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At least 19 recordsLinked to original sources
PubMed2001

Identification of the proton pathway in bacterial reaction centers: decrease of proton transfer rate by mutation of surface histidines at H126 and H128 and chemical rescue by imidazole identifies the initial proton donors.

The pathway for proton transfer to Q(B) was studied in the reaction center (RC) from Rhodobacter sphaeroides. The binding of Zn(2+) or Cd(2+) to the RC surface at His-H126, His-H128, and Asp-H124 inhibits the rate of proton transfer to Q(B), suggesting that the His may be important for proton transfer [Paddock, M. L., Graige, M. S., Feher, G. and Okamura, M. Y. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 6183-6188]. To assess directly the role of the histidines, mutant RCs were constructed in which either one or both His were replaced with Ala. In the single His mutant RCs, no significant effects were observed. In contrast, in the double mutant RC at pH 8.5, the observed rates of proton uptake associated with both the first and the second proton-coupled electron-transfer reactions k(AB)(()(1)()) [Q(A)(-)(*)Q(B)-Glu(-) + H(+) --> Q(A)(-)(*)Q(B)-GluH --> Q(A)Q(B)(-)(*)-GluH] and k(AB)(()(2)()) [Q(A)(-)(*)Q(B)(-)(*) + H(+) --> Q(A)(-)(*)(Q(B)H)(*) --> Q(A)(Q(B)H)(-)], were found to be slowed by factors of approximately 10 and approximately 4, respectively. Evidence that the observed changes in the double mutant RC are due to a reduction in the proton-transfer rate constants are provided by the observations: (i) k(AB)(1) at pH approximately pK(a) of GluH became biphasic, indicating that proton transfer is slower than electron transfer and (ii) k(AB)(2) became independent of the driving force for electron transfer, indicating that proton transfer is the rate-limiting step. These changes were overcome by the addition of exogenous imidazole which acts as a proton donor in place of the imidazole groups of His that were removed in the double mutant RC. Thus, we conclude that His-H126 and His-H128 facilitate proton transfer into the RC, acting as RC-bound proton donors at the entrance of the proton-transfer pathways.

Alanine↗
PubMed2006

Proton-proton correlations observed in two-proton radioactivity of 94Ag.

The stability and spontaneous decay of naturally occurring atomic nuclei have been much studied ever since Becquerel discovered natural radioactivity in 1896. In 1960, proton-rich nuclei with an odd or an even atomic number Z were predicted to decay through one- and two-proton radioactivity, respectively. The experimental observation of one-proton radioactivity was first reported in 1982, and two-proton radioactivity has now also been detected by experimentally studying the decay properties of 45Fe (refs 3, 4) and 54Zn (ref. 5). Here we report proton-proton correlations observed during the radioactive decay of a spinning long-lived state of the lightest known isotope of silver, 94Ag, which is known to undergo one-proton decay. We infer from these correlations that the long-lived state must also decay through simultaneous two-proton emission, making 94Ag the first nucleus to exhibit one- as well as two-proton radioactivity. We attribute the two-proton emission behaviour and the unexpectedly large probability for this decay mechanism to a very large deformation of the parent nucleus into a prolate (cigar-like) shape, which facilitates emission of protons either from the same or from opposite ends of the 'cigar'.

Journal Article↗
PubMed2006

Gas phase infrared multiple-photon dissociation spectra of methanol, ethanol and propanol proton-bound dimers, protonated propanol and the propanol/water proton-bound dimer.

The infrared multiphoton dissociation (IRMPD) spectra of three homogenous proton-bound dimers are presented and the major features are assigned based on comparisons with the neutral alcohol and with density functional theory calculations. As well, the IRMPD spectra of protonated propanol and the propanol/water proton-bound dimer (or singly hydrated protonated propanol) are presented and analysed. Two primary IRMPD photoproducts were observed for each of the alcohol proton bound dimers and were found to vary with the frequency of the radiation impinging upon the ions. For example, when the proton-bound dimer absorbs weakly a larger amount of S(N)2 product, protonated ether and water, are observed. When the proton-bound dimer absorbs more strongly, an increase in the simple dissociation product, protonated alcohol and neutral alcohol, is observed. With the aid of RRKM calculations this frequency dependence of the branching ratio is explained by assuming that photon absorption is faster than dissociation for these species and that only a few photons extra are necessary to make the higher-energy dissociation channel (simple cleavage) competitive with the lower energy (S(N)2) reaction channel.

1-Propanol↗
PubMed1989

Interactions of protons with single open L-type calcium channels. Location of protonation site and dependence of proton-induced current fluctuations on concentration and species of permeant ion.

We further investigated the rapid fluctuations between two different conductance levels promoted by protons when monovalent ions carry current through single L-type Ca channels. We tested for voltage dependence of the proton-induced current fluctuations and for accessibility of the protonation site from both sides of the membrane patch. The results strongly suggest an extracellular location of the protonation site. We also studied the dependence of the kinetics of the fluctuations and of the two conductance levels on the concentration of permeant ion and on external ionic strength. We find that saturation curves of channel conductance vs. [K] are similar for the two conductance levels. This provides evidence that protonation does not appreciably change the surface potential near the entry of the permeation pathway. The proton-induced conduction change must therefore result from an indirect interaction between the protonation site and the ion-conducting pathway. Concentration of permeant ion and ionic strength also affect the kinetics of the current fluctuations, in a manner consistent with our previous hypothesis that channel occupancy destabilizes the low conductance channel conformation. We show that the absence of measurable fluctuations with Li and Ba as charge carriers can be explained by significantly higher affinities of these ions for permeation sites. Low concentrations of Li reduce the Na conductance and abbreviate the lifetimes of the low conductance level seen in the presence of Na. We use whole-cell recordings to extrapolate our findings to the physiological conditions of Ca channel permeation and conclude that in the presence of 1.8 mM Ca no proton-induced fluctuations occur between pH 7.5 and 6.5. Finally, we propose a possible physical interpretation of the formal model of the protonation cycle introduced in the companion paper.

Animals↗
PubMed1976

Different proton-sugar stoichiometries for the uptake of glucose analogues by Chlorella vulgaris. Evidence for sugar-dependent proton uptake without concomitant sugar uptake by the proton-sugar symport system.

The uptake of hexoses by Chlorella vulgaris is accompanied by the uptake of protons. For 6-deoxyglucose a stoichiometry of one proton taken up per sugar molecule has been measured, whereas for 1-deoxyglucose approximately two protons are taken up per sugar molecule. It was found that in the presence of 1-deoxyglucose a considerable proportion of "carrier" catalyzes the transport of protons without the concomitant transport of sugar. Presumably, the binding of sugar initiates the translocation of the carrier-proton-sugar complex, but whereas 1-deoxyglucose can still dissociate from the complex at the external side of the cytoplasmic membrane, the translocation of the carrier-proton complex continues. This conclusion was reached since (a) the composition of the translocated carrier-proton-sugar complex is the same for both sugar. Its formation is a first order reaction with respect to protons. (b) When 6-deoxyglucose, present inside cells, is exchanged for external sugar, the exchange ratio is two to one when the external sugar is 1-deoxyglucose, two molecules of 6-deoxyglucose are lost for each molecule of 1-deoxyglucose entering. This result indicates that during uptake of 1-deoxyglucose statistically only each second carrier molecule appearing at the internal side of the cytoplasmic membrane is carrying sugar.

Binding Sites↗
PubMed1995

The F0 complex of the ATP synthase of Escherichia coli contains a proton pathway with large proton polarizability caused by collective proton fluctuation.

The F0 complex of the Escherichia coli ATP synthase embedded into cardiolipin liposomes was studied by FT-IR spectroscopy. For comparison, respective studies were performed with dried F0 liposomes and with F0 liposomes treated with N,N'-dicyclohexyl-carbodiimide (DCCD), which binds to Asp-61 of subunit c. Furthermore, the effect of H2O-->D2O exchange on the infrared spectrum was investigated. With F0 liposomes an infrared continuum is observed beginning at about 3000 cm-1 and extending toward smaller wavenumbers. In the DCCD-treated sample, this continuum is no longer observed. It vanishes also with drying of the liposomes. After H2O-->D2O exchange, this infrared continuum begins at about 2350 cm-1 and is less intense. All of these results demonstrate that a proton pathway in native F0 is present, in which the protons are shifted in a hydrogen-bonded chain with large proton polarizability due to collective proton tunneling. With the D2O-hydrated system, deuteron polarizability due to collective deuteron motion is observed, but the polarizability due to collective deuteron motion is smaller. Such pathways are very efficient, because they conduct protons or deuterons within picoseconds. These pathways lose their polarizability if the F0 complex is blocked by DCCD or if the liposomes are dried. On the basis of our results on the proton polarizability of hydrogen bonds and hydrogen-bonded systems and on the basis of structural data from the literature, the nature of the proton pathway of the F0 complex of E. coli is discussed.

Biophysical Phenomena↗
PubMed1989

The relative proton stoichiometries of the mitochondrial proton pumps are independent of the proton motive force.

Several different proton pumps were used to generate a proton motive force (delta p, proton motive force across the mitochondrial inner membrane) in isolated rat liver mitochondria, and the relationship between delta p and pump rate was investigated by titrating with various inhibitors of the pumps. It was found that this relationship was the same for mitochondria respiring on succinate irrespective of whether respiration was inhibited with malonate, antimycin or cyanide, indicating that the relationship was independent of the redox state of the respiratory chain. When delta p was generated by either the cytochrome bc1 complex, cytochrome oxidase, both together, or ATP hydrolysis (and transport), the reaction rates (in moles of electrons or ATP) were in the ratio of close to 3:1.5:1:1, respectively, at all accessible values of delta p. This suggests that the proton stoichiometries (H+/e and H+/ATP, where H+/e is the number of protons translocated vectorially across the inner membrane per electron transferred by the respiratory chain and H+/ATP is the number of protons translocated vectorially per ATP molecule hydrolyzed externally) were in the ratio of close to 1:2:3:3, respectively, at all values of delta p. Possible reasons for previous contradictory results are suggested.

Adenosine Triphosphate↗
PubMed2005

IFSERF, an isotope-filtered SERF experiment for the precise measurement of proton-proton coupling constants between chemically equivalent protons.

An isotope-filtered selective refocusing (IFSERF) experiment is presented for the sensitive and precise measurement of the proton-proton coupling constant between chemically equivalent protons. The 2D NMR method combines an initial doubly selective isotope filter based on heteronuclear cross-polarization followed by a selective J-resolved block. The coupling topologies obtained from several 2D variants of the IFSERF experiment are described for the simultaneous measurement of both proton-proton and proton-carbon coupling constants in the involved AA'XX' spin system. Application on the determination of the relative configuration of double bonds in symmetrical molecules is illustrated.

Journal Article↗
PubMed2002

Proton transfer from alkane radical cations to alkane molecules: selectivity with respect to the site of proton donation and proton acceptance.

Information on the donor and acceptor site selectivity in the proton transfer from n-alkane radical cations to n-alkane molecules is gathered from gamma-irradiated frozen CCl(3)F/n-alkane solutions (symmetric transfer) and mixed n-alkane crystals (asymmetric transfer) by EPR spectroscopy at 77 K and gas chromatographic analysis after melting. The proton-donor site is related very strictly to the structure of the semi-occupied molecular orbital of the parent radical cation, with proton transfer taking place from those C-H bonds that carry appreciable unpaired-electron and positive-charge density. Proton acceptance is restricted to C-H bonds at secondary carbon atoms (no proton transfer to C-C bonds nor to C-H bonds at primary carbon atoms), with a preference for the penultimate position and equal (but considerably lower) transfer to the interior sites. In mixed n-alkane crystals, additional selectivity with respect to the site of proton acceptance results from structural factors in combination with the donor site selectivity (structurally determined acceptor site selectivity).

Journal Article↗
PubMed1998

The precision of proton range calculations in proton radiotherapy treatment planning: experimental verification of the relation between CT-HU and proton stopping power.

The precision in proton radiotherapy treatment planning depends on the accuracy of the information used to calculate the stopping power properties of the tissues in the patient's body. This information is obtained from computed tomography (CT) images using a calibration curve to convert CT Hounsfield units into relative proton stopping power values. The validity of a stoichiometric method to create the calibration curve has been verified by measuring pairs of Hounsfield units and stopping power values for animal tissue samples. It was found that the agreement between measurement and calibration curve is better than 1% if beam hardening effects in the acquisition of the CT images can be neglected. The influence of beam hardening effects on the quantitative reading of the CT measurements is discussed and an estimation for the overall range precision of proton beams is given. It is expected that the range of protons in the human body can be controlled to better than +/-1.1% of the water equivalent range in soft tissue and +/-1.8% in bone, which translates into a range precision of about 1-3 mm in typical treatment situations.

Animals↗
PubMed1988

Deoxyribose ring conformation of [d(GGTATACC)]2: an analysis of vicinal proton-proton coupling constants from two-dimensional proton nuclear magnetic resonance.

Exchangeable and nonexchangeable protons of [d(GGTATACC)]2 in aqueous cacodylate solution were assigned from two-dimensional nuclear Overhausser effect (2D NOE) spectra. With phase-sensitive COSY and double quantum filtered COSY (DQF-COSY) experiments, the cross-peaks resulting from deoxyribose ring conformation sensitive proton-proton vicinal couplings, i.e., all 1'-2', 1'-2", 2'-3', and 3'-4' couplings and six from 2"-3' couplings, were observed. From the cross-peak fine structure, the 2',2" proton assignments can be confirmed; coupling constants J1'2' and J1'2" and sums of coupling constants involving H2' and H2" for all residues and H3' for C8 were obtained. The DISCO procedure [Kessler, H., Muller, A., & Oschkinat, H. (1985) Magn. Reson. Chem. 23, 844-852] was used to extract individual 1'-2' and 1'-2" coupling constants. The sum of coupling constants involving H1' or H3' was measured from the one-dimensional spectrum where signal overlap is not a problem. Analysis of the resulting coupling constants and sums of coupling constants, in the manner of Rinkel and Altona [Rinkel, L. J., & Altona, C. (1987) J. Biomol. Struct. Dyn. 4, 621-649], led to the following conclusion: C2'-endo deoxyribose ring conformation is predominant for every residue, but a significant amount of C3'-endo conformation may exist, ranging from 14% to 30%.

Carbohydrate Conformation↗
PubMed2002

Charged states of proteins. Reactions of doubly protonated alkyldiamines with NH(3): solvation or deprotonation. Extension of two proton cases to multiply protonated globular proteins observed in the gas phase.

The apparent gas-phase basicities (GB(app)'s) of basic sites in multiply protonated molecules, such as proteins, can be approximately predicted. An approach used by Williams and co-workers was to develop an equation for a diprotonated system, NH(3)(CH(2))(7)NH(3)(2+), and then extend it with a summation of pairwise interactions to multiply protonated systems. Experimental determinations of the rates of deprotonation of NH(3)(CH(2))(7)NH(3)(2+) by a variety of bases B, in the present work, showed that GB(app) = GB(NH(3)) = 196 kcal/mol. This result is supported also by determinations of the equilibria: NH(3)(CH(2))(p)NH(3)(2+) + NH(3) = NH(3)(CH(2))(p)NH(3) x NH(3)(2+), for p = 7, 8, 10, 12. The described experimental GB(app) is 14 kcal/mol higher than the value predicted by the equation used by Williams and co-workers but in agreement with an ab initio result by Gronert. Equations based on electrostatics are developed for the two proton and multiproton systems which allow the evaluation of GB(app) of the basic sites on proteins. These are applied for the evaluation of GB(app) of the basic sites and of N(SB), the maximum number of protons that the nondenatured proteins, carbonic anhydrase (CAII), cytochrome c (CYC), and pepsin, can hold. The N(SB) values are compared with the observed charges, Z(obs)'s, when the nondenatured proteins are produced by electrospray and found in agreement with the proposal by de la Mora that Z(obs) is determined by the number of charges provided by the droplet that contains the protein, according to the charge residue model (CRM). The GB(app) values of proteins have many other applications. They can be compared with experimental measurements and are also needed for the understanding of the thermal denaturing of charged proteins and the thermal dissociation of charged protein complexes.

Ammonia↗
PubMed2000

Collective proton transport with weak proton-proton coupling

A mechanism based on the peculiar dynamical properties of the hydrogen bond is suggested to describe fast proton transfers in hydrogen-bonded chains with realistic (weak) intersite proton-proton interactions. For this purpose, a two-sublattice model is suggested and studied analytically that admits an exact soliton solution. The solitons, which are topological objects (kinks and antikinks) on the one hand, but dynamical entities (like Boussinesq solitons) on the other hand, are shown to have a sufficiently large width to allow free propagation along the chain.

Journal Article↗
PubMed2005

Treatment planning with protons for pediatric retinoblastoma, medulloblastoma, and pelvic sarcoma: how do protons compare with other conformal techniques?

PURPOSE: To calculate treatment plans and compare the dose distributions and dose-volume histograms (DVHs) for photon three-dimensional conformal radiation therapy (3D-CRT), electron therapy, intensity-modulated radiation therapy (IMRT), and standard (nonintensity modulated) proton therapy in three pediatric disease sites. METHODS AND MATERIALS: The tumor volumes from 8 patients (3 retinoblastomas, 2 medulloblastomas, and 3 pelvic sarcomas) were studied retrospectively to compare DVHs from proton therapy with 3D-CRT, electron therapy, and IMRT. In retinoblastoma, several planning techniques were analyzed: A single electron appositional beam was compared with a single 3D-CRT lateral beam, a 3D-CRT anterior beam paired with a lateral beam, IMRT, and protons. In medulloblastoma, three posterior fossa irradiation techniques were analyzed: 3D-CRT, IMRT, and protons. Craniospinal irradiation (which consisted of composite plans of both the posterior fossa and craniospinal components) was also evaluated, primarily comparing spinal irradiation using 3D-CRT electrons, 3D-CRT photons, and protons. Lastly, in pelvic sarcoma, 3D-CRT, IMRT, and proton plans were assessed. RESULTS: In retinoblastoma, protons resulted in the best target coverage combined with the most orbital bone sparing (10% was the mean orbital bone volume irradiated at > or =5 Gy for protons vs. 25% for 3D-CRT electrons, 69% for IMRT, 41% for a single 3D lateral beam, 51% for a 3D anterolateral beam with a lens block, and 65% for a 3D anterolateral beam without a lens block). A single appositional electron field was the next best technique followed by other planning approaches. In medulloblastoma, for posterior fossa and craniospinal irradiation, protons resulted in the least dose to the cochlea (for only posterior fossa irradiation at > or =20 Gy, 34% was the mean cochlear volume irradiated for protons, 87% for IMRT, 89% for 3D-CRT) and hypothalamus-pituitary axis (for only posterior fossa irradiation at > or =10 Gy, 21% was the mean hypothalamus-pituitary volume irradiated for protons, 81% for IMRT, 91% for 3D-CRT); additional dose reductions to the optic chiasm, eyes, vertebrae, mandible, thyroid, lung, kidneys, heart, and liver were seen. Intensity-modulated radiotherapy appeared to be the second best technique for posterior fossa irradiation. For spinal irradiation 3D-CRT electrons were better than 3D-CRT photons in sparing dose to the thyroid, heart, lung, kidney, and liver. With pelvic sarcoma, protons were superior in eliminating any dose to the ovaries (0% of mean ovarian volume was irradiated at > or =2 Gy with protons) and to some extent, the pelvic bones and vertebrae. Intensity-modulated radiotherapy did show more bladder dose reduction than the other techniques in pelvic sarcoma irradiation. CONCLUSIONS: In the diseases studied, using various techniques of 3D-CRT, electrons, IMRT, and protons, protons are most optimal in treating retinoblastomas, medulloblastomas (posterior fossa and craniospinal), and pelvic sarcomas. Protons delivered superior target dose coverage and sparing of normal structures. As dose-volume parameters are expected to correlate with acute and late toxicity, proton therapy should receive serious consideration as the preferred technique for the treatment of pediatric tumors.

Adolescent↗
PubMed2006

Influence of the membrane potential on the protonation of bacteriorhodopsin: insights from electrostatic calculations into the regulation of proton pumping.

Proton binding and release are elementary steps for the transfer of protons within proteins, which is a process that is crucial in biochemical catalysis and biological energy transduction. Local electric fields in proteins affect the proton binding energy compared to aqueous solution. In membrane proteins, also the membrane potential affects the local electrostatics and can thus be crucial for protein function. In this paper, we introduce a procedure to calculate the protonation probability of titratable sites of a membrane protein in the presence of a membrane potential. In the framework of continuum electrostatics, we use a modified Poisson-Boltzmann equation to include the influence of the membrane potential. Our method considers that in a transmembrane protein each titratable site is accessible for protons from only one side of the membrane depending on the hydrogen bond pattern of the protein. We show that the protonation of sites receiving their protons from different sides of the membrane is differently influenced by the membrane potential. In addition, the effect of the membrane potential is combined with the effect of the pH gradient resulting from proton pumping. Our method is applied to bacteriorhodopsin, a light-activated proton pump. We find that the proton pumping of this protein might be regulated by Asp115, a conserved residue for which no function has been identified yet. According to our calculations, the interaction of Asp115 with Asp85 leads to the protonation of the latter if the pH gradient or the membrane potential becomes too large. Since Asp85 is the primary proton acceptor in the photocycle, bacteriorhodopsin molecules in which Asp85 is protonated cannot pump protons. Furthermore, we estimate how the membrane potential affects the energetics of the individual proton-transfer reactions of the photocycle. Most reactions, except the initial proton transfer from the Schiff base to Asp85, are influenced. Our calculations give new insights into the mechanism with which bacteriorhodopsin senses the membrane potential and the pH gradient and how the proton pumping is regulated by these parameters.

Animals↗
PubMed1999

Simulating proton translocations in proteins: probing proton transfer pathways in the Rhodobacter sphaeroides reaction center.

A general method for simulating proton translocations in proteins and for exploring the role of different proton transfer pathways is developed and examined. The method evaluates the rate constants for proton transfer processes using the energetics of the relevant proton configurations. The energies (DeltaG((m))) of the different protonation states are evaluated in two steps. First, the semimicroscopic version of the protein dipole Langevin dipole (PDLD/S) method is used to evaluate the intrinsic energy of bringing the protons to their protein sites, when the charges of all protein ionized residues are set to zero. Second, the interactions between the charged groups are evaluated by using a Coulomb's Law with an effective dielectric constant. This approach, which was introduced in an earlier study by one of the authors of the current report, allows for a very fast determination of any DeltaG((m)) and for practical evaluation of the time-dependent proton population: That is, the rate constants for proton transfer processes are evaluated by using the corresponding DeltaG((m)) values and a Marcus type relationship. These rate constants are then used to construct a master equation, the integration of which by a fourth-order Runge-Kutta method yields the proton population as a function of time. The integration evaluates, 'on the fly,' the changes of the rate constants as a result of the time-dependent changes in charge-charge interaction, and this feature benefits from the fast determination of DeltaG((m)). The method is demonstrated in a preliminary study of proton translocation processes in the reaction center of Rhodobacter sphaeroides. It is found that proton transfer across water chains involves significant activation barriers and that ionized protein residues probably are involved in the proton transfer pathways. The potential of the present method in analyzing mutation experiments is discussed briefly and illustrated. The present study also examines different views of the nature of proton translocations in proteins. It is shown that such processes are controlled mainly by the electrostatic interaction between the proton site and its surroundings rather than by the local bond rearrangements of water molecules that are involved in the proton pathways. Thus, the overall rate of proton transport frequently is controlled by the highest barrier along the conduction pathway. Proteins 1999;36:484-500.

Computer Simulation↗