Proton transfer, hydrogen bonds cluster formation

Figure 10 shows the proposed ubiquinol oxidation and electron bifurcation mechanism at Qp site. (A) In the absence of the ubiquinone, the side chain of Glu-271 is connected to the solvent in the mitochondrial intermembrane space via a water chain. (B) As a reduced ubiquinol molecule binds to the site, the side chain of Glu-271 flips to form a hydrogen bond to the bound ubiquinone. (C) Now, the ISP, which is moving around the intermediate position by thermal motion is trapped at the b" position by a hydrogen bond to the bound ubiquinone. (D,E) Coupled to deprotonation, the first electron transfer occurs. Since the Rieske FeS cluster has a much higher redox potential (ca. +300 mV) than heme bl (ca. 0 mV), the first electron is favorably transferred to ISP. This yields ubisemiquinone, (F,G). After ubisemiquinone formation, the hydrogen bond to the His-161 of ISP is destabilized. The ISP moves to the c position, where the electron is transferred from the Rieske FeS cluster to heme c. Now unstable ubisemiquinone is left in the Qp pocket. The redox potential of the deprotonated ubisemiquinone is assumed to be several hundred millivolts. Now the electron transfer to the heme bl is a downhill reaction. (H) Coupled to the second electron transfer, the second proton is transferred to Glu-271 and subsequently to the mitochondrial intermembrane space. The fully oxidized ubiquinone is released to the membrane. 

The N—H N hydrogen bond is responsible for the formation of the complexes between aniline and aliphatic amines (ammonia, methylamine, dimethylamine and tri-methylamine) which act as proton acceptors. Infrared photodissociation spectra and DFT calculation indicate208 that the clusters [aniline/ammonia]+ and [aniline/methylamine]+ have a non proton transferred (without the proton donation from the aniline moiety to the amine molecule) structure, while the complexes [aniline/dimethylamine]+, [aniline/ trimethylamine]+ possess a proton transferred structure. Reasonably, the proton transfer increases on increasing the proton affinity of the amine used as solvent. 

The interaction of protein with water is also an important consideration because the electrical conductivity of the adsorbed protein layer depends on the mechanism of charge transfer. The conduction in proteins with low water content is electronic, whereas at higher water contents it is protonic and/or due to small inorganic ions (35, 36). Water is considered (37) to exist in two structural forms clusters (ordered) formed by hydrogen bonds, and free unbounded water (monomeric). Any factors, such as temperature, that favor monomeric water tend to increase the protein s catalytic activity, and factors favoring cluster formation tend to decrease catalytic activity. In addition, increased catalytic activity is probably related to increased binding properties to foreign surfaces. 

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