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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↗
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↗
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↗
PubMed1981

Rapid calcium release and proton uptake at the disk membrane of isolated cattle rod outer segments. 1. Stoichiometry of light-stimulated calcium release and proton uptake.

We reported a rapid, light-stimulated release of calcium from isolated rod outer segments that is apparent only when both the disk membrane and the plasma membrane are made permeable to calcium by adding the ionophore A23187 [Kaupp, U. B., Schnetkamp, P. P. M., & Junge, W. (1979) Biochim. Biophys. Acta 552, 390-403]. In this paper, we have investigated the light-sensitive diskal binding sites and the calcium release mechanism in their dependence on the pH and the presence of mono- and divalent cations, including calcium itself. We have observed now that several different rod outer segment preparations (i.e., rod outer segments with an intact plasma membrane, broken cells, and sonicated material) possess a similar dependence of their calcium release on the ionic conditions, however, only if manipulated in a way that gives access to the outer conditions of sites within disks (namely, ionophore added in the case of intact rod outer segments). Monovalent cations, at concentrations between 20 and 40 mM, suppress light-induced calcium release. Divalent and trivalent cations are more efficient inhibitors by 1-2 and 2-3 orders of magnitude, respectively. These results suggest that calcium release is controlled by an interfacial potential. The optimum pH for calcium release is pH 6.3, and virtually no release occurs beyond pH 4.5 and 9. The drop for acidic pH is attributed to the pH dependence of calcium binding to disk membranes, and the drop for alkaline pH is attributed to the pH dependence of the metarhodopsin I/metarhodopsin II transition and the light-stimulated proton uptake. In general, calcium release parallels calcium binding as a function of pH and calcium concentrations, although the release saturates at lower calcium concentrations ((KDapp = 5 microM) than would be expected from the amount of calcium bound (KD = 30-60 microM). The maximum stoichiometry is approximately 1 mol of calcium release per mol of rhodopsin bleached. Concomitant measurements of the light-stimulated uptake of protons by the disk membrane revealed a maximal stoichiometry of 2.8 mol of protons taken up per mol of rhodopsin bleached. We present an integrated description of light-stimulated calcium release, proton uptake, and changes of the interfacial potential at the disk membrane.

Animals↗
PubMed1975

Conformation and interaction of short nucleic acid double-stranded helices. I. Proton magnetic resonance studies on the nonexchangeable protons of ribosyl ApApGpCpUpU.

1H nuclear magnetic resonance (NMR) spectra of a self-complementary ribosyl hexanucleotide, A2GCU2, are investigated as a function of temperature and ionic strength in D2O. Seventeen nonexchangeable base and ribose-H1' resonances are resolved, and unequivocally assigned by a systematic comparison with the spectra of a series of oligonucleotide fragments of the A2GCU2 sequence varying in chain length from 2 to 5. Changes in the chemical shifts of the 17 protons from the hexamer as well as the six H1'-H2' coupling constants are followed throughout a thermally induced helix-coil transition. These sigma vs. T and J vs. T (degrees C) profiles indicate that the transition is not totally cooperative and that substantial populations of partially bonded structures must exist at intermediate temperatures, with the central G-C region being most stable. Transitions in chemical shift for protons in the same base pair exhibit considerable differences in their Tm values as the data reflect both thermodynamic and local magnetic field effects in the structural transition, which are not readily separable. However, an average of the Tm values agrees well with the value predicted from studies of the thermally induced transition made by optical methods. The values of J1'-2' for all six residues become very small (less than 1.5 Hz) at low temperatures indicating that C3'-endo is the most heavily populated furanose conformation in the helix. The sigma values of protons in the duplex were compared with those calculated from the ring current magnetic anisotropies of nearest and next-nearest neighboring bases using the geometrical parameters of the A'-RNA and B-DNA models. The sigma values of the base protons in the duplex calculated assuming the A'-RNA geometry agree (+/- approximately 0.1 ppm) with the observed values much more accurately than those calculated on the basis of B-DNA geometry. The measured sigma values of the H1' are not accurately predicted from either model. The synthesis of 35 mg of A2GCU2 using primer-dependent polynucleotide phosphorylase is described in detail with extensive discussion in the microfilm edition.

Binding Sites↗
PubMed1975

Conformation and interaction of short nucleic acid double-stranded helices. II. Proton magnetic resonance studies on the hydrogen-bonded NH-N protons of ribosyl ApApGpCpUpU helix.

A self-complementary ribohexanucleotide, ApApGpCpUpU, was synthesized and its NH-N hydrogen-bonded protons were studied by proton magnetic resonance. At 1 degree C, 0.17 M Na+, pH 7.6 with 10 mM phosphate-0.1 mM EDTA in H2O, three proton resonances are found in the low-field region with the following chemical shifts and line widths at half-height: 13.2 ppm (80 Hz), 13.5 ppm (30 Hz), and 14.2 ppm (44 Hz). The existence of these resonances indicates the formation of a self-complementary, hydrogen-bonded duplex under these conditions. Upon elevation of temperature, these three resonances sequentially broaden and finally all disappear near 35 degrees C. Unambiguous assignments of these three resonances can be made to the terminal A(1)-U(6) pairs, interior A(2)-U(5) pairs, and to the middle G(3)-C(4) pairs. The assignments were based on (i) the differential sensitivities of the line widths of these resonances to thermal variation, as well as on (ii) a comparison of the computed chemical shifts with the observed chemical shifts. The quantitative aspects of the NH proton transfer between helix, coil, and water are discussed in relationship to the line widths of these resonances and the lifetime of the helix state. The computed chemical shifts of the NH-N resonances based on the A-RNA (or A'-RNA) model agree more closely with the observed chemical shifts than the computed values based on the B-DNA model. These results suggest that the helical duplex of A2GCU2 assumes a conformation similar to A-RNA (or A'-RNA) in aqueous solution. The results on both the NH-N resonances and the C-H resonances are summarized and discussed in terms of the helical conformation of (A2GCU2)2.

Hydrogen Bonding↗
PubMed2004

Proton transfer to nickel-thiolate complexes. 1. Protonation of [Ni(SC(6)H(4)R-4)(2)(Ph(2)PCH(2)CH(2)PPh(2))] (R = Me, MeO, H, Cl, or NO(2)).

The kinetics of the equilibrium reaction between [Ni(SC(6)H(4)R-4)(2)(dppe)] (R= MeO, Me, H, Cl, or NO(2); dppe = Ph(2)PCH(2)CH(2)PPh(2)) and mixtures of [lutH](+) and lut (lut = 2,6-dimethylpyridine) in MeCN to form [Ni(SHC(6)H(4)R-4)(SC(6)H(4)R-4)(dppe)](+) have been studied using stopped-flow spectrophotometry. The kinetics for the reactions with R = MeO, Me, H, or Cl are consistent with a single-step equilibrium reaction. Investigation of the temperature dependence of the reactions shows that DeltaG = 13.6 +/- 0.3 kcal mol(-)(1) for all the derivatives but the values of DeltaH and DeltaS vary with R (R = MeO, DeltaH() = 8.5 kcal mol(-)(1), DeltaS = -16 cal K(-)(1) mol(-)(1); R = Me, DeltaH() = 10.8 kcal mol(-)(1), DeltaS = -9.5 cal K(-)(1) mol(-)(1); R = Cl, DeltaH = 23.7 kcal mol(-)(1), DeltaS = +33 cal K(-)(1) mol(-)(1)). With [Ni(SC(6)H(4)NO(2)-4)(2)(dppe)] a more complicated rate law is observed consistent with a mechanism in which initial hydrogen-bonding of [lutH](+) to the complex precedes intramolecular proton transfer. It seems likely that all the derivatives operate by this mechanism, but only with R = NO(2) (the most electron-withdrawing substituent) does the intramolecular proton transfer step become sufficiently slow to result in the change in kinetics. Studies with [lutD](+) show that the rates of proton transfer to [Ni(SC(6)H(4)R-4)(2)(dppe)] (R = Me or Cl) are associated with negligible kinetic isotope effect. The possible reasons for this are discussed. The rates of proton transfer to [Ni(SC(6)H(4)R-4)(2)(dppe)] vary with the 4-R-substituent, and the Hammett plot is markedly nonlinear. This unusual behavior is attributable to the electronic influence of R which affects the electron density at the sulfur.

Journal Article↗
PubMed2001

Weak intramolecular proton-hydride and proton-fluoride interactions: experimental (NMR, X-ray) and DFT studies of the bis(NBH(3)) and bis(NBF(3)) adducts of 1,3-dimethyl-1,3-diazolidine.

Bis(NBH(3)), bis(NBF(3)), and NBF(3)/NBH(3) adducts 1-3 were prepared from 1,3-dimethyl-1,3-diazolidine and characterized by the (1)H, (13)C, (11)B, (19)F, 2D (1)H(-13)C HETCOR and NOESY NMR spectra. The structures and conformations of the adducts were established by the variable-temperature (1)H NMR spectra, the X-ray diffraction method (adduct 2A), and density functional calculations at different theoretical levels. The experimental and theoretical data have revealed that bis adducts 1-3 prefer trans orientations of the borane groups (1A, 2A, 3A) in solution, the solid state, and the gas phase. The studies have shown that the energetic preference of trans adducts with respect to cis compounds, decreasing as 2A (2.9 kcal/mol) > 3A (2.7 kcal/mol) > 1A (1.4 kcal/mol), is dictated by spatially repulsive interactions between the CH(3), BH(3), and BF(3) groups. The results of DFT calculations agree well with an experimental trans/cis isomeric ratio of 9:1 determined in solutions of adduct 1. The calculated geometry and energy, as well as the topological analysis of electronic densities, show that trans adducts 1-3 should exist in gas phase as twist conformations T-2 stabilized by the intramolecular C-H(delta+)...(-delta)H-B or C-H(delta+)...(-delta)F-B interactions. These interactions are characterized as closed-shell. The energy of one proton-hydride and proton-fluoride intramolecular contact, estimated as 1.9 (1A-T-2) and 0.7 (2A-T-2) kcal/mol, respectively, classifies the "elongated" intramolecular interactions CH(delta+)...(-delta)HB and CH(delta+)...(-delta)FB as weak ones. It has been established that, on going from gas phase to a condensed phase (solution and solid), the twist-conformations T-2 transform to conformations T-1, probably by intermolecular dipole-dipole interactions. The data presented in this work show that despite a weakness of the "elongated" proton-hydride and proton-fluoride interactions, they can play a significant role in the stabilization of conformational molecular states, especially when cooperativity is in action.

Journal Article↗
PubMed2004

Extreme projection of a proton into the pi-cloud of an aromatic ring: record shielding of an aromatic proton in trans-10b-methyl-10c-(1-naphthyl)-10b,10c-dihydropyrene.

A synthetic sequence involving dithiametacyclophane --> metacyclophanediene --> dihydropyrene was employed to prepare trans-10b-methyl-10c-(2-naphthyl)- and trans-10b-methyl-10c-(1-naphthyl)-10b,10c-dihydropyrene 5 and 6, respectively. Both exhibit a strong diamagnetic ring current despite the introduction of an internal bulky substituent within the pi-electron cloud. Their electronic spectra suggest interaction between the two near-perpendicular naphthyl and dihydropyrenyl pi systems, resulting in red shift and band broadening. All naphthyl protons are well resolved in their 1H NMR spectra due to a strong shielding effect of the dihydropyrene ring. The most shielded protons in 5 and 6 are H1' and H2' at delta 2.47 and 1.42, respectively, being 5.25 and 5.95 ppm shifted from those of reference protons. There is evidence for free rotation on the NMR time scale of the 2-naphthyl ring in 5 with a preference for a particular conformer, whereas the 1-naphthyl ring in 6 is conformationally rigid with its H2' projecting deeply into the pi-cloud, thus accounting for the most shielded aromatic proton (H2' in 6) reported to date.

Journal Article↗