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PubMed1982

Analysis of difference spectra of protonated DNA: determination of degree of protonation of nitrogen bases and the fractions of disordered nucleotide pairs.

The titration curves of nitrogen bases and fractions of disordered nucleotide pairs are obtained during DNA protonation. It is shown that purine bases are the first sites of the DNA double helix protonation. The cytosine protonation is due to proton-induced conformational transition within GC pairs with the sequence proton transfer from (N-7) of guanine to (N-3) of cytosine. Within DNA with unwound regions the bases are protonated in the following order: cytosine, adenine, guanine. It is shown that GC pairs are the primary centres in which the unwinding of protonated DNAs occurs.

Animals↗

PubMed2005

Proton slip in the ATP synthase of Rhodobacter capsulatus: induction, proton conduction, and nucleotide dependence.

FOF1-ATP synthase converts two energetic "currencies" of the cell (ATP and protonmotive force, pmf) by coupling two rotary motors/generators. Their coupling efficiency is usually very high. Uncoupled proton leakage (slip) has only been observed in chloroplast enzyme at unphysiologically low nucleotide concentration. We investigated the properties of proton slip in chromatophores (sub-bacterial vesicles) from Rhodobacter capsulatus in the single-enzyme-per-vesicle mode. The membrane was energized by excitation with flashing light and the relaxation of the transmembrane voltage and pH difference was photometrically detected. We found that: (1) Proton slip occurred only at low nucleotide concentration (<1 microM) and after pre-illumination over several seconds. (2) Slip induction by pmf was accompanied by the release of approximately 0.25 mol ADP per mole of enzyme. There was no detectable detachment of F1 from FO. (3) The transmembrane voltage and the pH difference were both efficient in slip induction. Once induced, slip persisted for hours, and was only partially reverted by the addition of ADP or ATP (>1 microM). (4) There was no pmf threshold for the proton transfer through the slipping enzyme; slip could be driven both by voltage and pH difference. (5) The conduction was ohmic and weakly pH-dependent in the range from 5.5 to 9.5. The rate constant of proton transfer under slip conditions was 185 s(-1) at pH 8. Proton slip probably presents the free-wheeling of the central rotary shaft, subunit gamma, in an open structure of the (alphabeta)3 hexagon with no nucleotides in the catalytic sites.

Bacterial Chromatophores↗

PubMed2006

Concerted involvement of cooperative proton-electron linkage and water production in the proton pump of cytochrome c oxidase.

In cytochrome c oxidase, oxido-reductions of heme a/Cu(A) and heme a3/Cu(B) are cooperatively linked to proton transfer at acid/base groups in the enzyme. H+/e- cooperative linkage at Fe(a3)/Cu(B) is envisaged to be involved in proton pump mechanisms confined to the binuclear center. Models have also been proposed which involve a role in proton pumping of cooperative H+/e- linkage at heme a (and Cu(A)). Observations will be presented on: (i) proton consumption in the reduction of molecular oxygen to H2O in soluble bovine heart cytochrome c oxidase; (ii) proton release/uptake associated with anaerobic oxidation/reduction of heme a/Cu(A) and heme a3/Cu(B) in the soluble oxidase; (iii) H+ release in the external phase (i.e. H+ pumping) associated with the oxidative (R-->O transition), reductive (O-->R transition) and a full catalytic cycle (R-->O-->R transition) of membrane-reconstituted cytochrome c oxidase. A model is presented in which cooperative H+/e- linkage at heme a/Cu(A) and heme a3/Cu(B) with acid/base clusters, C1 and C2 respectively, and protonmotive steps of the reduction of O2 to water are involved in proton pumping.

Animals↗

PubMed1991

Proton conductance by the gramicidin water wire. Model for proton conductance in the F1F0 ATPases?

The gramicidin channel contains a single strand of water molecules associated through hydrogen bonds. Previous work has shown that channels of similar size are formed by association of transmembrane alpha helices of synthetic leucine-serine peptides. Both types of channels translocate protons with considerable selectivity relative to other cations, and it has been proposed that the selectivity arises by proton "hopping" along hydrogen-bonded chains of water, whereas other cations must cross by ordinary diffusion processes. It is possible that a similar mechanism underlies proton transport in the Fo subunit of the F1F0 ATP synthase. Using the gramicidin channel as a model, we have tested whether a single strand of water is kinetically competent to translocate protons at a rate sufficient to support known rates of ATP synthesis. We found that the gramicidin channel saturates at approximately 530 pS of protonic current in 4 M HCl, more than sufficient for typical ATP synthesis rates. It follows that proton diffusion to a putative channel in Fo, rather than the channel itself, may limit ATP synthesis rates.

Gramicidin↗

PubMed1999

Observation of the protonated semiquinone intermediate in isolated reaction centers from Rhodobacter sphaeroides: implications for the mechanism of electron and proton transfer in proteins.

A proton-activated electron transfer (PAET) mechanism, involving a protonated semiquinone intermediate state, had been proposed for the electron-transfer reaction k(2)AB [Q(A)(-)(*)Q(B)(-)(*) + H(+) <--> Q(A)(-)(*)(Q(B)H)(*) --> Q(A)(Q(B)H)(-)] in reaction centers (RCs) from Rhodobacter sphaeroides [Graige, M. S., Paddock, M. L., Bruce, M. L., Feher, G., and Okamura, M. Y. (1996) J. Am. Chem. Soc. 118, 9005-9016]. Confirmation of this mechanism by observing the protonated semiquinone (Q(B)H)(*) had not been possible, presumably because of its low pK(a). By replacing the native Q(10) in the Q(B) site with rhodoquinone (RQ), which has a higher pK(a), we were able to observe the (Q(B)H)(*) state. The pH dependence of the semiquinone optical spectrum gave a pK(a) = 7.3 +/- 0.2. At pH < pK(a), the observed rate for the reaction was constant and attributed to the intrinsic electron-transfer rate from Q(A)(-)(*) to the protonated semiquinone (i.e., k(2)AB = k(ET)(RQ) = 2 x 10(4) s(-)(1)). The rate decreased at pH > pK(a) as predicted by the PAET mechanism in which fast reversible proton transfer precedes rate-limiting electron transfer. Consequently, near pH 7, the proton-transfer rate k(H) >> 10(4) s(-)(1). Applying the two step mechanism to RCs containing native Q(10) and taking into account the change in redox potential, we find reasonable values for the fraction of (Q(B)H)(*) congruent with 0.1% (consistent with a pK(a)(Q(10)) of approximately 4.5) and k(ET)(Q(10)) congruent with 10(6) s(-)(1). These results confirm the PAET mechanism in RCs with RQ and give strong support that this mechanism is active in RCs with Q(10) as well.

Benzoquinones↗

PubMed2001

On the importance of exchangeable NH protons in creatine for the magnetic coupling of creatine methyl protons in skeletal muscle.

The methyl protons of creatine in skeletal muscle exhibit a strong off-resonance magnetization transfer effect. The mechanism of this process is unknown. We previously hypothesized that the exchangeable amide/amino protons of creatine might be involved. To test this the characteristics of the creatine magnetization transfer effect were investigated in excised rat hindleg skeletal muscle that was equilibrated in either H2O or D2O solutions containing creatine. The efficiency of off-resonance magnetization transfer to the protons of mobile creatine in excised muscle was similar to that previously reported in intact muscle in vivo. Equilibrating the isolated muscle in D2O solution had no effect on the magnetic coupling to the immobile protons. It is concluded that exchangeable protons play a negligible role in the magnetic coupling of creatine methyl protons in muscle.

Animals↗

PubMed1985

Mechanism of surface peptide proton exchange in bovine pancreatic trypsin inhibitor. Salt effects and O-protonation.

The acid-catalyzed hydrogen exchange rate constants kH, and the base-catalyzed rate constants kOH, have been determined (in the preceding paper) for the 25 most rapidly exchanging NH groups of bovine pancreatic trypsin inhibitor. Most of these NH groups are at the protein-solvent interface. The correlation of kH, but not kOH, with the static accessibility and hydrogen bonding of the peptide carbonyl O atom indicates that the mechanism of acid catalysis in proteins involves O-protonation. Agreement between the ionic strength dependence observed for kH and kOH and the ionic strength dependence calculated for an O-protonation mechanism supports this conclusion. N-protonation for acid catalysis, as well as N-deprotonation for base catalysis, have traditionally been assumed in the mechanism of the chemical step in peptide amide proton exchange. A preference for the alternative O-protonation mechanism has far-reaching implications in the interpretation of protein hydrogen exchange kinetics. With an O-protonation mechanism, acid-catalyzed rates of surface NH groups are primarily a function of the average solvent accessibility of the carbonyl O atoms in the dynamic solution structure, while base-catalyzed rates of surface NH groups measure solvent accessibility of the peptide N. The relative dynamic accessibilities of peptide O atoms, as measured by relative values of kH (corrected for electrostatic effects), correlate with O static accessibilities in the crystal structure. A lower correlation of static accessibility of N atoms with kOH is observed for surface NH groups in peptide groups in which the carbonyl O is not hydrogen bonded. For some surface NH groups, the observed pH of minimum rate, pHmin, deviates widely from the pHmin of model compounds. This is explained as the combined result of electrostatic effects and of the differences in accessibility of the carbonyl O and N atoms that result in a change in the relative values of kH and kOH as compared to those of model peptides. A mechanism whereby exchange of interior sites is catalyzed by interactions of catalysis ions with protein surface atoms via charge transfer is suggested.

Amides↗

PubMed2003

What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals.

The nature of the control of water/proton selectivity in biological channels is a problem of a fundamental importance. Most studies of this issue have proposed that an interference with the orientational requirements of the so-called proton wire is the source of selectivity. The elucidation of the structures of aquaporins, which have evolved to prevent proton transfer (PT), provided a clear benchmark for exploring the selectivity problem. Previous simulations of this system have not examined, however, the actual issue of PT, but only considered the much simpler task of the transfer of water molecules. Here we take aquaporin as a benchmark and quantify the origin of the water/proton selectivity in this and related systems. This is done by evaluating in a consistent way the free energy profile for transferring a proton along the channel and relating this profile to the relevant PT rate constants. It is found that the water/proton selectivity is controlled by the change in solvation free energy upon moving the charged proton from water to the channel. The reason for the focus on the elegant concept of the proton wire and the related Grotthuss-type mechanism is also considered. It is concluded that these mechanisms are clearly important in cases with flat free energy surfaces (e.g., in bulk water, in gas phase water chains, and in infinitely long channels). However, in cases of biological channels, the actual PT mechanism is much less important than the energetics of transferring the proton charge from water to different regions in the channels.

Amino Acid Motifs↗

PubMed1998

Photovoltage evidence that Glu-204 is the intermediate proton donor rather than the terminal proton release group in bacteriorhodopsin.

Electrogenic events in the E204Q bacteriorhodopsin mutant have been studied. A two-fold decrease in the magnitude of microsecond photovoltage generation coupled to M intermediate formation in the E204Q mutant is shown. This means that deprotonation of E204 is an electrogenic process and its electrogenicity is comparable to that of the proton transfer from the Schiff base to D85. pH dependence of the electrogenicity of M intermediate formation in the wild-type bacteriorhodopsin reveals only one component corresponding to the protonation of D85 in the bacteriorhodopsin ground state and transition of the purple neutral form into the blue acid form. Thus, the pK of E204 in the M state is close to the pK of D85 in the bacteriorhodopsin ground state (< 3) and far below the pK of the terminal proton release group (approximately 6). It is concluded that E204 functions as the intermediate proton donor rather than the terminal proton release group in the bacteriorhodopsin proton pump.

Bacteriorhodopsins↗

PubMed1995

Proton transfer in cytochrome bo3 ubiquinol oxidase of Escherichia coli: second-site mutations in subunit I that restore proton pumping in the mutant Asp135-->Asn.

The ubiquinol oxidase, cytochrome bo3, of Escherichia coli is a member of the respiratory heme-copper oxidase family and conserves energy from the reduction of dioxygen to water by translocation of protons across the bacterial membrane. Mutation of an aspartic acid residue (Asp135) to asparagine in subunit I of this enzyme was previously found to impair proton translocation [Thomas et al. (1993) Biochemistry 32, 10923-10928]. This residue is located in an interhelical "loop" between transmembranous helices II and III, which contains six well-conserved residues (Asn124, Pro128, Gly132, Asp135, Pro139, and Asn142). Site-directed mutagenesis was performed to study the function of this entire domain. Nonconservative mutations of Asn124 and Asn142 also resulted in a loss of proton translocation, whereas their conservative substitution to glutamine had no effect. Mutations in eight other positions within this domain did not affect proton translocation. Introduction of an acidic group at positions 139 or 142, but not at eight other tested positions, restored proton pumping in the Asp135-->Asn mutated protein. These results suggest that the C-terminal part of the domain may be alpha-helical and that the entire "loop" plays an important structural and functional role as part of an input channel of the proton translocation machinery.

Amino Acid Sequence↗

PubMedDate not supplied

A computational study of intramolecular proton transfer in gaseous protonated glycine.

The minimum energy paths for intramolecular proton transfer between the amino nitrogen and carbonyl oxygen atoms in gaseous protonated glycine were estimated at the Hartree-Fock (HF) and second-order Møller-Plesset Perturbation (MP2) levels of theory. Potential energy profiles and their associated reactant, transition state, and product species calculated at the MP2/6-31G* level were shown to differ significantly from those obtained at the HF/6-31G* level. Effects of electron correlation and basis functions on the calculated geometries and energies of relevant species were examined at the HF, MP2, MP4, CCSD, and B3LYP levels using the 6-31G*, 6-31G**, 6-31+G**, 6-311+G**, 6-31+G(2d,2p), 6-311+G(3df,2p), cc-pVDZ, aug-cc-pVDZ, and cc-pVTZ basis sets. The HF and MP2 optimized levels with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** bases were used to calculate the thermodynamic and kinetic properties of the proton transfer reaction at 298.15 K and 1 atm, which include enthalpy, entropy, Gibbs free energy, equilibrium constant, potential energy barriers, tunneling transmission coefficients, and rate constants. Results indicate that the proton in a carbonyl O-protonated glycine undergoes a rapid migration to the amino nitrogen atom, while the reverse process is extremely unfavorable. The objective of this work is to develop practical theoretical procedures for studying proton transfer reactions in amino acids and peptides and to assemble physical data from these model calculations for future references.

Electrochemistry↗

PubMed2003

Protonation of gas-phase aromatic molecules: IR spectrum of the fluoronium isomer of protonated fluorobenzene.

The IR spectrum of the fluoronium isomer of protonated fluorobenzene (F-C(6)H(6)F(+), phenylfluoronium) is recorded in the vicinity of the C-H and F-H stretch fundamentals to obtain the first structured spectrum of an isolated protonated aromatic molecule in the gas phase. Stable F-C(6)H(6)F(+) ions are produced via proton transfer from CH(5)(+) to fluorobenzene (C(6)H(5)F) in a supersonic plasma expansion. The F-C(6)H(6)F(+) spectrum recorded between 2,540 and 4,050 cm(-1) is consistent with a weakly bound ion-dipole complex composed of HF and the phenyl cation, HF-C(6)H(5)(+). The strongest transition occurs at 3,645 cm(-1) and is assigned to the F-H stretch (sigma(FH)). The antisymmetric C-H stretch of the two ortho hydrogen atoms, sigma(CH) = 3,125 cm(-1), is nearly unshifted from bare C(6)H(5)(+), indicating that HF complexation has little influence on the C-H bond strength of C(6)H(5)(+). Despite the simultaneous production of the more stable ring protonated carbenium isomers of C(6)H(6)F(+) (fluorobenzenium) in the electron ionization source, F-C(6)H(6)F(+) can selectively be photodissociated into C(6)H(5)(+) and HF under the present experimental conditions, because it has a much lower dissociation energy than all carbenium isomers. Quantum chemical calculations at the B3LYP and MP2 levels of theory using the 6-311G(2df,2pd) basis support the interpretation of the experimental data and provide further details on structural, energetic, and vibrational properties of F-C(6)H(6)F(+), the carbenium isomers of C(6)H(6)F(+), and other weakly bound HF-C(6)H(5)(+) ion-dipole complexes. The dissociation energy of F-C(6)H(6)F(+) with respect to dehydrofluorination is calculated as D(0) = 4521 cm(-1) (approximately 54 kJ/mol). Analysis of the charge distribution in F-C(6)H(6)F(+) supports the notation of a HF-C(6)H(5)(+) ion-dipole complex, with nearly the whole positive charge of the added proton distributed over the C(6)H(5)(+) ring. As a result, protonation at the F atom strongly destabilizes the C-F bond in C(6)H(5)F.

Fluorobenzenes↗

PubMed2006

Carboxylates as proton-accepting groups in concerted proton-electron transfers. Electrochemistry of the 2,5-dicarboxylate 1,4-hydrobenzoquinone/2,5-dicarboxy 1,4-benzoquinone couple.

Concerted proton and electron transfers (CPET) currently attract considerable theoretical and experimental attention, notably in view of their likely involvement in many enzymatic reactions. The role of carboxylate groups as proton-accepting sites in CPET reactions is explored by means of a cyclic voltammetric investigation of the 2,5-dicarboxy 1,4-benzoquinone/2,5-dicarboxylate 1,4-hydrobenzoquinone couple in a nonaqueous medium. The presence of carboxylate groups ortho to the phenol groups induces the removal of an electron to be coupled with the transfer of the phenolic proton to a carboxylate oxygen. The kinetics of the electrochemical reaction and the observation of a significant hydrogen/deuterium kinetic isotope effect unambiguously indicate that electron transfer and proton transfer are concerted, thus providing an additional demonstration of the role of carboxylate groups as proton-accepting sites in concerted proton-electron transfer reactions.

Benzoquinones↗

PubMed2005

Excess proton solvation and delocalization in a hydrophilic pocket of the proton conducting polymer membrane nafion.

Solvation properties of the hydrated excess proton are studied in a hydrophilic pocket of Nafion 117 through a series of molecular dynamics simulations. The multistate empirical valence bond (MS-EVB) methodology, which enables the delocalization of the excess proton through the Grotthuss hopping mechanism, was employed for one of the excess protons in the simulation cell. Simulations were performed such that "classical" nondissociable hydronium cations and a single excess proton treated with the MS-EVB methodology were at a concentration ratio of 39:1. Two degrees of hydration of the Nafion polymer electrolyte membrane were simulated, each displaying the same marked difference between the solvation structures of the classical versus MS-EVB treated (Grotthuss shuttling) excess proton species. These differences are attributed to the solvent dynamics needed to transfer the cation between the solvent separated and contact pair positions about the sulfonic acid counterion. The results demonstrate that it is generally impossible to describe the low pH conditions in the hydrophilic domains of Nafion without the explicit treatment of Grotthuss delocalization in the underlying molecular dynamics model for the excess protons.

Fluorocarbon Polymers↗

PubMed1983

The mechanism of proton translocation by the cytochrome system of mitochondria. Characterization of proton-transfer reactions associated with oxidoreductions of terminal respiratory carriers.

A direct kinetic analysis is presented of rapid proton-releasing reactions at the outer or C-side of the membrane, in ox heart and rat liver mitochondria, associated with aerobic oxidation of reduced terminal respiratory carriers in the presence of antimycin. Valinomycin plus K+ enhances the rate of cytochrome c oxidation and the rate and extent of H+ release. In the presence of valinomycin the leads to H+/e- ratio, computed on the basis of total electron flow from respiratory carriers to oxygen, varies with pH, remaining always lower than 1, and is unaffected by N-ethylmaleimide. 2-Heptyl-4-hydroxyquinoline N-oxide and 5-(n-undecyl)-6-hydroxy-4,7-dioxobenzothiazole, at concentrations which inhibit in the presence of antimycin the oxygen-induced reduction of b cytochromes, cause also a marked depression of the H+ release associated with aerobic oxidation of terminal respiratory carriers. Aerobic oxidation of the cytochrome system in mitochondria and of isolated b-c1 complex and cytochrome c oxidase results in scalar proton release from ionizable groups (redox Bohr effects). In mitochondria and submitochondrial particles, about 70% of the oxidoreductions of the components of the cytochrome system are linked to scalar proton transfer by ionizable groups. In isolated b-c1 complex scalar proton transfer, resulting from redox Bohr effect, amounts to 0.9H+ per Fe-S protein (190 muT). In isolated cytochrome c oxidase, Bohr protons amount to 0.8 per haem a + a3. The results presented indicate that the H+ release from mitochondria during oxidation of terminal respiratory carriers derives from residual antimycin-insensitive electron flow in the quinone-cytochrome c span and from redox Bohr effects in the b-c1 complex and cytochrome c oxidase. There is no sign of proton pumping by cytochrome oxidase during its transition from the reduced to the active 'pulsed' state and the first one or two turnovers.

Animals↗

PubMed2005

Quantum and dynamical effects of proton donor-acceptor vibrational motion in nonadiabatic proton-coupled electron transfer reactions.

This paper presents a general theoretical formulation for proton-coupled electron transfer (PCET) reactions. The solute is represented by a multistate valence bond model, and the active electrons and transferring proton(s) are treated quantum mechanically. This formulation enables the classical or quantum mechanical treatment of the proton donor-acceptor vibrational mode, as well as the dynamical treatment of the proton donor-acceptor mode and the solvent. Nonadiabatic rate expressions are presented for PCET reactions in a number of well-defined limits for both dielectric continuum and molecular representations of the environment. The dynamical rate expressions account for correlations between the fluctuations of the proton donor-acceptor distance and the nonadiabatic PCET coupling. The quantities in the rate expressions can be calculated with a dielectric continuum model or a molecular dynamics simulation of the full system. The significance of the quantum and dynamical effects of the proton donor-acceptor mode is illustrated with applications to model PCET systems.

Computer Simulation↗

PubMed2000

The measurement of proton stopping power using proton-cone-beam computed tomography.

A cone-beam computed tomography (CT) system utilizing a proton beam has been developed and tested. The cone beam is produced by scattering a 160 MeV proton beam with a modifier that results in a signal in the detector system, which decreases monotonically with depth in the medium. The detector system consists of a Gd2O2S:Tb intensifying screen viewed by a cooled CCD camera. The Feldkamp-Davis-Kress cone-beam reconstruction algorithm is applied to the projection data to obtain the CT voxel data representing proton stopping power. The system described is capable of reconstructing data over a 16 x 16 x 16 cm3 volume into 512 x 512 x 512 voxels. A spatial and contrast resolution phantom was scanned to determine the performance of the system. Spatial resolution is significantly degraded by multiple Coulomb scattering effects. Comparison of the reconstructed proton CT values with x-ray CT derived proton stopping powers shows that there may be some advantage to obtaining stopping powers directly with proton CT. The system described suggests a possible practical method of obtaining this measurement in vivo.

Calibration↗

PubMed1985

Sugar specificity and sugar-proton interaction for the hexose-proton-symport system of Chlorella.

The substrate specificity of the glucose-proton symport system was studied to gain information about the spatial relationship between the binding sites for glucose and proton. Charged glucose analogues such as amino sugars or sugar acids were not transported by the uptake system, with the exception of 2-amino-2-deoxy-D-glucose. This glucosamine was taken up in the charged form in uniport mechanism, i.e. without symport of proton. This result was interpreted to mean that the proton-binding site of the symport system is close to the hydroxyl at carbon 2 of glucose. This interpretation was strengthened by the following facts: The steric position of hydroxyl groups at carbons 1, 2 or 3 of glucose were especially important for efficient transport. O-Methylation was not tolerated at carbon 1, but it was tolerated at carbons 3, 4 or 6. The stoichiometric flow of proton and sugar could be disturbed by removal of hydroxyl group at carbon 1 of glucose. The pH-dependence of sugar transport is sugar-specific, e.g. the amino group at carbon 2 of glucose improves transport at higher pH. The configuration at carbon 2 of glucose influences the specificity for the symported ion. It is concluded that the coupled flow of proton and glucose occurs by simultaneous coordinate movement of both in a transmembrane channel.

Biological Transport↗