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PubMed2006

Effect of electrolytes on the excited-state proton transfer and geminate recombination.

Time-resolved emission and steady-state fluorescence techniques are used to study the excited-state intermolecular proton transfer from 8-hydroxypyrene-1,3,6-trisulfonate (HPTS or pyranine) to water in the presence of inert salts, NaCl and MgCl(2). At low salt concentrations, up to about 0.5 M MgCl(2) or about 0.8 M NaCl, the time-resolved emission of both the photoacid and conjugate base can be quantitatively fitted by our diffusion-assisted geminate recombination model. In this concentration range, the proton transfer and geminate recombination rate constants are almost independent of the salt concentrations whereas the proton diffusion constant decreases as the salt concentration increases. At higher salt concentrations, the proton-transfer rate constant decreases while the recombination rate constant increases slightly. For the saturated solution of MgCl(2) (about 5 M at room temperature), the steady-state emission consists of only a single band of the protonated photoacid. Careful examination of the time-resolved emission of HPTS in the presence of a large concentration of MgCl(2) shows that the quality of the fit to the geminate recombination model is rather poor and we fail to find adjustable parameters for a good quality fitting. For this large concentration range of MgCl(2) we were able to get a good fit of the experimental data with a model based on a distribution of proton-transfer rates. The model is consistent with an inhomogeneous water environment next to the excited HPTS molecule in such concentrated solutions.

Arylsulfonates↗
PubMed2006

Proton character of the peptide unit in the Ca2+-binding sites of calcium pump.

The effect of forming calcium pump structures in biological systems on the proton character of the peptide unit has been studied theoretically using the density-functional theory calculations with a large basis set. One acetic acid, one acetate, and three acetamide molecules as well as the modeling peptide unit (MPU) have been employed to mimic the amino acid residues forming the Ca2+-binding sites. To highlight the limiting case of the Ca2+-binding effect on the proton property and the proton countertransport possibility in the direction opposite to the ion, the MPU bounded by the bare or the hydrated Ca2+ has also been investigated. The natural bond orbital (NBO) analysis indicates that the increase of the p-character of the (N-H) sigma orbital results in weakening of the N-H bond which is lengthened when a Ca2+ ion is introduced to the MPU. Calculated NMR shielding sigma(H1) of the MPU shifts upfield upon the Ca2+ ion combination, which reveals the donating of the electron from the amide H as represented by the increase of the calculated positive natural charge for amide H of the MPU. Moreover, the proton affinities (PA) and gas-phase basicities (GB) for the amide nitrogen active site of the MPU are reduced; that is, the acidity of the amide hydrogen gets stronger because of the influence of the Ca2+ ion. To prove the transport possibility of the N-H proton in the direction opposite to the Ca2+ ion along the N-H...O=C hydrogen bond in the helical peptide linkage, NH3 and H2O are used here to assist the dissociation of the amide H of the MPU, and the calculated results show the notable decrease of the deprotonation energies compared to that of the case without this assistance. Moreover, calculated results also reveal that the variation of the quantities discussed here for amide H of the MPU gets smaller when the acidity of Ca2+ ion decreases. Ionization states of the acidic residues forming the Ca2+-binding sites may influence the activity of the amide H of the MPU and further affect the transport tendency of the peptide unit proton in the direction opposite to Ca2+.

Binding Sites↗
PubMed2006

Characterization of the solvation and transport of the hydrated proton in the perfluorosulfonic acid membrane nafion.

The solvation and transport properties of the sulfonate-hydronium ion pair have been studied in hydrated Nafion through molecular dynamics simulation. Explicit proton and charge delocalization of the excess proton transport, via the Grotthuss hopping mechanism, were treated using the self-consistent multistate empirical valence bond (SCI-MS-EVB) method. The nature of the sulfonate-hydronium ion pair was characterized through analysis of free-energy profiles. It was found that, in general, the excess proton is solvated between two water molecules of a Zundel moiety while in the contact ion pair position, but then it transitions to an Eigen-like configuration in the solvent-separated pair position. Furthermore, the positive charge associated with the excess proton passes between the contact and solvent-separated ion pair positions through the Grotthuss mechanism rather than simple vehicular diffusion. The total proton diffusion was decomposed into vehicular and Grotthuss components and were found to be of the same relative magnitude, but with a strong negative correlation resulting in a smaller overall diffusion. Correlated motions between the ion pair were examined through the distinct portion of the van Hove correlation function, and a characteristic time scale of approximately 425 ps was observed. Additionally, the association of the hydrated proton with the hydrophobic polymer backbone suggests its amphiphile-like behavior (see Acc. Chem. Res. 2006, 39, 143; Phys. Rev. 1954, 95, 249; J. Chem. Phys. 2005, 123, 084309).

Chemistry, Physical↗
PubMed2001

Pulse sequences for detection of NH2...N hydrogen bonds in sheared G . A mismatches via remote, non-exchangeable protons.

The non-detectability of NH...N hydrogen bonds in nucleic acids due to exchange broadened imino/amino protons has recently been addressed via the use of non-exchangeable protons for detecting internucleotide 2hJ(NN) couplings. In these applications, the appropriate non-exchangeable proton is separated by two bonds from the NH...N bond. In this paper, we extend the scope of this approach to protons which are separated by four bonds from the NH...N moiety. Specifically, we consider the case of the commonly occurring sheared G x A mismatch alignment, in which we use the adenine H2 proton to report on the (A)N6H6(1.2)...N3(G) hydrogen bond, in the presence of undetectable, exchange broadened N6H6(1.2) protons. Two sequences, the 'straight-through' (H6)N6N3H2 and 'out-and-back' H2N6N3 experiments, are presented for observing these correlations in H2O and D2O solution, respectively. The sequences are demonstrated on two uniformly 15N,13C labelled DNA samples: d(G1G2G3T4T5C6A7G8G9)2, containing a G3 x (C6-A7) triad involving a sheared G3 x A7 mismatch, and d(G1G2G3C4A5G6G7T8)4, containing an A5 x (G3 x G6 x G3 x G6) x A5 hexad involving a sheared G3 x A5 mismatch.

Base Pair Mismatch↗
PubMed1998

Cardiolipins and mitochondrial proton-selective leakage.

The proton-selective leak (State 4 respiratory rate) but not delta psi, in mitochondria from thyroid-sensitive tissues, responds to in vivo stimuli in unique correlation with changes in cardiolipins, saturated and mono-unsaturated (extended) fatty acyl contents, cardiolipins/phospholipids ratios, and/or membrane outer-sidedness. Liver mitochondrial State 4 respiration, basal in fasted rats, contributes little to resting metabolic rate in fed rats, where State 3 depresses delta psi. In a proposed model, an essential inner-membrane outer-surface proton antenna collects protons and donates them, via a water-shuttle, to transmembrane porters: transient water-molecule-chains between extended phospholipid acyls; protonophores, and uncoupling proteins. Only cardiolipin microdomains can donate, from an anomalously-dissociating phosphate group in each headgroup; unadapted cardiolipins have few conducting water chains. Thyroid states regulate each cardiolipin property, and are permissive, via the proton antenna, for proton leaks, including those through adapted and possibly constitutive BAT and ectopic uncoupling proteins. Slow leakage in liposomes may reflect insufficient cardiolipin proton antennas.

Animals↗
PubMed1997

Proton pumping of mitochondrial complex I: differential activation by analogs of ubiquinone.

As part of the ongoing studies aimed at elucidating the mechanism of the energy conserving function of mitochondrial complex I, NADH: ubiquinone (Q) reductase, we have investigated how short-chain Q analogs activate the proton pumping function of this complex. Using a pH-sensitive fluorescent dye we have monitored both the extent and initial velocity of proton pumping of complex I in submitochondrial particles. The results are consistent with two sites of interaction of Q analogs with complex I, each having different proton pumping capacity. One is the physiological site which leads to a rapid proton pumping and a stoichiometric consumption of NADH associated with the reduction of the most hydrophobic Q analogs. Of these, heptyl-Q appears to be the most efficient substrate in the assay of proton pumping. Q analogs with a short-chain of less than six carbons interact with a second site which drives a slow proton pumping activity associated with NADH oxidation that is overstoichiometric to the reduced quinone acceptor. This activity is also nonphysiological, since hydrophilic Q analogs show little or no respiratory control ratio of their NADH:Q reductase activity, contrary to hydrophobic Q analogs.

Aminoacridines↗
PubMed1999

Proton translocation by cytochrome c oxidase.

Cell respiration in mitochondria and some bacteria is catalysed by cytochrome c oxidase, which reduces O2 to water, coupled with translocation of four protons across the mitochondrial or bacterial membrane. The enzyme's catalytic cycle consists of a reductive phase, in which the oxidized enzyme receives electrons from cytochrome c, and an oxidative phase, in which the reduced enzyme is oxidized by O2. Previous studies indicated that proton translocation is coupled energetically only to the oxidative phase, but this has been challenged. Here, with the purified enzyme inlaid in liposomes, we report time-resolved measurements of membrane potential, which show that half of the electrical charges due to proton-pumping actually cross the membrane during reduction after a preceding oxidative phase. pH measurements confirm that proton translocation also occurs during reduction, but only when immediately preceded by an oxidative phase. We conclude that all the energy for proton translocation is conserved in the enzyme during its oxidation by O2. One half of it is utilized for proton-pumping during oxidation, but the other half is unlatched for this purpose only during re-reduction of the enzyme.

Animals↗
PubMed2000

Molecular mechanism of vectorial proton translocation by bacteriorhodopsin.

Bacteriorhodopsin, a membrane protein with a relative molecular mass of 27,000, is a light driven pump which transports protons across the cell membrane of the halophilic organism Halobacterium salinarum. The chromophore retinal is covalently attached to the protein via a protonated Schiff base. Upon illumination, retinal is isomerized. The Schiff base then releases a proton to the extracellular medium, and is subsequently reprotonated from the cytoplasm. An atomic model for bacteriorhodopsin was first determined by Henderson et al, and has been confirmed and extended by work in a number of laboratories in the last few years. Here we present an atomic model for structural changes involved in the vectorial, light-driven transport of protons by bacteriorhodopsin. A 'switch' mechanism ensures the vectorial nature of pumping. First, retinal unbends, triggered by loss of the Schiff base proton, and second, a protein conformational change occurs. This conformational change, which we have determined by electron crystallography at atomic (3.2 A in-plane and 3.6 A vertical) resolution, is largely localized to helices F and G, and provides an 'opening' of the protein to protons on the cytoplasmic side of the membrane.

Bacteriorhodopsins↗
PubMed2002

Reduction of cytochrome c oxidase by a second electron leads to proton translocation.

Cytochrome c oxidase, the terminal enzyme of cellular respiration in mitochondria and many bacteria, reduces O(2) to water. This four-electron reduction process is coupled to translocation (pumping) of four protons across the mitochondrial or bacterial membrane; however, proton pumping is poorly understood. Proton pumping was thought to be linked exclusively to the oxidative phase, that is, to the transfer of the third and fourth electron. Upon re-evaluation of these data, however, this proposal has been questioned, and a transport mechanism including proton pumping in the reductive phase--that is, during the transfer of the first two electrons--was suggested. Subsequently, additional studies reported that proton pumping during the reductive phase can occur, but only when it is immediately preceded by an oxidative phase. To help clarify the issue we have measured the generation of the electric potential across the membrane, starting from a defined one-electron reduced state. Here we show that a second electron transfer into the enzyme leads to charge translocation corresponding to pumping of one proton without necessity for a preceding turnover.

Biological Transport↗
PubMed2005

Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy.

Much progress has been made in our understanding of water molecule reactions on surfaces, proton solvation in gas-phase water clusters and proton transfer through liquids. Compared with our advanced understanding of these physico-chemical systems, much less is known about individual water molecules and their cooperative behaviour in heterogeneous proteins during enzymatic reactions. Here we use time-resolved Fourier transform infrared spectroscopy (trFTIR) and in situ H2(18)O/H2(16)O exchange FTIR to determine how the membrane protein bacteriorhodopsin uses the interplay among strongly hydrogen-bonded water molecules, a water molecule with a dangling hydroxyl group and a protonated water cluster to transfer protons. The precise arrangement of water molecules in the protein matrix results in a controlled Grotthuss proton transfer, in contrast to the random proton migration that occurs in liquid water. Our findings support the emerging paradigm that intraprotein water molecules are as essential for biological functions as amino acids.

Amino Acid Substitution↗
PubMed1999

The significance and mechanism of mitochondrial proton conductance.

There is a futile cycle of pump and leak of protons across the mitochondrial inner membrane. The contribution of the proton cycle to standard metabolic rate is significant, particularly in skeletal muscle, and it accounts for 20% or more of the resting respiration of a rat. The mechanism of the proton leak is uncertain: basal proton conductance is not a simple biophysical leak across the unmodified phospholipid bilayer. Equally, the evidence that it is catalysed by homologues of the brown adipose uncoupling protein, UCP1, is weak. The yeast genome contains no clear UCP homologue but yeast mitochondria have normal basal proton conductance. UCP1 catalyses a regulated inducible proton conductance in brown adipose tissue and the possibility remains open that UCP2 and UCP3 have a similar role in other tissues, although this has yet to be demonstrated.

Animals↗
PubMed1973

Proton translocation coupled to quinol oxidation in ox heart mitochondria.

The suitability of ubiquinol(1) and duroquinol as pulse reductants for initiating respirationdriven proton translocation by aerobic ox heart mitochondria was investigated. At 25 degrees C the V(max.) for oxidation was close to 280nmol of quinol oxidized/min per mg of protein, and the K(m) values were 8mum for ubiquinol(1) and 28mum for duroquinol. Pulses of ubiquinol(1) and duroquinol were rapidly and completely oxidized by aerobic mitochondria with a simultaneous acidification of the suspending medium as detected with a glass electrode. The -->H(+)/2e(-) ratios (Mitchell, 1966) calculated from the observed extent of acidification and the amount of quinol added were 3.62 for ubiquinol(1) and 2.98 for duroquinol. These values are underestimates of the true value owing to proton back-flow across the membrane. An analogue computer model was used to correct the observed extent of respirationdriven acidification for proton back-flow. The corrected -->H(+)/2e(-) values were 4.01 for ubiquinol and 3.86 for duroquinol oxidation. Attempts to measure the rate of proton translocation with a pH-measuring system with a response time of 0.4s were not entirely satisfactory, owing to the relative slowness of the electrode response. Nevertheless the maximal rate of proton generation during ubiquinol(1) oxidation was about 1200ng-ions of H(+)/min per mg of mitochondrial protein. It is concluded, contrarily to Chance & Mela (1967), that mitochondria exhibit a proton-translocating ubiquinol oxidase activity with a -->H(+)/2e(-) ratio of 4.0.

Alcohols↗
PubMed1978

Proton translocation of the bovine chromaffin-granule membrane.

Bovine chromaffin granules were lysed and their membranes resealed to give osmotically sensitive 'ghosts'. These swell in the presence of salts and MgATP. It is shown that this is due to proton entry accompanied by anions. The rate of swelling depends on the anion present, but swelling is not limited to media containing permeant anions. It is quite marked in solutions of sulphates, phosphates and acetates. It is not uncoupler-sensitive, suggesting that at least one component of swelling is due to coupled proton and anion entry (non-electrogenic proton translocation). Direct measurements of transmembrane pH and potential gradients generated in the presence of MgATP shows that these are rapidly established in sucrose media, and are rather little affected by the presence of salts. They contribute roughly equally to the total protonmotive force. The potential gradient is establihsed very rapidly, but the pH gradient is generated over several minutes. The gradients are not completely dissipated by uncoupler, and it is shown that, in media containing sulphate but no permeant anion, sulphate can be taken up by the 'ghosts'. There thus appear to be two mechanisms of proton translocation across the membrane, both dependent on ATP hydrolysis: an electrogenic transfer of protons, and proton movement linked to an anion transporter of broad specificity.

Adenosine Triphosphate↗
PubMed1979

Limited-turnover studies on proton translocation in reconstituted cytochrome c oxidase-containing vesicles.

We have investigated ferrocytochrome c-induced proton ejection from reconstituted cytochrome c oxidase-containing vesicles using careful control of the number of enzyme turnovers. Ferrocytochrome c caused the appearance of protons at the vesicle exterior, and this could be abolished by using a protonophore. In addition, its decay was dependent on the permeability of the vesicle membranes to protons and the number of turnovers of the oxidase. These observations indicate that the ejection of protons was the result of genuine translocation. The possibility of this translocation occurring via a Mitchellian loop as a result of the presence of a reduced hydrogen carrier contaminating the enzyme was considered and excluded. Proton-translocating activity in this reconstituted system depended critically on the ratio of enzyme to lipid used in the reconstitution process and we propose a rationale to account for this. We conclude that our data provide strong support for the proposal that cytochrome c oxidase acts as a proton pump and that approx. 0.9 H+ is excluded per ferrocytochrome c molecule oxidized.

Binding Sites↗
PubMed2005

The basal proton conductance of mitochondria depends on adenine nucleotide translocase content.

The basal proton conductance of mitochondria causes mild uncoupling and may be an important contributor to metabolic rate. The molecular nature of the proton-conductance pathway is unknown. We show that the proton conductance of muscle mitochondria from mice in which isoform 1 of the adenine nucleotide translocase has been ablated is half that of wild-type controls. Overexpression of the adenine nucleotide translocase encoded by the stress-sensitive B gene in Drosophila mitochondria increases proton conductance, and underexpression decreases it, even when the carrier is fully inhibited using carboxyatractylate. We conclude that half to two-thirds of the basal proton conductance of mitochondria is catalysed by the adenine nucleotide carrier, independently of its ATP/ADP exchange or fatty-acid-dependent proton-leak functions.

Animals↗
PubMed2006

Inefficient coupling between proton transport and ATP synthesis may be the pathogenic mechanism for NARP and Leigh syndrome resulting from the T8993G mutation in mtDNA.

Mutations in the ATP6 gene of mtDNA (mitochondrial DNA) have been shown to cause several different neurological disorders. The product of this gene is ATPase 6, an essential component of the F1F0-ATPase. In the present study we show that the function of the F1F0-ATPase is impaired in lymphocytes from ten individuals harbouring the mtDNA T8993G point mutation associated with NARP (neuropathy, ataxia and retinitis pigmentosa) and Leigh syndrome. We show that the impaired function of both the ATP synthase and the proton transport activity of the enzyme correlates with the amount of the mtDNA that is mutated, ranging from 13-94%. The fluorescent dye RH-123 (Rhodamine-123) was used as a probe to determine whether or not passive proton flux (i.e. from the intermembrane space to the matrix) is affected by the mutation. Under state 3 respiratory conditions, a slight difference in RH-123 fluorescence quenching kinetics was observed between mutant and control mitochondria that suggests a marginally lower F0 proton flux capacity in cells from patients. Moreover, independent of the cellular mutant load the specific inhibitor oligomycin induced a marked enhancement of the RH-123 quenching rate, which is associated with a block in proton conductivity through F0 [Linnett and Beechey (1979) Inhibitors of the ATP synthethase system. Methods Enzymol. 55, 472-518]. Overall, the results rule out the previously proposed proton block as the basis of the pathogenicity of the mtDNA T8993G mutation. Since the ATP synthesis rate was decreased by 70% in NARP patients compared with controls, we suggest that the T8993G mutation affects the coupling between proton translocation through F0 and ATP synthesis on F1. We discuss our findings in view of the current knowledge regarding the rotary mechanism of catalysis of the enzyme.

Adenosine Triphosphate↗
PubMed2006

Synergy of fatty acid and reactive alkenal activation of proton conductance through uncoupling protein 1 in mitochondria.

The kinetics of proton transport through mammalian UCP1 (uncoupling protein 1) expressed in yeast mitochondria were measured. There was little or no UCP1 activity in the absence of added palmitate, but significant activity in its presence. The activator 4-HNE (4-hydroxy-2-nonenal) had little effect when added alone, but significantly enhanced proton conductance in the presence of added palmitate. Activation of the proton conductance of UCP1 was synergistic: proton conductance in the presence of both palmitate and 4-HNE was significantly greater than the sum of the individual effects. Mitochondria from control yeast transformed with empty vector showed no such synergy, showing that synergy is a property of UCP1. Activation by the 4-HNE analogue trans-cinnamate showed essentially the same characteristics as activation by 4-HNE. Mitochondria from brown adipose tissue also showed synergistic activation of GDP-sensitive proton conductance by palmitate and 4-HNE. These results show that reactive alkenals activate the proton conductance of UCP1 more strongly when fatty acids are also added, with implications for both mechanistic and physiological models of UCP1 activation.

Adipose Tissue, Brown↗
PubMed1983

The effect of pH on the exchangeability with deuterium of protons coupled to molybdenum(V) in the active and the desulpho forms of xanthine oxidase.

The effect of pH variation on the exchangeability with deuterium of protons strongly coupled to Mo(V) in the active and desulpho forms of xanthine oxidase was studied by e.p.r. and rapid freezing, in extension of the work of Gutteridge, Tanner & Bray [Biochem. J. (1978) 175, 887-897]. Above neutrality, exchange rates increased with increasing pH. Detailed studies were made on the desulpho enzyme under a variety of conditions, and exchange rate constants at 22 degrees C ranged from 0.16s -1 at pH 6.6 to 1.6s -1 at pH 11.3. The mechanism of proton exchange in the enzyme is discussed. The interpretation by the above workers that the strongly coupled proton of the active enzyme is on sulphur and that of the desulpho enzyme is on oxygen remains valid (and is in agreement with other work), as do their proposals for the structures of the protonated and deprotonated species. However, pK values cannot be calculated from the exchange data. It is likely that the relatively low rates of exchange observed are due to the difference of structure between the protonated and the deprotonated forms. In the case of the desulpho enzyme, an exchange mechanism, which involves the proton exchanging both as such and along with oxygen in the form of a hydroxyl ion, is discussed.

Deuterium↗