Proton transfer mechanism pumping

D. vulgaris and two ionizable centers in D. desulfuricans ATCC27774 that result in concerted two-electron/two-proton transfer steps has been called proton-thrusting, because it is akin to the redox-linked proton-transfer mechanisms seen in membrane-bound protein complexes involved in proton pumping. 

A perfect selective proton transfer mechanism is easily conceivable and its role appears particularly suggestive in relation to the paradigmatic frame of reference of the chemiosmotic theories, 13, However, we may fairly ask the question whether experimental proofs and theoretical argumentation are nowadays sufficiently conclusive in order to retain the predominant proton pump as the most plausible model for steady state electrogenic transfer in these cells. 

Rich (1995) has proposed that the proton pump in cytochrome c oxidase is driven mainly by electrostatic interactions (or repulsion) between protons in a proton trap and protons transferred from the matrix side to the O2 reduction site for neutralizing oxides (O ) are produced by O2 reduction. In this mechanism, a structural change for gating proton transfer from the matrix side to the proton trap is required for a complete cycle of redox-coupled proton pumping. However, no such structural change has been detected. 

Thirty years of research with bacteriorhodopsin has provided answers to many questions about how protons are transported by transmembrane pumps. In this small seven-transmembrane protein, absorption of light by the retinal chromophore Initiates a reaction cycle in which the initial state recovers through multiple conformational changes of the retinal and the protein, and a proton Is translocated stepwise from one side of the membrane to the other. Spectroscopy, extensive use of site-specific mutations, and crystallography have defined the photocycle reactions in atomic detail and provide a step-by-step description of the proton transfers, the transient local and global perturbations in the protein and how they arise, and the energy flow through the system, which add up to the mechanism of the pump. 

As already discussed, the model proposed by Tsukihara et alP depends on the so-scalled H-pathway of proton transfer and on the function of an aspartic acid that is not conserved in the bacterial oxidases. This model also depends crucially on the formyl group and on the hydroxyethyl farnesyl side chain of heme a. Many proton-pumping bacterial oxidases, such as cytochrome boj, from E. coll, have replaced heme a with a protoheme (heme B) that lacks both the formyl and the farnesyl side chain. Therefore, this model is restricted to heme a - containing oxidases, and implies different mechanisms of proton translocation in different members of the heme-copper oxidase superfamily. 

This finding suggests a possible mechanism of proton transfer in this region one branch of the water cluster can be used by pumped protons the other by chemical protons (Figure 4.14). There is driving force for both of these reactions [39]. The mechanism of gating of chemical and pumped protons, however, is not clear. 

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