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PubMed2005

The timing of proton migration in membrane-reconstituted cytochrome c oxidase.

In mitochondria and aerobic bacteria energy conservation involves electron transfer through a number of membrane-bound protein complexes to O2. The reduction of O2, accompanied by the uptake of substrate protons to form H2O, is catalyzed by cytochrome c oxidase (CcO). This reaction is coupled to proton translocation (pumping) across the membrane such that each electron transfer to the catalytic site is linked to the uptake of two protons from one side and the release of one proton to the other side of the membrane. To address the mechanism of vectorial proton translocation, in this study we have investigated the solvent deuterium isotope effect of proton-transfer rates in CcO oriented in small unilamellar vesicles. Although in H2O the uptake and release reactions occur with the same rates, in D2O the substrate and pumped protons are taken up first (tau(D) congruent with 200 micros, "peroxy" to "ferryl" transition) followed by a significantly slower proton release to the other side of the membrane (tau(D) congruent with 1 ms). Thus, the results define the order and timing of the proton transfers during a pumping cycle. Furthermore, the results indicate that during CcO turnover internal electron transfer to the catalytic site is controlled by the release of the pumped proton, which suggests a mechanism by which CcO orchestrates a tight coupling between electron transfer and proton translocation.

Detergents↗
PubMed1998

The mechanism of proton pumping by cytochrome c oxidasex127e [comments].

Cytochrome c oxidase catalyzes the reduction of oxygen to water that is accompanied by pumping of four protons across the mitochondrial or bacterial membrane. Triggered by the results of recent x-ray crystallographic analyses, published data concerning the coupling of individual electron transfer steps to proton pumping are reanalyzed: Conversion of the conventional oxoferryl intermediate F to the fully oxidized form O is connected to pumping of only one proton. Most likely one proton is already pumped during the double reduction of O, and only three protons during conversion of the "peroxy" forms P to O via the oxoferryl form F. Based on the available structural, spectroscopic, and mutagenesis data, a detailed mechanistic model, carefully considering electrostatic interactions, is presented. In this model, each of the four reductions of heme a during the catalytic cycle is coupled to the uptake of one proton via the D-pathway. These protons, but never more than two, are temporarily stored in the regions of the heme a and a3 propionates and are driven to the outside ("pumped") by electrostatic repulsion from protons entering the active site during turnover. The first proton is pumped by uptake of one proton via the K-pathway during reduction, the second and third proton during the P --> F transition when the D-pathway and the active site become directly connected, and the fourth one upon conversion of F to O. Atomic structures are assigned to each intermediate including F' with an alternative route to O.

Amino Acid Sequence↗
PubMed1974

The hexose-proton cotransport system of chlorella. pH-dependent change in Km values and translocation constants of the uptake system.

The proton concentration in the medium affects the maximal velocity of sugar uptake with a K(m) of 0.3 mM (high affinity uptake). By decreasing the proton concentration a decrease in high affinity sugar uptake is observed, in parallel the activity of a low affinity uptake system (K(m) of 50 mM) rises. Both systems add up to 100%. The existence of the carrier in two conformational states (protonated and unprotonated) has been proposed therefore, the protonated form with high affinity to 6-deoxyglucose, the unprotonated form with low affinity. A plot of extrapolated V(max) values at low substrate concentration versus proton concentration results in a K(m) for protons of 0.14 microM, i.e. half-maximal protonation of the carrier is achieved at pH 6.85. The stoichiometry of protons cotransported per 6-deoxyglucose is close to 1 at pH 6.0-6.5. At higher pH values the stoichiometry continuously decreases; at pH 8.0 only one proton is cotransported per four molecules of sugar. Whereas the translocation of the protonated carrier is strictly dependent on sugar this coupling is less strict for the unprotonated form. Therefore at alkaline pH a considerable net efflux of accumulated sugar can occur. The dependence of sugar accumulation on pH has been measured. The decrease in accumulation with higher pH values can quantitatively be explained by the decrease in the amount of protonated carrier. The properties of the unprotonated carrier resemble strikingly the properties of carrier at the inner side of the membrane. The inside pH of Chlorella was measured with the weak acid 5,5-dimethyl-2, 4-oxazolidinedion (DMO). At an outside pH of 6.5 the internal pH was found to be 7.2. To explain the extent of sugar accumulation it has to be assumed that the membrane potential also contributes to active sugar transport in this alga.

Biological Transport↗
PubMed2005

Meta-analysis: proton-pump inhibition in high-risk patients with acute peptic ulcer bleeding.

BACKGROUND: Recent data suggest that profound acid suppression may improve outcomes of patients in peptic ulcer bleeding. AIM: To better characterize the role of different pharmacological therapies in this population. METHODS: MEDLINE was used to identify randomized trials (01/1990-04/2003) that assessed the efficacy of pharmacological treatments for patients with bleeding peptic ulcers exhibiting high-risk stigmata (Forrest Ia-IIb). Three groups of treatment were assessed: proton-pump inhibitors given as high-dose bolus followed by intravenous constant infusion (40-80 mg and at least 6 mg/h), high-dose oral proton-pump inhibitors (at least twice the standard dosage), non-high-dose proton-pump inhibitors (other proton-pump inhibitors dosing schedules). Mixed-effect models were used to determine rate differences between treatment and control groups. RESULTS: Eighteen studies (1855 patients) were included. High-dose intravenous proton-pump inhibitors significantly reduced rebleeding (-14.6%), surgery (-5.4%) and mortality (-2.7%) compared with placebo, and rebleeding (-20.6%) compared with H(2)RA. Compared with placebo, high-dose oral proton-pump inhibitors significantly reduced only rebleeding (-11.8%), while non-high-dose proton-pump inhibitor treatment significantly improved all three outcomes. CONCLUSIONS: High-dose intravenous proton-pump inhibitor significantly decreases ulcer rebleeding, surgery and mortality. Early data on high-dose oral proton-pump inhibitor suggest improved rebleeding. The non-high-dose proton-pump inhibitor regimens, including a broad range of dosing, also improved outcomes, suggesting that doses inferior to those in the high-dose intravenous proton-pump inhibitor may be effective.

Administration, Oral↗
PubMed1984

Kinetic analysis of proton transfer between reactants adsorbed to the same micelle. The effect of proximity on the rate constants.

The dense packing of protogenic enzymes on the coupling membrane can furnish a route for a rapid proton flux which may avoid the adjacent bulk phase. In order to evaluate the role of proximity between reactants on the rate constant of proton transfer we generated a model system consisting of 2-naphthol and pH indicator (bromocresol green) both adsorbed on the same micelle of unchanged detergent. Excitation of the 2-naphthol by a short intensive laser pulse lowers its pK with subsequent synchronized proton ejection. The discharged protons are detected by their reaction with the indicator using a fast transient absorption technique. Evidence is produced that under certain conditions all of the observed proton flux represents proton transfer between 2-naphthol and indicator molecules sharing the same micelle. In this model system the entire proton flux proceeds through an aqueous phase fully accessible to phosphate ions. The high proximity of the reactants (the separation can not exceed approximately 6 nm) has a marked effect on the rate constant of the reaction k = 2.0 +/- 0.5 X 10(11) M-1 s-1. In spite of this extremely fast rate of reaction we observe unhindered competition, for the surface discharged proton, between the surface-bound reactants and phosphate ions in the bulk. Thus even in proton transfer between closely packed reactants on an interface, the diffusion of the proton is not limited to the interface. This finding implies that on bioenergetic surface the electrochemical potential of the proton on the surface will equal that of the bulk.

Adsorption↗
PubMed1985

Electrogenic active proton pump in Rana esculenta skin and its role in sodium ion transport.

Kinetic and electrophysiological studies were carried out in the in vitro Rana esculenta skin, bathed in dilute sodium solution, to characterize the proton pump and coupling between sodium absorption (JNa+n) and proton excretion (JH+n). JNa+n and JH+n were both dependent on transepithelial potential (psi ms); hyperpolarizing the skin decreased JNa+n and increased JH+n; depolarization produced the opposite effects. Amiloride (5 X 10(-5) M) at a clamped psi ms of +50 mV inhibited JNa+n without affecting JH+n. Variations of psi ms or pH had identical effects on JH+n. Ethoxzolamide inhibited JH+n and simultaneously increased psi ms by 15-30 mV. These changes were accompanied by depolarization of the apical membrane potential psi mc from -47 to -25 mV and an increase in apical membrane resistance of 30%; no significant effects on basolateral membrane potential (psi cs) and resistance (Rb) nor on shunt resistance (Rj) were observed. The proton pump appears to be localized at the apical membrane. The proton pump was also inhibited by deoxygenation, oligomycin, dicyclohexylcarbodiimide and vanadate (100, 78, 83 and 100% inhibition respectively). The variations of JH+n and of the measured electrical currents were significantly correlated. These findings are supportive evidence of a primary active proton pump, electrogenic and strictly linked to aerobic metabolism. The current-voltage (I-V) relation of the proton pump was obtained as the difference in the I-V curves of the apical membrane extracted before and after proton-pump inhibition by ethoxzolamide during amiloride block of sodium transport. The proton-pump current (IP) was best described by a saturable exponential function of psi mc. Maximal pump current (ImaxP) was calculated to be 200 nequiv h-1 cm-2 at a psi mc of +50 mV and the pump reversal potential ERP was -130 mV. The effect of ethoxzolamide to depolarize psi mc was dependent on the relation between psi mc and ERP. Maximal induced depolarization occurred at a psi mc of +50 mV whereas ethoxzolamide exerted minimal effect on psi mc when the ERP was approached either by voltage clamping the apical membrane or by the addition of amiloride. We show that electroneutral sodium-proton countertransport is not the mechanism of active proton excretion in frog skin but that it is the proton excretion which provides a favourable electrical driving force for passive apical sodium entry.(ABSTRACT TRUNCATED AT 400 WORDS)

Amiloride↗
PubMed2005

Proton sensitivity of ASIC1 appeared with the rise of fishes by changes of residues in the region that follows TM1 in the ectodomain of the channel.

The acid-sensitive ion channel 1 (ASIC1) is a neuronal Na+ channel insensitive to changes in membrane potential but is gated by external protons. Proton sensitivity is believed to be essential for the role of ASIC1 in modulating synaptic transmission and nociception in the mammalian nervous system. To examine the structural determinants that confer proton sensitivity, we cloned and functionally characterized ASIC1 from different species of the chordate lineage: lamprey, shark, toadfish and chicken. We observed that ASIC1s from early vertebrates (lamprey and shark) were proton insensitive in spite of a high degree of amino acid conservation (66-67%) with their mammalian counterparts. Sequence analysis showed that proton-sensitive ASIC1s could not be distinguished from proton-insensitive channels by any signature in the protein sequence. Chimeras made with rat ASIC1 (rASIC1) and lamprey or shark indicated that most of the ectodomain of rASIC1 was required to confer proton sensitivity and the distinct kinetics of activation and desensitization of the rat channel. Proton-sensitive chimeras contained the segment D78-E136, together with residues D351, Q358 and E359 of the rat sequence. However, none of the functional chimeras containing only part of the rat extracellular domain retained the kinetics of activation and desensitization of rASIC1, suggesting that residues distributed in several regions of the ectodomain contribute to allosteric changes underlying activation and desensitization. The results also demonstrate that gating by protons is not a feature common to all ASIC1 channels. Proton sensitivity arose recently in evolution, implying that agonists different from protons activate ASIC1 in lower vertebrates.

Acid Sensing Ion Channels↗
PubMed1998

Photosynthetic electron transport involved in PxcA-dependent proton extrusion in Synechocystis sp. Strain PCC6803: effect of pxcA inactivation on CO2, HCO3-, and NO3- uptake.

The product of pxcA (formerly known as cotA) is involved in light-induced Na+-dependent proton extrusion. In the presence of 2, 5-dimethyl-p-benzoquinone, net proton extrusion by Synechocystis sp. strain PCC6803 ceased after 1 min of illumination and a postillumination influx of protons was observed, suggesting that the PxcA-dependent, light-dependent proton extrusion equilibrates with a light-independent influx of protons. A photosystem I (PS I) deletion mutant extruded a large number of protons in the light. Thus, PS II-dependent electron transfer and proton translocation are major factors in light-driven proton extrusion, presumably mediated by ATP synthesis. Inhibition of CO2 fixation by glyceraldehyde in a cytochrome c oxidase (COX) deletion mutant strongly inhibited the proton extrusion. Leakage of PS II-generated electrons to oxygen via COX appears to be required for proton extrusion when CO2 fixation is inhibited. At pH 8.0, NO3- uptake activity was very low in the pxcA mutant at low [Na+] (approximately 100 microM). At pH 6.5, the pxcA strain did not take up CO2 or NO3- at low [Na+] and showed very low CO2 uptake activity even at 15 mM Na+. A possible role of PxcA-dependent proton exchange in charge and pH homeostasis during uptake of CO2, HCO3-, and NO3- is discussed.

Bacterial Proteins↗
PubMed1992

Proton transfer in reaction centers from photosynthetic bacteria.

Proton transfer in the bacterial RC associated with the reduction of the bound QB to the dihydroquinone is an important step in the energetics of photosynthetic bacteria. The binding of two protons by the quinone is associated with the transfer of the second electron to QB at a rate of ca. 10(3) s-1 (pH 7). Mutation of three protonatable residues, GluL212, SerL223, and AspL213, located near QB to nonprotonatable residues (Gln, Ala, and Asn, respectively) resulted in large reductions (by 2 to 3 orders of magnitude) in the rate or proton transfer to QB. These mutations can be grouped into two classes: those that blocked both proton transfer and electron transfer (SerL223, and AspL213) and those that blocked only proton transfer (GluL212). These results were interpreted in terms of a pathway for proton transport in which uptake of the first proton, required for the transfer of the second electron, occurs through a pathway involving AspL213 and SerL223. Uptake of the second proton, which follows electron transfer, occurs through a pathway involving GluL212 and possibly AspL213. Acidic residues near QB affect electron transfer rates via electrostatic interactions. One residue, with a pKa of ca. 10 interacting strongly with the charge on QB (delta pKa greater than 2), was shown to be GluL212. A second residue with a pKa of ca. 6, which interacts more weakly with the charge on QB (delta pK approximately 1), could be either AspL210 or AspL213. Several possible mechanisms for proton transfer are consistent with the observed experimental results and proposed proton pathways. These involve proton transfers from individual amino acid residues or internal water molecules either as single steps or in a concerted fashion. The determination of the dominant mechanism will require evaluation of the energetics of the various steps.

Bacteria↗
PubMed2003

Effects of internal hydrogen bonds between amide groups: protonation of alicyclic diamides.

The proton affinity (PA) of cyclopentane carboxamide 1, cyclohexane carboxamide 2 and their secondary and tertiary amide derivatives S1, S2, T1 and T2, was determined by the thermokinetic method and the kinetic method [PA(1) = 888 +/- 5 kJ mol(1); PA(2) = 892 +/- 5 kJ mol(1); PA(S1) = 920 +/- 6 kJ mol(1); PA(S2) = 920 +/- 6 kJ mol(1); PA(T1) = 938 +/- 6 kJ mol(1); PA(T2) = 938 +/- 6 kJ mol(1)]. Special entropy effects are not observed. Additionally, the effects of protonation have been studied using an advanced kinetic method for all isomers 37 of cyclopentane dicarboxamides and cyclohexane dicarboxamides (with the exception of cis-cyclopentane-1,2-dicarboxamide) and their bis-tertiary derivatives T3T7 by estimating the PA and the apparent entropy of protonation Delta(DeltaS(app)). Finally, the study was extended to bicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxamide 8 and its bis-tertiary derivative T8, to all stereoisomers of bicyclo[2.2.1]heptane-2,3-dicarboxamide 9, their secondary and tertiary amide derivatives S9 and T9, and to endoendobicyclo[2.2.1]heptane-2,5-dicarboxamide 10 and the corresponding secondary and tertiary derivatives S10 and T10. Compared with 1 and 2, all alicyclic diamides exhibit a significant increase of the PA (DeltaPA) and special entropy effects on protonation. For alicyclic diamides, which can not accommodate a conformation appropriate for building a proton bridge, the values of DeltaPA and Delta(DeltaS(app)) are small to moderate. This is explained by ion / dipole interactions between the protonated and neutral amide group which stabilize the protonated species but hinder the free rotation of the amide groups. If any of the conformations of the alicyclic diamide allows formation of a proton bridge, DeltaPA and Delta(DeltaS(app)) increase considerably. A spectacular case is cis-cyclohexane-1,4-dicarboxamide 7c which is the most basic monocyclic diamide, although generation of the proton bridge requires the unfavorable boat conformation with both amide substituents at a flagpole position. A pre-orientation of the two amide groups in such a 1,4-position in 10 results in a particularly large PA of < 1000 kJ mol(1). The observation of comparable values for Delta(DeltaS(app)) for linear and monocyclic diamides indicates that a major part of the entropy effects originates from freezing the free rotation of the amide groups by formation of the proton bridge. This is corroborated by observing corresponding effects during the protonation of dicarboxamides containing the rigid bicyclo[2.2.1]heptane carbon skeleton, where the only internal movements of the molecules corresponds to rotation of the amide substituents.

Amides↗
PubMed2006

Protonation of excited state pyrene-1-carboxylate by phosphate and organic acids in aqueous solution studied by fluorescence spectroscopy.

Pyrene-1-carboxylic acid has a pK of 4.0 in the ground state and 8.1 in the singlet electronic excited state. In the pH range of physiological interest (pH approximately 5-8), the ground state compound is largely ionized as pyrene-1-carboxylate, but protonation of the excited state molecule occurs when a proton donor reacts with the carboxylate during the excited state lifetime of the fluorophore. Both forms of the pyrene derivatives are fluorescent, and in this work the protonation reaction was measured by monitoring steady-state and time-resolved fluorescence. The rate of protonation of pyrene-COO(-) by acetic, chloroacetic, lactic, and cacodylic acids is a function of DeltapK, as predicted by Marcus theory. The rate of proton transfer from these acids saturates at high concentration, as expected for the existence of an encounter complex. Trihydrogen-phosphate is a much better proton donor than dihydrogen- and monohydrogen-phosphate, as can be seen by the pH dependence. The proton-donating ability of phosphate does not saturate at high concentrations, but increases with increasing phosphate concentration. We suggest that enhanced rate of proton transfer at high phosphate concentrations may be due to the dual proton donating and accepting nature of phosphate, in analogy to the Grotthuss mechanism for proton transfer in water. It is suggested that in molecular structures containing multiple phosphates, such as membrane surfaces and DNA, proton transfer rates will be enhanced by this mechanism.

Acids↗
PubMed1989

Theoretical study of the protonation and tautomerization of adenosine, formycin, and their 2-NH2 and 2-F derivatives: functional implications in the mechanism of reaction of adenosine deaminase.

A quantum chemical study of adenosine, formycin, and their 2-NH2 and 2-F derivatives is performed. The tautomerism of neutral and protonated species as well as the protonation of adenosine, formycin, and their derivatives are theoretically studied using semiempirical MNDO and AM1, as well as ab initio STO-3G methods. Calculations have been performed on a reduced model, in which the ribose moiety has been substituted by a hydroxy-methyl group. Results indicate that adenosine is mainly protonated at the N1 atom, whereas formycin can be protonated on N1 or N3, depending on the tautomeric form (N8-H or N7-H). The quantum chemical study of the N1-protonated molecules shows that a second protonation of adenosine is mainly on the N3 atom, whereas formycin can be protonated on N8 or N3, depending on the tautomeric form. On the other hand, results indicate that the protonation of formycin and its derivatives at the N1 atom leads to a change in their tautomeric preference from N7-H to N8-H. The importance of both tautomerism and protonation reactions in the mechanism of action of adenosine deaminase is studied by means of a quantitative structure activity relationships strategy. Significant correlations were found between several electronic parameters and the logarithm of the maximum rate of deamination (log Vm) of the studied compounds. For formycin and its derivatives, it was necessary to consider their N8-H tautomeric forms. The electronic parameters giving good correlations were as follows: energy of the minimum of the ab initio molecular electrostatic potential on N1, net charge over purine (pyrazolo-pyrimidine) and pyrimidine rings, and the N1 protonation energy. It must be noted that all these parameters are informative in relation to a proton attack. Adenosine and purine ribosides have been studied largely because of their high biological relevance. They are constituents of nucleic acids, intermediates in secondary metabolism, neuromodulators, and neurohormones. Their analogues have been extensively used because of their wide range of pharmacological effects (1). Formycin A (Fig. 1) is one of the most studied analogues of adenosine. It is a natural product extracted from Nocardia interforma (2) with proven antiviral (3-5), antibiotic (2), immunodepressant (6), antitumor (6), and antimetabolic (5) activities.

Adenosine↗
PubMed1998

A close look at 13C CPMAS linewidths in solids for rigid, strongly coupled carbons under CW proton decoupling

Ambient-temperature 13C linewidth (LW) and transverse relaxation (TC2) data are presented for the natural-abundance crystalline carbons of linear polyethylene (LPE) under CW proton decoupling conditions and magic angle spinning (MAS). This linewidth behavior typifies that seen for rigid methylene carbons whose attached protons are also strongly coupled to other protons. These data are presented for two LPE samples (unoriented, melt-crystallized and uniaxially oriented, extruded) as a function of several parameters including static field (1.4 T < B0 < 9.4 T), proton decoupling field strength (38 kHz < nuH1 < 90 kHz), MAS frequency (0.5 kHz < nur < 8 kHz) and RF frequency offsets from resonance (-4 kHz < Deltanuoff < 4 kHz). It is the ubiquitous nature of off-resonance proton irradiation (ORPI) (arising from fixed or rotationally dependent deviations from the true proton resonance condition) which provides the focus for this work. Corresponding contributions, LW(ORPI), to the total LW are treated within the general framework of the effective-field picture of CW decoupling. Then, considering the presence of spin fluctuations characteristic of the strongly-dipolar-coupled protons of LPE, LW(ORPI) can be traced to orbit-dependent TC2 contributions to LW. Important dependences demonstrated and discussed include: (1) For "off-resonance" decoupling, there is a quadratic dependence of LW(ORPI) on (Deltanuoff/nuH1) and there is a strong dependence of the corresponding parabolic coefficient on nur. From the latter dependence, characteristic times for spin fluctuations are also estimated. (2) For "on-resonance" decoupling, LW(ORPI) is proportional to (nuH1)-2 and shows very little sensitivity to nur. These LW(ORPI) contributions become more important at higher B0 since the principle reason for ORPI is the chemical shift anisotropy (CSA) of the 13C-bonded protons. The difference in sensitivities of LW(ORPI) to nur for the off-resonance and the on-resonance cases is traced back, respectively, to the scalar property of Deltanuoff for RF frequency offsets and to the tensorial character of the proton CSA. Contributions from LW(ORPI), possibly much larger than those seen in LPE, can be expected when protons near 13C nuclei sense any non-scalar, rotor-position-dependent magnetic fields, e.g., (a) local dipolar fields associated with third, magnetic nuclei or (b) perturbing magnetic-susceptibility fields arising from paramagnetic or ferromagnetic inclusions in a sample. By understanding the contributions to LW in LPE, one can forecast much more precisely what the potential benefits will be from new decoupling schemes like the recently reported "two-pulse phase modulation" (TPPM) since TPPM is designed to reduce LW(ORPI). Aside from LW(ORPI) contributions, the experimental LW data cover parameter space where another broadening mechanism, namely, MAS-assisted dipolar fluctuations (MADF), is seen. This mechanism, also recognized by others, creates a TC2-type linewidth contribution which increases rapidly as nuH1 decreases and which additionally has some orbit dependence. If the current trend in 13CCPMAS is toward higher B0 and nur, the nur-dependent MADF contributions can easily dominate LW relative to the B0-dependent LW(ORPI) contributions. One can avoid serious MADF broadening; however, the minimum acceptable values of nuH1 for good decoupling rise rapidly with B0. Finally, a few LW measurements are made on methyl-alpha-d-glucopyranoside tetraacetate (MGT), a rigid, polycrystalline material containing carbons with 0, 1, 2, and 3 attached protons. The behaviors of the methylene, methine, and methyl carbons at 9.4 T are compared with the behavior of LPE. Copyright 1998 Academic Press.

Journal Article↗
PubMed1998

Understanding structure and function in the light-driven proton pump bacteriorhodopsin.

The atomic structure of bacteriorhodopsin and the outlines of its proton transport mechanism are now available. Photoisomerization of the retinal in the chromophore creates a steric and electrostatic conflict at the retinal binding site. The free energy gain sets off a sequence of reactions in which directed proton transfers take place between the protonated retinal Schiff base, Asp-85, and Asp-96. These internal steps, and other proton transfers at and near the two aqueous interfaces, add up to the translocation of a proton from the cytoplasmic to the extracellular side of the membrane. Bound water plays a crucial role in proton conduction in both extracellular and cytoplasmic regions, but the means by which the protons move from site to site differ. Proton release to the extracellular surface is through interaction of a hydrogen-bonded chain of identified aspartic acid, arginine, water, and glutamic acid residues with Asp-85, while proton uptake from the cytoplasmic surface utilizes a single aspartic acid, Asp-96, whose protonation state appears to be regulated by the protein conformation dependent hydration of this region. The directionality of the translocation is ensured by the accessibility of the Schiff base to the extracellular and cytoplasmic directions after the retinal is photoisomerized, as well as the changing proton affinities of the acceptor Asp-85 and donor Asp-96.

Bacteriorhodopsins↗
PubMedDate not supplied

Transducer protein HtrI controls proton movements in sensory rhodopsin I.

Sensory rhodopsin I (SR-I lambda(max) 587 nm) is a phototaxis receptor in the archaeon Halobacterium salinarium. Photoisomerization of retinal in SR-I generates a long-lived intermediate with lambda(max) 373 nm which transmits a signal to the membrane-bound transducer protein HtrI. Although SR-I is structurally similar to the electrogenic proton pump bacteriorhodopsin (BR), early studies showed its photoreactions do not pump protons, nor result in membrane hyperpolarization. These studies used functionally active SR-I, that is, SR-I complexed with its transducer HtrI. Using recombinant DNA methods we have expressed SR-I protein containing mutations in ionizable residues near the protonated Schiff base, and studied wild-type and site-specifically mutated SR-I in the presence and absence of the transducer protein. UV-Vis kinetic absorption spectroscopy, FT-IR, and pH and membrane potential probes reveal transducer-free SR-I photoreactions result in vectorial proton translocation across the membrane in the same direction as that of BR. This proton pumping is suppressed by interaction with transducer which diverts the proton movements into an electroneutral path. A key step in this diversion is that transducer interaction raises the pK(a) of the aspartyl residue in SR-I (Asp76) which corresponds to the primary proton-accepting residue in the BR pump (Asp85). In transducer-free SR-I, our evidence indicates the pK(a) of Asp76 is 7.2, and ionized Asp76 functions as the Schiff base proton acceptor in the SR-I pump. In the SR-I/HtrI complex, the pK(a) of Asp76 is 8.5, and therefore at physiological pH (7.4) Asp76 is neutral. Protonation changes on Asp76 are clearly not required for signaling since the SR-I mutants D76N and D76A are active in phototaxis. The latent proton-translocation potential of SR-I may reflect the evolution of the SR-I sensory signaling mechanism from the proton pumping mechanism of BR.

Journal Article↗
PubMed1985

Epidermal growth factor from the mouse. Physical evidence for a tiered beta-sheet domain: two-dimensional NMR correlated spectroscopy and nuclear Overhauser experiments on backbone amide protons.

When H2O-exchanged, lyophilized mouse epidermal growth factor (mEGF) is dissolved in deuterium oxide at low pH (i.e., below approximately 6.0), 13 well-resolved, amide proton resonances are observed in the downfield region of an NMR spectrum (500 MHz). Under the conditions of these experiments, the lifetimes of these amide protons in exchange for deuterons of the deuterium oxide solvent suggest that these amide protons are hydrogen-bonded, backbone amide protons. Several of these amide proton resonances show splittings (i.e., JNH alpha-CH) of approximately 8-10 Hz, indicating that their associated amide protons are in some type of beta-structure. Selective nuclear Overhauser effect (NOE) experiments performed on all amide proton resonances strongly suggest that all 13 of these backbone amide protons are part of a single-tiered beta-sheet structural domain in mEGF. Correlation of 2D NMR correlated spectroscopy data, identifying scaler coupled protons, with NOE data, identifying protons close to the irradiated amide protons, allows tentative assignment of some resonances in the NOE difference spectra to specific amino acid residues. These data allow a partial structural model of the tiered beta-sheet domain in mEGF to be postulated.

Amino Acid Sequence↗
PubMed2002

Solvent reorganization controls the rate of proton transfer from neat alcohol solvents to singlet diphenylcarbene.

Femtosecond transient absorption spectroscopy was used to study singlet diphenylcarbene generated by photodissociation of diphenyldiazomethane with a UV pulse at 266 nm. Absorption by singlet diphenylcarbene was detected and characterized for the first time. Similar band shapes were observed in acetonitrile and in cyclohexane with lambda(max) approximately 370 nm. The singlet absorption decays by intersystem crossing to triplet diphenylcarbene at rates that agree with previous measurements. The singlet absorption band is completely formed 1 ps after the pump pulse. It is preceded by a strong and broad absorption band, which is tentatively assigned to excited-state absorption by a singlet diazo excited state. In neat alcohol solvents the growth and decay of the diphenylmethyl cation was observed. This species is formed by proton transfer from an alcohol molecule to singlet diphenylcarbene. Since a shell of solvent molecules surrounds each nascent carbene, the intrinsic rate of protonation in the absence of diffusion could be measured. In methanol, proton transfer occurs with a time constant of 9.0 ps, making this the fastest known intermolecular proton-transfer reaction to carbon. In O-deuterated methanol proton transfer occurs in 15.0 ps. Slower rates were observed in the longer alcohols. The protonation times correlate reasonably well with solvation times in these alcohols, suggesting that solvent fluctuations are the rate-limiting step. In all alcohols studied, the carbocations decay on a somewhat slower time scale to yield diphenylalkyl ethers. In methanol and ethanol the rate of decay is determined by reaction with neutral solvent nucleophiles. There is evidence in 2-propanol that geminate reaction within the initial ion pair is faster than reaction with solvent. No isotope effect was observed for the reaction of the diphenylmethyl carbocation in methanol. Using comparative actinometry the quantum yield of protonation was measured. In methanol, the quantum yield of carbocations reaches a maximum value of 0.18 approximately 18 ps after the pump pulse. According to our analysis, 30% of the photoexcited diazo precursor molecules are eventually protonated. Somewhat lower protonation efficiencies are observed in the other alcohols. Because the primary quantum yield for formation of singlet diphenylcarbene is still unknown, the importance of reaction channels that might exist in addition to protonation cannot be determined at present. Singlet carbenes are powerful, photogenerated bases that open new possibilities for fundamental studies of proton transfer in solution.

Journal Article↗
PubMed1983

NMR study of slowly exchanging imino protons in yeast tRNAasp.

We have monitored the exchange of imino and amino protons by NMR after quick transfer of yeast tRNAAsp in 2H2O solvent. When the concentration of exchange-catalyzing buffer is not too high, one imino proton exchanges considerably more slowly than any other (e.g., 100 hr versus 4 hr for the second-slowest imino proton at 18 degrees C in 15 mM Mg). This provides excellent conditions for identification, by the nuclear Overhauser effect, of the slowest exchanging proton, which we show to be the imino proton of the U-8 . A-14 reverse Hoogsteen tertiary-structure base pair; other slowly exchanging protons are identified as imino protons from A . U-11 and G . psi-13. In preliminary experiments, we find that the exchange of these protons is catalyzed by cacodylate or Tris buffer. The lifetimes of two other imino protons, ca. 10 min at 28 degrees C, are buffer independent. Slowly exchanging amino protons have also been observed. Correlation with the exchange of the uracil-8 imino proton suggests that they may be from adenine-14.

Base Sequence↗