in hydrogen-bonded networks containing water molecules is therefore an important step towards the elucidation of proton-pumping mechanisms. 

Fig. 21.5. Components of the electron transfer chain. NADH dehydrogenase (complex 1) spans the membrane and has a proton pumping mechanism involving CoQ. The electrons go from CoQ to c5riochrome b-cl complex (complex El), and electron transfer does NOT involve complex II. Succinate dehydrogenase (complex II), glycerol 3-phosphate dehydrogenase, and ETF Q oxidoreductase (shown in blue) all transfer electrons to CoQ, but do not span the membrane and do not have a proton pumping mechanism. As CoQ accepts protons from the matrix side, it is converted to QH2. Electrons are transferred from complex III to complex IV (cytochrome c oxidase) by cytochrome c, a small cytochrome in the intermembrane space that has reversible binding sites on the b-c, complex and cytochrome c oxidase.

COMPUTATIONAL STUDIES OF PROTON PUMPING MECHANISM IN CYTOCHROME OXIDASE... 

The key unknown in CcO proton pumping mechanism is the identity of the group that plays the role of the pump elemeut. Currently, most of the researches in the area agree that the most likely mechanism of pumping involves an intermediate proton... 

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