Proton channel

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.,...

Two classes of inhibitors for influenza virus are currently available (Hayden 2006). The M2 proton channel inhibitors amantadine and rimantadine and the neuraminidase (NA) inhibitors oseltamivir carboxylate and zanamivir. Chapter 5 provides more details about the class of NA inhibitors. 

Fig. 27. A schematic representation of the seven transmembrane helical peptide chains (A-G) viewed from inside the cell. The numbering denotes the first and last amino acid residues. The proton channel is believed to be the volume between helices C, D, F and G...

Figure 23 Calculation of the shape of the actively compensated pulse can be carried out on the software. (A) shows the real (red line) and the imaginary (green line) component of an example of the target pulse shape t>,(f). Its leading and the trailing edges have a cosine shape with a transition time of 1.25 xs in 50 steps, and the width of the plateau is 5 ps. (B) Laplace transformation B(s) multiplied by the Laplace transformed step function U(s). (C) It was then divided by the Laplace transformation Y(s) of the measured step response y(t) of the proton channel of a 3.2-mm Varian T3 probe tuned at 400.244 MHz to obtain V(s). (D) Finally, inverse Laplace transformation was performed on V(s) to obtain the compensated pulse that results in the RF pulse with the target shape. Time resolution was 25 ns, and o = 20 was used for the Laplace and inverse Laplace transformations.

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... 

Fig. 14.4 Pulse sequences used for the experiments described in this chapter. A [ N HJ-HSQC with water flip back and PFGs. The shaped pulse on the proton channel is a sine-shaped, 1.5 ms soft pulse all other pulses are hard pulses. Gradients are applied as square or sine-shaped pulses. The sign of the last gradient is reversed for anti-echo selection together with the sign of phase 6. B CPMG sequence. C bpPFGLED sequence. The delay T denotes the diffusion delay. Typically, r is set to 1 ms, T to 50-100 ms and Te to 1.2 ms.

In each of these cases, the gradient is utilized by an ATP synthase (4) to form ATP. ATP synthases consist of two components—a proton channel (Fq) and an inwardly directed protein complex (Fi), which conserves the energy of back-flowing protons through ATP synthesis (see p. 142). 

The ATP synthase (EC3.6.1.34, complex V) that transports H"" is a complex molecular machine. The enzyme consists of two parts—a proton channel (Fq, for oligomycin-sensitive ) that is integrated into the membrane and a catalytic unit (Fi) that protrudes into the matrix. The Fo part consists of 12 membrane-spanning c-peptides and one a-subunit. The head of the Fi part is composed of three a and three p subunits, between which there are three active centers. The stem between Fo and Fi consists of one y and one e subunit. Two more polypeptides, b and 8, form a kind of stator, fixing the a and p subunits relative to the Fo part. 

Fig. 4. Bottom the Double-Band-Filtered COSY spectrum obtained by selection through DANTE-Z of the H region (prior to the evolution interval) and by the selection through SPlN-PlNGING [11] of the amide region (before the acquisition interval) of toxin 7. Top the corresponding region of a standard COSY spectrum. Note, in the bottom diagram, the considerable increase in spectral resolution as well as the occurrence of additional crosspeaks (indicated with asterisks). Experiments were performed at 360 MHz (Bruker AMX360) in H2O at 318 K. The 50 W class C amplifier of the proton channel was used as transmitter.

The conformation of membrane-bound enzymes is undoubtedly restricted by the membrane. However, the mechanism of action of these enzymes appears to be similar to that of soluble enzymes, so that the presence of clefts and conformational flexibility is to be expected. The mitochondrial coupling factor apparently contains both the ATP synthesizing enzyme and a proton channel conformational changes undoubtedly play a role in the function of this system. A large movement of polypeptide chains has been proposed in the functioning of this system (and for other membrane-bound enzymes), but no convincing experimental evidence is available to support such a hypothesis. 

Chemiosmotic theory readily explains the dependence of electron transfer on ATP synthesis in mitochondria. When the flow of protons into the matrix through the proton channel of ATP synthase is blocked (with oligomycin, for example), no path exists for the return of protons to the matrix, and the continued extrusion of protons driven by the activity of the respiratory chain generates a large proton gradient. The proton-motive force builds up until the cost (free energy) of pumping... 

This hypothesis presumes that early free-living prokaryotes had the enzymatic machinery for oxidative phosphorylation and predicts that their modern prokaryotic descendants must have respiratory chains closely similar to those of modern eukaryotes. They do. Aerobic bacteria carry out NAD-linked electron transfer from substrates to 02, coupled to the phosphorylation of cytosolic ADP. The dehydrogenases are located in the bacterial cytosol and the respiratory chain in the plasma membrane. The electron carriers are similar to some mitochondrial electron carriers (Fig. 19-33). They translocate protons outward across the plasma membrane as electrons are transferred to 02. Bacteria such as Escherichia coli have F0Fi complexes in their plasma membranes the F portion protrudes into the cytosol and catalyzes ATP synthesis from ADP and P, as protons flow back into the cell through the proton channel of F0. 

A porphyrin template has also been used by DeGrado and coworkers [35] for developing a well-defined four a-helix structure (41) that has proton channel activity (see Sect. 3.2). Following modeling studies, they used a tetraphenyl porphyrin with four carboxylic acids at the meta positions as attachment points for the peptide segments. 

The proton channel rotates and this motion is transmitted to the rotor in Fi sector. 

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