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At least 1,441 records · Page 80Linked to original sources
PubMed2004

Fragmentation of protonated oligoalanines: amide bond cleavage and beyond.

The fragmentation reactions of the singly-protonated oligoalanines trialanine to hexaalanine have been studied using energy-resolved mass spectrometry in MS(2) and MS(3) experiments. The primary fragmentation reactions are rationalized in terms of the b(x)-y(z) pathway of amide bond cleavage which results in formation of a proton-bound complex of an oxazolone and a peptide/amino acid; on decomposition of this complex the species of higher proton affinity preferentially retains the proton. For protonated pentaalanine and protonated hexaalanine the major primary fragmentation reaction involves cleavage of the C-terminal amide bond to form the appropriate b ion. The lower mass b ions originate largely, if not completely, by further fragmentation of the initially formed b ion. MS(3) energy-resolved experiments clearly show the fragmentation sequence b(n) --> b(n-1) --> b(n-2). A more minor pathway for the alanines involves the sequence b(n) --> a(n) --> b(n-1) --> b(n-2). The a(5) ion formed from hexaalanine loses, in part, NH(3) to begin the sequence of fragmentation reactions a(5) --> a(5)* --> a(4)* --> a(3)* where a(n)* = a(n) - NH(3). The a(3)* ion also is formed from the b(3) ion by the sequence b(3) --> a(3) --> a(3)* with the final step being sufficiently facile that the a(3) ion is not observed with significant intensity in CID mass spectra. A cyclic structure is proposed for the a(3)* ion.

Alanine↗
PubMed2006

Collisionally activated dissociation of protonated 2'-deoxycytidine, 2'-deoxyuridine, and their oxidatively damaged derivatives.

We examined the collisionally activated dissociation (CAD) pathways of protonated 2'-deoxycytidine (dC), 5-formyl-2'-deoxycytidine (5-FmdC), 5-hydroxy-2'-deoxycytidine (5-OHdC), 5-hydroxymethyl-2'-deoxycytidine (5-HmdC), and their corresponding stable isotope-labeled compounds to gain insights into the effects of modifications on the fragmentation pathways of the pyrimidine bases. Multi-stage MS (MSn) results showed that protonated cytosine, its 5-hydroxyl- and 5-hydroxymethyl-substituted derivatives, but not its 5-formyl-substituted analog, could undergo Dimroth-like rearrangement in the gas-phase. The elimination of HNCO was one of the major fragmentation pathways observed for the protonated ions of all dC derivatives except for 5-hydroxymethylcytosine, which underwent this loss only after a H2O molecule had been eliminated. In addition, the protonated cytosine and 5-hydroxycytosine can undergo a facile elimination of NH3 molecule. This loss, however, was not observed for protonated 5-hydroxymethylcytosine, 5-formylcytosine, and their uracil analogs. Taken together, our study demonstrated that modifications could alter markedly the CAD patterns of the protonated pyrimidine bases. The results from this study provided a basis for the identifications of other modified pyrimidine bases/nucleosides by tandem mass spectrometry.

Chromatography, High Pressure Liquid↗
PubMed2004

Protonation status of metal-bound ligands can be determined by quantum refinement.

The protonation status of key residues and bound ligands are often important for the function of a protein. Unfortunately, protons are not discerned in normal protein crystal structures, so their positions have to be determined by more indirect methods. We show that the recently developed quantum refinement method can be used to determine the position of protons in crystal structures. By replacing the molecular-mechanics potential, normally used in crystallographic refinement, by more accurate quantum chemical calculations, we get information about the ideal structure of a certain protonation state. By comparing the refined structures of different protonation states, the one that fits the crystallographic raw data best can be decided using four criteria: the R factors, electron density maps, strain energy, and divergence from the unrestrained quantum chemical structure. We test this method on alcohol dehydrogenase, for which the pK(a) of the zinc-bound solvent molecule is experimentally known. We show that we can predict the correct protonation state for both a deprotonated alcohol and a neutral water molecule.

Alcohol Dehydrogenase↗
PubMed2004

Structural determinants of proton blockage in aquaporins.

Aquaporins are an important class of membrane channels selective for water and linear polyols but impermeable to ions, including protons. Recent computational studies have revealed that the relay of protons through the water-conduction pathway of aquaporin channels is opposed by a substantial free energy barrier peaking at the signature NPA motifs. Here, free-energy simulations and continuum electrostatic calculations are combined to examine the nature and the magnitude of the contribution of specific structural elements to proton blockage in the bacterial glycerol uptake facilitator, GlpF. Potential of mean-force profiles for both hop and turn steps of structural diffusion in the narrow pore are obtained for artificial variants of the GlpF channel in which coulombic interactions between the pore contents and conserved residues Asn68 and Asn203 at the NPA signature motifs, Arg206 at the selectivity filter, and the peptidic backbone of the two half-helices M3 and M7, which are arranged in head-to-head fashion around the NPA motifs, are turned off selectively. A comparison of these results with electrostatic energy profiles for the translocation of a probe cation throughout the water permeation pathway indicates that the free-energy profile for proton movement inside the narrow pore is dominated by static effects arising from the distribution of charged and polar groups of the channel, whereas dielectric effects contribute primarily to opposing the access of H+ to the pore mouths (desolvation penalty). The single most effective way to abolish the free-energy gradients opposing the movement of H+ around the NPA motif is to turn off the dipole moments of helices M3 and M7. Mutation of either of the two NPA Asn residues to Asp compensates for charge-dipole and dipole-dipole effects opposing the hop and turn steps of structural diffusion, respectively, and dramatically reduces the free energy barrier of proton translocation, suggesting that these single mutants could leak protons.

Aquaporins↗
PubMed2002

Influence of the physical states of membrane surface area and center area on lysosomal proton permeability.

The physical state of the lysosomal membrane was modulated with the membrane fluidizers n-propanol and n-octanol and with the membrane rigidifiers cholesteryl hemisuccinate and cholesterol. Membrane fluidity was examined by the steady-state fluorescence anisotropy of 2-(9-anthroyloxy) palmitic acid and 16-(9-anthroyloxy) palmitic acid. Fluidizing the membranes at the surface and center areas increased the proton permeability coefficient by 92.8 and 18.0%, respectively. Rigidifying the membranes at the surface and center areas decreased the coefficient by 68.2 and 40.2%, respectively. Proton leakage of the lysosomes increased and decreased similar to the coefficient changes with the treatments. The results indicate that lysosomal proton permeability is affected by its membrane's physical state, and the physical state of the membrane surface area affects the proton permeability more markedly. The proton permeability coefficient of liposomes was similar to that of lysosomes, suggesting that efflux of lysosomal protons might occur through the lipid part of the bilayer but not transmembrane proteins.

1-Octanol↗
PubMed2000

Proton transport by sensory rhodopsins and its modulation by transducer-binding.

The study of light-induced proton transfers in the archaeal sensory rhodopsins (SR), phototaxis receptors in Halobacterium salinarum, has contributed important insights into their mechanism of signaling to their cognate transducer subunits in the signaling complex. Essential features of the bacteriorhodopsin (BR) pumping mechanism have been conserved in the evolution of the sensors, which carry out light-driven electrogenic proton transport when their transducers are removed. The interaction of SRI with its transducer blocks proton-conducting channels in the receptor thereby inhibiting its proton pumping, indicating that the pump machinery, rather than the transport activity itself, is functionally important for signaling. Analysis of SRII mutants has shown that the salt bridge between the protonated Schiff base and its counterion Asp73 constrains the receptor in its inactive conformation. Similarly, in BR, the corresponding salt bridge between the protonated Schiff base and Asp85 contributes to constraining the protein in a conformation in which its cytoplasmic channel is closed. Transducer chimera studies further indicate that the receptor conformational changes are transmitted from the sensors to their cognate transducers through transmembrane helix-helix interaction. These and other results reviewed here support a signaling mechanism in which tilting of helices on the cytoplasmic side (primarily outward tilting of helix F), similar to that which occurs in BR in its open cytoplasmic channel conformation, causes structural alterations in the transducer transmembrane helices.

Archaeal Proteins↗
PubMed2001

Mitochondrial proton leak and the uncoupling protein 1 homologues.

Mitochondrial proton leak is the largest single contributor to the standard metabolic rate (SMR) of a rat, accounting for about 20% of SMR. Yet the mechanisms by which proton leak occurs are incompletely understood. The available evidence suggests that both phospholipids and proteins in the mitochondrial inner membrane are important determinants of proton conductance. The uncoupling protein 1 homologues (e.g. UCP2, UCP3) may play a role in mediating proton leak, but it is unlikely they account for all of the observed proton conductance. Experimental data regarding the functions of these proteins include important ambiguities and contradictions which must be addressed before their function can be confirmed. The physiological role of the proton leak, and of the uncoupling protein 1 homologues, remains similarly unclear.

Amino Acid Sequence↗
PubMed2003

Water-gated mechanism of proton translocation by cytochrome c oxidase.

Cytochrome c oxidase is essential for aerobic life as a membrane-bound energy transducer. O(2) reduction at the haem a(3)-Cu(B) centre consumes electrons transferred via haem a from cytochrome c outside the membrane. Protons are taken up from the inside, both to form water and to be pumped across the membrane (M.K.F. Wikström, Nature 266 (1977) 271; M. Wikström, K. Krab, M. Saraste, Cytochrome Oxidase, A Synthesis, Academic Press, London, 1981 ). The resulting electrochemical proton gradient drives ATP synthesis (P. Mitchell, Chemiosmotic Coupling in Oxidative and Photosynthetic Phosphorylation, Glynn Research, Bodmin, UK, 1966 ). Here we present a molecular mechanism for proton pumping coupled to oxygen reduction that is based on the unique properties of water in hydrophobic cavities. An array of water molecules conducts protons from a conserved glutamic acid, either to the Delta-propionate of haem a(3) (pumping), or to haem a(3)-Cu(B) (water formation). Switching between these pathways is controlled by the redox-state-dependent electric field between haem a and haem a(3)-Cu(B), which determines the water-dipole orientation, and therefore the proton transfer direction. Proton transfer via the propionate provides a gate to O(2) reduction. This pumping mechanism explains the unique arrangement of the metal cofactors in the structure. It is consistent with the large body of biochemical data, and is shown to be plausible by molecular dynamics simulations.

Electron Transport↗
PubMed1997

Proton-translocation by membrane-bound NADH:ubiquinone-oxidoreductase (complex I) through redox-gated ligand conduction.

For the catalytic mechanism of proton-translocating NADH-dehydrogenase (complex I, EC 1.6.99.3) a number of hypothetical models have been proposed over the last three decades. These models are discussed in the light of recent substantial progress on the structure and function of this very complicated multiprotein complex. Only the high-potential iron-sulfur center N-2 and ubiquinone seem to contribute to the proton-translocating machinery of complex I: Based on the pH dependent midpoint potential of iron-sulfur cluster N-2 and the physical properties of ubiquinone intermediates a novel mechanism is proposed. The model builds on a series of defined chemical reactions taking place at three different ubiquinone-binding sites. Therefore, some aspects of this redox-gated ligand conduction mechanism are reminiscent to the proton-motive Q-cycle. However, its central feature is the abstraction of a proton from ubihydroquinone by a redox-Bohr group associated with iron-sulfur cluster N-2. Thus, in the proposed mechanism proton translocation is driven by a direct linkage between redox dependent protonation of iron-sulfur cluster N-2 and the redox chemistry of ubiquinone.

Animals↗
PubMed1997

Light-induced electrogenic events associated with proton uptake upon forming QB- in bacterial wild-type and mutant reaction centers.

Light-induced voltage changes (electrogenic events) were measured in wild-type and site-directed mutants of reaction centers (RCs) from Rhodobacter sphaeroides oriented in a lipid monolayer adsorbed to a Teflon film. A rapid increase in voltage associated with charge separation was followed by a slower increase attributed to proton transfer from solution to protonatable amino-acid residues in the vicinity of the QB site. In native reaction centers the proton-transfer voltage had a pH-dependent amplitude with two peaks at pH 4.5 and pH 9.7, respectively. In the Glu-L212-->Gln RCs the high-pH peak was absent, whereas in the Asp-L213-->Asn RCs the low-pH peak was absent and the high-pH peak was shifted to lower pH by about 1.3 pH units. The amplitudes of the electrogenic phases as a function of pH follow approximately the measured proton uptake from solution (P.H. McPherson, M.Y. Okamura, G. Feher, Biochim. Biophys. Acta, vol. 934, 1988, pp. 348-368) and are ascribed to proton transfer to amino acid residues upon QB- formation. The peak around pH 9.7 is ascribed to proton uptake predominantly by Glu-L212 and the peak around pH 4.5 to proton uptake predominantly by Asp-L213 or a residue strongly interacting with Asp-L213.

Hydrogen-Ion Concentration↗
PubMed1997

Effects of proton pump inhibitors on thyroid hormone metabolism in rats: a comparison of UDP-glucuronyltransferase induction.

The effects of proton pump inhibitors on thyroid hormone metabolism in rats were examined. Pantoprazole, omeprazole, and lansoprazole were administered repeatedly to female SD rats at doses of 5, 50, and 300 mg/kg/day for 1 week, and changes in UDP-glucuronyltransferase activities were examined. Increases in o-aminophenol UDP-glucuronyltransferase activity, which was measured as that responsible for the glucuronidation of thyroxine, were evident following 7-day high-dose administration of all the proton pump inhibitors tested. Of the three proton pump inhibitors investigated, o-aminophenol UDP-glucuronyltransferase activity was greatest following the high-dose administration of omeprazole. Androsterone UDP-glucuronyltransferase activity in rats treated with the proton pump inhibitors increased significantly, but these increases were smaller than those of o-aminophenol UDP-glucuronyltransferase. Pantoprazole and omeprazole treatment did not affect plasma T4 or T3 significantly, whereas lansoprazole treatment produced marked reductions in plasma T4 but did not affect plasma T3 significantly. After administration of 125I-labeled thyroid hormone to rats treated with the proton pump inhibitors, biliary excretion of radioactivity increased significantly in omeprazole- and lansoprazole-treated rats; these increases were attributed to induction of liver thyroxine UDP-glucuronyltransferase activities. The order of biliary excretion of radioactivity, as well as the o-aminophenol UDP-glucuronyltransferase activity, in the treated animals was: omeprazole > lansoprazole > pantoprazole. Therefore, repeated administration of the proton pump inhibitors increased thyroxine-metabolizing activity via induction of UDP-glucuronyltransferase, and this induction by pantoprazole was less pronounced than that by omeprazole or lansoprazole.

2-Pyridinylmethylsulfinylbenzimidazoles↗
PubMed2000

A study on the mechanism of the proton transport in bacteriorhodopsin: the importance of the water molecule.

The mechanism of proton transport around the Schiff base in bacteriorhodopsin was investigated by ab initio molecular orbital (MO) calculations. Computations were performed for the case where there is a water molecule between the Schiff base and the Asp residue and for the case where there is no water molecule. Changes in the atomic configuration and potential energy through the proton transport process were compared between two cases. In the absence of water, the protonated Schiff base was not stable, and a proton was spontaneously detached from the Schiff base. On the other hand, a stable structure of the protonated Schiff base was obtained in the presence of water. This suggests that the presence of a water molecule is required for stability in the formation of a protonated Schiff base.

Aspartic Acid↗
PubMed2000

A combined molecular dynamics and diffusion model of single proton conduction through gramicidin.

We develop a model for proton conduction through gramicidin based on the molecular dynamics simulations of Pomès and Roux (Biophys. J. 72:A246, 1997). The transport of a single proton through the gramicidin pore is described by a potential of mean force and diffusion coefficient obtained from the molecular dynamics. In addition, the model incorporates the dynamics of a defect in the hydrogen bonding structure of pore waters without an excess proton. Proton entrance and exit were not simulated by the molecular dynamics. The single proton conduction model includes a simple representation of these processes that involves three free parameters. A reasonable value can be chosen for one of these, and the other two can be optimized to yield a good fit to the proton conductance data of, Ann. N.Y. Acad. Sci. 339:8-20) for pH > or = 1.7. A sensitivity analysis shows the significance of this fit.

Biophysics↗
PubMed2001

The formation and dynamics of proton wires in channel environments.

By virtue of an accurate interaction model, the equilibrium and dynamical properties of an excess proton in aqueous systems are studied, in which the water and excess proton are confined to hydrophobic cylindrical channels. Solvation structures of the excess proton and its mobility along the channel are considered as a function of the channel radius. It is found that when the aqueous proton systems are sufficiently constricted there is a substantial increase in the diffusion of the excess proton charge accompanied by a decrease in the diffusion of water molecules along the channel. Such systems present clear evidence for the possible existence of "proton wires."

Biophysical Phenomena↗
PubMed1993

Effects of alcohol-induced lipid interdigitation on proton permeability in L-alpha-dipalmitoylphosphatidylcholine vesicles.

6-Carboxyfluorescein was employed to examine the effect of alcohol-induced lipid interdigitation on proton permeability in L-alpha-dipalmitoylphosphatidylcholine (DPPC) large unilamellar vesicles. Proton permeability was measured by monitoring the decrease of 6-carboxyfluorescein fluorescence after a pH gradient from 3.5 (outside the vesicle) to 8.0 (inside the vesicle) was established. At 20 degrees C and below 1.2 M ethanol, the fluorescence decrease is best described by a single exponential function. Above 1.2 M ethanol, the intensity decrease is better described by a two-exponential decay law. Using the fitted rate constants and the vesicle radii determined from light-scattering measurements, the proton permeability coefficient, P, in DPPC vesicles was calculated as a function of ethanol concentration. At 20 degrees C, P increases monotonically with increasing ethanol content up to 1.0 M, followed by an abrupt increase at 1.2 M. The vesicle size also exhibits a sudden increase at around 1.2 M ethanol, which has been shown to result from vesicle aggregation rather than vesicle fusion. The abrupt increases in P and in vesicle size occur at the concentration region close to the critical ethanol concentration for the formation of the fully interdigitated gel state of DPPC. At 14 degrees C, the abrupt change in P shifts to 1.9-2.0 M ethanol, completely in accordance with the ethanol-temperature phase diagram of interdigitated DPPC. Effects of methanol and benzyl alcohol on lipid interdigitation have also been examined. At 20 degrees C, DPPC large unilamellar vesicles exhibit a dramatic change in P at 3 M methanol and at 40 mM benzyl alcohol. These concentrations come close to the critical methanol and benzyl alcohol concentrations for the formation of fully interdigitated DPPC structures determined previously by others. It can be concluded that proton permeability increases dramatically as DPPC is transformed from the noninterdigitated gel to the fully interdigitated gel state by high concentrations of alcohol. This marked increase in proton permeability can be attributed to the combined effect of the changes in membrane thickness and surface charge density, due to the ethanol-induced lipid interdigitation. The possible effects of the increased proton permeability caused by ingested ethanol on gastric mucosal membranes are discussed.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1999

Inhibition of alphabeta epithelial sodium channels by external protons indicates that the second hydrophobic domain contains structural elements for closing the pore.

We have examined the effect of extracellular protons on the activity of epithelial sodium channels (ENaCs). We found that alphabeta channels, but not alphabetagamma or alphagamma channels, are inhibited by low extracellular pH. External protons induced short and long closed states that markedly decreased the open probability of alphabeta channels. External protons did not change the single-channel conductance or amiloride binding. Analysis of the proton-induced changes on the kinetics of single channels indicates that at least two protons sequentially bind to the extracellular domain at sites that are not in the ion pathway. Conformational changes induced by protonation of those sites are transmitted to the second hydrophobic domain (M2) of the subunits to induce closure of the pore. The results suggest that elements located in the carboxy-terminal half of M2 participate in the gating mechanism of ENaCs.

Animals↗
PubMed2001

Zn(2+) binding to the cytoplasmic side of Paracoccus denitrificans cytochrome c oxidase selectively uncouples electron transfer and proton translocation.

Using a combination of stopped-flow spectrophotometric proton pumping measurements and time-resolved potential measurements on black lipid membranes, we have investigated the effect of Zn(2+) ions on the proton transfer properties of Paracoccus denitrificans cytochrome c oxidase. When zinc was enclosed in the interior of cytochrome c oxidase containing liposomes, the H/e stoichiometry was found to gradually decrease with increasing Zn(2+) concentration. Half-inhibition of proton pumping was observed at [Zn(2+)](i)=75 microM corresponding to about 5-6 Zn(2+) ions per oxidase molecule. In addition, there was a significant increase in the respiratory control ratio of the proteoliposomes upon incorporation of Zn(2+). Time-resolved potential measurements on a black lipid membrane showed that the electrogenic phases slowed down in the presence of Zn(2+) correspond to phases that have been attributed to proton uptake from the cytoplasmic side and to proton pumping. We conclude that Zn(2+) ions bind close to or within the two proton transfer pathways of the bacterial cytochrome c oxidase.

Binding Sites↗
PubMed1997

Proton release from water oxidation by photosystem II: similar stoichiometries are stabilized in thylakoids and PSII core particles by glycerol.

During the four-stepped catalytic cycle of water oxidation by photosystem II (PSII) molecular oxygen is released in only one of the four reaction steps whereas the release of four protons is distributed over all steps. In principle, the pattern of proton production could be taken as indicative of the partial reactions with bound water. In thylakoids the extent and rate of proton release varies as function of the redox transition and of the pH without concomitant variations of the redox pattern. The variation has allowed to discriminate between deprotonation events of peripheral amino acids (Bohr effects) as opposed to the chemical deprotonation of a particular redox cofactor, and of water. In contrast, in thylakoids grown under intermittent light, as well as in PSII core particles the pattern of proton release is flat and independent of the pH. This has been attributed to the lack in these materials of the chlorophyll a,b-binding (CAB) proteins. We now found that a thylakoid-like, oscillatory pattern of proton release was restored simply by the addition of glycerol which modifies the protein-protein interaction. Being a further proof for the electrostatic origin of the greater portion of proton release, this effect will serve as an important tool in further studies of water oxidation.

Cyanobacteria↗