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Properties of pseudouridine N1 imino protons located in the major groove of an A-form RNA duplex.

The exchangeable N1 imino protons of two pseudouridine (psi) bases located at adjacent internal positions within an undecamer RNA duplex (5'AUAC psi psi ACCUG/3'UAUGAAUGGUC) can report on the environment of the major groove of an A-form double-stranded nucleic acid. The psi N1 imino protons of these residues (which are not involved in interstrand Watson-Crick hydrogen bonding) are protected from chemical exchange with the solvent water and thus are observable in the proton NMR spectrum in H2O (1). These protons will exchange readily at increased pH values or upon thermal denaturation of the duplex. The longitudinal (T1) relaxation times of the psi N1 imino protons in 100 mM NaCl or in 10 mM MgCl2 and 100 mM NaCl are approximately two-fold faster than those of the psi N3 imino protons which are involved in Watson-Crick base pairing. With the addition of spermidine, the psi N1 imino protons become readily exchangeable at a temperature some 20 degrees C below the melting temperature of the duplex.

Base Sequence↗

Acid denaturation steps of Streptomyces subtilisin inhibitor. A proton magnetic resonance study of individual histidine environment.

Resonance positions and intensities of the C(2) protons of histidyl residues (His 43 His 106) were followed in the NMR spectrum of a protein, Streptomyces subtilisin inhibitor (MW 23,000), in the pH range 2-9 at 30 degrees C, in order to clarify the microenvironment of the individual histidyl residues and the acid denaturation processes of the protein. The large difference in the 1H-2H exchange rate between the C(2) protons of the two histidyl residues indicates that, whereas His 106 is well exposed to the solvent, His 43 is highly shielded from the solvent. Protonation of His 106 occurs in the pH range 5-9, giving a pKa of 6.0 +/- 0.1. In contrast, His 43 can not be protonated in the native conformation, but is protonation occurs simultaneously with the acid denaturation of the protein in a narrow pH range 2.7-3.6, with pHmid of transition at 3.25. On the other hand, the denaturation of the His 106 environment starts at pH 5.0 and finishes at pH 2.7 with pHmid of transition at 3.7. The denaturation transitions are reversible with pH for both His 43 and His 106, but the rates of these transitions are slow (less than 25 s-1). The Hill coefficient for the His 106 transition was found to be 0.9 +/- 0.1 in the pH range 3.5-5.0, but to be distinctively larger than unity below pH 3.5. On the other hand, the Hill coefficient for the His 43 transition was found to be 4.4 +/- 0.6 for the whole range of transition (pH 2.7-3.6). These results combined with available information about the crystal structure lead us to conclude that the transition of His 106 in the pH range 3.5-5.0 represents a local denaturation caused by the protonation of one neighboring residue, probably Glu 102, whereas the transition of His 43 occurs as a result of cooperative protonation of several residues probably including Phe 113 and Asp 52, and is a denaturation step accompanied by the destruction of the major hydrophobic core.

Bacterial Proteins↗

Hydrogen bond topology and the ice VII/VIII and Ih/XI proton ordering phase transitions.

Ice Ih, ordinary ice at atmospheric pressure, is a proton-disordered crystal that when cooled under special conditions is believed to transform to ferroelectric proton-ordered ice XI, but this transformation is still subject to controversy. Ice VII, also proton disordered throughout its region of stability, transforms to proton-ordered ice VIII upon cooling. In contrast to the ice Ih/XI transition, the VII/VIII transition and the crystal structure of ice VIII are well characterized. In order to shed some light on the ice Ih proton ordering transition, we present the results of periodic electronic density functional theory calculations and statistical simulations. We are able to describe the small energy differences among the innumerable H-bond configurations possible in a large simulation cell by using an analytic theory to extrapolate from electronic DFT calculations on small unit cells to cells large enough to approximate the thermodynamic limit. We first validate our methods by comparing our predictions to the well-characterized ice VII/VIII proton ordering transition, finding agreement with respect to both the transition temperature and structure of the low-temperature phase. For ice Ih, our results indicate that a proton-ordered phase is attainable at low temperatures, the structure of which is in agreement with the experimentally proposed ferroelectric structure. The predicted transition temperature of is in qualitative agreement with the observed transition at on KOH-doped ice samples.

Journal Article↗

Localization and capacity of proton pumps in roots of intact sunflower plants.

Proton extrusion by roots of intact sunflower plants (Helianthus annuus L.) was studied in nutrient solutions or in agar media with a pH indicator. Proton extrusion was enhanced by either iron deficiency, addition of fusicoccin, or single salt solutions of ammonium or potassium salts. The three types of proton extrusion differ in both localization along the roots and capacity. From their sensitivity to ATPase inhibitors it seems justified to characterize them as proton pumps driven by plasma membrane APTases.Enhanced proton extrusion induced by preferential cation uptake from (NH(4))(2)SO(4) or K(2)SO(4) was uniformly distributed over the whole root system. In contrast, the enhancement effect of fusicoccin was confined to the basal root zones and that of iron deficiency to the apical root zones. Also the rates of proton extrusion per unit of root fresh weight differed remarkably and increased in the order: Fusicoccin << K(2)SO(4) < (NH(4))(2)SO(4) < iron deficiency.Under iron deficiency the average values of proton extrusion for the whole root system are 5.6 micromoles H(+) per gram fresh weight per hour; however, for the apical root zones values of about 28 micromoles H(+) can be calculated. This high capacity is most probably related to the iron deficiency-induced formation of rhizodermal transfer cells in the apical root zones. It can be assumed that the various types of root-induced acidification of the rhizosphere are of considerable ecological importance for the plant-soil relationships in general and for mobilization of mineral nutrients from sparingly soluble sources in particular.

Journal Article↗

Proton-Translocating Inorganic Pyrophosphatase in Red Beet (Beta vulgaris L.) Tonoplast Vesicles.

The substrate and ionic requirements of ATP and inorganic pyrophosphate (PPi) hydrolysis by tonoplast vesicles isolated from storage tissue of red beet (Beta vulgaris L.) were compared with the requirements of ATP-and PPi-dependent proton translocation by the same material. Both ATP hydrolysis and ATP-dependent proton translocation are most stimulated by Cl(-) and inhibited by NO(3) (-). NaCl and KCl support similar rates of ATP hydrolysis and ATP-dependent proton translocation while K(2)SO(4) supports lesser rates for both. PPi hydrolysis and PPi-dependent proton translocation are most stimulated by K(+). KCl and K(2)SO(4) support similar rates of PPi hydrolysis and PPi-dependent proton translocation but NaCl has only a small stimulatory effect on both. Since PPi does not inhibit ATP hydrolysis and ATP does not interfere with PPi hydrolysis, it is inferred that the two phosphohydrolase and proton translocation activities are mediated by different tonoplast-associated enzymes. The results indicate the presence of an energy-conserving proton-translocating pyrophosphatase in the tonoplast of red beet.

Journal Article↗

Time-resolved dynamics of proton transfer in proteinous systems.

The dynamics of proton dissociation from an acidic moiety and its subsequent dispersion in the bulk is regulated by the physical chemical properties of the solvent. The solvent has to provide a potential well to accommodate the discharged proton, screen it from the negative charge of the conjugated base, and provide an efficient mode for the diffusion of the proton to the bulk. On measuring the dynamics of proton dissociation in the time-resolved domain, the kinetic analysis of the reaction can quantitate the properties of the immediate environment. In this review we implement the kinetic analysis for evaluating the properties of small cavities in proteins and the diffusion of protons within narrow channels. On the basis of this analysis,we discuss how the clustering of proton-binding sites on a surface can endow the surface with enhanced capacity to attract protons and to funnel them toward a specific site.

Journal Article↗

Is intestinal peptide transport energized by a proton gradient?

Transport of intact peptides, followed by intracellular hydrolysis in the intestinal mucosal cells, plays an important role in the absorption of protein digestion products in the mammalian small intestine. Even though earlier studies on peptide absorption in intact-tissue preparations have indicated that peptides are transported by an active Na+-dependent mechanism, recent studies with purified brush-border membrane vesicles have unequivocally demonstrated that Na+ does not play a direct role in the translocation of peptides across the membrane. Like most amino acids, peptides are also transported as zwitterions. However, peptide transport causes depolarization of the brushborder membrane in intact mucosal cells as well as in purified membrane vesicles, and the depolarization is the result of a net transfer of positive charge across the membrane during peptide transport. This electrogenic nature of peptide transport is observed even in the absence of Na+. Peptide transport is enhanced by an interior-negative membrane potential and inhibited by an interior-positive membrane potential. An inward proton gradient stimulates peptide transport, and this stimulation is reduced when the proton gradient is subjected to rapid dissipation by the presence of a proton ionophore. These observations strongly suggest that peptides are cotransported with protons in the intestine. There is substantial evidence for the existence of an inward proton gradient in the mammalian small intestine, and therefore it is very likely that this proton gradient is the in vivo energy source for the uphill transport of peptides. The Na+-H+ exchanger in the brush-border membrane, in conjunction with Na+-K+-ATPase at the basolateral membrane, is probably responsible for the generation and maintenance of the proton gradient and may thus be involved indirectly in the intestinal absorption of peptides.

Amino Acids↗

Proton-induced sodium current in frog isolated dorsal root ganglion cells.

1. The proton-induced current was examined in isolated frog dorsal root ganglion (DRG) cells by the use of the "concentration-clamp" technique, which allows intracellular perfusion and rapid change of external solution with various pH (pHo) within 2 ms under single-electrode voltage-clamp condition. 2. Over one-half of the examined neurons showed no response for a "step" reduction of pHo even in a Ca2(+)-free external solution. In smaller neurons having a diameter less than 20 microns, the persistent and reliable proton-induced responses were obtained, though the current amplitude and the activation and inactivation varied considerably for each cell. 3. The decrease of external Na+ concentration ([Na+]o) reduced the proton response. The proton response reversed the direction and the Na+ equilibrium potential (ENa). 4. With decreasing pHo from 7.4, proton response increased in a sigmoidal fashion. The threshold was around pH 7.0 and the maximum response appeared at pH 5.2, whereas pKa and Hill coefficient were 6.0 and 1.97, respectively. 5. The activation and inactivation phases of the proton-induced current behaved as a single exponential function. The time constants of activation (tau a) and inactivation (tau i) were not affected by changing either the holding membrane potential (VH) or the low external Ca2+ concentration [( Ca2+]o) between 10(-6) and 5 X 10(-3) M. But the decrease of pHo up to 5.2 decreased both tau a and tau i in a saturable manner. 6. In the inactivation curve of proton-induced current obtained by decreasing pHo from various conditioning pHo to 5.5, half inactivation occurred at pHo 7.45.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Temporal evolution of ischemic damage in rat brain measured by proton nuclear magnetic resonance imaging.

We studied the effect of focal cerebral ischemia on the "state" of brain water using proton nuclear magnetic resonance imaging. Focal cerebral ischemia was induced in five halothane-anesthetized rats via tandem occlusion of the left common carotid artery and the left middle cerebral artery. The proton transverse relaxation time, the proton density, and the water diffusion coefficient were measured at various times from the same region of brain tissue from 1.5 to 168 hours after occlusion. Early measurements indicated significant changes in the transverse relaxation time (p = 0.004) and water diffusion coefficient (p = 0.002) of ischemic brain tissue compared with a homologous region from the contralateral hemisphere. However, the transverse relaxation time, proton density, and water diffusion coefficient in ischemic brain tissue showed different temporal evolutions over the study period. Diffusion coefficient weighting was superior to relaxation time and proton density weighting for the visualization of early cerebral ischemia. Our data suggest that nuclear magnetic resonance imaging is sensitive in detecting changes in proton-associated parameters during early cerebral ischemia and confirm significant changes (p less than or equal to 0.01) in the temporal evolution of transverse relaxation times, proton densities, and diffusion coefficients following middle cerebral artery occlusion.

Animals↗

Proton beam irradiation for treatment of experimental human retinoblastoma.

Proton beam irradiation was used to treat human retinoblastoma (Y-79 cell line) grown subcutaneously in the athymic "nude" mouse. Thirty-four tumors were included in the experimental groups, of which twenty-three were irradiated and eleven served as controls. Tumors were irradiated with protons produced at the 160 megavolts Harvard cyclotron. The dose delivered to the tumor ranged from 7.5 to 27.5 proton gray in a single treatment, and 25.0 proton gray delivered in two fractions separated by 24 hours. Reduction of tumor growth was significantly greater than controls (p less than 0.001) with treatment doses greater than or equal to 17.5 proton gray. Histologic examination revealed a marked decrease of mitotic activity in all specimens examined 48 hours after treatment at these higher doses. Total regression without evidence of remaining malignant cells was noted in three tumors treated at 17.5 proton gray or above. Our results indicate that human retinoblastoma in a murine host, with a tumor mass similar to that seen in a clinical setting, is sensitive to radiation by high energy protons.

Animals↗

A quantum chemical study of the protonation of phenylphosphine and its halogenated derivatives.

The protonation and methylation of phenylphosphine (C(6)H(5)PH(2)) and its mono-halogenated derivatives have been studied using ab initio quantum chemical calculations. Density functional theory (B3LYP) calculations using the 6-311++G(d,p) basis set consistently confirm that protonation of phenylphosphines takes place at the phosphorus atom; the C(4)-protonated phenylphosphine lying about 66 kJ mol(-1) above the P-protonated isomer. Similarly, methylation of phosphines consistently occurs at phosphorus. The proton and methyl cation affinities are estimated as follows: PA(phenylphosphine) = 863 +/- 10 kJ mol(-1) and MCA(phenylphosphine) = 515 -/+ 12 kJ mol(-1). Mono-halogen substitution appears to reduce the proton affinites by up to 20 kJ mol(-1). In this context, following P-protonation of either ameta- or a para-X-C(6)H(4)-PH(2), an elimination of the halogen X-atom under collisional activation (CA) conditions is expected to lead to a distonic radical cation, a low-energy isomer being 50 kJ mol(-1) above ionized phenylphosphine.

Journal Article↗

Calcium transport driven by a proton gradient and inverted membrane vesicles of Escherichia coli.

Calcium transport into inverted vesicles of Escherichia coli was observed to occur without an exogenous energy source when an artificial proton gradient was used. The orientation of the proton gradient was acid inside and alkaline outside. Either phosphate or oxalate was necessary for transport, as was found for respiratory-driven or ATP-driven uptake (Tsuchiya, T., and Rosen, B.P. (1975) J. Biol. Chem. 250, 7687-7692). Phosphate accumulation was found to occur in conjunction with calcium accumulation. Calcium transport driven by an artificial proton gradient was stimulated by dicyclohexylcarbodiimide, an inhibitor of the Mg2+ATPase (EC 3.6.1.3). Valinomycin, which catalyzes electrogenic potassium movement, stimulated calcium accumulation, while nigericin, which catalyzes electroneutral exchange of potassium and protons, inhibited both artificial proton gradient-driven transport and respiratory-driven transport. Other properties of the proton gradient-driven system and the previously reported energy-linked calcium transport system are similar, indicating that calcium is transported by the same carrier whether energy is supplied through an artificial proton gradient or an energized membrane state. These results suggest the existence of a calcium/proton antiport.

Biological Transport, Active↗

Proton pump-generated electrochemical gradients in rat liver multivesicular bodies. Quantitation and effects of chloride.

Endocytic vesicles possess an electrogenic proton pump, and measurements of ATPase activity suggest that Cl- may stimulate proton pump activity. This study was undertaken to measure the steady-state pH, potential (delta psi), and total proton electrochemical gradients established by the rat liver multivesicular body (MVB) proton pump and to examine the effects of Cl- (0.5-140 mM) on these gradients. Radiolabeled [( 14C] methylamine and 36Cl-) and fluorescent (fluorescein isothiocyanate-conjugated low density lipoproteins) probes were used to assess internal pH (pHi) and delta psi. In the absence of ATP, pHi averaged 7.37 +/- 0.05 (extracellular pH 7.31 +/- 0.02), and delta psi ranged from -32 to -71 mV; but neither pHi nor delta psi varied consistently with [Cl-]. In the presence of ATP, pHi decreased progressively with increasing [Cl-] to a plateau value of about 5.89 at greater than or equal to 25 mM Cl-, and MVB exhibited an interior positive delta psi that was maximal at the lowest Cl- concentration (+65.5 mV) and decreased as medium Cl- increased. The total ATP-dependent proton electrochemical gradient (proton-motive force (delta p] averaged 118.0 +/- 4.3 mV and did not change in any consistent manner as [Cl-] varied almost 300-fold. However, initial rates of MVB acidification increased with increasing [Cl-]. These studies indicate that: (a) in the absence of ATP, isolated MVB exhibited a negative delta psi, probably a Donnan potential; (b) in the presence of ATP and at a [Cl-] similar to that in hepatocyte cytoplasm (25 mM), MVB pHi was 5.89, and delta psi was +9.6 mV; and (c) over the range of [Cl-] tested, the magnitudes of delta pH and delta psi were inversely related, apparently related to Cl- availability, but the ATP-dependent delta p did not vary. Therefore, it is concluded that Cl- increases the initial rate of vesicle acidification in MVB and also affects the relative chemical and electrical contributions of the steady-state proton pump-determined delta p. Cl-, however, does not alter steady-state delta p.

Adenosine Triphosphatases↗

ATP-driven proton fluxes across membranes of secretory organelles.

The ATP-dependent proton uptake by chromaffin granule membranes, lysosomes, and synaptosomes was examined. In synaptosomes the reaction was absolutely dependent on the presence of chloride, while in chromaffin granules chloride had a profound effect and in lysosomes only a minor effect. The presence of chloride markedly increases the rate of collapse of delta pH by carbonyl cyanide p-trifluoromethoxyphenylhydrazone in all three organelles. Ascorbate with phenazine methosulfate uncoupled the ATP-dependent proton uptake by chromaffin granules, but had no effect on lysosomes and synaptosomes. Proton uptake by submitochondrial particles was about 50-fold more sensitive to dicyclohexylcarbodiimide than the proton uptake by chromaffin granule membranes. Chromaffin granule membranes were treated with 2 M sodium bromide to inactivate the mitochondrial ATPase. The treatment caused a complete inhibition of the ATP-dependent proton uptake. Solubilization of these membranes by sodium cholate, followed by reconstitution by cholate dilution revealed the ATP-dependent proton uptake of the system. It is concluded that the genuine ATPase enzyme of chromaffin granules is a proton translocator.

Adenosine Triphosphate↗

Loss of lysosomal integrity caused by the decrease of proton translocation in methylene blue-mediated photosensitization.

Loss of lysosomal integrity is a critical event for killing tumor cells in the photodynamic therapy of cancers. To elucidate the mechanism of photodamage induced lysosomal disintegration, we investigated the role of losing lysosomal proton translocation in latency loss of photosensitized lysosomes. Isolated rat liver lysosomes were light exposed in the presence of Methylene blue. Through monitoring lysosomal delta pH with Acridine orange and measuring its membrane potential with 3,3'-dipropylthiadicarbocyanine iodide, loss of Mg-ATP dependent proton translocation and decrease in electrogenicity of the proton pump were observed after lysosomes were photosensitized. When normal lysosomes were incubated for 60 min in K+ contained medium, percentage free activity of lysosomal enzyme beta-galactosidase increased, i.e. lysosomal latency decreased. In the presence of Mg-ATP, the latency loss of incubated lysosomes reduced. Addition of n-ethylmaleimide, a potent inhibitor of lysosomal H(+)-ATPase, abolished the effect of Mg-ATP on lysosomal latency. It suggests a role of proton translocation in protecting lysosomal integrity. Under the same conditions, Methylene blue photosensitized lysosomes increasingly lost latency of beta-hexosaminidase and beta-galactosidase with light exposure, presumably due to the photodamage induced loss of proton pumping. In contrast, the photosensitization did not decrease lysosomal latency in the absence of Mg-ATP, implying that lysosomal integrity might not be impaired via other photodamage effects under the conditions of this study. These results indicate that lysosomal integrity can be photodestructed via the loss of proton translocation.

Animals↗

Significant reduction of normal tissue dose by proton radiotherapy compared with three-dimensional conformal or intensity-modulated radiation therapy in Stage I or Stage III non-small-cell lung cancer.

PURPOSE: To compare dose-volume histograms (DVH) in patients with non-small-cell lung cancer (NSCLC) treated by photon or proton radiotherapy. METHODS AND MATERIALS: Dose-volume histograms were compared between photon, including three-dimensional conformal radiation therapy (3D-CRT), intensity-modulated radiation therapy (IMRT), and proton plans at doses of 66 Gy, 87.5 Gy in Stage I (n=10) and 60-63 Gy, and 74 Gy in Stage III (n=15). RESULTS: For Stage I, the mean total lung V5, V10, and V20 were 31.8%, 24.6%, and 15.8%, respectively, for photon 3D-CRT with 66 Gy, whereas they were 13.4%, 12.3%, and 10.9%, respectively, with proton with dose escalation to 87.5 cobalt Gray equivalents (CGE) (p=0.002). For Stage III, the mean total lung V5, V10, and V20 were 54.1%, 46.9%, and 34.8%, respectively, for photon 3D-CRT with 63 Gy, whereas they were 39.7%, 36.6%, and 31.6%, respectively, for proton with dose escalation to 74 CGE (p=0.002). In all cases, the doses to lung, spinal cord, heart, esophagus, and integral dose were lower with proton therapy even compared with IMRT. CONCLUSIONS: Proton treatment appears to reduce dose to normal tissues significantly, even with dose escalation, compared with standard-dose photon therapy, either 3D-CRT or IMRT.

Carcinoma, Non-Small-Cell Lung↗

Proton or photon irradiation for hemangiomas of the choroid? A retrospective comparison.

PURPOSE: The aim of this study was to compare, on a retrospective basis, the results of therapy in patients with uveal hemangioma treated with photon or proton irradiation at a single center. METHODS: From 1993 to 2002 a total of 44 patients were treated. Until 1998 radiotherapy was given with 6 MV photons in standard fractionation of 2.0 Gy 5 times per week. In 1998 proton therapy became available and was used since then. A dose of 20 to 22.5 Cobalt Gray Equivalent (CGE) 68 MeV protons was given on 4 consecutive days. Progressive symptoms or deterioration of vision were the indications for therapy. RESULTS: Of the 44 patients treated, 36 had circumscribed choroidal hemangiomas and 8 had diffuse choroidal hemangiomas (DCH) and Sturge-Weber syndrome. Of the patients, 19 were treated with photons with a total dose in the range of 16 to 30 Gy. A total of 25 patients were irradiated with protons. All patients with DCH but 1 were treated with photons. Stabilization of visual acuity was achieved in 93.2% of all patients. Tumor thickness decreased in 95.4% and retinal detachment resolved in 92.9%. Late effects, although generally mild or moderate, were frequently detected. In all, 40.9% showed radiation-induced optic neuropathy, maximum Grade I. Retinopathy was found in 29.5% of cases, but only 1 patient experienced more than Grade II severity. Retinopathy and radiation-induced optic neuropathy were reversible in some of the patients and in some resolved completely. No differences could be detected between patients with circumscribed choroidal hemangiomas treated with protons and photons. Treatment was less effective in DCH patients (75%). CONCLUSIONS: Radiotherapy is effective in treating choroidal hemangiomas with respect to visual acuity and tumor thickness but a benefit of proton therapy could not be detected. Side effects are moderate but careful monitoring for side effects should be part of the follow-up procedures.

Adolescent↗

Economic evaluation of proton radiation therapy in the treatment of breast cancer.

BACKGROUND AND PURPOSE: Proton beam therapy offers potential clinical advantages compared with conventional radiation therapy for many cancer patients. The benefits are mainly a result of a more favourable dose distribution. The treatment cost with proton radiation is higher than for conventional radiation, mainly due to the large investment cost of building a proton therapy facility. It is therefore important to evaluate whether the medical benefits of proton therapy are large enough to justify the higher treatment costs, compared with conventional radiation therapy. PATIENTS AND METHODS: The cost-effectiveness of proton therapy in the treatment of 55-year old women with left-sided breast cancer was assessed. A Markov cohort simulation model was used to simulate the life of patients diagnosed with breast cancers and treated with radiation. Cost and quality adjusted life years (QALYs) were the primary outcome measures. RESULTS: The study found a cost per QALY gained of 67,000 Euro for the base case analysis of an average breast cancer patient. The cost per QALY gained would, however, be considerably lower if a population with high-risk of developing cardiac disease was treated. Sensitivity analyses showed that the results were stable and that the risk of cardiac disease was the most important parameter. CONCLUSIONS: The results indicate that proton therapy for breast cancer can be cost-effective if appropriate risk groups are chosen as targets for the therapy.

Breast Neoplasms↗