Final Proton Research Articles

X-ray structure of an AdoMet radical activase reveals an anaerobic solution for formylglycine posttranslational modification

Arylsulfatases require a maturating enzyme to perform a co- or posttranslational modification to form a catalytically essential formylglycine (FGly) residue. In organisms that live aerobically, molecular oxygen is used enzymatically to oxidize cysteine to FGly. Under anaerobic conditions, S-adenosylmethionine (AdoMet) radical chemistry is used. Here we present the structures of an anaerobic sulfatase maturating enzyme (anSME), both with and without peptidyl-substrates, at 1.6-1.8 Å resolution. We find that anSMEs differ from their aerobic counterparts in using backbone-based hydrogen-bonding patterns to interact with their peptidyl-substrates, leading to decreased sequence specificity. These anSME structures from Clostridium perfringens are also the first of an AdoMet radical enzyme that performs dehydrogenase chemistry. Together with accompanying mutagenesis data, a mechanistic proposal is put forth for how AdoMet radical chemistry is coopted to perform a dehydrogenation reaction. In the oxidation of cysteine or serine to FGly by anSME, we identify D277 and an auxiliary [4Fe-4S] cluster as the likely acceptor of the final proton and electron, respectively. D277 and both auxiliary clusters are housed in a cysteine-rich C-terminal domain, termed SPASM domain, that contains homology to ~1,400 other unique AdoMet radical enzymes proposed to use [4Fe-4S] clusters to ligate peptidyl-substrates for subsequent modification. In contrast to this proposal, we find that neither auxiliary cluster in anSME bind substrate, and both are fully ligated by cysteine residues. Instead, our structural data suggest that the placement of these auxiliary clusters creates a conduit for electrons to travel from the buried substrate to the protein surface.

Simulation of Catalytic Water Activation in Mitochondrial F1-ATPase Using a Hybrid Quantum Mechanics/Molecular Mechanics Approach: An Alternative Role for β-Glu 188

The use of quantum mechanics/molecular mechanics simulations to study the free energy landscape of the water activation at the catalytic site of mitochondrial F(1)-ATPase affords us insight into the generation of the nucleophile OH(-) prior to ATP hydrolysis. As a result, the ATP molecule was found to be the final proton acceptor. In the simulated pathway, the transfer of a proton to the nucleotide was not direct but occurred via a second water molecule in a manner similar to the Grotthuss mechanism proposed for proton diffusion. Residue β-Glu 188, previously described as the putative catalytic base, was found to be involved in the stabilization of a transient hydronium ion during water activation. Simulations in the absence of the carboxylate moiety of β-Glu 188 support this role.

Reaction Dynamics of ATP Hydrolysis in Actin Determined by ab Initio Molecular Dynamics Simulations.

Energy released by the hydrolysis of the high-energy phosphate bond of nucleoside triphosphate (NTP) cofactors is the driving force behind most biological processes. To understand how this energy is used to induce differences in protein structure and function, we examine the transfer of vibrational energy into the nucleotide-bound actin active site immediately after reaction activation. To this end, we perform Born-Oppenheimer molecular dynamics simulations of the active site at the level of density functional theory (DFT) starting at the calculated transition state (TS) structure. Similarly to the mechanism determined in many nucleotide-bound protein systems, the Os-Pγ bond is first elongated. Then, nucleophilic attack of the lytic water on Pγ occurs. Subsequently, protons are transferred in a cycle formed by water molecules, a protein residue, Asp154, and the γ-phosphate group, resulting in the formation of H2PO4(-). To investigate the possible creation of excited vibrational states in the products, power spectra of bond-length autocorrelation functions for relevant bonds within the active site are compared for simulations that start at the TS, at reactants, and at reaction end products. The hydroxyl bond formed in the final proton transfer to the phosphate molecule is observed to exhibit relatively high kinetic energies and large oscillations during reaction. It is also likely that some of the energy released by the reaction is captured by the low-energy stretching vibrations of the phosphoryl bonds of orthophosphate, which oscillate with large amplitudes in nonequilibrium simulations of end products.

Polarization Components inπ0Photoproduction at Photon Energies up to 5.6 GeV

We present new data for the polarization observables of the final state proton in the (1)H(γ,p)π(0) reaction. These data can be used to test predictions based on hadron helicity conservation and perturbative QCD. These data have both small statistical and systematic uncertainties and were obtained with beam energies between 1.8 and 5.6 GeV and for π(0) scattering angles larger than 75° in the center-of-mass frame. The data extend the polarization measurements database for neutral pion photoproduction up to E(γ)=5.6 GeV. The results show a nonzero induced polarization above the resonance region. The polarization transfer components vary rapidly with the photon energy and π(0) scattering angle in the center-of-mass frame. This indicates that hadron helicity conservation does not hold and that the perturbative QCD limit is still not reached in the energy regime of this experiment.

Differential cross section and analysing power of the [formula omitted] reaction at 353 MeV

The differential cross section dσ/dΩ and analysing power Ay of the p→p→{pp}sπ0 reaction have been measured at COSY-ANKE at 353 MeV. The final proton pair was detected at very low excitation energy, leading to an S-wave diproton, denoted here as {pp}s. The angular dependence of both dσ/dΩ and Ay can be described in terms of s- and d-wave pion production. By using phase information from elastic pp scattering, unique solutions are derived for the corresponding amplitudes only as a result of the combined analysis of both experimental observables. The large d-wave term thus obtained is important for the tests of the current state-of-the-art chiral perturbation theory approach. The amplitudes will also help towards determining the isospin dependence of pion production in nucleon–nucleon collisions with diproton formation.

Measurement of dijet production in diffractive deep-inelastic scattering with a leading proton at HERA

The cross section of diffractive deep-inelastic scattering ep \rightarrow eXp is measured, where the system X contains at least two jets and the leading final state proton is detected in the H1 Forward Proton Spectrometer. The measurement is performed for fractional proton longitudinal momentum loss xIP < 0.1 and covers the range 0.1 < |t| < 0.7 GeV2 in squared four-momentum transfer at the proton vertex and 4 < Q2 < 110 GeV2 in photon virtuality. The differential cross sections extrapolated to |t| < 1 GeV2 are in agreement with next-toleading order QCD predictions based on diffractive parton distribution functions extracted from measurements of inclusive and dijet cross sections in diffractive deep-inelastic scattering. The data are also compared with leading order Monte Carlo models.

Measurement and analysis of thepp→ppγreaction at 310 MeV

The $\mathit{pp}\ensuremath{\rightarrow}\mathit{pp}\ensuremath{\gamma}$ reaction has been studied at a beam energy of 310 MeV by detecting both final protons at the PROMICE-WASA facility and identifying the photon through the resulting missing-mass peak. The photon angular distribution in the center-of-mass system and those of the proton-proton relative momentum with respect to the beam direction and to that of the recoil photon were determined reliably up to a final $\mathit{pp}$ excitation energy of ${E}_{\mathit{pp}}~30$ MeV. Except for very small ${E}_{\mathit{pp}}$ values, the behavior of these distributions with excitation energy is well reproduced by a new refined model of the hard bremsstrahlung process. The model reproduces absolutely the total cross section and its energy dependence to within the experimental and theoretical uncertainties.

DNA Binding Restricts the Intrinsic Conformational Flexibility of Methyl CpG Binding Protein 2 (MeCP2)

Mass spectrometry-based hydrogen/deuterium exchange (H/DX) has been used to define the polypeptide backbone dynamics of full-length methyl CpG binding protein 2 (MeCP2) when free in solution and when bound to unmethylated and methylated DNA. Essentially the entire MeCP2 polypeptide chain underwent H/DX at rates faster than could be measured (i.e. complete exchange in ≤10 s), with the exception of the methyl DNA binding domain (MBD). Even the H/DX of the MBD was rapid compared with that of a typical globular protein. Thus, there is no single tertiary structure of MeCP2. Rather, the full-length protein rapidly samples many different conformations when free in solution. When MeCP2 binds to unmethylated DNA, H/DX is slowed several orders of magnitude throughout the MBD. Binding of MeCP2 to methylated DNA led to additional minor H/DX protection, and only locally within the N-terminal portion of the MBD. H/DX also was used to examine the structural dynamics of the isolated MBD carrying three frequent mutations associated with Rett syndrome. The effects of the mutations ranged from very little (R106W) to a substantial increase in conformational sampling (F155S). Our H/DX results have yielded fine resolution mapping of the structure of full-length MeCP2 in the absence and presence of DNA, provided a biochemical basis for understanding MeCP2 function in normal cells, and predicted potential approaches for the treatment of a subset of RTT cases caused by point mutations that destabilize the MBD.

Measurement of the cross section for diffractive deep-inelastic scattering with a leading proton at HERA

The cross section for the diffractive deep-inelastic scattering process ep -> e X p is measured, with the leading final state proton detected in the H1 Forward Proton Spectrometer. The data sample covers the range x_pom<0.1 in fractional proton longitudinal momentum loss, 0.1 < |t| < 0.7 GeV^2 in squared four-momentum transfer at the proton vertex and 4 < Q^2 < 700 GeV^2 in photon virtuality. The cross section is measured four-fold differentially in t, x_pom, Q^2 and beta=x/x_pom, where x is the Bjorken scaling variable. The t and x_pom dependences are interpreted in terms of an effective pomeron trajectory and a sub-leading exchange. The data are compared to perturbative QCD predictions at next-to-leading order based on diffractive parton distribution functions previously extracted from complementary measurements of inclusive diffractive deep-inelastic scattering. The ratio of the diffractive to the inclusive ep cross section is studied as a function of Q^2, beta and x_pom.

Energy dependence of hard bremsstrahlung production in proton–proton collisions in the Δ(1232) region

Hard bremsstrahlung production in proton–proton collisions has been studied with the ANKE spectrometer at COSY-Jülich in the energy range of 353–800 MeV by detecting the final proton pair {pp}s from the pp → {pp}sγ reaction with very low excitation energy. Differential cross sections were measured at small diproton c.m. angles from 0° to 20° and the average over this angular interval reveals a broad peak at a beam energy around 650 MeV with a FWHM ≈ 220 MeV, suggesting the influence of Δ(1232)N intermediate states. Comparison with deuteron photodisintegration shows that the cross section for diproton production is up to two orders of magnitude smaller, due largely to differences in the selection rules.

Electrochemical Proton-Coupled Electron Transfer of an Osmium Aquo Complex: Theoretical Analysis of Asymmetric Tafel Plots and Transfer Coefficients

Electrochemical proton-coupled electron transfer of an osmium aquo complex attached to a self-assembled monolayer on a gold electrode is studied with a recently developed theoretical formulation. The calculated hydrogen/deuterium kinetic isotope effect for the standard rate constant, the cathodic transfer coefficient at zero overpotential, and the Tafel plot are in excellent agreement with experimental data. The input quantities to the heterogeneous rate constant expressions were calculated with density functional theory in conjunction with dielectric continuum models, and no parameters were fit to experimental data. The theoretical calculations indicate that the asymmetry of the Tafel plot and the deviation of the transfer coefficient at zero overpotential from the standard value of one-half arise from the change in the equilibrium proton donor-acceptor distance upon electron transfer. The direction of the asymmetry and deviation from one-half is determined by the sign of this distance change, and the magnitude of these effects is determined by the magnitude of this distance change, as well as the reorganization energy and the distance dependence of the overlap between the initial and final proton vibrational wave functions. This theory provides experimentally testable predictions for the impact of specific system properties on the qualitative behavior of the Tafel plots.

GEANT4 simulations for low energy proton computerized tomography

This work presents the recent results of computer simulations for the low energy proton beam tomographic scanner installed at the cyclotron CV-28 of IEN/CNEN. New computer simulations were performed in order to adjust the parameters of previous simulation within the first experimental results and to understand some specific effects that affected the form of the final proton energy spectra. To do this, the energy and angular spread of the initial proton beam were added, and the virtual phantom geometry was specified more accurately in relation to the real one. As a result, a more realistic view on the measurements was achieved.

Hard bremsstrahlung in the [formula omitted] reaction

The pp→ppγ reaction has been measured at a beam energy of 310 MeV by detecting both final protons in the PROMICE-WASA facility and identifying a missing-mass peak. For those events where the pp excitation is less than 3 MeV, the final diproton is almost purely in the S01 state and, under these conditions, there is complete coverage in the photon c.m. angle θγ. The linear behaviour observed in cos2θγ shows that there is almost no influence of an E2 multipole at this energy, though the E1 and M2 must be rather similar in size.

DIPROTON FINAL STATES: A NEW TOOL FOR HADRON PHYSICS AT ANKE-COSY

The ANKE spectrometer at COSY-Juelich provides the possibility to select proton pairs with small excitation energy in the final state. This opens a new way to study hadron interactions at intermediate energies. The final proton pairs with small excitation energy are found presumably in the 1S0 state which simplifies significantly the theoretical analysis. This approach has been successfully applied to the reactions pd → {pp}sn at high and low momentum transfer kinematics, as well as to the pp → {pp}sπ0 and pp → {pp}sγ processes.

HADRON PHYSICS WITH DIPROTON FINAL STATES AT ANKE-COSY

The possibility to select reliably the diproton final state with small excitation energy with the ANKE spectrometer at COSY-Juelich provides a new tool to study hadron interactions at intermediate energies. In this case the final proton pairs are found presumably in the 1S0 state which simplifies significantly the theoretical analysis. This approach has been successfully applied to the reactions pd → {pp}sn at high and low momentum transfer kinematics, as well as to the pp → {pp}sπ0 and pp → {pp}sγ processes.

Proton affinity and enthalpy of formation of formaldehyde

AbstractThe proton affinity and the enthalpy of formation of the prototypical carbonyl, formaldehyde, have been determined by the first‐principles composite focal‐point analysis (FPA) approach. The electronic structure computations employed the all‐electron coupled‐cluster method with up to single, double, triple, quadruple, and even pentuple excitations. In these computations the aug‐cc‐p(C)VXZ [X = 2(D), 3(T), 4(Q), 5, and 6] correlation‐consistent Gaussian basis sets for C and O were used in conjunction with the corresponding aug‐cc‐pVXZ (X = 2–6) sets for H. The basis set limit values have been confirmed via explicitly correlated computations. Our FPA study supersedes previous computational work for the proton affinity and to some extent the enthalpy of formation of formaldehyde by accounting for (a) electron correlation beyond the “gold standard” CCSD(T) level; (b) the non‐additivity of core electron correlation effects; (c) scalar relativity; (d) diagonal Born–Oppenheimer corrections computed at a correlated level; (e) anharmonicity of zero‐point vibrational energies, based on global potential energy surfaces and variational vibrational computations; and (f) thermal corrections to enthalpies by direct summation over rovibrational energy levels. Our final proton affinities at 298.15 (0.0) K are ΔpaHo (H2CO) = 711.02 (704.98) ± 0.39 kJ mol−1. Our final enthalpies of formation at 298.15 (0.0) K are ΔfHo (H2CO) = −109.23 (−105.42) ± 0.33 kJ mol−1. The latter values are based on the enthalpy of the H2 + CO → H2CO reaction but supported by two further reaction schemes, H2O + C → H2CO and 2H + C + O → H2CO. These values, especially ΔpaHo (H2CO), have better accuracy and considerably lower uncertainty than the best previous recommendations and thus should be employed in future studies. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

Possible method for measuring the proton form factors in processes with and without proton spin flip

The ratio of the squares of the electric and magnetic proton form factors is shown to be proportional to the ratio of the cross sections for the elastic scattering of an unpolarized electron on a partially polarized proton with and without proton spin flip. The initial proton at rest should be polarized along the direction of the motion of the final proton. Similar results are valid for both radiative ep scattering and the photoproduction of pairs on a proton in the Bethe-Heitler kinematics. When the initial proton is fully polarized in the direction of the motion of the final proton, the cross section for the ep → ep process, as well as for the ep → epγ and γp → \( e\bar ep \) processes, without (with) proton spin flip is expressed only in terms of the square of the electric (magnetic) proton form factor. Such an experiment on the measurement of the cross sections without and with proton spin flip would make it possible to acquire new independent data on the behavior of GE2(Q2) and GM2(Q2), which are necessary for resolving the contradictions appearing after the experiment of the JLab collaboration on the measurement of the proton form factors with the method of polarization transfer from the initial electron to the final proton.

The Mechanism of the Stetter Reaction – A DFT Study

AbstractOn the basis of Breslow's mechanism for benzoin condensation, a model asymmetric Stetter reaction has been investigated using DFT methods. In contrast to the concerted benzoin condensation, after formation of the Breslow intermediate the Stetter reaction is found to be a two‐step process in which the rate‐determining C–C coupling of the Breslow intermediate and the Michael acceptor precedes final proton transfer. In addition, the enolamine is found to play a significant role in the stereochemistry of the product, with the energy difference between stereoisomers of this intermediate reflected throughout the remainder of the reaction sequence. Consequently, electronic and steric control of the stereochemistry of this intermediate should directly enhance the ee values of the product. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2008)

Fully integrated transport approach to heavy ion reactions with an intermediate hydrodynamic stage

We present a coupled Boltzmann and hydrodynamics approach to relativistic heavy ion reactions. This hybrid approach is based on the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) transport approach with an intermediate hydrodynamical evolution for the hot and dense stage of the collision. Event-by-event fluctuations are directly taken into account via the nonequilibrium initial conditions generated by the initial collisions and string fragmentations in the microscopic UrQMD model. After a (3+1)-dimensional ideal hydrodynamic evolution, the hydrodynamical fields are mapped to hadrons via the Cooper-Frye equation and the subsequent hadronic cascade calculation within UrQMD proceeds to incorporate the important final state effects for a realistic freeze-out. This implementation allows us to compare pure microscopic transport calculations with hydrodynamic calculations using exactly the same initial conditions and freeze-out procedure. The effects of the change in the underlying dynamics--ideal fluid dynamics versus nonequilibrium transport theory--is explored. The freeze-out and initial state parameter dependencies are investigated for different observables. The time evolution of the baryon density and particle yields are also discussed. We find that the final pion and proton multiplicities are lower in the hybrid model calculation owing to the isentropic hydrodynamic expansion whereas the yields for strange particles are enhanced owing to the localmore » equilibrium in the hydrodynamic evolution. The results of the different calculations for the mean transverse mass excitation function, rapidity, and transverse mass spectra for different particle species at three different beam energies are discussed in the context of the available data.« less

Anchoring the Absolute Proton Affinity Scale.

Converged first-principles proton affinities (PA) of ammonia and carbon monoxide have been determined by the focal-point analysis (FPA) approach, thus fixing the high and low ends of the molecular proton affinity scale. The electronic structure computations employed the all-electron (AE) coupled-cluster (CC) method up to single, double, triple, quadruple, and pentuple excitations. Aug-cc-pCVXZ [X = 2(D), 3(T), 4(Q), 5, and 6] correlation-consistent (cc) Gaussian basis sets for C, N, and O were used in conjunction with the corresponding aug-cc-pVXZ (X = 2-6) sets for H. Our FPA study supersedes previous computational work by accounting for (a) electron correlation beyond the "gold standard" CCSD(T) level; (b) the nonadditivity of core electron correlation effects; (c) scalar relativity; (d) diagonal Born-Oppenheimer corrections (DBOC); (e) anharmonicity of zero-point vibrational energies, based on accurate AE-CCSD(T)/cc-pCVQZ internal coordinate quartic force fields and fully variational vibrational computations; and (f) thermal corrections to enthalpies by direct summation over rovibrational energy levels. Our final proton affinities at 298.15(0.0) K are ΔpaH°(NH3) = 852.6(846.4) ± 0.3 kJ mol(-1) and ΔpaH°(CO) = 592.4(586.5) ± 0.2 kJ mol(-1). These values have better accuracy and considerably lower uncertainty than the best previous recommendations and thus anchor the proton affinity scale of molecules for future use.