Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Protons”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 181 records · Page 10Linked to original sources
PubMed2003

Discrimination of 13C NMR signals in solid material with liquid-like behavior presenting residual dipolar proton-proton homonuclear interactions: application on seeds.

In this communication, we propose, a modified spin echo fourier transform (SEFT) experiment run under magic angle spinning (MAS) to obtain structural informations of the liquid-like domains inside complex organic materials. It includes a proton-proton dipolar decoupling such as BLEW12 or Lee-Goldburg sequence just after the 180 degrees 13C refocusing pulse and short echo delays are used in order to overcome T(2) relaxation. This very easy implemented sequence allows a clear discrimination among fast relaxing 13C signals between those with a pure liquid-like behavior and those presenting residual proton-proton dipolar coupling. The interests of the sequence, combined with other classical NMR experiments, are illustrated on whole vegetable seeds that represent an example of a complex material.

Chemical Phenomena↗
PubMed2003

Analysis of proton-proton transfer dynamics in rotating solids and their use for 3D structure determination.

A detailed analysis of proton-proton-transfer dynamics under magic angle spinning NMR is presented. Results obtained on model compounds are evaluated under different experimental conditions and NMR mixing schemes. It is shown that the resulting buildup rates can be interpreted in terms of internuclear proton-proton distances provided that an appropriate theoretical description is chosen. As demonstrated in two test applications, these dependencies can be used in the context of a three-dimensional structure determination in the solid state.

Alanine↗
PubMed2003

A novel mechanism of proton transfer in protonated peptides.

The study presents quantum-chemical calculations on proton transfer in protonated N-acetylglycyl-N1-methylglycinamide (AGA) as a short oligopeptide model. All calculations employ the B3LYP functional and the 6-31++G** basis set. Two different mechanisms of proton transfer are discussed. The rate-determining step of the first mechanism exhibits an energy barrier of about 17.7 kcal mol-1, and it is represented by an isomerization of the proton around the double bond of the carbonyl group. The second mechanism is based on the large conformational flexibility of AGA, where all carbonyl oxygens cooperate. The rate-determining step of this mechanism exhibits an energy barrier of only 8.3 kcal mol-1.

Glycine↗
PubMed2006

Spectroscopic determination of proton position in the proton-coupled electron transfer pathways of donor-acceptor supramolecule assemblies.

A homologous set of porphyrin derivatives possessing an isocyclic five-membered ring appended with an amidinium functionality has been used to examine proton-coupled electron transfer (PCET) through well-characterized amidine-carboxylic acid interfaces. Conjugation between the porphyrin chromophore and the amidinium interface can be altered by selective reduction of the isocyclic ring of an amidinium-purpurin to produce an amidinium-chlorin. The highly conjugated amidinium-purpurin displays large spectral shifts in the visible region upon alteration of the amidinium/amidine protonation state; no such change is observed for the chlorin homologue. Analysis of the UV-vis absorption and emission profiles of the amidinium-purpurin upon deprotonation allows for the measurement of the porphyrinic-amidinium acidity constant for the ground state (pKa = 9.55 +/- 0.1 in CH3CN) and excited state (pKa)= 10.40 +/- 0.1 in CH3CN). The absorption spectrum of the purpurin also provides a convenient handle for determining the protonation state of assembled interfaces. In this way, the purpurin macrocycle provides a general tool for PCET studies because it can be used to determine the location of a proton within PCET interfaces formed from carboxylic acid electron acceptors including dinitrobenzenes (DNBs) and naphthalenediimide (NI), which have been used extensively in previous PCET studies. An amidine-carboxylic acid interface is observed for electron-rich acceptors, whereas the ionized amidinium-carboxylate interface is observed for electron-poor acceptors. The PCET kinetics for purpurin/chlorin associated to NI are consistent with an amidine-carboxylic acid interface, which is also verified spectrally.

Algorithms↗
PubMed2005

Proton transfer in nanoconfined polar solvents. II. Adiabatic proton transfer dynamics.

The reaction dynamics for a model phenol-amine proton transfer system in a confined methyl chloride solvent have been simulated by mixed quantum-classical molecular dynamics. In this approach, the proton vibration is treated quantum mechanically (and adiabatically), while the rest of the system is described classically. Nonequilibrium trajectories are used to determine the proton transfer reaction rate constant. The reaction complex and methyl chloride solvent are confined in a smooth, hydrophobic spherical cavity, and radii of 10, 12, and 15 A have been considered. The effects of the cavity radius and the heavy atom (hydrogen bond) distance on the reaction dynamics are considered, and the mechanism of the proton transfer is examined in detail by analysis of the trajectories.

Kinetics↗
PubMed2006

DFT/B3LYP study of the substituent effect on the reaction enthalpies of the individual steps of single electron transfer-proton transfer and sequential proton loss electron transfer mechanisms of phenols antioxidant action.

The reaction enthalpies related to the individual steps of two phenolic antioxidants action mechanisms, single electron transfer-proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET), for 30 meta and para-substituted phenols (ArOH) were calculated using DFT/B3LYP method. These mechanisms represent the alternative ways to the extensively studied hydrogen atom transfer (HAT) mechanism. Except the comparison of calculated reaction enthalpies with available experimental and/or theoretical values, obtained enthalpies were correlated with Hammett constants. We have found that electron-donating substituents induce the rise in the enthalpy of proton dissociation (PDE) from ArOH+* radical cation (second step in SET-PT) and in the proton affinities of phenoxide ions ArO- (reaction enthalpy of the first step in SPLET). Electron-withdrawing groups cause the increase in the reaction enthalpies of the processes where electron is abstracted, i.e., in the ionization potentials of ArOH (first step in SET-PT) and in the enthalpy of electron transfer from ArO- (second step in SPLET). Found results indicate that all dependences of reaction enthalpies on Hammett constants of the substituents are linear. The calculations of liquid-phase reaction enthalpies for several para-substituted phenols indicate that found trends hold also in water, although substituent effects are weaker. From the thermodynamic point of view, entering SPLET mechanism represents the most probable process in water.

Antioxidants↗
PubMed2006

Catalytic asymmetric protonation of lithium enolates using amino acid derivatives as chiral proton sources.

[reaction: see text] Asymmetric protonation of lithium enolates was examined using commercially available amino acid derivatives as chiral proton sources. Among the amino acid derivatives tested, Nbeta-l-aspartyl-l-phenylalanine methyl ester was found to cause significant asymmetric induction in the protonation of lithium enolates. The enantiomeric excess (up to 88% ee) of the products obtained in the presence of a catalytic amount of the chiral proton source was higher than those obtained in the stoichiometric reaction.

Amino Acids↗
PubMed1986

Changes in permeability to protons and other cations at high proton motive force in rat liver mitochondria.

We have confirmed that the respiration rate of rat liver mitochondria can be substantially inhibited with only a small drop in proton motive force. We have directly measured the passive proton permeability as a function of delta psi by using K+ diffusion potentials and have shown that there is a large increase in proton permeability at high delta psi. This can quantitatively account for the inhibitor titrations of respiration. delta psi and delta pH were shown to have roughly equal effects on the relatively high respiration rate in static head. The permeabilities to K+, tetramethylammonium+ and choline+ were shown to increase greatly at high delta psi, in a similar way to proton permeability, indicating a similar mechanism of entry.

Animals↗
PubMed2003

Resolving intermediates in biological proton-coupled electron transfer: a tyrosyl radical prior to proton movement.

The coupling of proton chemistry with redox reactions is important in many enzymes and is central to energy transduction in biology. However, the mechanistic details are poorly understood. Here, we have studied tyrosine oxidation, a reaction in which the removal of one electron from the amino acid is linked to the release of its phenolic proton. Using the unique photochemical properties of photosystem II, it was possible to oxidize the tyrosine at 1.8 K, a temperature at which proton and protein motions are limited. The state formed was detected by high magnetic field EPR as a high-energy radical intermediate trapped in an unprecedentedly electropositive environment. Warming of the protein allows this state to convert to a relaxed, stable form of the radical. The relaxation event occurs at 77 K and seems to involve proton migration and only a very limited movement of the protein. These reactions represent a stabilization process that prevents the back-reaction and determines the reactivity of the radical.

Biophysical Phenomena↗
PubMed2004

Site-directed mutation of arginine 282 to glutamate uncouples the movement of peptides and protons by the rabbit proton-peptide cotransporter PepT1.

A conserved positive residue in the seventh transmembrane domain of the mammalian proton-coupled di- and tripeptide transporter PepT1 has been shown by site-directed mutagenesis to be a key residue for protein function. Substitution of arginine 282 with a glutamate residue (R282E-PepT1) gave a protein at the plasma membrane of Xenopus laevis oocytes that was able to transport the non-hydrolyzable dipeptide [3H]d-Phe-l-Gln, although unlike the wild type, the rate of transport by R282E-PepT1 was independent of the extracellular pH level, and the substrate could not be accumulated above equilibrium. The binding affinity of the mutant transport protein was unchanged from the wild type. Thus, R282E-Pept1 appears to have been changed from a proton-driven to a facilitated transporter for peptides. In addition, peptide transport by R282E-PepT1 still induced depolarization as measured by microelectrode recordings of membrane potential. A more detailed study by two-electrode voltage clamping revealed that R282E-PepT1 behaved as a peptide-gated non-selective cation channel with the ion selectivity series lithium > sodium > N-methyl-d-glucamine at pH 7.4. There was also a proton conductance (comparing pH 7.4 and 8.4), and at pH 5.5 the predominant conductance was for potassium ions. Therefore, it can be concluded that changing arginine 282 to a glutamate not only uncouples the cotransport of protons and peptides of the wild-type PepT1 but also creates a peptide-gated cation channel in the protein.

Animals↗
PubMed1993

Proton block of rat brain sodium channels. Evidence for two proton binding sites and multiple occupancy.

The acid titration function of bilayer-incorporated batrachotoxin (BTX)-modified sodium channels was examined in experiments in which the pH was decreased symmetrically, on both sides of the membrane, or asymmetrically, on only one side. In an attempt to minimize interpretational ambiguities, the experiments were done in 1.0 M NaCl (buffered to the appropriate pH) with channels incorporated into net neutral bilayers. When the pH was decreased symmetrically (from 7.4 to 4.5), the small-signal conductance (g) decreased in accordance with the predictions of a simple (single-site) titration function with a pK of approximately 4.9. As the pH was decreased below 6.5, the single-channel current-voltage (i-V) relation became increasingly rectifying, with the inward current being decreased more than the outward current. When the pH was decreased asymmetrically (with the pH of the other solution being held constant at 7.4), the titration behavior was different for extra- and intracellular acidification. With extracellular acidification, the reduction in g could still be approximated by a simple titration function with a pK of approximately 4.6, and there was a pronounced rectification at pHs < or = 6 (cf. Woodhull, A. M. 1973. Journal of General Physiology. 61:687-708). The voltage dependence of the block could be described by assuming that protons enter the pore and bind to a site with a pK of approximately 4.6 at an apparent electrical distance of approximately 0.1 from the extracellular entrance. With intracellular acidification there was only a slight reduction in g, and the g-pH relation could not be approximated by a simple titration curve, suggesting that protons can bind to several sites. The i-V relations were still rectifying, and the voltage-dependent block could be approximated by assuming that protons enter the pore and bind to a site with a pK of approximately 4.1 at an apparent electrical distance of approximately 0.2 from the intracellular entrance. Based on the difference between the three g-pH relations, we conclude that there are at least two proton binding sites in the pore and that they can be occupied simultaneously.

Animals↗
PubMed2005

Patient specific optimization of the relation between CT-hounsfield units and proton stopping power with proton radiography.

The purpose of this work is to show the feasibility of using in vivo proton radiography of a radiotherapy patient for the patient individual optimization of the calibration from CT-Hounsfield units to relative proton stopping power. Water equivalent tissue (WET) calibrated proton radiographs of a dog patient treated for a nasal tumor were used as baseline in comparison with integrated proton stopping power through the calibrated CT of the dog. In an optimization procedure starting with a stoichiometric calibration curve, the calibration was modified randomly. The result of this iteration is an optimized calibration curve which was used to recalculate the dose distribution of the patient. One result of this experiment was that the mean value of the deviations between WET calculations based on the stoichiometric calibration curve and the measurements was shifted systematically away from zero. The calibration produced by the optimization procedure reduced this shift to around 0.4 mm. Another result was that the precision of the calibration, reflected as the standard deviation of the normally distributed deviations between WET calculation and measurement, could be reduced from 7.9 to 6.7 mm with the optimized calibration. The dose distributions based on the two calibration curves showed major deviations at the distal end of the target volume.

Animals↗
PubMed1991

Effect of the delta subunit on assembly and proton permeability of the F0 proton channel of Escherichia coli F1F0 ATPase.

During the assembly of the Escherichia coli proton-translocating ATPase, the subunits of F1 interact with F0 to increase the proton permeability of the transmembrane proton channel. We tested the involvement of the delta subunit in this process by partially and completely deleting uncH (delta subunit) from a plasmid carrying the genes for the F0 subunits and delta and testing the effects of those F0 plasmids on the growth of unc+ and unc mutant E. coli strains. We found that the delta subunit was required for inhibition of growth of unc+ cells. We also tested membranes isolated from unc-deleted cells containing F0 plasmids for F1-binding ability. In unc-deleted cells, these plasmids produced F0 in amounts comparable to those found in normal unc+ E. coli cells, while having only small effects on cell growth. These studies demonstrate that the delta subunit plays an important role in opening the F0 proton channel but that it does not serve as a temporary plug of F0 during assembly, as had been previously speculated (S. Pati and W. S. A. Brusilow, J. Biol. Chem. 264:2640-2644, 1989).

Adenosine Triphosphate↗
PubMedDate not supplied

[Proton transfer via the external proton channel of bacteriorhodopsin].

The process of proton transfer across the membrane via the external proton channel in bacteriorhodopsin is considered. A possible amino acid composition of the channel is suggested and the step-by-step mechanism of proton transfer is proposed which agrees with the experimental data. The rate of proton transfer between fixed centers at several chains of the channel was estimated for which the spectroscopic data are available.

Bacteriorhodopsins↗
PubMed1983

Alternative hypotheses of proton ejection in cytochrome oxidase vesicles. Transmembrane proton pumping or redox-linked deprotonation of phospholipid-cytochrome c complex(es).

A review of published experimental and interpretative knowledge concerning proton ejection associated with cytochrome c oxidation by artificial phospholipid vesicles inlaid with cytochrome c oxidase indicates that the detailed characteristics of the redox-linked proton ejection cannot be simply explained by proton pumping. We propose an alternative hypothesis according to which proton ejection is due to the redox-linked deprotonation of a complex involving phospholipid and cytochrome c at the surface of the vesicles. The postulates upon which this hypothesis depends are explicitly outlined, and some methods of testing the hypothesis are suggested.

Carbonyl Cyanide m-Chlorophenyl Hydrazone↗
PubMed1976

Proton NMR study of coordinated imidazoles in low-spin ferric heme complexes. Assignment of single proton histidine resonance in hemoproteins.

The proton signals for the coordinated axial imidazoles in a series of low-spin ferric bis-imidazole complexes with natural porphyrin derivatives have been located and assigned. The methyl signals of several methyl-substituted imidazoles have also been resolved for the mixed ligand complexes of imidazole and cyanide ion. The imidazole spectra for the bis complexes are essentially the same as those reported earlier for synthetic porphyrins, with the hyperfine shifts exhibiting comparable contributions from the dipolar and contact interactions. The contact contribution reflects spin transfer into a vacant imidazole pi orbital. The spectra of both the mono- and bis-imidazole complex concur in predicting that only the 2-H and 5-CH2 signals of an axial histidine are likely to resonate clearly outside the diamagnetic 0 to --10 ppm from TMS region in hemoproteins. However, both the 2-H and 4-H imidazole peaks are found to be too broad to detect in a hemoprotein. Hence, it is suggested that the pair of non-heme, single-proton resonances in low-spin met-myoglobin cyanides arise from the non-equivalent methylene protons at the 5-position of the histidyl imidazole. Both the resonance positions and relative linewidths in the model compounds are consistent with the data for this pair of protons in myoglobins. The possible interpretations of the average downfield bias of these signals as well as the magnitude of their spacing, are discussed in terms of the conformation of the proximal histidine relative to the heme group.

Chemical Phenomena↗
PubMed1981

Proton magnetic resonance characterization of the dynamic stability of the heme pocket in myoglobin by the exchange behavior of the labile proton of the proximal histidyl imidazole.

The assigned exchangeable proton signals in the proton nuclear magnetic resonance spectra of sperm whale deoxy and Met-cyano myoglobin in H2O solution were found to exhibit pH-dependent saturation transfer from the bulk water, which allowed determination of the kinetics and mechanism of the labile proton exchange with solvent. The exchange rates are base catalyzed for both protein forms, with the rate eight times faster in Met-cyano than in deoxy myoglobin. The exchange rate is taken as a measure of the magnitude of the fluctuation in the protein conformation near the heme cavity. On the basis of tritium exchange methods, the greater stability of the unligated relative to the ligated state in myoglobin has also been reported for hemoglobin. The present study, however, localizes the differential kinetic stability on the F helix whose flexibility has been implicated in the mechanism of cooperativity. The observation that filling the hydrophobic vacancy on the proximal side of the heme near the proximal histidine in Met-cyano myoglobin wih cyclopropane increases the proton lability argues against the role for this hole in facilitating the flexibility of the F helix in the native protein.

Animals↗
PubMed2003

Impurity proton NMR signals from common "proton-free" laboratory materials.

For the study of small samples (tens of microns cubed) by NMR, impurities from the environment and construction materials (Teflon, Kel-F, glass NMR tubes, etc.) can dominate the signal, in particular for proton NMR. Using pulsed NMR with a resolution of several microseconds, we have studied a number of common construction materials considered to be proton-free and find considerable proton impurity. We present results in terms of impurity proton spins per milligram and discuss procedures to minimize the effects of impurity signal.

Magnetic Resonance Spectroscopy↗