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Sample records for proton structure functions

  1. Proton structure functions at HERA

    NASA Astrophysics Data System (ADS)

    Stella, Bruno

    2001-10-01

    The electron-proton collider HERA, like an electron-mycroscope, explores the structure of the proton down to 10-16 cm and up to the situation of very high parton densities. The proton energy was upgraded from 820 to 920 GeV in the Fall of '98 and the luminosity has also substantially improved, with another factor of 3 upgrade expected to follow this year. Inclusive proton structure functions have been studied with incident e+ and e- of 27 GeV in the neutral (NC) and charged (CC) current interactions as functions of the squared four-momentum transfer, Q2, and of the fractional proton momentum carried by partons, x. The structure function F2, as well as the γ-Z0 interference term xF3, have been measured in a range of Q2 and 1/x that extends by orders of magnitude that reached by fixed target experiments. The DGLAP evolution equations [1] allow for a perturbative NLO QCD fit of the measured non-perturbative structure functions in the available kinematic range: αS and the gluon density at low x are fitted at the same time with good precision. The longitudinal structure function, FL, can be determined within the DGLAP formalism. With CC, the electroweak unification has been tested; at high x, a first flavor decomposition of the light quarks is achieved. The contribution to F2 of the charm quark has been measured and results to be relevant. Bounds on the radius of quarks and on compositeness are derived from the data at the highest Q2, 100

  2. Proton structure functions at HERA

    NASA Astrophysics Data System (ADS)

    H1; ZEUS Collaborations,

    2001-10-01

    The electron-proton collider HERA, like an electron-mycroscope, explores the structure of the proton down to 10-16 cm and up to the situation of very high parton densities. The proton energy was upgraded from 820 to 920 GeV in the Fall of '98 and the luminosity has also substantially improved, with another factor of 3 upgrade expected to follow this year. Inclusive proton structure functions have been studied with incident e+ and e- of 27 GeV in the neutral (NC) and charged (CC) current interactions as functions of the squared four-momentum transfer, Q2, and of the fractional proton momentum carried by partons, x. The structure function F2, as well as the γ-Z0 interference term xF3, have been measured in a range of Q2 and 1/x that extends by orders of magnitude that reached by fixed target experiments. The DGLAP evolution equations [1] allow for a perturbative NLO QCD fit of the measured non-perturbative structure functions in the available kinematic range: αS and the gluon density at low x are fitted at the same time with good precision. The longitudinal structure function, FL, can be determined within the DGLAP formalism. With CC, the electroweak unification has been tested; at high x, a first flavor decomposition of the light quarks is achieved. The contribution to F2 of the charm quark has been measured and results to be relevant. Bounds on the radius of quarks and on compositeness are derived from the data at the highest Q2, 100

  3. Proton structure functions at small x

    DOE PAGES

    Hentschinski, Martin

    2015-01-01

    Proton structure functions are measured in electron-proton collision through inelastic scattering of virtual photons with virtuality Q on protons; x denotes the momentum fraction carried by the struck parton. Proton structure functions are currently described with excellent accuracy in terms of scale dependent parton distribution functions, defined in terms of collinear factorization and DGLAP evolution in Q. With decreasing x however, parton densities increase and are ultimately expected to saturate. In this regime DGLAP evolution will finally break down and non-linear evolution equations w.r.t x are expected to take over. In the first part of the talk we present recentmore » result on an implementation of physical DGLAP evolution. Unlike the conventional description in terms of parton distribution functions, the former describes directly the Q dependence of the measured structure functions. It is therefore physical insensitive to factorization scheme and scale ambiguities. It therefore provides a more stringent test of DGLAP evolution and eases the manifestation of (non-linear) small x effects. It however requires a precise measurement of both structure functions F2 and FL, which will be only possible at future facilities, such as an Electron Ion Collider. In the second part we present a recent analysis of the small x region of the combined HERA data on the structure function F2. We demonstrate that (linear) next-to-leading order BFKL evolution describes the effective Pomeron intercept, determined from the combined HERA data, once a resummation of collinear enhanced terms is included and the renormalization scale is fixed using the BLM optimal scale setting procedure. We also provide a detailed description of the Q and x dependence of the full structure functions F2 in the small x region, as measured at HERA. As a result, predictions for the structure function FL are found to be in agreement with the existing HERA data.« less

  4. Proton structure functions at small x

    SciTech Connect

    Hentschinski, Martin

    2015-01-01

    Proton structure functions are measured in electron-proton collision through inelastic scattering of virtual photons with virtuality Q on protons; x denotes the momentum fraction carried by the struck parton. Proton structure functions are currently described with excellent accuracy in terms of scale dependent parton distribution functions, defined in terms of collinear factorization and DGLAP evolution in Q. With decreasing x however, parton densities increase and are ultimately expected to saturate. In this regime DGLAP evolution will finally break down and non-linear evolution equations w.r.t x are expected to take over. In the first part of the talk we present recent result on an implementation of physical DGLAP evolution. Unlike the conventional description in terms of parton distribution functions, the former describes directly the Q dependence of the measured structure functions. It is therefore physical insensitive to factorization scheme and scale ambiguities. It therefore provides a more stringent test of DGLAP evolution and eases the manifestation of (non-linear) small x effects. It however requires a precise measurement of both structure functions F2 and FL, which will be only possible at future facilities, such as an Electron Ion Collider. In the second part we present a recent analysis of the small x region of the combined HERA data on the structure function F2. We demonstrate that (linear) next-to-leading order BFKL evolution describes the effective Pomeron intercept, determined from the combined HERA data, once a resummation of collinear enhanced terms is included and the renormalization scale is fixed using the BLM optimal scale setting procedure. We also provide a detailed description of the Q and x dependence of the full structure functions F2 in the small x region, as measured at HERA. As a result, predictions for the structure function FL are found to be in agreement with the existing HERA

  5. Spin-dependent structure functions for the proton and neutron

    NASA Astrophysics Data System (ADS)

    Schäfer, Andreas

    1988-07-01

    We present a phenomenological model for the spin-dependent structure functions g1(x) of the proton and neutron. The model is an extension of the one proposed by Carlitz and Kaur. We use improved unpolarized structure functions and include effects due to the mass difference between up and down quark and due to the mass difference between spin 1/2 and 3/2 baryons. Our results for the proton agree with the data.

  6. On the analytic proton structure function with heavy quarks

    NASA Astrophysics Data System (ADS)

    Hu, Y.; Zeng, J.; Li, Q.; Zhou, F.; Zhou, D.; Xiang, W.

    2015-12-01

    The analytic proton structure function including quark mass is derived in the framework of color glass condensate. To get the massive proton structure function we keep the quark mass in photon wave function in the derivation process although the calculation is much more complicated than the massless case. It shows that the quark mass plays a key role in the description of the experimental data of proton structure function, and the cross-section of γ^{ast}p scattering will be divergent without quark mass regulation. To have the right threshold behavior and a smooth transition in the limit Q2→ 0, the quark mass has to include in the cross-section.

  7. Polarized Structure Functions: Proton/Deuteron Measurements in Hall C

    SciTech Connect

    Oscar A. Rondon

    2005-02-01

    The study of the nucleon polarized structure functions has matured beyond the inclusive measurements of the past to the investigation of all eight quark distribution functions in the nucleon. Jefferson Lab's Hall C program of polarized structure functions studies started with a measurement of the proton and deuteron spin structure in the resonances at Q2 {approx} 1.3 [GeV/c]2. This work will be extended for the proton to more than 5 [GeV/c]2 for both DIS and the resonances in the upcoming SANE experiment. SANE will use a novel non-magnetic very large solid angle detector, BETA. Semi-inclusive asymmetries will be measured to determine the flavor composition of the nucleon spin in the recently approved Semi-SANE experiment. The 11 GeV energy upgrade will open new opportunities to study other functions, such as the transversity, Collins and Sievers functions, using vertical polarized targets.

  8. Higher Twist Analysis of the Proton g{sub 1} Structure Function

    SciTech Connect

    Mikhail Osipenko; Wolodymyr Melnitchouk; Silvano Simula; Peter Bosted; Volker Burkert; Eric Christy; Keith Griffioen; Cynthia Keppel; Sebastian Kuhn

    2004-04-01

    We perform a global analysis of all available spin-dependent proton structure function data, covering a large range of Q{sup 2}, 1 < Q{sup 2} < 30 GeV{sup 2}, and calculate the lowest moment of the g{sub 1} structure function as a function of Q{sup 2}. The moment at high Q{sup 2} is used to obtain a value of the singlet axial charge, consistent with all the proton data. From the Q{sup 2} dependence of the lowest moment we extract matrix elements of twist-4 operators, and determine the color electric and magnetic polarizabilities of the proton.

  9. Analysis of Small x Behaviour of Longitudinal and Heavy Favour Structure Functions of Proton

    NASA Astrophysics Data System (ADS)

    Baruah, Nomita; Das, Mrinal Kumar; Sarma, Jayanta Kumar

    2015-10-01

    The behaviour of structure functions F L , with respect to Bjorken variable x are studied using Taylor series expansion method at small x. At small values of x, all these quantities are dominated by the gluon content of the proton. Here, we use the input distribution of gluon from Donnachie-Landshoff (DL) model to determine the longitudinal and heavy flavour structure function of proton. We compare our results with the recent HERA data and results of DL and Colour Dipole models which shows good agreement with data and fit. We use our results of heavy flavour structure function to analyze the behaviour of DIS cross section ratio R h ( x, Q 2) and reduced cross section in heavy quark lepto-production at small values of x. We have also studied the behaviour of the heavy quark content of the F L structure functions with respect to x.

  10. Leading and higher twists in proton, neutron and deuteron unpolarized structure functions F2

    SciTech Connect

    S. Simula

    2007-03-01

    We summarize the results of a recent global analysis of proton and deuteron F2 structure function world data performed over a large range of kinematics, including recent measurements done at JLab with the CLAS detector. From these data the lowest moments (n≤10) of the unpolarized structure functions are determined with good statistics and systematics. The Q2 evolution of the extracted moments is analyzed in terms of an OPE-based twist expansion, taking into account soft-gluon effects at large x. A clean separation among the leading- and higher-twist terms is achieved. By combining proton and deuteron measurements the lowest moments of the neutron F2 structure function are determined and its leading-twist term is extracted. Particular attention is paid to nuclear effects in the deuteron, which become increasingly important for the higher moments. Our results for the non-singlet, isovector (p-n) combination of the leading-twist moments are used to test recent lattice simulations. We also determine the lowest few moments of the higher-twist contributions, and find these to be approximately isospin independent, suggesting the possible dominance of ud correlations over uu and dd in the nucleon.

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

    PubMed

    Lanyi, J K

    1998-12-15

    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.

  12. Advances in functional and structural imaging of the human lung using proton MRI.

    PubMed

    Miller, G Wilson; Mugler, John P; Sá, Rui C; Altes, Talissa A; Prisk, G Kim; Hopkins, Susan R

    2014-12-01

    The field of proton lung MRI is advancing on a variety of fronts. In the realm of functional imaging, it is now possible to use arterial spin labeling (ASL) and oxygen-enhanced imaging techniques to quantify regional perfusion and ventilation, respectively, in standard units of measurement. By combining these techniques into a single scan, it is also possible to quantify the local ventilation-perfusion ratio, which is the most important determinant of gas-exchange efficiency in the lung. To demonstrate potential for accurate and meaningful measurements of lung function, this technique was used to study gravitational gradients of ventilation, perfusion, and ventilation-perfusion ratio in healthy subjects, yielding quantitative results consistent with expected regional variations. Such techniques can also be applied in the time domain, providing new tools for studying temporal dynamics of lung function. Temporal ASL measurements showed increased spatial-temporal heterogeneity of pulmonary blood flow in healthy subjects exposed to hypoxia, suggesting sensitivity to active control mechanisms such as hypoxic pulmonary vasoconstriction, and illustrating that to fully examine the factors that govern lung function it is necessary to consider temporal as well as spatial variability. Further development to increase spatial coverage and improve robustness would enhance the clinical applicability of these new functional imaging tools. In the realm of structural imaging, pulse sequence techniques such as ultrashort echo-time radial k-space acquisition, ultrafast steady-state free precession, and imaging-based diaphragm triggering can be combined to overcome the significant challenges associated with proton MRI in the lung, enabling high-quality three-dimensional imaging of the whole lung in a clinically reasonable scan time. Images of healthy and cystic fibrosis subjects using these techniques demonstrate substantial promise for non-contrast pulmonary angiography and detailed

  13. The role of N7 protonation of guanine in determining the structure, stability and function of RNA base pairs.

    PubMed

    Halder, Antarip; Bhattacharya, Sohini; Datta, Ayan; Bhattacharyya, Dhananjay; Mitra, Abhijit

    2015-10-21

    The roles of protonated nucleobases in stabilizing different structural motifs and in facilitating catalytic functions of RNA are well known. Among different polar sites of all the nucleobases, N7 of guanine has the highest protonation propensity at physiological pH. However, unlike other easily protonable sites such as N1 and N3 of adenine or N3 of cytosine, N7 protonation of guanine does not lead to the stabilization of base pairs involving its protonated Hoogsteen edge. It also does not facilitate its participation in any acid-base catalysis process. To explore the possible roles of N7 protonated guanine, we have studied its base pairing potentials involving WatsonCrick and sugar edges, which undergo major charge redistribution upon N7 protonation. We have carried out quantum chemical geometry optimization at the M05-2X/6-311G+(2d,2p) level, followed by interaction energy calculation at the MP2/aug-cc-pVDZ level, along with the analysis of the context of occurrence for selected base pairs involving the sugar edge or the WatsonCrick edge of guanine within a non-redundant set of 167 RNA crystal structures. Our results suggest that, four base pairs - G:C W:W trans, G:rC W:S cis, G:G W:H cis and G:G S:H trans may involve N7 protonated guanine. These base pairs deviate significantly from their respective experimental geometries upon QM optimization, but they retain their experimental geometries if guanine N7 protonation is considered during optimization. Our study also reveals the role of guanine N7 protonation (i) in stabilizing important RNA structural motifs, (ii) in providing a framework for designing pH driven molecular motors and (iii) in providing an alternative strategy to mimic the effect of post-transcriptional changes. PMID:26382322

  14. The Structure of the Proton

    DOE R&D Accomplishments Database

    Chambers, E. E.; Hofstadter, R.

    1956-04-01

    The structure and size of the proton have been studied by means of the methods of high-energy electron scattering. The elastic scattering of electrons from protons in polyethylene has been investigated at the following energies in the laboratory system: 200, 300, 400, 500, 550 Mev. The range of laboratory angles examined has been 30 degrees to 135 degrees. At the largest angles and the highest energy, the cross section for scattering shows a deviation below that expected from a point proton by a factor of about nine. The magnitude and variation with angle of the deviations determine a structure factor for the proton, and thereby determine the size and shape of the charge and magnetic-moment distributions within the proton. An interpretation, consistent at all energies and angles and agreeing with earlier results from this laboratory, fixes the rms radius at 0.77 {plus or minus} 0.10 x 10{sup -13} cm for each of the charge and moment distributions. The shape of the density function is not far from a Gaussian with rms radius 0.70 x 10{sup -13} cm or an exponential with rms radius 0.80 x 10 {sup -13} cm. An equivalent interpretation of the experiments would ascribe the apparent size to a breakdown of the Coulomb law and the conventional theory of electromagnetism.

  15. Structural Basis for the Function and Inhibition of an Influenze Virus Proton Channel

    SciTech Connect

    Stouffer,A.; Acharya, R.; Salom, D.; Levine, A.; Di Costanzo, L.; Soto, C.; Tershko, V.; Nanda, V.; Stayrook, S.; DeGrado, W.

    2008-01-01

    The M2 protein from influenza A virus is a pH-activated proton channel that mediates acidification of the interior of viral particles entrapped in endosomes. M2 is the target of the anti-influenza drugs amantadine and rimantadine; recently, resistance to these drugs in humans, birds and pigs has reached more than 90% (ref. 1). Here we describe the crystal structure of the transmembrane-spanning region of the homotetrameric protein in the presence and absence of the channel-blocking drug amantadine. pH-dependent structural changes occur near a set of conserved His and Trp residues that are involved in proton gating2. The drug-binding site is lined by residues that are mutated in amantadine-resistant viruses3, 4. Binding of amantadine physically occludes the pore, and might also perturb the pKa of the critical His residue. The structure provides a starting point for solving the problem of resistance to M2-channel blockers.

  16. Proton and deuteron F2 structure function at low Q2

    SciTech Connect

    Tvaskis, Vladas; Asaturyan, Razmik; Baker, Oliver; Blok, Henk; Bosted, Peter; Boswell, Melissa; Bruell, Antje; Christy, Michael; Cochran, Anthony; Ent, Rolf; Filippone, Bradley; Gasparian, Ashot; Keppel, Cynthia; Kinney, Edward; Lapikas, L; Lorenzon, Wolfgang; Mammei, Juliette; Martin, J W; Mkrtchyan, Hamlet; Niculescu, Maria-Ioana; Piercey, Rodney; Potterveld, David; Smith, Gregory; Spurlock, Kurt; Van der Steenhoven, Gerard; Stepanyan, Stepan; Tadevosyan, Vardan; Wood, Stephen

    2010-06-01

    Measurements of the proton and deuteron F2 structure functions are presented. The data, taken at Jefferson Lab Hall C, span the four-momentum transfer range 0.062<2.8GeV2 and Bjorken x values from 0.009 to 0.45, thus extending the knowledge of F2 to low values of Q2 at low x. Next-to-next-to-leading-order calculations using recent parton distribution functions start to deviate from the data for Q2<2 GeV2 at the low and high x values. Down to the lowest value of Q2, the structure function is in good agreement with a parametrization of F2 based on data that have been taken at much higher values of Q2 or much lower values of x, and which are constrained by data at the photon point. The ratio of the deuteron and proton structure functions at low x remains well described by a logarithmic dependence on Q2 at low Q2.

  17. From protons to OXPHOS supercomplexes and Alzheimer's disease: structure-dynamics-function relationships of energy-transducing membranes.

    PubMed

    Seelert, H; Dani, D N; Dante, S; Hauss, T; Krause, F; Schäfer, E; Frenzel, M; Poetsch, A; Rexroth, S; Schwassmann, H J; Suhai, T; Vonck, J; Dencher, N A

    2009-06-01

    By the elucidation of high-resolution structures the view of the bioenergetic processes has become more precise. But in the face of these fundamental advances, many problems are still unresolved. We have examined a variety of aspects of energy-transducing membranes from large protein complexes down to the level of protons and functional relevant picosecond protein dynamics. Based on the central role of the ATP synthase for supplying the biological fuel ATP, one main emphasis was put on this protein complex from both chloroplast and mitochondria. In particular the stoichiometry of protons required for the synthesis of one ATP molecule and the supramolecular organisation of ATP synthases were examined. Since formation of supercomplexes also concerns other complexes of the respiratory chain, our work was directed to unravel this kind of organisation, e.g. of the OXPHOS supercomplex I(1)III(2)IV(1), in terms of structure and function. Not only the large protein complexes or supercomplexes work as key players for biological energy conversion, but also small components as quinones which facilitate the transfer of electrons and protons. Therefore, their location in the membrane profile was determined by neutron diffraction. Physico-chemical features of the path of protons from the generators of the electrochemical gradient to the ATP synthase, as well as of their interaction with the membrane surface, could be elucidated by time-resolved absorption spectroscopy in combination with optical pH indicators. Diseases such as Alzheimer's dementia (AD) are triggered by perturbation of membranes and bioenergetics as demonstrated by our neutron scattering studies.

  18. Proposal to measure spin-structure functions and semi-exclusive asymmetries for the proton and neutron at HERA

    SciTech Connect

    Jackson, H.E.; Hansen, J.O.; Jones, C.E.

    1995-08-01

    Nucleon spin physics will be studied in the HERMES experiment, that will use polarized internal targets of essentially pure atomic H, D, and {sup 3}He in the HERA electron storage ring at DESY. A series of measurements of spin-dependent properties of the nucleon and few-body nuclei will be made; the spin structure function g{sub 1}(x) of the proton and neutron will be measured to test the Bjorken sum rule and study the fraction of the nucleon spin carried by quarks; the spin structure function g{sub 2}W, sensitive to quark-gluon correlations, and the structure functions b{sub 1}(x), and {Delta}(x), sensitive to nuclear binding effects, will be measured; and, using the particle identification capability of the HERMES detector, pions will be detected in coincidence with the scattered electrons. The coincident hadron measurements represent the most important extension that can be made at this time to the existing measurements on the nucleon spin structure functions because they provide information about the flavor-dependence of the quark spin distribution in the nucleon. Argonne is providing the Cerenkov counter to be used for particle identification and developing the drifilm coating technique for the ultrathin target cell required for this experiment. The HERMES collaboration intends to use polarized targets with the highest available figures of merit, and the Argonne laser-driven source offers the most promise for a significant advance in present-day targets.

  19. A Kinematically Complete Measurement of the Proton Structure Function F2 in the Resonance Region and Evaluation of Its Moments

    SciTech Connect

    Mikhail Osipenko; Et. Al.

    2003-05-01

    We measured the inclusive electron-proton cross section in the nucleon resonance region (W<2.5 GeV) at momentum transfers Q2 below 4.5 (GeV/c)2 with the CLAS detector. The large acceptance of CLAS allowed the measurement of the cross section in a large, contiguous two-dimensional range of Q2 and x, making it possible to perform an integration of the data at fixed Q2 over the significant x interval. >From these data we extracted the structure function F2 and, by including other world data, we studied the Q2 evolution of its moments, Mn(Q2), in order to estimate higher twist contributions. The small statistical and systematic uncertainties of the CLAS data allow a precise extraction of the higher twists and will require significant improvements in theoretical predictions if a meaningful comparison with these new experimental results is to be made.

  20. Function of chromatin structure and dynamics in DNA damage, repair and misrepair: γ-rays and protons in action.

    PubMed

    Ježková, Lucie; Falk, Martin; Falková, Iva; Davídková, Marie; Bačíková, Alena; Štefančíková, Lenka; Vachelová, Jana; Michaelidesová, Anna; Lukášová, Emilie; Boreyko, Alla; Krasavin, Evgeny; Kozubek, Stanislav

    2014-01-01

    According to their physical characteristics, protons and ion beams promise a revolution in cancer radiotherapy. Curing protocols however reflect rather the empirical knowledge than experimental data on DNA repair. This especially holds for the spatio-temporal organization of repair processes in the context of higher-order chromatin structure-the problematics addressed in this work. The consequences for the mechanism of chromosomal translocations are compared for gamma rays and proton beams.

  1. Global Analysis of Data on the Proton Structure Function g{sub 1} and Extraction of its Moments

    SciTech Connect

    Mikhail Osipenko; Silvano Simula; Wolodymyr Melnitchouk; Peter Bosted; Volker Burkert; Eric Christy; Keith Griffioen; Cynthia Keppel; Sebastian Kuhn; Giovani Ricco

    2005-01-01

    Inspired by recent measurements with the CLAS detector at Jefferson Lab, we perform a self-consistent analysis of world data on the proton structure function g{sub 1} in the range 0.17 < Q{sup 2} < 30 (GeV/c){sup 2}. We compute low-order moments g{sub 1} and study their evolution from small to large values of Q{sup 2}. The analysis takes includes the latest data on the unpolarized inclusive cross sections, the recent results for the ratio R = {sigma}{sub L}/{sigma}{sub T}, and a new model for the transverse asymmetry A{sub 2} in the resonance region. The contributions of both leading and higher twists are extracted, taking into account effects from radiative corrections beyond the next-to-leading order by means of soft-gluon resummation techniques. The contribution of higher twists to the g{sub 1} moments is found to be significantly larger than in the case of the unpolarized structure function F{sub 2}.

  2. The spin structure function g1p of the proton and a test of the Bjorken sum rule

    NASA Astrophysics Data System (ADS)

    Adolph, C.; Akhunzyanov, R.; Alexeev, M. G.; Alexeev, G. D.; Amoroso, A.; Andrieux, V.; Anosov, V.; Austregesilo, A.; Azevedo, C.; Badełek, B.; Balestra, F.; Barth, J.; Baum, G.; Beck, R.; Bedfer, Y.; Bernhard, J.; Bicker, K.; Bielert, E. R.; Birsa, R.; Bisplinghoff, J.; Bodlak, M.; Boer, M.; Bordalo, P.; Bradamante, F.; Braun, C.; Bressan, A.; Büchele, M.; Burtin, E.; Capozza, L.; Chang, W.-C.; Chiosso, M.; Choi, I.; Chung, S. U.; Cicuttin, A.; Crespo, M. L.; Curiel, Q.; Dalla Torre, S.; Dasgupta, S. S.; Dasgupta, S.; Denisov, O. Yu.; Dhara, L.; Donskov, S. V.; Doshita, N.; Duic, V.; Dziewiecki, M.; Efremov, A.; Eversheim, P. D.; Eyrich, W.; Ferrero, A.; Finger, M.; Finger, M.; Fischer, H.; Franco, C.; du Fresne von Hohenesche, N.; Friedrich, J. M.; Frolov, V.; Fuchey, E.; Gautheron, F.; Gavrichtchouk, O. P.; Gerassimov, S.; Giordano, F.; Gnesi, I.; Gorzellik, M.; Grabmüller, S.; Grasso, A.; Grosse-Perdekamp, M.; Grube, B.; Grussenmeyer, T.; Guskov, A.; Haas, F.; Hahne, D.; von Harrach, D.; Hashimoto, R.; Heinsius, F. H.; Herrmann, F.; Hinterberger, F.; Horikawa, N.; d'Hose, N.; -Yu Hsieh, C.; Huber, S.; Ishimoto, S.; Ivanov, A.; Ivanshin, Yu.; Iwata, T.; Jahn, R.; Jary, V.; Jörg, P.; Joosten, R.; Kabuß, E.; Ketzer, B.; Khaustov, G. V.; Khokhlov, Yu. A.; Kisselev, Yu.; Klein, F.; Klimaszewski, K.; Koivuniemi, J. H.; Kolosov, V. N.; Kondo, K.; Königsmann, K.; Konorov, I.; Konstantinov, V. F.; Kotzinian, A. M.; Kouznetsov, O.; Krämer, M.; Kremser, P.; Krinner, F.; Kroumchtein, Z. V.; Kuchinski, N.; Kunne, F.; Kurek, K.; Kurjata, R. P.; Lednev, A. A.; Lehmann, A.; Levillain, M.; Levorato, S.; Lichtenstadt, J.; Longo, R.; Maggiora, A.; Magnon, A.; Makins, N.; Makke, N.; Mallot, G. K.; Marchand, C.; Martin, A.; Marzec, J.; Matousek, J.; Matsuda, H.; Matsuda, T.; Meshcheryakov, G.; Meyer, W.; Michigami, T.; Mikhailov, Yu. V.; Miyachi, Y.; Nagaytsev, A.; Nagel, T.; Nerling, F.; Neyret, D.; Nikolaenko, V. I.; Novy, J.; Nowak, W.-D.; Nunes, A. S.; Olshevsky, A. G.; Orlov, I.; Ostrick, M.; Panzieri, D.; Parsamyan, B.; Paul, S.; Peng, J.-C.; Pereira, F.; Pesek, M.; Peshekhonov, D. V.; Platchkov, S.; Pochodzalla, J.; Polyakov, V. A.; Pretz, J.; Quaresma, M.; Quintans, C.; Ramos, S.; Regali, C.; Reicherz, G.; Riedl, C.; Rocco, E.; Rossiyskaya, N. S.; Ryabchikov, D. I.; Rychter, A.; Samoylenko, V. D.; Sandacz, A.; Santos, C.; Sarkar, S.; Savin, I. A.; Sbrizzai, G.; Schiavon, P.; Schmidt, K.; Schmieden, H.; Schönning, K.; Schopferer, S.; Selyunin, A.; Shevchenko, O. Yu.; Silva, L.; Sinha, L.; Sirtl, S.; Slunecka, M.; Sozzi, F.; Srnka, A.; Stolarski, M.; Sulc, M.; Suzuki, H.; Szabelski, A.; Szameitat, T.; Sznajder, P.; Takekawa, S.; ter Wolbeek, J.; Tessaro, S.; Tessarotto, F.; Thibaud, F.; Tosello, F.; Tskhay, V.; Uhl, S.; Veloso, J.; Virius, M.; Weisrock, T.; Wilfert, M.; Windmolders, R.; Zaremba, K.; Zavertyaev, M.; Zemlyanichkina, E.; Ziembicki, M.; Zink, A.

    2016-02-01

    New results for the double spin asymmetry A1p and the proton longitudinal spin structure function g1p are presented. They were obtained by the COMPASS Collaboration using polarised 200 GeV muons scattered off a longitudinally polarised NH3 target. The data were collected in 2011 and complement those recorded in 2007 at 160 GeV, in particular at lower values of x. They improve the statistical precision of g1p (x) by about a factor of two in the region x ≲ 0.02. A next-to-leading order QCD fit to the g1 world data is performed. It leads to a new determination of the quark spin contribution to the nucleon spin, ΔΣ, ranging from 0.26 to 0.36, and to a re-evaluation of the first moment of g1p. The uncertainty of ΔΣ is mostly due to the large uncertainty in the present determinations of the gluon helicity distribution. A new evaluation of the Bjorken sum rule based on the COMPASS results for the non-singlet structure function g1NS (x ,Q2) yields as ratio of the axial and vector coupling constants |gA /gV | = 1.22 ± 0.05 (stat.) ± 0.10 (syst.), which validates the sum rule to an accuracy of about 9%.

  3. The proton-linked monocarboxylate transporter (MCT) family: structure, function and regulation.

    PubMed Central

    Halestrap, A P; Price, N T

    1999-01-01

    Monocarboxylates such as lactate and pyruvate play a central role in cellular metabolism and metabolic communication between tissues. Essential to these roles is their rapid transport across the plasma membrane, which is catalysed by a recently identified family of proton-linked monocarboxylate transporters (MCTs). Nine MCT-related sequences have so far been identified in mammals, each having a different tissue distribution, whereas six related proteins can be recognized in Caenorhabditis elegans and 4 in Saccharomyces cerevisiae. Direct demonstration of proton-linked lactate and pyruvate transport has been demonstrated for mammalian MCT1-MCT4, but only for MCT1 and MCT2 have detailed analyses of substrate and inhibitor kinetics been described following heterologous expression in Xenopus oocytes. MCT1 is ubiquitously expressed, but is especially prominent in heart and red muscle, where it is up-regulated in response to increased work, suggesting a special role in lactic acid oxidation. By contrast, MCT4 is most evident in white muscle and other cells with a high glycolytic rate, such as tumour cells and white blood cells, suggesting it is expressed where lactic acid efflux predominates. MCT2 has a ten-fold higher affinity for substrates than MCT1 and MCT4 and is found in cells where rapid uptake at low substrate concentrations may be required, including the proximal kidney tubules, neurons and sperm tails. MCT3 is uniquely expressed in the retinal pigment epithelium. The mechanisms involved in regulating the expression of different MCT isoforms remain to be established. However, there is evidence for alternative splicing of the 5'- and 3'-untranslated regions and the use of alternative promoters for some isoforms. In addition, MCT1 and MCT4 have been shown to interact specifically with OX-47 (CD147), a member of the immunoglobulin superfamily with a single transmembrane helix. This interaction appears to assist MCT expression at the cell surface. There is still

  4. Chemistry as a function of the fine-structure constant and the electron-proton mass ratio

    NASA Astrophysics Data System (ADS)

    King, Rollin A.; Siddiqi, Ali; Allen, Wesley D.; Schaefer, Henry F., III

    2010-04-01

    In standard computations in theoretical quantum chemistry the accepted values of the fundamental physical constants are assumed. Alternatively, the tools of computational quantum chemistry can be used to investigate hypothetical chemistry that would result from different values of these constants, given the same physical laws. In this work, the dependence of a variety of basic chemical quantities on the values of the fine-structure constant and the electron-proton mass ratio is explored. In chemistry, the accepted values of both constants may be considered small, in the sense that their increase must be substantial to seriously impact bond energies. It is found that if the fine-structure constant were larger, covalent bonds between light atoms would be weaker, and the dipole moment and hydrogen-bonding ability of water would be reduced. Conversely, an increase in the value of the electron-proton mass ratio increases dissociation energies in molecules such as H2, O2, and CO2. Specifically, a sevenfold increase in the fine-structure constant decreases the strength of the O-H bond in the water molecule by 7 kcal mol-1 while reducing its dipole moment by at least 10%, whereas a 100-fold increase in the electron-proton mass ratio increases the same bond energy by 11 kcal mol-1.

  5. Structural and Dynamic Mechanisms for the Function and Inhibition of the M2 Proton Channel From Influenza A Virus

    PubMed Central

    Wang, Jun; Qiu, Jade Xiaoyan; Soto, Cinque; DeGrado, William F.

    2011-01-01

    The M2 proton channel from influenza A virus, a prototype for a class of viral ion channels known as viroporins, conducts protons along a chain of water molecules and ionizable side chains, including His37. Recent studies highlight a delicate interplay between protein folding, proton binding and proton conduction through the channel. Drugs inhibit proton conduction by binding to an aqueous cavity adjacent to M2’s proton-selective filter, thereby blocking access of proton to the filter, and altering the energetic landscape of the channel and the energetics of proton-binding to His37. PMID:21247754

  6. Anatomy of the differential gluon structure function of the proton from the experimental data on F2p(x,Q2)

    NASA Astrophysics Data System (ADS)

    Ivanov, I. P.; Nikolaev, N. N.

    2002-03-01

    The differential gluon structure function of the proton F(x,Q2) introduced by Fadin, Kuraev, and Lipatov in 1975 is used in many applications of small-x QCD. We report here ready-to-use parametrizations of F(x,Q2) from the κ-factorization phenomenology of the experimental data on the small-x proton structure function F2p(x,Q2). These parametrizations are based partly on the available Dokshitzer-Gribov-Lipatov-Altarelli-Parisi (DGLAP) evolution fits [Glück-Reya-Vogt, Coordinated Theoretical/Experimental Project on QCD Phenomenology (CTEQ), and Martin-Roberts-Stirling] to parton distribution functions and on realistic extrapolations into a soft region. We discuss the impact of soft gluons on various observables. The x dependence of the F(x,Q2) so determined varies strongly with Q2 and does not exhibit simple Regge properties. Nonetheless, the hard-to-soft diffusion is found to give rise to a viable approximation of the proton structure function F2p(x,Q2) by the soft and hard Regge components with intercepts Δsoft=0 and Δhard~0.4.

  7. Transmembrane Communication: General Principles and Lessons from the Structure and Function of the M2 Proton Channel, K+ Channels, and Integrin Receptors

    PubMed Central

    Grigoryan, Gevorg; Moore, David T.; DeGrado, William F.

    2013-01-01

    Signal transduction across biological membranes is central to life. This process generally happens through communication between different domains and hierarchical coupling of information. Here, we review structural and thermodynamic principles behind transmembrane (TM) signal transduction and discuss common themes. Communication between signaling domains can be understood in terms of thermodynamic and kinetic principles, and complex signaling patterns can arise from simple wiring of thermodynamically coupled domains. We relate this to functions of several signal transduction systems: the M2 proton channel from influenza A virus, potassium channels, integrin receptors, and bacterial kinases. We also discuss key features in the structural rearrangements responsible for signal transduction in these systems. PMID:21548783

  8. Transmembrane communication: general principles and lessons from the structure and function of the M2 proton channel, K⁺ channels, and integrin receptors.

    PubMed

    Grigoryan, Gevorg; Moore, David T; DeGrado, William F

    2011-01-01

    Signal transduction across biological membranes is central to life. This process generally happens through communication between different domains and hierarchical coupling of information. Here, we review structural and thermodynamic principles behind transmembrane (TM) signal transduction and discuss common themes. Communication between signaling domains can be understood in terms of thermodynamic and kinetic principles, and complex signaling patterns can arise from simple wiring of thermodynamically coupled domains. We relate this to functions of several signal transduction systems: the M2 proton channel from influenza A virus, potassium channels, integrin receptors, and bacterial kinases. We also discuss key features in the structural rearrangements responsible for signal transduction in these systems.

  9. Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity.

    PubMed

    Hsu, Min-Feng; Fu, Hsu-Yuan; Cai, Chun-Jie; Yi, Hsiu-Pin; Yang, Chii-Shen; Wang, Andrew H-J

    2015-12-01

    Retinal bound light-driven proton pumps are widespread in eukaryotic and prokaryotic organisms. Among these pumps, bacteriorhodopsin (BR) proteins cooperate with ATP synthase to convert captured solar energy into a biologically consumable form, ATP. In an acidic environment or when pumped-out protons accumulate in the extracellular region, the maximum absorbance of BR proteins shifts markedly to the longer wavelengths. These conditions affect the light-driven proton pumping functional exertion as well. In this study, wild-type crystal structure of a BR with optical stability under wide pH range from a square halophilic archaeon, Haloquadratum walsbyi (HwBR), was solved in two crystal forms. One crystal form, refined to 1.85 Å resolution, contains a trimer in the asymmetric unit, whereas another contains an antiparallel dimer was refined at 2.58 Å. HwBR could not be classified into any existing subgroup of archaeal BR proteins based on the protein sequence phylogenetic tree, and it showed unique absorption spectral stability when exposed to low pH values. All structures showed a unique hydrogen-bonding network between Arg(82) and Thr(201), linking the BC and FG loops to shield the retinal-binding pocket in the interior from the extracellular environment. This result was supported by R82E mutation that attenuated the optical stability. The negatively charged cytoplasmic side and the Arg(82)-Thr(201) hydrogen bond may play an important role in the proton translocation trend in HwBR under acidic conditions. Our findings have unveiled a strategy adopted by BR proteins to solidify their defenses against unfavorable environments and maintain their optical properties associated with proton pumping.

  10. Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity*

    PubMed Central

    Hsu, Min-Feng; Fu, Hsu-Yuan; Cai, Chun-Jie; Yi, Hsiu-Pin; Yang, Chii-Shen; Wang, Andrew H.-J.

    2015-01-01

    Retinal bound light-driven proton pumps are widespread in eukaryotic and prokaryotic organisms. Among these pumps, bacteriorhodopsin (BR) proteins cooperate with ATP synthase to convert captured solar energy into a biologically consumable form, ATP. In an acidic environment or when pumped-out protons accumulate in the extracellular region, the maximum absorbance of BR proteins shifts markedly to the longer wavelengths. These conditions affect the light-driven proton pumping functional exertion as well. In this study, wild-type crystal structure of a BR with optical stability under wide pH range from a square halophilic archaeon, Haloquadratum walsbyi (HwBR), was solved in two crystal forms. One crystal form, refined to 1.85 Å resolution, contains a trimer in the asymmetric unit, whereas another contains an antiparallel dimer was refined at 2.58 Å. HwBR could not be classified into any existing subgroup of archaeal BR proteins based on the protein sequence phylogenetic tree, and it showed unique absorption spectral stability when exposed to low pH values. All structures showed a unique hydrogen-bonding network between Arg82 and Thr201, linking the BC and FG loops to shield the retinal-binding pocket in the interior from the extracellular environment. This result was supported by R82E mutation that attenuated the optical stability. The negatively charged cytoplasmic side and the Arg82–Thr201 hydrogen bond may play an important role in the proton translocation trend in HwBR under acidic conditions. Our findings have unveiled a strategy adopted by BR proteins to solidify their defenses against unfavorable environments and maintain their optical properties associated with proton pumping. PMID:26483542

  11. The spin structure of the proton

    SciTech Connect

    Bass, Steven D.

    2005-10-15

    This article reviews the present understanding of the QCD spin structure of the proton. The author first outlines the proton spin puzzle and its possible resolution in QCD. Then the review explores the present and next generation of experiments being undertaken to resolve the proton's spin-flavor structure, explaining the theoretical issues involved, the present status of experimental investigation, and the open questions and challenges for future investigation.

  12. Proton Spin Structure in the Resonance Region

    SciTech Connect

    F. R. Wesselmann; K. Slifer; S. Tajima; A. Aghalaryan; A. Ahmidouch; R. Asaturyan; F. Bloch; W. Boeglin; P. Bosted; C. Carasco; R. Carlini; J. Cha; J. P. Chen; M. E. Christy; L. Cole; L. Coman; D. Crabb; S. Danagoulian; D. Day; J. Dunne; M. Elaasar; R. Ent; H. Fenker; E. Frlez; L. Gan; D. Gaskell; J. Gomez; B. Hu; M. K. Jones; J. Jourdan; C. Keith; C. E. Keppel; M. Khandaker; A. Klein; L. Kramer; Y. Liang; J. Lichtenstadt; R. Lindgren; D. Mack; P. McKee; D. McNulty; D. Meekins; H. Mkrtchyan; R. Nasseripour; I. Niculescu; K. Normand; B. Norum; D. Pocanic; Y. Prok; B. Raue; J. Reinhold; J. Roche; D. Rohe; O. A. Rondon; N. Savvinov; B. Sawatzky; M. Seely; I. Sick; C. Smith; G. Smith; S. Stepanyan; L. Tang; G. Testa; W. Vulcan; K. Wang; G. Warren; S. Wood; C. Yan; L. Yuan; Junho Yun; Markus Zeier; Hong Guo Zhu

    2006-10-11

    The RSS collaboration has measured the spin structure functions g{sub 1} and g{sub 2} of the proton at Jefferson Lab using the lab's polarized electron beam, the Hall C HMS spectrometer and the UVa polarized solid target. The asymmetries A{sub parallel} and A{sub perp} were measured at the elastic peak and in the region of the nucleon resonances (1.085 GeV < W < 1.910 GeV) at an average four momentum transfer of Q{sup 2} = 1.3 GeV{sup 2}. The extracted spin structure functions and their kinematic dependence make a significant contribution in the study of higher-twist effects and polarized duality tests.

  13. Understanding the proton's spin structure

    SciTech Connect

    Fred Myhrer; Thomas, Anthony W.

    2010-02-01

    We discuss the tremendous progress that has been towards an understanding of how the spin of the proton is distributed on its quark and gluon constituents. This is a problem that began in earnest twenty years ago with the discovery of the proton "spin crisis" by the European Muon Collaboration. The discoveries prompted by that original work have given us unprecedented insight into the amount of spin carried by polarized gluons and the orbital angular momentum of the quarks.

  14. Structural Changes and Proton Transfer in Cytochrome c Oxidase.

    PubMed

    Vilhjálmsdóttir, Jóhanna; Johansson, Ann-Louise; Brzezinski, Peter

    2015-08-27

    In cytochrome c oxidase electron transfer from cytochrome c to O2 is linked to transmembrane proton pumping, which contributes to maintaining a proton electrochemical gradient across the membrane. The mechanism by which cytochrome c oxidase couples the exergonic electron transfer to the endergonic proton translocation is not known, but it presumably involves local structural changes that control the alternating proton access to the two sides of the membrane. Such redox-induced structural changes have been observed in X-ray crystallographic studies at residues 423-425 (in the R. sphaeroides oxidase), located near heme a. The aim of the present study is to investigate the functional effects of these structural changes on reaction steps associated with proton pumping. Residue Ser425 was modified using site-directed mutagenesis and time-resolved spectroscopy was used to investigate coupled electron-proton transfer upon reaction of the oxidase with O2. The data indicate that the structural change at position 425 propagates to the D proton pathway, which suggests a link between redox changes at heme a and modulation of intramolecular proton-transfer rates.

  15. Fine structure in deformed proton emitters.

    SciTech Connect

    Sonzogni, A. A.; Davids, C. N.; Woods, P. J.; Seweryniak, D.; Carpenter, M. P.; Ressler, J. J.; Schwartz, J.; Uusitalo, J.; Walters, W. B.

    1999-12-07

    In a recent experiment to study the proton radioactivity of the highly deformed {sup 131}Eu nucleus, two proton lines were detected. The higher energy one was assigned to the ground-state to ground-state decay, while the lower energy, to the ground-state to the 2{sup +} state decay. This constitutes the first observation of fine structure in proton radioactivity. With these four measured quantities, proton energies, half-life and branching ratio, it is possible to determine the Nilsson configuration of the ground state of the proton emitting nucleus as well as the 2{sup +} energy and nuclear deformation of the daughter nucleus. These results will be presented and discussed.

  16. One-Proton Halo Structure in 23Al

    NASA Astrophysics Data System (ADS)

    Fang, De-Qing; Ma, Chun-Wang; Ma, Yu-Gang; Cai, Xiang-Zhou; Chen, Jin-Gen; Chen, Jin-Hui; Guo, Wei; Tian, Wen-Dong; Wang, Kun; Wei, Yi-Bin; Yan, Ting-Zhi; Zhong, Chen; Zuo, Jia-Xu; Shen, Wen-Qing

    2005-03-01

    The Glauber theory is used to investigate the reaction cross section of proton-rich nucleus 23Al. A core plus a proton structure is assumed for 23Al. HO-type density distribution is used for the core while the density distribution for the valence proton is calculated by solving the eigenvalue problem of Woods-Saxon potential. The transparency function in an analytical expression is obtained by adopting multi-Gaussian expansion for the density distribution. Coulomb correction and finite-range interaction are introduced. This modified Glauber model is suitable for halo nuclei. A dominate s-wave is suggested for the last proton in 23Al from our analysis which is possible in the calculation of relativistic mean-field theory.

  17. Spin Structure Moments of the Proton and Deuteron

    SciTech Connect

    Slifer, Karl; Rondon-Aramayo, Oscar; Aghalaryan, Aram; Ahmidouch, Abdellah; Asaturyan, Razmik; Bloch, Frederic; Boeglin, Werner; Bosted, Peter; Carasco, Cedric; Carlini, Roger; Cha, Jinseok; Chen, Jian-Ping; Christy, Michael; Cole, Leon; Coman, Luminita; Crabb, Donald; Danagoulian, Samuel; Day, Donal; Dunne, James; Elaasar, Mostafa; Ent, Rolf; Fenker, Howard; Frlez, Emil; Gaskell, David; Gan, Liping; Gomez, Javier; Hu, Bitao; Jourdan, Juerg; Jones, Mark; Keith, Christopher; Keppel, Cynthia; Khandaker, Mahbubul; Klein, Andreas; Kramer, Laird; Liang, Yongguang; Lichtenstadt, Jechiel; Lindgren, Richard; Mack, David; McKee, Paul; McNulty, Dustin; Meekins, David; Mkrtchyan, Hamlet; Nasseripour, Rakhsha; Niculescu, Maria-Ioana; Normand, Kristoff; Norum, Blaine; Pocanic, Dinko; Prok, Yelena; Raue, Brian; Reinhold, Joerg; Roche, Julie; Rohe, Daniela; Savvinov, Nikolai; Sawatzky, Bradley; Seely, Mikell; Sick, Ingo; Smith, C.; Smith, G.; Stepanyan, Samuel; Tang, Liguang; Tajima, Shigeyuki; Testa, Giuseppe; Vulcan, William; Wang, Kebin; Warren, G.; Wesselmann, Frank; Wood, Stephen; Yan, Chen; Yuan, Lulin; Yun, Junho; Zeier, Markus; Guo Zhu, Hong

    2009-01-01

    Moments of the spin structure functions g1 and g2 of the proton and deuteron have been measured in the resonance region at intermediate four momentum transfer. We perform a Nachtmann moment analysis of this data, along with isovector and isoscalar combinations, in order to rigorously account for target mass effects. This analysis provides the first definitive evidence for dynamic higher twists.

  18. Structural determinants of proton blockage in aquaporins.

    PubMed

    Chakrabarti, Nilmadhab; Roux, Benoît; Pomès, Régis

    2004-10-15

    Aquaporins are an important class of membrane channels selective for water and linear polyols but impermeable to ions, including protons. Recent computational studies have revealed that the relay of protons through the water-conduction pathway of aquaporin channels is opposed by a substantial free energy barrier peaking at the signature NPA motifs. Here, free-energy simulations and continuum electrostatic calculations are combined to examine the nature and the magnitude of the contribution of specific structural elements to proton blockage in the bacterial glycerol uptake facilitator, GlpF. Potential of mean-force profiles for both hop and turn steps of structural diffusion in the narrow pore are obtained for artificial variants of the GlpF channel in which coulombic interactions between the pore contents and conserved residues Asn68 and Asn203 at the NPA signature motifs, Arg206 at the selectivity filter, and the peptidic backbone of the two half-helices M3 and M7, which are arranged in head-to-head fashion around the NPA motifs, are turned off selectively. A comparison of these results with electrostatic energy profiles for the translocation of a probe cation throughout the water permeation pathway indicates that the free-energy profile for proton movement inside the narrow pore is dominated by static effects arising from the distribution of charged and polar groups of the channel, whereas dielectric effects contribute primarily to opposing the access of H+ to the pore mouths (desolvation penalty). The single most effective way to abolish the free-energy gradients opposing the movement of H+ around the NPA motif is to turn off the dipole moments of helices M3 and M7. Mutation of either of the two NPA Asn residues to Asp compensates for charge-dipole and dipole-dipole effects opposing the hop and turn steps of structural diffusion, respectively, and dramatically reduces the free energy barrier of proton translocation, suggesting that these single mutants could

  19. Tests of proton structure functions using leptons at CDF and DØ: W charge asymmetry and Drell-Yan production

    NASA Astrophysics Data System (ADS)

    Barbaro, Pawel de

    1996-02-01

    High statistics W charge asymmetry measurements at the Tevatron p¯p collider significantly constrain the u and d quark distributions, and specifically the slope of the d(x)/u(x) in the x range 0.007 to 0.27. We present measurements of the lepton charge asymmetry as a function of lepton rapidity, A(yl) at √s=1.8 TeV for ‖yl‖<2.0, for W decays to electrons and muons recorded by the CDF detector during the 1992-93 run (≊20 pb-1), and the first ≊50 pb-1 of data from the 1994-95 run. These precise data make possible further discrimination between sets of modern parton distributions. In particular it is found that the most recent parton distributions, which included the CDF 1992-93 W asymmetry data in their fits (MRSA, CTEQ3M and GRV94) are still in good agreement with the more precise data from the 1994-95 run. W charge asymmetry results from DO/ based on ≊6.5 pb-1 of data from the 1992-93 run and ≊29.7 pb-1 of data from the 1994-1995 run, using the W decays to muons, are also presented and are found to be consistent with CDF results. In addition, we present preliminary measurement of the Drell-Yan cross-section by CDF using a dielectron sample collected during the 1993-94 run (≊20 pb-1) and a high mass dimuon sample from the combined 1993-94 and 1994-95 runs (≊70 pb-1). The measurement is in good agreement with predictions using the most recent parton density functions in a dilepton mass range between 11 and 350 GeV/c2.

  20. Proton Coupled Electron Transfer and Redox Active Tyrosines: Structure and Function of the Tyrosyl Radicals in Ribonucleotide Reductase and Photosystem II

    PubMed Central

    Barry, Bridgette A.; Chen, Jun; Keough, James; Jenson, David; Offenbacher, Adam; Pagba, Cynthia

    2012-01-01

    Proton coupled electron transfer (PCET) reactions are important in many biological processes. Tyrosine oxidation/reduction can play a critical role in facilitating these reactions. Two examples are photosystem II (PSII) and ribonucleotide reductase (RNR). RNR is essential in DNA synthesis in all organisms. In E. coli RNR, a tyrosyl radical, Y122•, is required as a radical initiator. Photosystem II (PSII) generates molecular oxygen from water. In PSII, an essential tyrosyl radical, YZ•, oxidizes the oxygen evolving center. However, the mechanisms, by which the extraordinary oxidizing power of the tyrosyl radical is controlled, are not well understood. This is due to the difficulty in acquiring high-resolution structural information about the radical state. Spectroscopic approaches, such as EPR and UV resonance Raman (UVRR), can give new information. Here, we discuss EPR studies of PCET and the PSII YZ radical. We also present UVRR results, which support the conclusion that Y122 undergoes an alteration in ring and backbone dihedral angle when it is oxidized. This conformational change results in a loss of hydrogen bonding to the phenolic oxygen. Our analysis suggests that access of water is an important factor in determining tyrosyl radical lifetime and function. TOC graphic PMID:22662289

  1. Tests of proton structure functions using leptons at CDF and DO/: {ital W} charge asymmetry and Drell-Yan production

    SciTech Connect

    Barbaro, P.d.

    1996-02-01

    High statistics {ital W} charge asymmetry measurements at the Tevatron {bar {ital p}}{ital p} collider significantly constrain the {ital u} and {ital d} quark distributions, and specifically the slope of the {ital d}({ital x})/{ital u}({ital x}) in the {ital x} range 0.007 to 0.27. We present measurements of the lepton charge asymmetry as a function of lepton rapidity, {ital A}({ital y}{sub {ital l}}) at {radical}{ital s}=1.8 TeV for {parallel}{ital y}{sub {ital l}}{parallel}{lt}2.0, for {ital W} decays to electrons and muons recorded by the CDF detector during the 1992{endash}93 run ({approx_equal}20 {ital pb}{sup {minus}1}), and the first {approx_equal}50 {ital pb}{sup {minus}1} of data from the 1994{endash}95 run. These precise data make possible further discrimination between sets of modern parton distributions. In particular it is found that the most recent parton distributions, which included the CDF 1992{endash}93 W asymmetry data in their fits (MRSA, CTEQ3M and GRV94) are still in good agreement with the more precise data from the 1994{endash}95 run. {ital W} charge asymmetry results from DO/ based on {approx_equal}6.5 {ital pb}{sup {minus}1} of data from the 1992{endash}93 run and {approx_equal}29.7 {ital pb}{sup {minus}1} of data from the 1994{endash}1995 run, using the W decays to muons, are also presented and are found to be consistent with CDF results. In addition, we present preliminary measurement of the Drell-Yan cross-section by CDF using a dielectron sample collected during the 1993{endash}94 run ({approx_equal}20 {ital pb}{sup {minus}1}) and a high mass dimuon sample from the combined 1993{endash}94 and 1994{endash}95 runs ({approx_equal}70 {ital pb}{sup {minus}1}). The measurement is in good agreement with predictions using the most recent parton density functions in a dilepton mass range between 11 and 350 GeV/{ital c}{sup 2}. {copyright} {ital 1996 American Institute of Physics.}

  2. Simulating the function of sodium/proton antiporters

    PubMed Central

    Alhadeff, Raphael; Warshel, Arieh

    2015-01-01

    The molecular basis of the function of transporters is a problem of significant importance, and the emerging structural information has not yet been converted to a full understanding of the corresponding function. This work explores the molecular origin of the function of the bacterial Na+/H+ antiporter NhaA by evaluating the energetics of the Na+ and H+ movement and then using the resulting landscape in Monte Carlo simulations that examine two transport models and explore which model can reproduce the relevant experimental results. The simulations reproduce the observed transport features by a relatively simple model that relates the protein structure to its transporting function. Focusing on the two key aspartic acid residues of NhaA, D163 and D164, shows that the fully charged state acts as an Na+ trap and that the fully protonated one poses an energetic barrier that blocks the transport of Na+. By alternating between the former and latter states, mediated by the partially protonated protein, protons, and Na+ can be exchanged across the membrane at 2:1 stoichiometry. Our study provides a numerical validation of the need of large conformational changes for effective transport. Furthermore, we also yield a reasonable explanation for the observation that some mammalian transporters have 1:1 stoichiometry. The present coarse-grained model can provide a general way for exploring the function of transporters on a molecular level. PMID:26392528

  3. Simulating the function of sodium/proton antiporters.

    PubMed

    Alhadeff, Raphael; Warshel, Arieh

    2015-10-01

    The molecular basis of the function of transporters is a problem of significant importance, and the emerging structural information has not yet been converted to a full understanding of the corresponding function. This work explores the molecular origin of the function of the bacterial Na+/H+ antiporter NhaA by evaluating the energetics of the Na+ and H+ movement and then using the resulting landscape in Monte Carlo simulations that examine two transport models and explore which model can reproduce the relevant experimental results. The simulations reproduce the observed transport features by a relatively simple model that relates the protein structure to its transporting function. Focusing on the two key aspartic acid residues of NhaA, D163 and D164, shows that the fully charged state acts as an Na+ trap and that the fully protonated one poses an energetic barrier that blocks the transport of Na+. By alternating between the former and latter states, mediated by the partially protonated protein, protons, and Na+ can be exchanged across the membrane at 2:1 stoichiometry. Our study provides a numerical validation of the need of large conformational changes for effective transport. Furthermore, we also yield a reasonable explanation for the observation that some mammalian transporters have 1:1 stoichiometry. The present coarse-grained model can provide a general way for exploring the function of transporters on a molecular level.

  4. Structure in the Proton and the Neutron

    DOE R&D Accomplishments Database

    Hofstadter, R.

    1958-06-01

    A survey of the recent work on the structures of the proton and the neutron carried out by high-energy electron-scattering methods is presented. Early work established finite size effects in the proton and led to information about the charge and magnetic density distributions in the proton. The rms size was established to be close to (0.77 plus or minus 0.10) x 10{sup -13} cm, and the density distributions of charge and anomalous magnetic moment were shown to be approximately of the same shape. The form factors could be described in terms of several alternative models given, for example, by an exponential, gaussian, hollow exponential, hollow gaussian, etc., distribution of densities. Many other shapes were excluded by the experimental data. Recent work by Bumiller and Hofstadter now fixes one among these models that is appropriate to the proton and provides an extremely good fit at all angles between energies of 200 and 650 Mev. The new evidence clearly favors the exponential model with rms radius (0.80 plus or minus 0.04) 10{sup -13} cm. Recent studies of the proton have attempted to answer the question: how closely similar are the charge and magnetic form factors? This work now shows that the distributions have the same sizes and shapes to within 10 per cent, and each distribution is given very closely by the exponential model described above with radius (0.80 plus or minus 0.04) x 10{sup -13}. Certain other similar models will be discussed. Early work on the inelastic continuum in the deuteron established that the neutron's magnetic structure was extended and not a point. It was further shown that the neutron's size was approximately the same as that of the proton. This work has recently been extended by Yearian and Hofstadter to a determination of the variation of the neutron's magnetic form factor over the range where the proton's form factor is known. The new results show: (1) the neutron is not a point, (2) the neutron's magnetic structure has a size lying

  5. Internal spin structure of the proton from high energy polarized e-p scattering

    SciTech Connect

    Hughes, V.W.; Baum, G.; Bergstroem, M.R.

    1981-02-01

    A review is given of experimental knowledge of the spin dependent structure functions of the proton, which is based on inclusive high energy scattering of longitudinal polarized electrons by longitudinally polarized protons in both the deep inelastic and resonance regions, and includes preliminary results from our most recent SLAC experiment. Implications for scaling, sum rules, models of proton structure, and the hyperfine structure interval in hydrogen are given. Possible future directions of research are indicated.

  6. Local Structure of Proton-Conducting Lanthanum Tungstate La28-xW4+xO54+δ: a Combined Density Functional Theory and Pair Distribution Function Study

    SciTech Connect

    Kalland, Liv-Elisif; Magrasó, Anna; Mancini, Alessandro; Tealdi, Cristina; Malavasi, Lorenzo

    2013-10-02

    Lanthanum tungstate (La28–xW4+xO54+δ) is a good proton conductor and exhibits a complex fluorite-type structure. To gain further understanding of the short-range order in the structure we correlate the optimized configurations obtained by density functional theory (DFT) with the experimental atomic pair distribution function analysis (PDF) of time-of-flight neutron and synchrotron X-ray data, collected at room temperature. The local atomic arrangements cannot be described by means of any average symmetric structure. Tungsten forms WO6 octahedra in alternating directions, La1 is mainly 8-fold coordinated in relatively symmetric cubes, and La2 is coordinated with 6 or 7 oxygens in heavily distorted cubes. Both DFT and PDF confirm that the excess tungsten (x) is incorporated in La2 (1/4, 1/4, 1/4) sites in the La27W5O55.5 composition. This additional tungsten can be considered as a donor self-dopant in the material and has implications to the conducting properties and the defect structure.

  7. Proton-neutron interaction and nuclear structure

    SciTech Connect

    Casten, R.F.

    1986-01-01

    The pervasive role of the proton-neutron interaction in nuclear structure is discussed. Particular emphasis is given to its influence on the onset of collectivity and deformation, on intruder states, and on the evolution of subshell structure. The N/sub p/N/sub n/ scheme is outlined and some applications of it to collective model calculations and to nuclei far off stability are described. The concept of N/sub p/N/sub n/ multiplets is introduced. 32 refs., 20 figs.

  8. Fast Proton-Coupled Electron Transfer Observed for a High-Fidelity Structural and Functional [2Fe–2S] Rieske Model

    PubMed Central

    2015-01-01

    Rieske cofactors have a [2Fe–2S] cluster with unique {His2Cys2} ligation and distinct Fe subsites. The histidine ligands are functionally relevant, since they allow for coupling of electron and proton transfer (PCET) during quinol oxidation in respiratory and photosynthetic ET chains. Here we present the highest fidelity synthetic analogue for the Rieske [2Fe–2S] cluster reported so far. This synthetic analogue 5x– emulates the heteroleptic {His2Cys2} ligation of the [2Fe–2S] core, and it also serves as a functional model that undergoes fast concerted proton and electron transfer (CPET) upon reaction of the mixed-valent (ferrous/ferric) protonated 5H2– with TEMPO. The thermodynamics of the PCET square scheme for 5x– have been determined, and three species (diferric 52–, protonated diferric 5H–, and mixed-valent 53–) have been characterized by X-ray diffraction. pKa values for 5H– and 5H2– differ by about 4 units, and the reduction potential of 5H– is shifted anodically by about +230 mV compared to that of 52–. While the N–H bond dissociation free energy of 5H2– (60.2 ± 0.5 kcal mol–1) and the free energy, ΔG°CPET, of its reaction with TEMPO (−6.3 kcal mol–1) are similar to values recently reported for a homoleptic {N2/N2}-coordinated [2Fe–2S] cluster, CPET is significantly faster for 5H2– with biomimetic {N2/S2} ligation (k = (9.5 ± 1.2) × 104 M–1 s–1, ΔH‡ = 8.7 ± 1.0 kJ mol–1, ΔS‡ = −120 ± 40 J mol–1 K–1, and ΔG‡ = 43.8 ± 0.3 kJ mol–1 at 293 K). These parameters, and the comparison with homoleptic analogues, provide important information and new perspectives for the mechanistic understanding of the biological Rieske cofactor. PMID:24506804

  9. Protonated sugars: vibrational spectroscopy and conformational structure of protonated O-methyl α-D-galactopyranoside

    NASA Astrophysics Data System (ADS)

    Rudić, Svemir; Xie, Hong-bin; Gerber, R. Benny; Simons, John P.

    2012-08-01

    'Bridging' protons provide a common structural motif in biological assemblies such as proton wires and proton-bound dimers. Here we present a 'proof-of-principle' computational and vibrational spectroscopic investigation of an 'intra-molecular proton-bound dimer,' O-methyl α-D-galactopyranoside (αMeGal-H+), generated in the gas phase through photo-ionisation of its complex with phenol in a molecular beam. Its vibrational spectrum corresponds well with a classical molecular dynamics simulation conducted 'on-the-fly' and also with the lowest-energy structures predicted by DFT and ab initio calculations. They reveal proton-bound structures that bridge neighbouring pairs of oxygen atoms, preferentially O6 and O4, linked together within the carbohydrate scaffold. Motivated by the possibility of an entry into the microscopic mechanism of its acid (or enzyme)-catalysed hydrolysis, we also report the corresponding predictions for its singly hydrated complex.

  10. Theoretical Approaches to the Spin Structure of the Proton

    NASA Astrophysics Data System (ADS)

    Gonzalez Hernandez, Jose Osvaldo

    Many aspects of the structure of the proton are still unknown. One of the most noticeable unanswered question is the one of spin, that is, how can the fundamental degrees of freedom, quarks and gluons, account for the spin of the parent proton? It is known that quarks and gluons carry not only intrinsic but also orbital angular momentum. These two, combined, should in principle should add up to the value 1/2, which characterizes the spin of the proton. The mechanism responsible for this it is yet to be understood. It is not even clear how to define or "separate" the orbital angular momentum from the intrinsic angular momentum of the constituent particles. In recent years, one promising approach to this puzzle known as the spin crisis, is the possibility of accessing the transverse structure of the proton by means of the so called Generalized Parton Distributions (GPDs). These functions appear in the description of exclusive scattering processes. Since GPDs cannot be calculated from first principles, they must be extracted based upon models and experimental data. This dissertation presents the development of a new flexible parametrization, based on a "Reggeized" diquark approach, for chiral-even GPDs. This model is then used to analyze the significance of the different GPDs in some Deeply Virtual Compton Scattering measurements from Jlab; the results from this analysis are extended to the kinematical region relevant at the HERMES experiment. Subsequently, the model is extended to chiral-odd GPDs. With the tool of this model in hand, a study of the flavor dependence of Dirac and Pauli form factors is conducted. The connections between GPDs and other distribution functions are addressed in the last chapter, in the context of Wigner Distributions and possible probabilistic interpretations.

  11. Structural and energetic determinants of proton transfer in bacteriorhodopsin

    SciTech Connect

    Bondar, A.N.; Smith, Jeremy C; Fischer, S.

    2006-05-01

    In the light-driven bacteriorhodopsin proton pump, the first proton transfer step is from the retinal Schiff base to a nearby carboxylate group. The mechanism of this transfer step is highly controversial, in particular whether a direct proton jump is allowed. Here, we review the structural and energetic determinants of the direct proton transfer path computed by using a combined quantum mechanical/molecular mechanical approach. Both protein flexibility and electrostatic interactions play an important role in shaping the proton transfer energy profile. Detailed analysis of the energetics of putative transitions in the first half of the photocycle focuses on two elements that determine the likelihood that a given configuration of the active site is populated during the proton-pumping cycle. First, the rate-limiting barrier for proton transfer must be consistent with the kinetics of the photocycle. Second, the active-site configuration must be compatible with a productive overall pumping cycle.

  12. Optimized enzymatic dual functions of PaPrx protein by proton irradiation

    PubMed Central

    Park, Chul-Hong; Lee, Seung Sik; Kim, Kye Ryung; Jung, Myung Hwan; Lee, Sang Yeol; Cho, Eun Ju; Singh, Sudhir; Chung, Byung Yeoup

    2014-01-01

    We investigated the effects of proton irradiation on the function and structure of the Pseudomonas aeruginosa peroxiredoxin (PaPrx). Polyacrylamide gel demonstrated that PaPrx proteins exposed to proton irradiation at several doses exhibited simultaneous formation of high molecular weight (HMW) complexes and fragmentation. Size-exclusion chromatography (SEC) analysis revealed that the number of fragments and very low molecular weight (LMW) structures increased as the proton irradiation dose increased. The peroxidase activity of irradiated PaPrx was preserved, and its chaperone activity was significantly increased by increasing the proton irradiation dose. The chaperone activity increased about 3–4 fold after 2.5 kGy proton irradiation, compared with that of non-irradiated PaPrx, and increased to almost the maximum activity after 10 kGy proton irradiation. We previously obtained functional switching in PaPrx proteins, by using gamma rays and electron beams as radiation sources, and found that the proteins exhibited increased chaperone activity but decreased peroxidase activity. Interestingly, in this study we newly found that proton irradiation could enhance both peroxidase and chaperone activities. Therefore, we can suggest proton irradiation as a novel protocol for conserved 2-Cys protein engineering. PMID:23753570

  13. Proton NMR studies of functionalized nanoparticles in aqueous environments

    NASA Astrophysics Data System (ADS)

    Tataurova, Yulia Nikolaevna

    in high-resolution NMR spectra. This technique is selective for protons on the surface organic functional groups due to their motional averaging in solution. In this study, 1H solution NMR spectroscopy was used to investigate the interface of the organic functional groups in D2O. The pKa for these functional groups covalently bound to the surface of nanoparticles was determined using an NMR-pH titration method based on the variation in the proton chemical shift for the alkyl group protons closest to the amine group with pH. The adsorption of toxic contaminants (chromate and arsenate anions) on the surface of functionalized silicalite-1 and mesoporous silica nanoparticles has been studied by 1H solution NMR spectroscopy. With this method, the surface bound contaminants are detected. The analysis of the intensity and position of these peaks allows quantitative assessment of the relative amounts of functional groups with adsorbed metal ions. These results demonstrate the sensitivity of solution NMR spectroscopy to the electronic environment and structure of the surface functional groups on porous nanomaterials.

  14. Dynamic Short Hydrogen Bonds in Histidine Tetrad of Full-Length M2 Proton Channel Reveal Tetrameric Structural Heterogeneity and Functional Mechanism.

    PubMed

    Miao, Yimin; Fu, Riqiang; Zhou, Huan-Xiang; Cross, Timothy A

    2015-12-01

    The tetrameric M2 protein from influenza A conducts protons into the virus upon acid activation of its His37 tetrad and is a proven drug target. Here, in studies of full-length M2 protein solubilized in native-like liquid-crystalline lipid bilayers, a pH titration monitored by solid-state nuclear magnetic resonance revealed a clustering of the first three His37 pKas (6.3, 6.3, and 5.5). When the +2 state of the tetrad accepts a third proton from the externally exposed portion of the channel pore and releases a proton to the internally exposed pore, successful proton conductance is achieved, but more frequently the tetrad accepts and returns the proton to the externally exposed pore, resulting in a futile cycle. Both dynamics and conformational heterogeneity of the His37 tetrad featuring short hydrogen bonds between imidazolium-imidazole pairs are characterized, and the heterogeneity appears to reflect oligomeric helix packing and the extent of transmembrane helical bending around Gly34.

  15. The causes and functions of mitochondrial proton leak.

    PubMed

    Brand, M D; Chien, L F; Ainscow, E K; Rolfe, D F; Porter, R K

    1994-08-30

    The non-linear relationship between respiration rate and protonmotive force in isolated mitochondria is explained entirely by delta p-dependent changes in the proton conductance of the mitochondrial inner membrane and is not caused by redox slip in the proton pumps. Mitochondrial proton leak occurs in intact cells and tissues: the futile cycle of proton pumping and proton leak accounts for 26% +/- 7% of the total oxygen consumption rate or 33% +/- 7% of the mitochondrial respiration rate of isolated hepatocytes (mean +/- S.D. for 43 rats); 52% of the oxygen consumption rate of resting perfused muscle and up to 38% of the basal metabolic rate of a rat, suggesting that heat production may be an important function in the proton leak in homeotherms. Together with non-mitochondrial oxygen consumption, it lowers the effective P/O ratio in cells from maximum possible values of 2.33 (palmitate oxidation) or 2.58 (glucose oxidation) to as low as 1.1 in liver or 0.8 in muscle. The effective P/O ratio increases in response to ATP demand; the ability to allow rapid switching of flux from leak to ATP turnover may be an even more important function of the leak reaction than heat production. The mitochondrial proton conductance in isolated mitochondria and in hepatocytes is greatly modulated by thyroid hormones, by phylogeny and by body mass. Usually the reactions of ATP turnover change in parallel so that the coupling ratio is not greatly affected. Changes in proton leak in tissues are brought about in the short term by changes in mitochondrial protonmotive force and in the longer term by changes in the surface area and proton permeability of the mitochondrial inner membrane. Permeability changes are probably caused by changes in the fatty acid composition of the membrane phospholipids.

  16. Exchangers man the pumps: Functional interplay between proton pumps and proton-coupled Ca(2+) exchangers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tonoplast-localised proton-coupled Ca(2+) transporters encoded by cation/H(+) exchanger (CAX) genes play a critical role in sequestering Ca(2+) into the vacuole. These transporters may function in coordination with Ca(2+) release channels, to shape stimulus-induced cytosolic Ca(2+) elevations. Recen...

  17. Structure of fully protonated proteins by proton-detected magic-angle spinning NMR.

    PubMed

    Andreas, Loren B; Jaudzems, Kristaps; Stanek, Jan; Lalli, Daniela; Bertarello, Andrea; Le Marchand, Tanguy; Cala-De Paepe, Diane; Kotelovica, Svetlana; Akopjana, Inara; Knott, Benno; Wegner, Sebastian; Engelke, Frank; Lesage, Anne; Emsley, Lyndon; Tars, Kaspars; Herrmann, Torsten; Pintacuda, Guido

    2016-08-16

    Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that, at 100-kHz MAS and above, spectral resolution is high enough to detect resolved correlations from amide and side-chain protons of all residue types, and to reliably measure a dense network of (1)H-(1)H proximities that define a protein structure. The high data quality allowed the correct identification of internuclear distance restraints encoded in 3D spectra with automated data analysis, resulting in accurate, unbiased, and fast structure determination. Additionally, we find that narrower proton resonance lines, longer coherence lifetimes, and improved magnetization transfer offset the reduced sample size at 100-kHz spinning and above. Less than 2 weeks of experiment time and a single 0.5-mg sample was sufficient for the acquisition of all data necessary for backbone and side-chain resonance assignment and unsupervised structure determination. We expect the technique to pave the way for atomic-resolution structure analysis applicable to a wide range of proteins. PMID:27489348

  18. Structure of fully protonated proteins by proton-detected magic-angle spinning NMR.

    PubMed

    Andreas, Loren B; Jaudzems, Kristaps; Stanek, Jan; Lalli, Daniela; Bertarello, Andrea; Le Marchand, Tanguy; Cala-De Paepe, Diane; Kotelovica, Svetlana; Akopjana, Inara; Knott, Benno; Wegner, Sebastian; Engelke, Frank; Lesage, Anne; Emsley, Lyndon; Tars, Kaspars; Herrmann, Torsten; Pintacuda, Guido

    2016-08-16

    Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that, at 100-kHz MAS and above, spectral resolution is high enough to detect resolved correlations from amide and side-chain protons of all residue types, and to reliably measure a dense network of (1)H-(1)H proximities that define a protein structure. The high data quality allowed the correct identification of internuclear distance restraints encoded in 3D spectra with automated data analysis, resulting in accurate, unbiased, and fast structure determination. Additionally, we find that narrower proton resonance lines, longer coherence lifetimes, and improved magnetization transfer offset the reduced sample size at 100-kHz spinning and above. Less than 2 weeks of experiment time and a single 0.5-mg sample was sufficient for the acquisition of all data necessary for backbone and side-chain resonance assignment and unsupervised structure determination. We expect the technique to pave the way for atomic-resolution structure analysis applicable to a wide range of proteins.

  19. A Proton-Cyclotron Wave Storm Generated by Unstable Proton Distribution Functions in the Solar Wind

    NASA Technical Reports Server (NTRS)

    Wicks, R. T.; Alexander, R. L.; Stevens, M.; Wilson, L. B., III; Moya, P. S.; Vinas, A.; Jian, L. K.; Roberts, D. A.; O’Modhrain, S.; Gilbert, J. A.; Zurbuchen, T. H.

    2016-01-01

    We use audification of 0.092 seconds cadence magnetometer data from the Wind spacecraft to identify waves with amplitudes greater than 0.1 nanoteslas near the ion gyrofrequency (approximately 0.1 hertz) with duration longer than 1 hour during 2008. We present one of the most common types of event for a case study and find it to be a proton-cyclotron wave storm, coinciding with highly radial magnetic field and a suprathermal proton beam close in density to the core distribution itself. Using linear Vlasov analysis, we conclude that the long-duration, large-amplitude waves are generated by the instability of the proton distribution function. The origin of the beam is unknown, but the radial field period is found in the trailing edge of a fast solar wind stream and resembles other events thought to be caused by magnetic field footpoint motion or interchange reconnection between coronal holes and closed field lines in the corona.

  20. Spin Structure Function Measurements in Hall C at Jefferson Lab

    SciTech Connect

    Wood, Stephen A.

    2008-11-01

    This presentation introduces the spin structure functions and resonant spin structure, and it discusses the experimental approaches for studying spin structure via polarized electron beam interactions with frozen polarized proton and deuteron targets.

  1. The quark and gluon structure of the proton.

    PubMed

    Perez, E; Rizvi, E

    2013-04-01

    In this paper we present a review of the structure of the proton and the current status of our knowledge of the parton distribution functions (PDFs). The lepton-nucleon scattering experiments which provide the main constraints in PDF extractions are introduced and their measurements are discussed. Particular emphasis is given to the HERA data which cover a wide kinematic region. Hadron-hadron scattering measurements which provide supplementary information are also discussed. The methods used by various groups to extract the PDFs in QCD analyses of hard scattering data are presented and their results are compared. The use of existing measurements allows predictions for cross sections at the LHC to be made. A comparison of these predictions for selected processes is given. First measurements from the LHC experiments are compared to predictions and some initial studies of the impact of this new data on the PDFs are presented. PMID:23503469

  2. Function of Proton Channels in Lung Epithelia.

    PubMed

    Fischer, Horst

    2012-05-01

    The properties of the voltage-dependent H(+) channel have been studied in lung epithelial cells for many years, and recently HVCN1 mRNA expression has been linked directly to H(+) channel function in lung epithelium. The H(+) channel is activated by strong membrane depolarization, intracellular acidity, or extracellular alkalinity. Early on it was noted that these are surprising physiological channel characteristics when considering that lung epithelial cells have rather stable membrane potentials and a well pH-buffered intracellular milieu. This raised the question under which conditions the H(+) channel is active in lung epithelium and what is its physiological function there. Current understanding of the HVCN1 H(+) channel in lung epithelial acid secretion, its activation by an alkaline mucosal extracellular pH, and its role in the regulation of the mucosal pH of the lung has resulted in a model of mucosal pH regulation based on the parallel function of the HVCN1 H(+) channel and the CFTR HCO(3) (-) channel, which suggests that HVCN1 is a critical factor that maintains a neutral surface pH in the lung.

  3. Structures of protonated methanol clusters and temperature effects.

    PubMed

    Fifen, Jean Jules; Nsangou, Mama; Dhaouadi, Zoubeida; Motapon, Ousmanou; Jaidane, Nejm-Eddine

    2013-05-14

    The accurate evaluation of pKa's, or solvation energies of the proton in methanol at a given temperature is subject to the determination of the most favored structures of various isomers of protonated (H(+)(MeOH)n) and neutral ((MeOH)n) methanol clusters in the gas phase and in methanol at that temperature. Solvation energies of the proton in a given medium, at a given temperature may help in the determination of proton affinities and proton dissociation energies related to the deprotonation process in that medium and at that temperature. pKa's are related to numerous properties of drugs. In this work, we were interested in the determination of the most favored structures of various isomers of protonated methanol clusters in the gas phase and in methanol, at a given temperature. For this aim, the M062X/6-31++G(d,p) and B3LYP/6-31++G(d,p) levels of theory were used to perform geometries optimizations and frequency calculations on various isomers of (H(+)(MeOH)n) in both phases. Thermal effects were retrieved using our homemade FORTRAN code. Thus, we accessed the relative populations of various isomers of protonated methanol clusters, in both phases for temperatures ranging from 0 to 400 K. As results, in the gas phase, linear structures are entropically more favorable at high temperatures, while more compact ones are energetically more favorable at lower temperatures. The trend is somewhat different when bulk effects are taken into account. At high temperatures, the linear structure only dominates the population for n ≤ 6, while it is dominated by the cyclic structure for larger cluster sizes. At lower temperatures, compact structures still dominate the population, but with an order different from the one established in the gas phase. Hence, temperature effects dominate solvent effects in small cluster sizes (n ≤ 6), while the reverse trend is noted for larger cluster sizes. PMID:23676038

  4. Measurements of the Q{sup 2}-Dependence of the Proton and Neutron Spin Structure Functions g{sub 1}{sup p} and g{sub 1}{sup n}

    SciTech Connect

    Perry Anthony; R.G. Arnold; Todd Averett; H.R. Band; M.C. Berisso; H. Borel; Peter Bosted; Stephen Bueltmann; M. Buenerd; T. Chupp; Steve Churchwell; G.R. Court; Donald Crabb; Donal Day; Piotr Decowski; P. DePietro; Robin D. Erbacher; R. Erickson; A. Feltham; Helene Fonvieille; Emil Frlez; R. Gearhart; V. Ghazikhanian; Javier Gomez; Keith Griffioen; C. Harris; M.A. Houlden; Emlyn Hughes; Charles Hyde-wright; G. Igo; Sebastien Incerti; John Jensen; J.R. Johnson; Paul King; Yu.G. Kolomensky; Sebastian Kuhn; Richard Lindgren; R.M. Lombard-Nelsen; Jacques Marroncle; James Mccarthy; Paul Mckee; Werner Meyer; Gregory Mitchell; Joseph Mitchell; Michael Olson; Seppo Penttila; Gerald Peterson; Gerassimos Petratos; R. Pitthan; Dinko Pocanic; R. Prepost; C. Prescott; Liming Qin; Brian Raue; D. Reyna; L.S. Rochester; Stephen Rock; Oscar Rondon-aramayo; Franck Sabatie; Ingo Sick; Tim Smith; Lee Sorrell; F. Staley; S. St. Lorant; L.M. Stuart; Z. Szalata; Y. Terrien; William Tobias; Luminita Todor; T. Toole; S. Trentalange; D. Walz; Robert Welsh; Frank Wesselmann; T.R. Wright; C.C. Young; Markus Zeier; Hong Guo Zhu; Benedikt Zihlmann

    2000-11-09

    The structure functions g{sub 1}{sup p} and g{sub 1}{sup n} have been measured over the range 0.014 < x < 0.9 and 1 < Q{sup 2} < 40 GeV{sup 2} using deep-inelastic scattering of 48 GeV longitudinally polarized electrons from polarized protons and deuterons. We find that the Q{sup 2} dependence of g{sub 1}{sup p} (g{sub 1}{sup n}) at fixed x is very similar to that of the spin-averaged structure function F{sub 1}{sup p} (F{sub 1}{sup n}). From a NLO QCD fit to all available data we find {Gamma}{sub 1}{sup p} - {Gamma}{sub 1}{sup n} = 0.176 {+-} 0.003 {+-} 0.007 at Q{sup 2} = 5 GeV{sup 2}, in agreement with the Bjorken sum rule prediction of 0.182 {+-} 0.005.

  5. Jet fragmentation functions in proton-proton collisions using soft-collinear effective theory

    NASA Astrophysics Data System (ADS)

    Chien, Yang-Ting; Kang, Zhong-Bo; Ringer, Felix; Vitev, Ivan; Xing, Hongxi

    2016-05-01

    The jet fragmentation function describes the longitudinal momentum distribution of hadrons inside a reconstructed jet. We study the jet fragmentation function in proton-proton collisions in the framework of soft-collinear effective theory (SCET). We find that, up to power corrections, the jet fragmentation function can be expressed as the ratio of the fragmenting jet function and the unmeasured jet function. Using renormalization group techniques, we are able to resum large logarithms of jet radii R in the perturbative expansion of the cross section. We use our theoretical formalism to describe the jet fragmentation functions for light hadron and heavy meson production measured at the Large Hadron Collider (LHC). Our calculations agree very well with the experimental data for the light hadron production. On the other hand, although our calculations for the heavy meson production inside jets are consistent with the PYTHIA simulation, they fail to describe the LHC data. We find that the jet fragmentation function for heavy meson production is very sensitive to the gluon-to-heavy-meson fragmentation function.

  6. ``PROTON Sponges": a Rigid Organic Scaffold to Reveal the Quantum Structure of the Intramolecular Proton Bond

    NASA Astrophysics Data System (ADS)

    Deblase, Andrew F.; Johnson, Mark A.; Scerba, Michael T.; Bloom, Steven; Lectka, Thomas; Dudding, Travis

    2012-06-01

    Spectroscopic analysis of systems containing charged hydrogen bonds (e.g. the Zundel ion, {H}5{O}2+) in a vibrationally cold regime is useful in decongesting numerous anharmonic features common to room temperature measurements.[Roscioli, J. R.; et. al. Science 2007] This approach has been extended to conjugate acids of the ``Proton Sponge" family of organic compounds, which contain strong intramolecular hydrogen bonds between proton donor (D) and acceptor (A) groups at the 1- and 8-positions. By performing {H}_2/{D}_2 vibrational predissociation spectroscopy on cryogenically cooled ions, we explore how the proximity and spatial orientation of D and A moieties relates to the spectroscopic signature of the shared proton. In the cases studied ({D = Me2N-H+; A = OH, O(C=O)Ph}), we observe strong anharmonic couplings between the shared proton and dark states that persist at these cryogenic temperatures. This leads to intense NH stretching features throughout the nominal CH stretching region (2800-3000 {cm}-1). Isotopic substitution has verified that the oscillator strength of these broad features is driven by NH stretching. Furthermore, the study of A = O(C=O)Ph has provided a spectroscopic snapshot of the shared proton at work as an active catalytic moiety fostering ester hydrolysis by first order acylium fission ({AAC1}). This is apparent by the high frequency carbonyl stretch at 1792 {cm}-1, which is a consequence of the strong hydrogen bond to the ether-ester oxygen atom. Thus, these ``Proton Sponges" are useful model systems that unearth the quantum structure and reactivity of shared proton interactions in organic compounds.

  7. Insight into proton transfer in phosphotungstic acid functionalized mesoporous silica-based proton exchange membrane fuel cells.

    PubMed

    Zhou, Yuhua; Yang, Jing; Su, Haibin; Zeng, Jie; Jiang, San Ping; Goddard, William A

    2014-04-01

    We have developed for fuel cells a novel proton exchange membrane (PEM) using inorganic phosphotungstic acid (HPW) as proton carrier and mesoporous silica as matrix (HPW-meso-silica) . The proton conductivity measured by electrochemical impedance spectroscopy is 0.11 S cm(-1) at 90 °C and 100% relative humidity (RH) with a low activation energy of ∼14 kJ mol(-1). In order to determine the energetics associated with proton migration within the HPW-meso-silica PEM and to determine the mechanism of proton hopping, we report density functional theory (DFT) calculations using the generalized gradient approximation (GGA). These DFT calculations revealed that the proton transfer process involves both intramolecular and intermolecular proton transfer pathways. When the adjacent HPWs are close (less than 17.0 Å apart), the calculated activation energy for intramolecular proton transfer within a HPW molecule is higher (29.1-18.8 kJ/mol) than the barrier for intermolecular proton transfer along the hydrogen bond. We find that the overall barrier for proton movement within the HPW-meso-silica membranes is determined by the intramolecular proton transfer pathway, which explains why the proton conductivity remains unchanged when the weight percentage of HPW on meso-silica is above 67 wt %. In contrast, the activation energy of proton transfer on a clean SiO2 (111) surface is computed to be as high as ∼40 kJ mol(-1), confirming the very low proton conductivity on clean silica surfaces observed experimentally.

  8. Molecular structures and protonation state of 2-Mercaptopyridine in aqueous solution

    NASA Astrophysics Data System (ADS)

    Eckert, S.; Miedema, P. S.; Quevedo, W.; O'Cinneide, B.; Fondell, M.; Beye, M.; Pietzsch, A.; Ross, M.; Khalil, M.; Föhlisch, A.

    2016-03-01

    The speciation of 2-Mercaptopyridine in aqueous solution has been investigated with nitrogen 1s Near Edge X-ray Absorption Fine Structure spectroscopy and time dependent Density Functional Theory. The prevalence of distinct species as a function of the solvent basicity is established. No indications of dimerization towards high concentrations are found. The determination of different molecular structures of 2-Mercaptopyridine in aqueous solution is put into the context of proton-transfer in keto-enol and thione-thiol tautomerisms.

  9. The structural basis of water permeation and proton exclusion in aquaporins.

    PubMed

    Fu, Dax; Lu, Min

    2007-01-01

    Aquaporins (AQPs) represent a ubiquitous class of integral membrane proteins that play critical roles in cellular osmoregulations in microbes, plants and mammals. AQPs primarily function as water-conducting channels, whereas members of a sub-class of AQPs, termed aquaglyceroporins, are permeable to small neutral solutes such as glycerol. While AQPs facilitate transmembrane permeation of water and/or small neutral solutes, they preclude the conduction of protons. Consequently, openings of AQP channels allow rapid water diffusion down an osmotic gradient without dissipating electrochemical potentials. Molecular structures of AQPs portray unique features that define the two central functions of AQP channels: effective water permeation and strict proton exclusion. This review describes AQP structures known to date and discusses the mechanisms underlying water permeation, proton exclusion and water permeability regulation. PMID:17710641

  10. The QCD Analysis Of The World Data On Structure Functions g{sub 1}{sup p,d,n} For Proton, Deuteron And Neutron

    SciTech Connect

    Savin, I. A.

    2007-06-13

    The fits of all published data on g1, including the new COMPASS measurements of g{sub 1}{sup d}(x,Q{sup 2}), have been performed by using two different QCD evolution formalisms in the next-to-leading-order (NLO) approximation. In both methods we obtain two solutions for fitted parameters of the parton distribution functions (PDFs), one with {delta}G>0 and the other - with {delta}G<0, where {delta}G is the first moment of the polarized gluon distribution in nucleon.

  11. Proton affinity determinations and proton-bound dimer structure indications in C2 to C15, (alpha),(omega)-alkyldiamines

    NASA Technical Reports Server (NTRS)

    Karpas, Z.; Harden, C. S.; Smith, P. B. W.

    1995-01-01

    The 'kinetic method' was used to determine the proton affinity (PA) of a,coalkyldiamines from collision induced dissociation (CID) studies of protonated heterodimers. These PA values were consistently lower than those reported in the proton affinity scale. The apparent discrepancy was rationalized in terms of differences in the conformation of the protonated diamine monomers. The minimum energy species, formed by equilibrium proton transfer processes, have a cyclic conformation and the ion charge is shared by both amino-groups which are bridged by the proton. On the other hand, the species formed through dissociation of protonated dimers have a linear structure and the charge is localized on one of the amino-groups. Thus, the difference in the PA values obtained by both methods is a measure of the additional stability acquired by the protonated diamines through cyclization and charge delocalization. The major collision dissociation pathway of the protonated diamine monomers involved elimination of an ammonia moiety. Other reactions observed included loss of the second amino-group and several other bond cleavages. CID of the protonated dimers involved primarily formation of a protonated monomer through cleavage of the weaker hydrogen bond and subsequently loss of ammonia at higher collision energies. As observed from the CID studies, doubly charged ions were also formed from the diamines under conditions of the electrospray ionization.

  12. Photon structure function

    SciTech Connect

    Bardeen, W.A.

    1980-11-01

    Theoretical understanding of the photon structure function is reviewed. As an illustration of the pointlike component, the parton model is briefly discussed. However, the systematic study of the photon structure function is presented through the framework of the operator product expansion. Perturbative QCD is used as the theoretical basis for the calculation of leading contributions to the operator product expansion. The influence of higher order QCD effects on these results is discussed. Recent results for the polarized structure functions are discussed.

  13. Tests of proton structure functions using leptons at CDF and D0: W charge asymmetry and Drell-Yan production. Version 1.0

    SciTech Connect

    Barbaro, P. de

    1995-06-13

    High statistics W charge asymmetry measurements at the Tevatron {bar p}p collider significantly constrain the u and d quark distributions, and specifically the slope of the d(x)/u(x) in the x range 0.007 to 0.27. The authors present measurements of lepton charge asymmetry as a function of lepton rapidity, A(y{sub l}) at {radical}s = 1.8 TeV for {vert_bar}y{sub l}{vert_bar} < 2.0, for the W decays to electrons and muons recorded by the CDF detector during the 1992-93 run ({approx} 20 pb{sup {minus}1}), and the first {approx} 50 pb{sup {minus}1} of data from the 1994-95 run. These precise data make possible further discrimination between sets of modern parton distributions. In particular it is found that the most recent parton distributions, which included the CDF 1992-93 W asymmetry data in their fits (MRSA, CTEQ3M and GRV94) are still in good agreement with the more precise data from the 1994-95 run. W charge asymmetry results from D0 based on {approx} 6.5 pb{sup {minus}1} data from 1992-1993 run and {approx} 29.7 pb{sup {minus}1} data from 1994-1995 run, using the W decays to muons, are also presented and are found to be consistent with CDF results. In addition, the authors present preliminary measurement of the Drell-Yan cross-section by CDF using a dielectron sample collected during the 1993-94 run ({approx} 20 pb{sup {minus}1}) and a high mass dimuon sample from the combined 1993-94 and 1994-95 runs ({approx} 70 pb{sup {minus}1}). The measurement is in good agreement with predictions using the most recent PDFs in a dilepton mass range between 11 and 350 GeV/c{sup 2}.

  14. Outcomes of Proton Therapy for Patients With Functional Pituitary Adenomas

    SciTech Connect

    Wattson, Daniel A.; Tanguturi, Shyam K.; Spiegel, Daphna Y.; Niemierko, Andrzej; Biller, Beverly M.K.; Nachtigall, Lisa B.; Bussière, Marc R.; Swearingen, Brooke; Chapman, Paul H.; Loeffler, Jay S.; Shih, Helen A.

    2014-11-01

    Purpose/Objective(s): This study evaluated the efficacy and toxicity of proton therapy for functional pituitary adenomas (FPAs). Methods and Materials: We analyzed 165 patients with FPAs who were treated at a single institution with proton therapy between 1992 and 2012 and had at least 6 months of follow-up. All but 3 patients underwent prior resection, and 14 received prior photon irradiation. Proton stereotactic radiosurgery was used for 92% of patients, with a median dose of 20 Gy(RBE). The remainder received fractionated stereotactic proton therapy. Time to biochemical complete response (CR, defined as ≥3 months of normal laboratory values with no medical treatment), local control, and adverse effects are reported. Results: With a median follow-up time of 4.3 years (range, 0.5-20.6 years) for 144 evaluable patients, the actuarial 3-year CR rate and the median time to CR were 54% and 32 months among 74 patients with Cushing disease (CD), 63% and 27 months among 8 patients with Nelson syndrome (NS), 26% and 62 months among 50 patients with acromegaly, and 22% and 60 months among 9 patients with prolactinomas, respectively. One of 3 patients with thyroid stimulating hormone—secreting tumors achieved CR. Actuarial time to CR was significantly shorter for corticotroph FPAs (CD/NS) compared with other subtypes (P=.001). At a median imaging follow-up time of 43 months, tumor control was 98% among 140 patients. The actuarial 3-year and 5-year rates of development of new hypopituitarism were 45% and 62%, and the median time to deficiency was 40 months. Larger radiosurgery target volume as a continuous variable was a significant predictor of hypopituitarism (adjusted hazard ratio 1.3, P=.004). Four patients had new-onset postradiosurgery seizures suspected to be related to generously defined target volumes. There were no radiation-induced tumors. Conclusions: Proton irradiation is an effective treatment for FPAs, and hypopituitarism remains the primary

  15. Structural characteristics of hydrated protons in the conductive channels: effects of confinement and fluorination studied by molecular dynamics simulation.

    PubMed

    Zhang, Ning; Song, Yuechun; Ruan, Xuehua; Yan, Xiaoming; Liu, Zhao; Shen, Zhuanglin; Wu, Xuemei; He, Gaohong

    2016-09-21

    The relationship between the proton conductive channel and the hydrated proton structure is of significant importance for understanding the deformed hydrogen bonding network of the confined protons which matches the nanochannel. In general, the structure of hydrated protons in the nanochannel of the proton exchange membrane is affected by several factors. To investigate the independent effect of each factor, it is necessary to eliminate the interference of other factors. In this paper, a one-dimensional carbon nanotube decorated with fluorine was built to investigate the independent effects of nanoscale confinement and fluorination on the structural properties of hydrated protons in the nanochannel using classical molecular dynamics simulation. In order to characterize the structure of hydrated protons confined in the channel, the hydrogen bonding interaction between water and the hydrated protons has been studied according to suitable hydrogen bond criteria. The hydrogen bond criteria were proposed based on the radial distribution function, angle distribution and pair-potential energy distribution. It was found that fluorination leads to an ordered hydrogen bonding structure of the hydrated protons near the channel surface, and confinement weakens the formation of the bifurcated hydrogen bonds in the radial direction. Besides, fluorination lowers the free energy barrier of hydronium along the nanochannel, but slightly increases the barrier for water. This leads to disintegration of the sequential hydrogen bond network in the fluorinated CNTs with small size. In the fluorinated CNTs with large diameter, the lower degree of confinement produces a spiral-like sequential hydrogen bond network with few bifurcated hydrogen bonds in the central region. This structure might promote unidirectional proton transfer along the channel without random movement. This study provides the cooperative effect of confinement dimension and fluorination on the structure and hydrogen

  16. Surface, structural and tensile properties of proton beam irradiated zirconium

    NASA Astrophysics Data System (ADS)

    Rafique, Mohsin; Chae, San; Kim, Yong-Soo

    2016-02-01

    This paper reports the surface, structural and tensile properties of proton beam irradiated pure zirconium (99.8%). The Zr samples were irradiated by 3.5 MeV protons using MC-50 cyclotron accelerator at different doses ranging from 1 × 1013 to 1 × 1016 protons/cm2. Both un-irradiated and irradiated samples were characterized using Field Emission Scanning Electron Microscope (FESEM), X-ray Diffraction (XRD) and Universal Testing Machine (UTM). The average surface roughness of the specimens was determined by using Nanotech WSxM 5.0 develop 7.0 software. The FESEM results revealed the formation of bubbles, cracks and black spots on the samples' surface at different doses whereas the XRD results indicated the presence of residual stresses in the irradiated specimens. Williamson-Hall analysis of the diffraction peaks was carried out to investigate changes in crystallite size and lattice strain in the irradiated specimens. The tensile properties such as the yield stress, ultimate tensile stress and percentage elongation exhibited a decreasing trend after irradiation in general, however, an inconsistent behavior was observed in their dependence on proton dose. The changes in tensile properties of Zr were associated with the production of radiation-induced defects including bubbles, cracks, precipitates and simultaneous recovery by the thermal energy generated with the increase of irradiation dose.

  17. Infrared Structural Biology: Detect Functionally Important Structural Motions of Proteins

    NASA Astrophysics Data System (ADS)

    Xie, Aihua

    Proteins are dynamic. Lack of dynamic structures of proteins hampers our understanding of protein functions. Infrared structural biology (IRSB) is an emerging technology. There are several advantages of IRSB for mechanistic studies of proteins: (1) its excellent dynamic range (detecting structural motions from picoseconds to >= seconds); (2) its high structural sensitivity (detect tiny but functionally important structural motions such as proton transfer and changes in hydrogen bonding interaction); (3) its ability to detect different structural motions simultaneously. Successful development of infrared structural biology demands not only new experimental techniques (from infrared technologies to chemical synthesis and cell biology), but also new data processing (how to translate infrared signals into quantitative structural information of proteins). These topics will be discussed as well as examples of how to use IRSB to study structure-function relationship of proteins. This work was supported by NSF DBI1338097 and OCAST HR10-078.

  18. Proton Conduction in Sulfonated Organic-Inorganic Hybrid Monoliths with Hierarchical Pore Structure.

    PubMed

    von der Lehr, Martin; Seidler, Christopher F; Taffa, Dereje H; Wark, Michael; Smarsly, Bernd M; Marschall, Roland

    2016-09-28

    Porous organic-inorganic hybrid monoliths with hierarchical porosity exhibiting macro- and mesopores are prepared via sol-gel process under variation of the mesopore size. Organic moieties in the pore walls are incorporated by substituting up to 10% of the silicon precursor tetramethylorthosilicate with bisilylated benzene molecules. After functionalization with sulfonic acid groups, the resulting sulfonated hybrid monoliths featuring a bimodal pore structure are investigated regarding proton conduction depending on temperature and relative humidity. The hierarchical pore system and controlled mesopore design turn out to be crucial for sulfonation and proton conduction. These sulfonated hybrid hierarchical monoliths containing only 10% organic precursor exhibit higher proton conduction at different relative humidities than sulfonated periodic mesoporous organosilica made of 100% bisilylated precursors exhibiting solely mesopores, even with a lower concentration of sulfonic acid groups. PMID:27598017

  19. Proton Conduction in Sulfonated Organic-Inorganic Hybrid Monoliths with Hierarchical Pore Structure.

    PubMed

    von der Lehr, Martin; Seidler, Christopher F; Taffa, Dereje H; Wark, Michael; Smarsly, Bernd M; Marschall, Roland

    2016-09-28

    Porous organic-inorganic hybrid monoliths with hierarchical porosity exhibiting macro- and mesopores are prepared via sol-gel process under variation of the mesopore size. Organic moieties in the pore walls are incorporated by substituting up to 10% of the silicon precursor tetramethylorthosilicate with bisilylated benzene molecules. After functionalization with sulfonic acid groups, the resulting sulfonated hybrid monoliths featuring a bimodal pore structure are investigated regarding proton conduction depending on temperature and relative humidity. The hierarchical pore system and controlled mesopore design turn out to be crucial for sulfonation and proton conduction. These sulfonated hybrid hierarchical monoliths containing only 10% organic precursor exhibit higher proton conduction at different relative humidities than sulfonated periodic mesoporous organosilica made of 100% bisilylated precursors exhibiting solely mesopores, even with a lower concentration of sulfonic acid groups.

  20. Structure function monitor

    DOEpatents

    McGraw, John T.; Zimmer, Peter C.; Ackermann, Mark R.

    2012-01-24

    Methods and apparatus for a structure function monitor provide for generation of parameters characterizing a refractive medium. In an embodiment, a structure function monitor acquires images of a pupil plane and an image plane and, from these images, retrieves the phase over an aperture, unwraps the retrieved phase, and analyzes the unwrapped retrieved phase. In an embodiment, analysis yields atmospheric parameters measured at spatial scales from zero to the diameter of a telescope used to collect light from a source.

  1. Systematic Structural Elucidation for the Protonated Form of Rare Earth Bis(porphyrinato) Double-Decker Complexes: Direct Structural Evidence of the Location of the Attached Proton.

    PubMed

    Yamashita, Ken-Ichi; Sakata, Naoya; Ogawa, Takuji

    2016-09-01

    Direct structural evidence of the presence and location of the attached proton in the protonated form of rare earth bis(porphyrinato) double-decker complexes is obtained from an X-ray diffraction study of single crystals for a series of protonated forms of bis(tetraphenylporphyrinato) complexes [M(III)(tpp)(tppH)] (M = Tb, Y, Sm, Nd, and La). When CHCl3 is used as a solvent for crystallization of the complexes, their nondisordered molecular structures are obtained and the attached proton is identified on one of the eight nitrogen atoms. Use of other solvents affords another type of crystal, in which the position of the proton is disordered and thus the molecular structure is averaged. La complex also affords the disordered average structure even when CHCl3 is used for crystallization. A variable-temperature diffraction study for the Tb complex reveals that the dynamics of the proton in the nondisordered crystal is restricted. PMID:27541189

  2. Systematic Structural Elucidation for the Protonated Form of Rare Earth Bis(porphyrinato) Double-Decker Complexes: Direct Structural Evidence of the Location of the Attached Proton.

    PubMed

    Yamashita, Ken-Ichi; Sakata, Naoya; Ogawa, Takuji

    2016-09-01

    Direct structural evidence of the presence and location of the attached proton in the protonated form of rare earth bis(porphyrinato) double-decker complexes is obtained from an X-ray diffraction study of single crystals for a series of protonated forms of bis(tetraphenylporphyrinato) complexes [M(III)(tpp)(tppH)] (M = Tb, Y, Sm, Nd, and La). When CHCl3 is used as a solvent for crystallization of the complexes, their nondisordered molecular structures are obtained and the attached proton is identified on one of the eight nitrogen atoms. Use of other solvents affords another type of crystal, in which the position of the proton is disordered and thus the molecular structure is averaged. La complex also affords the disordered average structure even when CHCl3 is used for crystallization. A variable-temperature diffraction study for the Tb complex reveals that the dynamics of the proton in the nondisordered crystal is restricted.

  3. Periodic Interference Structures in the Timelike Proton Form Factor.

    PubMed

    Bianconi, Andrea; Tomasi-Gustafsson, Egle

    2015-06-12

    An intriguing and elusive feature of the timelike hadron form factor is the possible presence of an imaginary part associated to rescattering processes. We find evidence of that in the recent and precise data on the proton timelike form factor measured by the BABAR Collaboration. By plotting these data as a function of the 3-momentum of the relative motion of the final proton and antiproton, a systematic sinusoidal modulation is highlighted in the near-threshold region. Our analysis attributes this pattern to rescattering processes at a relative distance of 0.7-1.5 fm between the centers of the forming hadrons. This distance implies a large fraction of inelastic processes in pp interactions, and a large imaginary part in the related e(+)e(-)→pp reaction because of unitarity. PMID:26196793

  4. Proton irradiation of germanium isotope multilayer structures at elevated temperatures

    NASA Astrophysics Data System (ADS)

    Schneider, S.; Bracht, H.; Petersen, M. C.; Hansen, J. Lundsgaard; Larsen, A. Nylandsted

    2008-02-01

    Irradiation of germanium (Ge) isotope heterostructures with 2.5 MeV protons have been performed at 550 °C. The applied proton flux was varied between 1.0 and 1.5 μA leading to various rates of Frenkel pair production. After irradiation, concentration profiles of the Ge isotopes were recorded by means of secondary ion mass spectrometry (SIMS). An inhomogeneous broadening of the isotope structure was observed. In addition to the effect of irradiation enhanced self-diffusion, an influence of the formation of microscopic defects on the detected broadening was ascertained. Atomic force and scanning electron microscopy show that the microscopic defects are most probably resulting from an aggregation of vacancies formed during irradiation. Numerical analysis of Ge profiles not disturbed by microdefect formation indicates a significant contribution of self-interstitials to self-diffusion under irradiation.

  5. Characteristics of proton velocity distribution functions in the near-lunar wake from Chandrayaan-1/SWIM observations

    NASA Astrophysics Data System (ADS)

    Dhanya, M. B.; Bhardwaj, Anil; Futaana, Yoshifumi; Barabash, Stas; Alok, Abhinaw; Wieser, Martin; Holmström, Mats; Wurz, Peter

    2016-06-01

    Due to the high absorption of solar wind plasma on the lunar dayside, a large scale wake structure is formed downstream of the Moon. However, recent in-situ observations have revealed the presence of protons in the near-lunar wake (100 km to 200 km from the surface). The solar wind, either directly or after interaction with the lunar surface (including magnetic anomalies), is the source of these protons in the near-wake region. Using the entire data from the SWIM sensor of the SARA experiment onboard Chandrayaan-1, we analyzed the velocity distribution of the protons observed in the near-lunar wake. The average velocity distribution functions, computed in the solar wind rest frame, were further separated based on the angle between the upstream solar wind velocity and the IMF. Although the protons enter the wake parallel as well as perpendicular to the IMF, the velocity distribution were not identical for the different IMF orientations, indicating the control of IMF in the proton entry processes. Several proton populations were identified from the velocity distribution and their possible entry mechanism were inferred based on the characteristics of the velocity distribution. These entry mechanisms include (i) diffusion of solar wind protons into the wake along IMF, (ii) the solar wind protons with finite gyro-radii that are aided by the wake boundary electric field, (iii) solar wind protons with gyro-radii larger than lunar radii from the tail of the solar wind velocity distribution, and (iv) scattering of solar wind protons from the dayside lunar surface or from magnetic anomalies. In order to gain more insight into the entry mechanisms associated with different populations, backtracing is carried out for each of these populations. For most of the populations, the source of the protons obtained from backtracing is found to be in agreement with that inferred from the velocity distribution. There are few populations that could not be explained by the known mechanisms

  6. Dynamic versus Static Hadronic Structure Functions

    SciTech Connect

    Brodsky, Stanley J.; /SLAC

    2009-01-09

    'Static' structure functions are the probabilistic distributions computed from the square of the light-front wavefunctions of the target hadron. In contrast, the 'dynamic' structure functions measured in deep inelastic lepton-hadron scattering include the effects of rescattering associated with the Wilson line. Initial- and final-state rescattering, neglected in the parton model, can have a profound effect in QCD hard-scattering reactions, producing single-spin asymmetries, diffractive deep inelastic scattering, diffractive hard hadronic reactions, the breakdown of the Lam-Tung relation in Drell-Yan reactions, nuclear shadowing, and non-universal nuclear antishadowing|novel leading-twist physics not incorporated in the light-front wavefunctions of the target computed in isolation. I also review how 'direct' higher-twist processes--where a proton is produced in the hard subprocess itself--can explain the anomalous proton-to-pion ratio seen in high centrality heavy ion collisions.

  7. Structure of an Inward Proton-Transporting Anabaena Sensory Rhodopsin Mutant: Mechanistic Insights.

    PubMed

    Dong, Bamboo; Sánchez-Magraner, Lissete; Luecke, Hartmut

    2016-09-01

    Microbial rhodopsins are light-activated, seven-α-helical, retinylidene transmembrane proteins that have been identified in thousands of organisms across archaea, bacteria, fungi, and algae. Although they share a high degree of sequence identity and thus similarity in structure, many unique functions have been discovered and characterized among them. Some function as outward proton pumps, some as inward chloride pumps, whereas others function as light sensors or ion channels. Unique among the microbial rhodopsins characterized thus far, Anabaena sensory rhodopsin (ASR) is a photochromic sensor that interacts with a soluble 14-kDa cytoplasmic transducer that is encoded on the same operon. The sensor itself stably interconverts between all-trans-15-anti and 13-cis-15-syn retinal forms depending on the wavelength of illumination, although only the former participates in a photocycle with a signaling M intermediate. A mutation in the cytoplasmic half-channel of the protein, replacing Asp217 with Glu (D217E), results in the creation of a light-driven, single-photon, inward proton transporter. We present the 2.3 Å structure of dark-adapted D217E ASR, which reveals significant changes in the water network surrounding Glu217, as well as a shift in the carbon backbone near retinal-binding Lys210, illustrating a possible pathway leading to the protonation of Glu217 in the cytoplasmic half-channel, located 15 Å from the Schiff base. Crystallographic evidence for the protonation of nearby Glu36 is also discussed, which was described previously by Fourier transform infrared spectroscopy analysis. Finally, two histidine residues near the extracellular surface and their possible role in proton uptake are discussed. PMID:27602724

  8. Structure of Protonated Threonine Dimers in the Gas Phase: Salt-Bridged or Charge-Solvated?

    NASA Astrophysics Data System (ADS)

    Yin, Hong; Kong, Xianglei

    2015-09-01

    For homodimers of amino acids, their salt-bridged structures are gradually stabilized as the proton affinity of the component amino acid increases. Threonine has a proton affinity value located in the middle of the list of 20 natural amino acids. Thus, identifying whether the most stable isomer of protonated threonine dimer (Thr2H+) has a charge-solvated or salt-bridged structure is important and helpful for understanding the structures of other homodimers. By combining infrared photodissociation (IRPD) spectroscopy and theoretical calculations, the structures of Thr2H+ were investigated. Based on calculations at the M062X/6-311++G(d,p)//M062X/6-311++G(d,p) level, the most stable isomer of Thr2H+ was computed to be a charge-solvated structure, with an energy 3.87 kcal/mol lower than the most stable salt-bridged isomer. The predicted infrared spectrum is in good agreement with the experimental spectrum. To evaluate the temperature effect on the distribution of different isomers, the relative concentrations of the six isomers of Thr2H+ were calculated at different temperatures, according to their partition functions and enthalpies. The results show that the isomers are dominated by charge-solvated structures at a temperature of 300 K.

  9. Proton Transport in Imidazoles: Unraveling the Role of Supramolecular Structure

    DOE PAGES

    Cosby, James T.; Holt, Adam P.; Griffin, Phillip; Wang, Yangyang; Sangoro, Joshua R.

    2015-09-18

    The impact of supramolecular hydrogen bonded networks on dynamics and charge transport in 2-ethyl-4-methylimidazole (2E4MIm), a model proton-conducting system, is investigated by broadband dielectric spectroscopy, depolarized dynamic light scattering, viscometry, and calorimetry. It is observed that the slow, Debye-like relaxation reflecting the supramolecular structure in neat 2E4MIm is eliminated upon the addition of minute amounts of levulinic acid. This is attributed to the dissociation of imidazole molecules and the breaking down of hydrogen-bonded chains, which leads to a 10-fold enhancement of ionic conductivity.

  10. Static and dynamic aspect of covariant density functional theory in proton rich nuclei

    SciTech Connect

    Ring, P.; Lalazissis, G. A.; Paar, N.; Vretenar, D.

    2007-11-30

    Proton rich nuclei are investigated in the framework of Covariant Density Functional Theory (CDFT). The Relativistic Hartree Bogoliubov (RHB) model is used to study the proton drip line in the region of heavy and superheavy nuclei. The dynamical behavior of nuclei with a large proton excess is studied within the Relativistic Quasiparticle Random Phase Approximation (RQRPA). Low lying El-strength is observed and it is shown that it corresponds to an oscillation of the proton skin against the isospin saturated neutron-proton core. This mode is in full analogy to the neutron pygmy resonances found in many nuclei with neutron excess.

  11. Spin structure functions

    SciTech Connect

    Jian-ping Chen, Alexandre Deur, Sebastian Kuhn, Zein-eddine Meziani

    2011-06-01

    Spin-dependent observables have been a powerful tool to probe the internal structure of the nucleon and to understand the dynamics of the strong interaction. Experiments involving spin degrees of freedom have often brought out surprises and puzzles. The so-called "spin crisis" in the 1980s revealed the limitation of naive quark-parton models and led to intensive worldwide efforts, both experimental and theoretical, to understand the nucleon spin structure. With high intensity and high polarization of both the electron beam and targets, Jefferson Lab has the world's highest polarized luminosity and the best figure-of-merit for precision spin structure measurements. It has made a strong impact in this subfield of research. This chapter will highlight Jefferson Lab's unique contributions in the measurements of valence quark spin distributions, in the moments of spin structure functions at low to intermediate Q2, and in the transverse spin structure.

  12. Controlled multiple functionalization of mesoporous silica nanoparticles: homogeneous implementation of pairs of functionalities communicating through energy or proton transfers.

    PubMed

    Noureddine, Achraf; Lichon, Laure; Maynadier, Marie; Garcia, Marcel; Gary-Bobo, Magali; Zink, Jeffrey I; Cattoën, Xavier; Wong Chi Man, Michel

    2015-07-14

    The synthesis of mesoporous silica nanoparticles bearing organic functionalities is strained by the careful adjustment of the reaction parameters, as the incorporation of functional and/or voluminous organosilanes during the sol-gel synthesis strongly affects the final structure of the nanoparticles. In this paper we describe the design of new clickable mesoporous silica nanoparticles as spheres or rods, synthesized by the co-condensation of TEOS with two clickable organosilanes (bearing alkyne and azide groups) and readily multi-functionalizable by CuAAC click chemistry. We show that controlled loadings of clickable functions can be homogeneously distributed within the MSN, allowing us to efficiently click-graft various pairs of functionalities while preserving the texture and morphology of the particles. The homogeneous distribution of the grafted functionalities was probed by FRET experiments between two anchored fluorophores. Moreover, a communication by proton transfer between two functions was demonstrated by constructing a light-actuated nanomachine that works through a proton transfer between a photoacid generator and a pH-sensitive supramolecular nanogate. The activation of the nanomachine enabled the successful release of rhodamine B in buffered solutions and the delivery of doxorubicin in breast cancer cells (MCF-7) upon blue irradiation.

  13. Analysis of proton radioactivity of nuclei by using proximity potential with a new universal function

    NASA Astrophysics Data System (ADS)

    Guo, C. L.; Zhang, G. L.

    2014-12-01

    The nuclear potential between proton and the daughter nuclei is calculated in the frame of the proximity potential with a new universal function. We obtained and analyzed the half-lives of proton radioactivity of the mother nuclei. By comparing to the experimental data and the other calculation results of ground and isomer states of proton emitters, it is found that the present calculation results can reproduce the order of magnitude of the experimental data well. It indicates that the proximity potential with a new universal function can estimate the half-life of proton radioactivity.

  14. Protonation-deprotonation and structural dynamics of antidiabetic drug metformin.

    PubMed

    Hernández, Belén; Pflüger, Fernando; Kruglik, Sergei G; Cohen, Régis; Ghomi, Mahmoud

    2015-10-10

    Since the late 1950s, metformin is the worldwide first-line pharmacologic treatment for type 2 diabetes. Beyond the fact that the mode of action of this drug has always been very difficult to elucidate, little is known about its physicochemical properties in aqueous solution. Herein, we focus on the protonation-deprotonation features of metformin by using jointly Raman scattering and theoretical calculations. Vibrational markers evidence the fact that within a wide pH interval extended at either side of the physiological one, i.e. ∼7 ± 4, metformin is mainly monoprotonated. Although the biprotonated form appears as major population at very low pH values (<1.5), Raman markers of neutral species do not dominate even at very high pH values (>13), presumably because of the extreme basicity of metformin as described by recent NMR measurements. Density functional theory calculations using both explicit and implicit hydration models, have led to presume a possible coexistence of two possible monoprotonated forms in aqueous environment. In conclusion, the biophysical features of this molecule and the amount used in clinical practice might certainly explain the pleiotropic actions toward several targets where metformin could be a permanent cationic partner, a proton donor/acceptor, as well as a good candidate for stabilizing the so-called π→π interactions.

  15. A Proton Wire and Water Channel Revealed in the Crystal Structure of Isatin Hydrolase

    PubMed Central

    Bjerregaard-Andersen, Kaare; Sommer, Theis; Jensen, Jan K.; Jochimsen, Bjarne; Etzerodt, Michael; Morth, J. Preben

    2014-01-01

    The high resolution crystal structures of isatin hydrolase from Labrenzia aggregata in the apo and the product state are described. These are the first structures of a functionally characterized metal-dependent hydrolase of this fold. Isatin hydrolase converts isatin to isatinate and belongs to a novel family of metalloenzymes that include the bacterial kynurenine formamidase. The product state, mimicked by bound thioisatinate, reveals a water molecule that bridges the thioisatinate to a proton wire in an adjacent water channel and thus allows the proton released by the reaction to escape only when the product is formed. The functional proton wire present in isatin hydrolase isoform b represents a unique catalytic feature common to all hydrolases is here trapped and visualized for the first time. The local molecular environment required to coordinate thioisatinate allows stronger and more confident identification of orthologous genes encoding isatin hydrolases within the prokaryotic kingdom. The isatin hydrolase orthologues found in human gut bacteria raise the question as to whether the indole-3-acetic acid degradation pathway is present in human gut flora. PMID:24917679

  16. Electronic band structure effects in the stopping of protons in copper

    NASA Astrophysics Data System (ADS)

    Quashie, Edwin E.; Saha, Bidhan C.; Correa, Alfredo A.

    2016-10-01

    We present an ab initio study of the electronic stopping power of protons in copper over a wide range of proton velocities v =0.02 -10 a .u . where we take into account nonlinear effects. Time-dependent density functional theory coupled with molecular dynamics is used to study electronic excitations produced by energetic protons. A plane-wave pseudopotential scheme is employed to solve the time-dependent Kohn-Sham equations for a moving ion in a periodic crystal. The electronic excitations and the band structure determine the stopping power of the material and alter the interatomic forces for both channeling and off-channeling trajectories. Our off-channeling results are in quantitative agreement with experiments, and at low velocity they unveil a crossover region of superlinear velocity dependence (with a power of ˜1.5 ) in the velocity range v =0.07 -0.3 a .u . , which we associate to the copper crystalline electronic band structure. The results are rationalized by simple band models connecting two separate regimes. We find that the limit of electronic stopping v →0 is not as simple as phenomenological models suggest and it is plagued by band-structure effects.

  17. Visualizing proton antenna in a high-resolution green fluorescent protein structure.

    PubMed

    Shinobu, Ai; Palm, Gottfried J; Schierbeek, Abraham J; Agmon, Noam

    2010-08-18

    "Proton-collecting antenna" are conjectured to consist of several carboxylates within hydrogen-bond (HB) networks on the surface of proteins, which funnel protons to the orifice of an internal proton wire leading to the protein's active site. Yet such constructions were never directly visualized. Here we report an X-ray structure of green fluorescent protein (GFP) of the highest resolution to date (0.9 A). It allows the identification of some pivotal hydrogen atoms pertinent to uncertainties concerning the protonation state of the chromophore. Applying a computer algorithm for mapping proton wires in proteins reveals the previously observed "active site wire" connecting Glu222 with the surface carboxylate Glu5. In addition, it is now possible to identify what appears to be a proton-collecting apparatus of GFP. It consists of a negative surface patch containing carboxylates, threonines, and water molecules, connected by a HB network to Glu5. Furthermore, we detect exit points via Asn146 and His148 to a hydrophobic surface region. The more extensive HB network of the present structure, as compared with earlier GFP structures, is not accidental. A systematic investigation of over 100 mutants shows a clear correlation between the observed water content of GFP X-ray structures and their resolution. With increasing water content, the proton wires become progressively larger. These findings corroborate the scenario in which the photodissociated proton from wild-type GFP can leak outside, whereafter another proton is recruited via the proton-collecting apparatus reported herein.

  18. Interplay between structure and relaxations in perfluorosulfonic acid proton conducting membranes.

    PubMed

    Giffin, Guinevere A; Haugen, Gregory M; Hamrock, Steven J; Di Noto, Vito

    2013-01-16

    This study focuses on changes in the structure of ionomer membranes, provided by the 3M Fuel Cells Component Group, as a function of the equivalent weight (EW) and the relationship between the structure and the properties of the membrane. Wide-angle X-ray diffraction results showed evidence of both non-crystalline and crystalline ordered hydrophobic regions in all the EW membranes except the 700 EW membrane. The spectral changes evident in the vibrational spectra of the 3M membranes can be associated with two major phenomena: (1) dissociation of the proton from the sulfonic acid groups even in the presence of small amounts of water; and (2) changes in the conformation or the degree of crystallinity of the poly(tetrafluoroethylene) hydrophobic domains both as a function of EW and membrane water content. All the membranes, regardless of EW, are thermally stable up to 360 °C. The wet membranes have conductivities between 7 and 20 mS/cm at 125 °C. In this condition, the conductivity values follow VTF behavior, which suggests that the proton migration occurs via proton exchange processes between delocalization bodies (DBs) that are facilitated by the dynamics of the host polymer. The conductivity along the interface between the hydrophobic and hydrophilic domains makes a larger contribution in the smaller EW membranes likely due to the existence of a greater number of interfaces in the membrane. The larger crystalline domains present in the higher EW membranes provide percolation pathways for charge migration between DBs, which reduces the probability of charge transfer along the interface. Therefore, at higher EWs although there is charge migration along the interface within the hydrophobic-hydrophilic domains, the exchange of protons between different DBs is likely the rate-limiting step of the overall conduction process. PMID:23249300

  19. Neutron spin structure with polarized deuterons and spectator proton tagging at EIC

    DOE PAGES

    Cosyn, W.; Guzey, V.; Higinbotham, D. W.; Hyde, C.; Kuhn, S.; Nadel-Turonski, P.; Park, K.; Sargsian, M.; Strikman, M.; Weiss, C.

    2014-10-27

    The neutron's deep-inelastic structure functions provide essential information for the flavor separation of the nucleon parton densities, the nucleon spin decomposition, and precision studies of QCD phenomena in the flavor-singlet and nonsinglet sectors. Thus, traditional inclusive measurements on nuclear targets are limited by dilution from scattering on protons, Fermi motion and binding effects, final-state interactions, and nuclear shadowing at x << 0.1. An Electron-Ion Collider (EIC) would enable next-generation measurements of neutron structure with polarized deuteron beams and detection of forward-moving spectator protons over a wide range of recoil momenta (0 < pR << several 100 MeV in the nucleusmore » rest frame). The free neutron structure functions could be obtained by extrapolating the measured recoil momentum distributions to the on-shell point. The method eliminates nuclear modifications and can be applied to polarized scattering, as well as to semi-inclusive and exclusive final states. We review the prospects for neutron structure measurements with spectator tagging at EIC, the status of R&D efforts, and the accelerator and detector requirements.« less

  20. Neutron spin structure with polarized deuterons and spectator proton tagging at EIC

    SciTech Connect

    Cosyn, W.; Guzey, V.; Higinbotham, D. W.; Hyde, C.; Kuhn, S.; Nadel-Turonski, P.; Park, K.; Sargsian, M.; Strikman, M.; Weiss, C.

    2014-10-27

    The neutron's deep-inelastic structure functions provide essential information for the flavor separation of the nucleon parton densities, the nucleon spin decomposition, and precision studies of QCD phenomena in the flavor-singlet and nonsinglet sectors. Thus, traditional inclusive measurements on nuclear targets are limited by dilution from scattering on protons, Fermi motion and binding effects, final-state interactions, and nuclear shadowing at x << 0.1. An Electron-Ion Collider (EIC) would enable next-generation measurements of neutron structure with polarized deuteron beams and detection of forward-moving spectator protons over a wide range of recoil momenta (0 < pR << several 100 MeV in the nucleus rest frame). The free neutron structure functions could be obtained by extrapolating the measured recoil momentum distributions to the on-shell point. The method eliminates nuclear modifications and can be applied to polarized scattering, as well as to semi-inclusive and exclusive final states. We review the prospects for neutron structure measurements with spectator tagging at EIC, the status of R&D efforts, and the accelerator and detector requirements.

  1. Proton currents constrain structural models of voltage sensor activation

    PubMed Central

    Randolph, Aaron L; Mokrab, Younes; Bennett, Ashley L; Sansom, Mark SP; Ramsey, Ian Scott

    2016-01-01

    The Hv1 proton channel is evidently unique among voltage sensor domain proteins in mediating an intrinsic ‘aqueous’ H+ conductance (GAQ). Mutation of a highly conserved ‘gating charge’ residue in the S4 helix (R1H) confers a resting-state H+ ‘shuttle’ conductance (GSH) in VGCs and Ci VSP, and we now report that R1H is sufficient to reconstitute GSH in Hv1 without abrogating GAQ. Second-site mutations in S3 (D185A/H) and S4 (N4R) experimentally separate GSH and GAQ gating, which report thermodynamically distinct initial and final steps, respectively, in the Hv1 activation pathway. The effects of Hv1 mutations on GSH and GAQ are used to constrain the positions of key side chains in resting- and activated-state VS model structures, providing new insights into the structural basis of VS activation and H+ transfer mechanisms in Hv1. DOI: http://dx.doi.org/10.7554/eLife.18017.001 PMID:27572256

  2. The formic acid-nitric acid complex: microwave spectrum, structure, and proton transfer.

    PubMed

    Mackenzie, Rebecca B; Dewberry, Christopher T; Leopold, Kenneth R

    2014-09-11

    Rotational spectra are reported for seven isotopologues of the complex HCOOH-HNO3 in a supersonic jet. The system is planar and bound by a pair of hydrogen bonds, much like the more widely studied carboxylic acid dimers. Double proton exchange interconverts the system between a pair of equivalent structures, as revealed by a splitting of the a-type spectrum that disappears when one of the hydrogen bonding protons is replaced by deuterium. The observation of relative intensities that are consistent with nuclear spin statistics in a symmetric and antisymmetric pair of tunneling states provides additional evidence for such a motion. The observed splittings in the pure rotational spectrum are 1-2 orders of magnitude smaller than those recently reported in the pure rotational spectra of several related carboxylic acid dimers. This is a curious difference, although we note that because the observed spectra do not cross the tunneling doublet, the splittings are a measure of the difference in effective rotational constants for the two states, not the tunneling frequency itself. The observed rotational constants have been used to determine an accurate vibrationally averaged structure for the complex. The two hydrogen bond lengths, 1.686(17) Å and 1.813(10) Å for the hydrogen bonds involving the HNO3 and HCOOH protons, respectively, differ by 0.127(27) Å. Likewise, the associated oxygen-oxygen distances determined for the parent species, 2.631 and 2.794 Å, differ by 0.163 Å. These results suggest that the double proton transfer is necessarily accompanied by substantial motion of the heavy atom frame, and thus this system, in principle, provides an excellent prototype for multidimensional tunneling processes. Ab initio calculations of the binding energy and the barrier height are presented. Excellent agreement between the calculated equilibrium structure and the experimental, vibrationally averaged structure suggests that the vibrational wave function is not highly

  3. A density functional study of crystalline acetic acid and its proton transfer polymorphic forms

    NASA Astrophysics Data System (ADS)

    Rovira, Carme; Novoa, Juan J.

    2000-11-01

    We present a density functional study of the structure and dynamics of solid acetic acid. Our calculations are based on density functional theory combined with molecular dynamics, within the Car-Parrinello scheme. The computed structure of the acetic acid crystal, optimized without symmetry constraints, is in very good agreement with the experiment and reproduces the changes in the intramolecular structure when going from the gas phase to the solid. The cell parameters of the experimental structure are also well reproduced. Cooperative effects along the molecular chains building the crystal are found to be small (1.2 kcal/mol), although larger than it had been previously estimated. The anti conformation of the COOH fragment leads to a stable structure up to 250 K, with an energy of only 3 kcal/mol above that of the known syn form. The energy barrier associated with the most likely pathway for the syn to anti conformations, involving proton transfer along the OH⋯O units (<5.8 kcal/mol) is much smaller than the experimental barrier for the syn/anti isomerism in gas phase and in solution. Intramolecular and intermolecular reorganizations upon change to the anti structure are analyzed. Overall, our results pinpoint the anti form as a good candidate for a possible acetic acid polymorph.

  4. DNA structure and function.

    PubMed

    Travers, Andrew; Muskhelishvili, Georgi

    2015-06-01

    The proposal of a double-helical structure for DNA over 60 years ago provided an eminently satisfying explanation for the heritability of genetic information. But why is DNA, and not RNA, now the dominant biological information store? We argue that, in addition to its coding function, the ability of DNA, unlike RNA, to adopt a B-DNA structure confers advantages both for information accessibility and for packaging. The information encoded by DNA is both digital - the precise base specifying, for example, amino acid sequences - and analogue. The latter determines the sequence-dependent physicochemical properties of DNA, for example, its stiffness and susceptibility to strand separation. Most importantly, DNA chirality enables the formation of supercoiling under torsional stress. We review recent evidence suggesting that DNA supercoiling, particularly that generated by DNA translocases, is a major driver of gene regulation and patterns of chromosomal gene organization, and in its guise as a promoter of DNA packaging enables DNA to act as an energy store to facilitate the passage of translocating enzymes such as RNA polymerase.

  5. Hydrophobic plug functions as a gate in voltage-gated proton channels.

    PubMed

    Chamberlin, Adam; Qiu, Feng; Rebolledo, Santiago; Wang, Yibo; Noskov, Sergei Y; Larsson, H Peter

    2014-01-14

    Voltage-gated proton (Hv1) channels play important roles in the respiratory burst, in pH regulation, in spermatozoa, in apoptosis, and in cancer metastasis. Unlike other voltage-gated cation channels, the Hv1 channel lacks a centrally located pore formed by the assembly of subunits. Instead, the proton permeation pathway in the Hv1 channel is within the voltage-sensing domain of each subunit. The gating mechanism of this pathway is still unclear. Mutagenic and fluorescence studies suggest that the fourth transmembrane (TM) segment (S4) functions as a voltage sensor and that there is an outward movement of S4 during channel activation. Using thermodynamic mutant cycle analysis, we find that the conserved positively charged residues in S4 are stabilized by countercharges in the other TM segments both in the closed and open states. We constructed models of both the closed and open states of Hv1 channels that are consistent with the mutant cycle analysis. These structural models suggest that electrostatic interactions between TM segments in the closed state pull hydrophobic residues together to form a hydrophobic plug in the center of the voltage-sensing domain. Outward S4 movement during channel activation induces conformational changes that remove this hydrophobic plug and instead insert protonatable residues in the center of the channel that, together with water molecules, can form a hydrogen bond chain across the channel for proton permeation. This suggests that salt bridge networks and the hydrophobic plug function as the gate in Hv1 channels and that outward movement of S4 leads to the opening of this gate.

  6. Ab Initio Molecular Dynamics Simulations of an Excess Proton in a Triethylene Glycol-Water Solution: Solvation Structure, Mechanism, and Kinetics.

    PubMed

    McDonnell, Marshall T; Xu, Haixuan; Keffer, David J

    2016-06-16

    We investigate the solvation shell structures, the distribution of protonic defects, mechanistic details, kinetics, and dynamics of proton transfer for an excess proton in bulk water and for an excess proton in an aqueous solution of triethylene glycol (TEG) via Car-Parrinello molecular dynamics simulations. The PW91, PBE, and PBE with the Tkatchenko-Scheffler (TS) density-dependent dispersion functionals were used and compared for bulk water and the TEG-water mixtures. The excess proton is found to reside predominantly on water molecules but also resides on hydroxyl groups of TEG. The lifetimes associated with structural diffusion time scales of the protonated water were found to be on the order of ∼1 ps. All three functionals studied support the presolvation requirement for structural diffusion. The highest level of theory shows a reduction in the free energy barrier for water-water proton transfer in TEG-water mixtures compared to bulk water. The effect of TEG shows no strong change in the kinetics for TEG-water mixtures compared to bulk water for this same level of theory. The excess proton displays burst-rest behavior in the presence of TEG, similar to that found in bulk water. We find that the TEG chain disrupts the hydrogen-bond network, causing the solvation shell around water to be populated by TEG chain groups instead of other waters, reducing the rigidity of the hydrogen-bond network. Methylene is a dominant hydrogen bond donor for the protonated water in hydrogen-bond networks associated with proton transfer and structural diffusion. This is consistent with previous studies that have found the hydronium ion to be amphiphilic in nature and to have higher proton mobility at oil-water interfaces. PMID:27218455

  7. Vortex Dust Structures in the Track Plasma of a Proton Beam

    SciTech Connect

    Fortov, V.E.; Filinov, V.S.; Vladimirov, V.I.; Deputatova, L.V.; Petrov, O.F.; Molotkov, V.I.; Rykov, V.A.; Budnik, A.P.; D'yachenko, P.P.; Rykov, K.V.; Khudyakov, A.V.

    2005-07-15

    Results are presented from experimental and theoretical investigations of the behavior of dust grains in a track plasma produced by a beam of accelerated protons. The dynamic ordered dust structures in a proton-beam-produced plasma are obtained for the first time. The processes leading to the formation of such structures are simulated numerically. The experimentally obtained dynamic vortex dust structures in a track plasma of a proton beam are explained theoretically, and the theoretical model developed to describe such a plasma is verified experimentally. Numerical investigations carried out by the method of Brownian dynamics made it possible to qualitatively explain the characteristic features of the formation of vortex dust structures.

  8. Multi-functional composite structures

    DOEpatents

    Mulligan, Anthony C.; Halloran, John; Popovich, Dragan; Rigali, Mark J.; Sutaria, Manish P.; Vaidyanathan, K. Ranji; Fulcher, Michael L.; Knittel, Kenneth L.

    2010-04-27

    Fibrous monolith processing techniques to fabricate multifunctional structures capable of performing more than one discrete function such as structures capable of bearing structural loads and mechanical stresses in service and also capable of performing at least one additional non-structural function.

  9. Multi-functional composite structures

    DOEpatents

    Mulligan, Anthony C.; Halloran, John; Popovich, Dragan; Rigali, Mark J.; Sutaria, Manish P.; Vaidyanathan, K. Ranji; Fulcher, Michael L.; Knittel, Kenneth L.

    2004-10-19

    Fibrous monolith processing techniques to fabricate multifunctional structures capable of performing more than one discrete function such as structures capable of bearing structural loads and mechanical stresses in service and also capable of performing at least one additional non-structural function.

  10. Structure and Proton Conductivity in Mixtures of Poly(acrylic acid) and Imidazole

    NASA Astrophysics Data System (ADS)

    Yang, Han-Chang; Griffin, Philip J.; Winey, Karen I.; University of Pennsylvania Team

    2015-03-01

    Proton conductivity in polymer electrolyte membranes (PEMs) typically involves water, which requires that during operation the humidity of the PEM be carefully controlled. In contrast, anhydrous protic polymer membranes promote proton transport by incorporating heterocyclic molecules, such as imidazole and its derivatives, into acid-containing polymers. In this work, we explore the interplay between nanoscale-structure and proton conduction of poly(acrylic acid) (PAA) blended at varying compositions with 2-ethyl-4-methylimidazole (EMI). We present the glass transition temperature from differential scanning calorimetry, morphology characterization from X-ray scattering, and proton conductivity from electrical impedance spectroscopy.

  11. Structural transitions in polycytidylic acid: proton buffer capacity data.

    PubMed

    Zarudnaya, Margarita I; Samijlenko, Svitlana P; Potyahaylo, Andriy L; Hovorun, Dmytro M

    2002-01-01

    The pH-dependences of proton buffer capacity of poly(C) were computed on the basis of the literature data. In these curves there were observed four peaks: two narrow and two wide ones. The first narrow peak reflects the process of cooperative formation of double helices, which is induced by protonation of the N3 atom of nucleotide bases. The first wide peak is assigned to noncooperative process of poly(C) double helices protonation at the N3 nitrogen atom. It is proposed that the second wide peak corresponds to noncooperative protonation of the neutral cytosine bases at the oxygen atom. This reaction causes cooperative dissociation of the poly(C) double helices. The second narrow peak reflects the dissociation process. PMID:11991140

  12. Microdosimetry of the full slowing down of protons using Monte Carlo track structure simulations.

    PubMed

    Liamsuwan, T; Uehara, S; Nikjoo, H

    2015-09-01

    The article investigates two approaches in microdosimetric calculations based on Monte Carlo track structure (MCTS) simulations of a 160-MeV proton beam. In the first approach, microdosimetric parameters of the proton beam were obtained using the weighted sum of proton energy distributions and microdosimetric parameters of proton track segments (TSMs). In the second approach, phase spaces of energy depositions obtained using MCTS simulations in the full slowing down (FSD) mode were used for the microdosimetric calculations. Targets of interest were water cylinders of 2.3-100 nm in diameters and heights. Frequency-averaged lineal energies ([Formula: see text]) obtained using both approaches agreed within the statistical uncertainties. Discrepancies beyond this level were observed for dose-averaged lineal energies ([Formula: see text]) towards the Bragg peak region due to the small number of proton energies used in the TSM approach and different energy deposition patterns in the TSM and FSD of protons.

  13. Proton transfer from the inactive gas-phase nicotine structure to the bioactive aqueous-phase structure.

    PubMed

    Gaigeot, Marie-Pierre; Cimas, Alvaro; Seydou, Mahamadou; Kim, Ju-Young; Lee, Sungyul; Schermann, Jean-Pierre

    2010-12-29

    The role of water in the structural change of nicotine from its inactive form in the gas phase to its bioactive form in aqueous solution has been investigated by two complementary theoretical approaches, i.e., geometry optimizations and molecular dynamics. Structures of the lowest-energy nicotineH(+)-(H(2)O)(n) complexes protonated either on the pyridine (inactive form) or pyrrolidine (active form) ring have been calculated, as well as the free-energy barriers for the proton-transfer tautomerization between the two cycles. These structures show chains of 2-4 water molecules bridging the two protonation sites. The room-temperature free-energy barrier to tautomerization along the minimum-energy path from the pyridine to the pyrrolidine cycle drops rapidly when the number of water molecules increases from 0 to 4, but still remains rather high (16 kJ/mol with four water molecules), indicating that the proton transfer is a rather difficult and rare event. We compare results obtained through this explicit water molecule approach to those obtained by means of continuum methods. Car-Parrinello molecular dynamics (CPMD) simulations of the proton-transfer process in bulk with explicit water molecules have been conducted at room temperature. No spontaneous proton transfers have been observed during the dynamics, and biased CPMD simulations have therefore been performed in order to measure the free-energy profile of the proton transfer in the aqueous phase and to reveal the proton-transfer mechanism through water bridges. The MD bias involves pulling the proton from the pyridine ring to the surrounding bulk. Dynamics show that this triggers the tautomerization toward the pyrrolidine ring, proceeding without energy barrier. The proton transfer is extremely fast, and protonation of the pyrrolidine ring was achieved within 0.5 ps. CPMD simulations confirmed the pivotal role played by the water molecules that bridge the two protonation sites of nicotine within the bulk of the

  14. Experimental moments of the nucleon structure function F2

    SciTech Connect

    Mikhail Osipenko; W. Melnitchouk; Silvano Simula; Sergey Kulagin; Giovanni Ricco

    2007-12-01

    Experimental data on the F2 structure functions of the proton and deuteron, including recent results from CLAS at Jefferson Lab, have been used to construct their n<=12 moments. A comprehensive analysis of the moments in terms of the operator product expansion has been performed to separate the moments into leading and higher twist contributions. Particular attention was paid to the issue of nuclear corrections in the deuteron, when extracting the neutron moments from data. The difference between the proton and neutron moments was compared directly with lattice QCD simulations. Combining leading twist moments of the neutron and proton we found the d/u ratio at x->1 approaching 0, although the precision of the data did not allow to exclude the 1/5 value. The higher twist components of the proton and neutron moments suggest that multi-parton correlations are isospin independent.

  15. Structure functions of unstable lithium isotopes

    NASA Astrophysics Data System (ADS)

    Saito, K.; Ueda, M.; Tsushima, K.; Thomas, A. W.

    2002-07-01

    We study the spin-average and spin-dependent structure functions of the lithium isotopes. It is found that the light-cone momentum distribution of the valence neutron in the halo of 11Li is very sharp and symmetric around y=1, because of the weak binding. This implies that such neutrons are in an environment very close to that of a free neutron. The EMC ratios for Li isotopes are then calculated. Furthermore, we investigate a new ratio, given by the difference between the Li structure functions of mass number A ( F2A) and A-1 ( F2A-1 ) divided by the difference between the structure functions of the deuteron and free proton. We study the possibility of extracting the neutron structure function from data for the nuclear structure functions of the Li isotopes. In particular, the ratios for A=9 and 11 present an attractive possibility for extracting the free neutron structure function. Next, as an example, we calculate the spin-dependent structure function of 9Li isotope, which has spin 3/2. The spin structure function is given in terms of the multipole spin structure functions; 3/21g 1, which is analogous to the usual spin structure function, g1, for a target with spin 1/2, and a new one, 3/23g 1, which first arises for a target with spin 3/2. The effect of the nuclear binding and Fermi motion on 3/21g 1 is about 10% in the region x<0.7, but it becomes quite important at large x. The spin structure function, 3/23g 1, is negative at small x but it becomes positive in the region 0.2< x<0.5. However, the magnitude is very small. At large x it is again negative and its absolute value becomes large because of the Fermi motion. Finally, we discuss the modification of the Gottfried and Bjorken integrals in a nuclear medium and point out several candidates for a pair of mirror nuclei to study the flavor-nonsinglet quark distributions in nuclei.

  16. A density functional theory study of dimers of hydrophosphoryl compounds and proton transfer in them

    NASA Astrophysics Data System (ADS)

    Babin, Yu. V.; Prisyazhnyuk, A. V.; Ustynyuk, Yu. A.

    2008-01-01

    The structures of dimers of several types of dimethylphosphinous acid (CH3)2POH and dimethylphosphine oxide (CH3)2P(O)H and dimers of the corresponding perfluorinated derivatives (CF3)2POH and (CF3)2P(O)H were studied in detail by density functional theory with the PBE gradient-corrected functional and the TZ2 p basis set. Fairly strong dimeric associates (2.50-10.5 kcal/mol) were shown to form thanks to O-H···O, O-H···P, and C-H···O H-bonds and dipole-dipole interactions of polar phosphoryl groups P → O of two monomer molecules. The existence of C-H···O and the absence of P-H···O H-bonds in (CH3)2P(O)H dimers was substantiated by an AIM (atoms in molecules) analysis of their structures according to Bader. The reaction coordinates were calculated for synchronous transfer of two protons in (CH3)2POH and (CF3)2P(O)H dimers. Both rearrangements were shown to occur via symmetrical six-membered planar transition states with activation barriers of less than 20 kcal/mol, which was much lower than for intramolecular transfer in the corresponding monomers (47 kcal/mol for the (CH3)2P(O)H → (CH3)2POH pair). The tautomeric transitions between the phosphinous acid and phosphine oxide forms observed experimentally in nonpolar media under mild conditions in the absence of molecules that could act as proton carriers were shown to proceed as bimolecular reactions with the intermediate formation of the corresponding dimers.

  17. The Spin Structure of the Proton in the Resonance Region

    SciTech Connect

    Renee Fatemi

    2002-01-01

    Inclusive double spin asymmetries have been measured for {rvec p}({rvec e},e{prime}) using the CLAS detector and a polarized {sup 15}NH{sub 3} target at Jefferson Lab in 1998. The virtual photon asymmetry A{sub 1}, the longitudinal spin structure function, g{sub 1} (x, Q{sup 2}), and the first moment {Gamma}{sub 1}{sup p}, have been extracted for a Q{sup 2} range of 0.15-2.0 GeV{sup 2}. These results provide insight into the low Q{sup 2} evolution of spin dependent asymmetries and structure functions as well as the transition of {Gamma}{sub 1}{sup p} from the photon point, where the Gerasimov, Drell and Hearn Sum Rule is expected to be satisfied, to the deep inelastic region.

  18. Using AN Organic Scaffold to Modulate the Quantum Structure of AN Intramolecular Proton Bond: Cryogenic Vibrational Predissociation Spectroscopy of H2 on Protonated 8-NAPHTHALENE-1-AMINE

    NASA Astrophysics Data System (ADS)

    Deblase, Andrew F.; Guasco, Timothy L.; Leavitt, Christopher M.; Johnson, Mark A.; Lectka, Thomas

    2011-06-01

    The quantum structure of the intermolecular proton bond is a key aspect in understanding proton transfer events that govern the efficiency of fuel cells and various biological membranes. Previously, we have constructed a soft binding motif, that consists of a "point contact" between the lone pairs of two small molecules (combinations of ethers, alcohols, ammonia, and water) that are linked by a shared proton [Science 2007, 613, 249]. Although the frequency of the shared proton vibration has been correlated with effects of acid and base structure, such as proton affinities and dipole moments, the spatial arrangement of the proton donor and acceptor remains unexplored. Towards this aim, we have obtained a molecule of rigid topology that contains a proton donor and acceptor capable of intramolecular proton-bonding (protonated 8-flouronaphthalene-1-amine). Using electrospray ionization coupled with a novel cryogenic mass spectrometry scheme, we employ vibrational predissociation spectroscopy of H2 tagged ions to elucidate how a forced spatial configuration of the acid and base perturbs the energetics of the proton bond.

  19. Evidence for dimer structure of proton-pumping cytochrome c oxidase, an analysis by radiation inactivation.

    PubMed Central

    Sone, N; Kosako, T

    1986-01-01

    Cytochrome c oxidases, purified from bovine heart and the thermophilic bacterium PS3, were irradiated with a high-energy electron beam. The proton transport activities of both preparations and their electron transfer activities decreased as single exponential functions of the radiation dosage. Applying the target theory with alkaline phosphatase as an internal standard, the following functional molecular weights were obtained for cytochrome c oxidation and H+ pumping: 63-73 kd and 160-220 kd, respectively, for the bovine enzyme, and 80-100 kd and 190-230 kd for the PS3 enzyme. The results suggest that a dimer structure is necessary for H+ pumping, while a core part of monomer (presumably the largest two subunits, i.e. subunits I and II) is sufficient for cytochrome c oxidation. PMID:3017697

  20. Protons stabilize the closed conformation of gain-of-function mutants of the TRPV1 channel.

    PubMed

    Boukalova, Stepana; Teisinger, Jan; Vlachova, Viktorie

    2013-03-01

    The vanilloid transient receptor potential channel TRPV1 is a molecular integrator of noxious stimuli, including capsaicin, heat and protons. Despite clear similarities between the overall architecture of TRPV1 and voltage-dependent potassium (Kv) channels, the extent of conservation in the molecular logic for gating is unknown. In Kv channels, a small contact surface between S1 and the pore-helix is required for channel functioning. To explore the function of S1 in TRPV1, we used tryptophan-scanning mutagenesis and characterized the responses to capsaicin and protons. Wild-type-like currents were generated in 9 out of 17 mutants; three mutants (M445W, A452W, R455W) were non-functional. The conservative mutation R455K in the extracellular extent of S1 slowed down capsaicin-induced activation and prevented normal channel closure. This mutant was neither activated nor potentiated by protons, on the contrary, protons promoted a rapid deactivation of its currents. Similar phenotypes were found in two other gain-of-function mutants and also in the pore-helix mutant T633A, known to uncouple proton activation. We propose that the S1 domain contains a functionally important region that may be specifically involved in TRPV1 channel gating, and thus be important for the energetic coupling between S1-S4 sensor activation and gate opening. Analogous to Kv channels, the S1-pore interface might serve to stabilize conformations associated with TRPV1 channel gating.

  1. Toward proton MR spectroscopic imaging of stimulated brain function

    SciTech Connect

    Singh, M. . Dept. of Radiology)

    1992-08-01

    With the objective of complementing local cerebral metabolic studies of PET, and as a prelude to spectroscopic imaging, the authors have performed the first localized proton spectroscopic study of the stimulated human auditory cortex. Water suppressed localized spectroscopy (voxel size 3cm [times] 3cm [times] 3cm enclosing the auditory cortex, Te = 272ms, Tr = 3s) was performed on a 1.5T MRI/MRS system and spectra were acquired during stimulation with a 1kHz tone presented at 2Hz. Measurements were conducted for 30-40 min with a temporal resolution of 3.2 min (64 averages per time block). Results included in this paper from six subjects show a lactate peak which increases during stimulation compared to baseline values. These results suggest an increase in anaerobic glycolysis during stimulation and provide unique and valuable information that should complement glucose metabolism and flood flow studies of PET.

  2. Crystal structure of the sodium–proton antiporter NhaA dimer and new mechanistic insights

    PubMed Central

    Lee, Chiara; Yashiro, Shoko; Dotson, David L.; Uzdavinys, Povilas; Iwata, So; Sansom, Mark S.P.; von Ballmoos, Christoph

    2014-01-01

    Sodium–proton antiporters rapidly exchange protons and sodium ions across the membrane to regulate intracellular pH, cell volume, and sodium concentration. How ion binding and release is coupled to the conformational changes associated with transport is not clear. Here, we report a crystal form of the prototypical sodium–proton antiporter NhaA from Escherichia coli in which the protein is seen as a dimer. In this new structure, we observe a salt bridge between an essential aspartic acid (Asp163) and a conserved lysine (Lys300). An equivalent salt bridge is present in the homologous transporter NapA, but not in the only other known crystal structure of NhaA, which provides the foundation of most existing structural models of electrogenic sodium–proton antiport. Molecular dynamics simulations show that the stability of the salt bridge is weakened by sodium ions binding to Asp164 and the neighboring Asp163. This suggests that the transport mechanism involves Asp163 switching between forming a salt bridge with Lys300 and interacting with the sodium ion. pKa calculations suggest that Asp163 is highly unlikely to be protonated when involved in the salt bridge. As it has been previously suggested that Asp163 is one of the two residues through which proton transport occurs, these results have clear implications to the current mechanistic models of sodium–proton antiport in NhaA. PMID:25422503

  3. Diagnostic NH and OH Vibrations for Oxazolone and Diketopiperazine Structures: b2 from Protonated Triglycine

    NASA Astrophysics Data System (ADS)

    Wang, Da; Gulyuz, Kerim; Stedwell, Corey N.; Polfer, Nick C.

    2011-07-01

    We present infrared multiple photon dissociation (IRMPD) spectra in the hydrogen stretching region of the simplest b fragment, b2 from protonated triglycine, contrasted to that of protonated cyclo(Gly-Gly). Both spectra confirm the presence of intense, diagnostic vibrations linked to the site of proton attachment. Protonated cyclo(Gly-Gly) serves as a reference spectrum for the diketopiperazine structure, showing a diagnostic O-H+ stretch of the protonated carbonyl group at 3585 cm-1. Conversely, b2 from protonated triglycine exhibits a strong band at 3345 cm-1, associated with the N-H stretching mode of the protonated oxazolone ring structure. Other weaker N-H stretches can also be discerned, such as the amino NH2 and amide NH bands. These results demonstrate the usefulness of the hydrogen stretching region, and hence benchtop optical parametric oscillator/amplifier (OPO/A) set-ups, in making structural assignments of product ions in collision-induced dissociation (CID) of peptides.

  4. ELECTROMAGNETIC SIMULATIONS OF LINEAR PROTON ACCELERATOR STRUCTURES USING DIELECTRIC WALL ACCELERATORS

    SciTech Connect

    Nelson, S; Poole, B; Caporaso, G

    2007-06-15

    Proton accelerator structures for medical applications using Dielectric Wall Accelerator (DWA) technology allow for the utilization of high electric field gradients on the order of 100 MV/m to accelerate the proton bunch. Medical applications involving cancer therapy treatment usually desire short bunch lengths on the order of hundreds of picoseconds in order to limit the extent of the energy deposited in the tumor site (in 3D space, time, and deposited proton charge). Electromagnetic simulations of the DWA structure, in combination with injections of proton bunches have been performed using 3D finite difference codes in combination with particle pushing codes. Electromagnetic simulations of DWA structures includes these effects and also include the details of the switch configuration and how that switch time affects the electric field pulse which accelerates the particle beam.

  5. High-x structure function of the virtually free neutron

    NASA Astrophysics Data System (ADS)

    Cosyn, Wim; Sargsian, Misak M.

    2016-05-01

    The pole extrapolation method is applied to the semi-inclusive inelastic electron scattering off the deuteron with tagged spectator protons to extract the high-x structure function of the neutron. This approach is based on the extrapolation of the measured cross sections at different momenta of the spectator proton to the nonphysical pole of the bound neutron in the deuteron. The advantage of the method is in the possibility of suppression of the nuclear effects in a maximally model-independent way. The neutron structure functions obtained in this way demonstrate a surprising x dependence at x ≥0.6 and 1.6 ≤Q2≤3.38 GeV2 , indicating a possible rise of the neutron-to-proton structure functions ratio. If the observed rise is valid in the true deep inelastic region then it may indicate new dynamics in the generation of high-x quarks in the nucleon. One such mechanism we discuss is the possible dominance of short-range isosinglet quark-quark correlations that can enhance the d -quark distribution in the proton.

  6. Proton nuclear Overhauser effect study of the heme active site structure of Coprinus macrorhizus peroxidase.

    PubMed

    Dugad, L B; Goff, H M

    1992-07-13

    Proton nuclear Overhauser effect and paramagnetic relaxation measurements have been used to define more extensively the heme active site structure of Coprinus macrorhizus peroxidase, CMP (previously known as Coprinus cinereus peroxidase), as the ferric low-spin cyanide ligated complex. The results are compared with other well-characterized peroxidase enzymes. The NMR spectrum of CMPCN shows changes in the paramagnetically shifted resonances as a function of time, suggesting a significant heme disorder for CMP. The presence of proximal and distal histidine amino acid residues are common to the heme environments of both CMPCN and HRPCN. However, the upfield distal arginine signals of HRPCN are not evident in the 1H-NMR spectra of CMPCN.

  7. USING KAPPA FUNCTIONS TO CHARACTERIZE OUTER HELIOSPHERE PROTON DISTRIBUTIONS IN THE PRESENCE OF CHARGE-EXCHANGE

    SciTech Connect

    Zirnstein, E. J.; McComas, D. J. E-mail: dmccomas@swri.edu

    2015-12-10

    Kappa functions have long been used in the analysis and modeling of suprathermal particles in various space plasmas. In situ observations of the supersonic solar wind show its distribution contains a cold ion core and power-law tail, which is well-represented by a kappa function. In situ plasma observations by Voyager, as well as observations of energetic neutral atom (ENA) spectra by the Interstellar Boundary Explorer (IBEX), showed that the compressed and heated inner heliosheath (IHS) plasma beyond the termination shock can also be represented by a kappa function. IBEX exposes the IHS plasma properties through the detection of ENAs generated by charge-exchange in the IHS. However, charge-exchange modifies the plasma as it flows through the IHS, and makes it difficult to ascertain the parent proton distribution. In this paper we investigate the evolution of proton distributions, initially represented by a kappa function, that experience losses due to charge-exchange in the IHS. In the absence of other processes, it is no longer representable by a single kappa function due to the energy-dependent, charge-exchange process. While one can still fit a kappa function to the evolving proton distribution over limited energy ranges, this yields fitting parameters (pseudo-density, pseudo-temperature, pseudo-kappa index) that depend on the energy range of the fit. We discuss the effects of fitting a kappa function to the IHS proton distribution over limited energy ranges, its dependence on the initial proton distribution properties at the termination shock, and implications for understanding the observations.

  8. Using Kappa Functions to Characterize Outer Heliosphere Proton Distributions in the Presence of Charge-exchange

    NASA Astrophysics Data System (ADS)

    Zirnstein, E. J.; McComas, D. J.

    2015-12-01

    Kappa functions have long been used in the analysis and modeling of suprathermal particles in various space plasmas. In situ observations of the supersonic solar wind show its distribution contains a cold ion core and power-law tail, which is well-represented by a kappa function. In situ plasma observations by Voyager, as well as observations of energetic neutral atom (ENA) spectra by the Interstellar Boundary Explorer (IBEX), showed that the compressed and heated inner heliosheath (IHS) plasma beyond the termination shock can also be represented by a kappa function. IBEX exposes the IHS plasma properties through the detection of ENAs generated by charge-exchange in the IHS. However, charge-exchange modifies the plasma as it flows through the IHS, and makes it difficult to ascertain the parent proton distribution. In this paper we investigate the evolution of proton distributions, initially represented by a kappa function, that experience losses due to charge-exchange in the IHS. In the absence of other processes, it is no longer representable by a single kappa function due to the energy-dependent, charge-exchange process. While one can still fit a kappa function to the evolving proton distribution over limited energy ranges, this yields fitting parameters (pseudo-density, pseudo-temperature, pseudo-kappa index) that depend on the energy range of the fit. We discuss the effects of fitting a kappa function to the IHS proton distribution over limited energy ranges, its dependence on the initial proton distribution properties at the termination shock, and implications for understanding the observations.

  9. Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum.

    PubMed

    Furuse, Munenori; Tamogami, Jun; Hosaka, Toshiaki; Kikukawa, Takashi; Shinya, Naoko; Hato, Masakatsu; Ohsawa, Noboru; Kim, So Young; Jung, Kwang Hwan; Demura, Makoto; Miyauchi, Seiji; Kamo, Naoki; Shimono, Kazumi; Kimura-Someya, Tomomi; Yokoyama, Shigeyuki; Shirouzu, Mikako

    2015-11-01

    Although many crystal structures of microbial rhodopsins have been solved, those with sufficient resolution to identify the functional water molecules are very limited. In this study, the Acetabularia rhodopsin I (ARI) protein derived from the marine alga A. acetabulum was synthesized on a large scale by the Escherichia coli cell-free membrane-protein production method, and crystal structures of ARI were determined at the second highest (1.52-1.80 Å) resolution for a microbial rhodopsin, following bacteriorhodopsin (BR). Examinations of the photochemical properties of ARI revealed that the photocycle of ARI is slower than that of BR and that its proton-transfer reactions are different from those of BR. In the present structures, a large cavity containing numerous water molecules exists on the extracellular side of ARI, explaining the relatively low pKa of Glu206(ARI), which cannot function as an initial proton-releasing residue at any pH. An interhelical hydrogen bond exists between Leu97(ARI) and Tyr221(ARI) on the cytoplasmic side, which facilitates the slow photocycle and regulates the pKa of Asp100(ARI), a potential proton donor to the Schiff base, in the dark state.

  10. Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria

    PubMed Central

    Gushchin, Ivan; Chervakov, Pavel; Kuzmichev, Pavel; Popov, Alexander N.; Round, Ekaterina; Borshchevskiy, Valentin; Ishchenko, Andrii; Petrovskaya, Lada; Chupin, Vladimir; Dolgikh, Dmitry A.; Arseniev, Alexander S.; Kirpichnikov, Mikhail; Gordeliy, Valentin

    2013-01-01

    Light-driven proton pumps are present in many organisms. Here, we present a high-resolution structure of a proteorhodopsin from a permafrost bacterium, Exiguobacterium sibiricum rhodopsin (ESR). Contrary to the proton pumps of known structure, ESR possesses three unique features. First, ESR's proton donor is a lysine side chain that is situated very close to the bulk solvent. Second, the α-helical structure in the middle of the helix F is replaced by 310- and π-helix–like elements that are stabilized by the Trp-154 and Asn-224 side chains. This feature is characteristic for the proteorhodopsin family of proteins. Third, the proton release region is connected to the bulk solvent by a chain of water molecules already in the ground state. Despite these peculiarities, the positions of water molecule and amino acid side chains in the immediate Schiff base vicinity are very well conserved. These features make ESR a very unusual proton pump. The presented structure sheds light on the large family of proteorhodopsins, for which structural information was not available previously. PMID:23872846

  11. Reversible proton-switchable fluorescence controlled by conjugation effect in an organically-functionalized polyoxometalate

    PubMed Central

    Lv, Chunlin; Chen, Kun; Hu, Junjie; Zhang, Jin; Khan, Rao Naumaan Nasim; Wei, Yongge

    2016-01-01

    A novel monosubstituted organoimido hexamolybdate containing 6-nitroquinoline moiety has been successfully synthesized. This organically-functionalized polyoxometalate exhibits proton-induced switchable fluorescence property in aqueous acetonitrile solution at room temperature. Experimental and theoretical investigations of this reversible “on” and “off” switching mechanism have been carried out, and it is found that the protonation and deprotonation at the heterocyclic nitrogen atom within quinoline fragment leads to the breaking and reformation of the conjugation through strong d-π interaction between the hexamolybdate anionic cluster and the quinoline moiety, resulting in “on” and “off” luminescence signal. PMID:27321576

  12. On the complex structural diffusion of proton holes in nanoconfined alkaline solutions within slit pores

    PubMed Central

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-01-01

    The hydroxide anion OH−(aq) in homogeneous bulk water, that is, the solvated proton hole, is known to feature peculiar properties compared with excess protons solvated therein. In this work, it is disclosed that nanoconfinement of such alkaline aqueous solutions strongly affects the key structural and dynamical properties of OH−(aq) compared with the bulk limit. The combined effect of the preferred hypercoordinated solvation pattern of OH−(aq), its preferred perpendicular orientation relative to the confining surfaces, the pronounced layering of nanoconfined water and the topology of the hydrogen bond network required for proton hole transfer lead to major changes of the charge transport mechanism, in such a way that the proton hole migration mechanism depends exquisitely on the width of the confined space that hosts the water film. Moreover, the anionic Zundel complex, which is of transient nature in homogeneous bulk solutions, can be dynamically trapped as a shallow intermediate species by suitable nanoconfinement conditions. PMID:27550616

  13. On the complex structural diffusion of proton holes in nanoconfined alkaline solutions within slit pores

    NASA Astrophysics Data System (ADS)

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-08-01

    The hydroxide anion OH-(aq) in homogeneous bulk water, that is, the solvated proton hole, is known to feature peculiar properties compared with excess protons solvated therein. In this work, it is disclosed that nanoconfinement of such alkaline aqueous solutions strongly affects the key structural and dynamical properties of OH-(aq) compared with the bulk limit. The combined effect of the preferred hypercoordinated solvation pattern of OH-(aq), its preferred perpendicular orientation relative to the confining surfaces, the pronounced layering of nanoconfined water and the topology of the hydrogen bond network required for proton hole transfer lead to major changes of the charge transport mechanism, in such a way that the proton hole migration mechanism depends exquisitely on the width of the confined space that hosts the water film. Moreover, the anionic Zundel complex, which is of transient nature in homogeneous bulk solutions, can be dynamically trapped as a shallow intermediate species by suitable nanoconfinement conditions.

  14. A functional [NiFe]-hydrogenase model compound that undergoes biologically relevant reversible thiolate protonation.

    PubMed

    Weber, Katharina; Krämer, Tobias; Shafaat, Hannah S; Weyhermüller, Thomas; Bill, Eckhard; van Gastel, Maurice; Neese, Frank; Lubitz, Wolfgang

    2012-12-26

    Two model compounds of the active site of [NiFe]-hydrogenases with an unusual {S(2)Ni(μ-S)(μ-CO)Fe(CO)(2)S}-coordination environment around the metals are reported. The neutral compound [Ni(xbsms)(μ-CO)(μ-S)Fe(CO)(2)('S')], (1) (H(2)xbsms = 1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) is converted to [1H][BF(4)] by reversible protonation using HBF(4)·Et(2)O. The protonation takes place at the terminal thiolate sulfur atom that is coordinated to nickel. Catalytic intermediates with a protonated terminal cysteinate were suggested for the native protein but have not yet been confirmed experimentally. [1H][BF(4)] is the first dinuclear [NiFe] model compound for such a species. Both complexes have been synthesized and characterized by X-ray crystallography, NMR-, FTIR-, and (57)Fe-Mössbauer spectroscopy as well as by electronic absorption and resonance Raman spectroscopy. The experimental results clearly show that the protonation has a significant impact on the electronic structure of the iron center, although it takes place at the nickel site. DFT calculations support the interpretation of the spectroscopic data and indicate the presence of a bonding interaction between the metal ions, which is relevant for the enzyme as well. Electrochemical experiments show that both 1 and [1H][BF(4)] are active for electrocatalytic proton reduction in aprotic solvents.

  15. A functional [NiFe]-hydrogenase model compound that undergoes biologically relevant reversible thiolate protonation.

    PubMed

    Weber, Katharina; Krämer, Tobias; Shafaat, Hannah S; Weyhermüller, Thomas; Bill, Eckhard; van Gastel, Maurice; Neese, Frank; Lubitz, Wolfgang

    2012-12-26

    Two model compounds of the active site of [NiFe]-hydrogenases with an unusual {S(2)Ni(μ-S)(μ-CO)Fe(CO)(2)S}-coordination environment around the metals are reported. The neutral compound [Ni(xbsms)(μ-CO)(μ-S)Fe(CO)(2)('S')], (1) (H(2)xbsms = 1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) is converted to [1H][BF(4)] by reversible protonation using HBF(4)·Et(2)O. The protonation takes place at the terminal thiolate sulfur atom that is coordinated to nickel. Catalytic intermediates with a protonated terminal cysteinate were suggested for the native protein but have not yet been confirmed experimentally. [1H][BF(4)] is the first dinuclear [NiFe] model compound for such a species. Both complexes have been synthesized and characterized by X-ray crystallography, NMR-, FTIR-, and (57)Fe-Mössbauer spectroscopy as well as by electronic absorption and resonance Raman spectroscopy. The experimental results clearly show that the protonation has a significant impact on the electronic structure of the iron center, although it takes place at the nickel site. DFT calculations support the interpretation of the spectroscopic data and indicate the presence of a bonding interaction between the metal ions, which is relevant for the enzyme as well. Electrochemical experiments show that both 1 and [1H][BF(4)] are active for electrocatalytic proton reduction in aprotic solvents. PMID:23194246

  16. Spin structure functions: a window into the structure of hadrons

    SciTech Connect

    Dodge, Gail

    2005-08-01

    A large program of spin structure measurements is underway in Jefferson Lab's Hall B. Of particular interest is the first moment of the spin structure function g1, which goes through a rapid transition from the photon point (Q2 = 0), where it is constrained by the Gerasimov-Drell-Hearn sum rule, to the deep inelastic limit where it is sensitive to the nucleon spin fraction carried by quarks. One can then study the transition from hadronic to quark degrees of freedom over the whole range of Q2. It is also interesting to look for the onset of quark-hadron duality in spin structure functions. We use longitudinally polarized electrons with energies from 1.6 to 5.7 GeV incident upon polarized NH3 and ND3 targets to investigate proton and deuteron spin observables in and above the resonance region. We present the GDH and Bjorken integrals using the 1.6 and 5.7 GeV data and comment on the validity of local quark-hadron duality over the wide kinematical range (0.05 ? Q2 ? 4.5 GeV2 and W < 3.2

  17. Structured Functional Principal Component Analysis

    PubMed Central

    Shou, Haochang; Zipunnikov, Vadim; Crainiceanu, Ciprian M.; Greven, Sonja

    2015-01-01

    Summary Motivated by modern observational studies, we introduce a class of functional models that expand nested and crossed designs. These models account for the natural inheritance of the correlation structures from sampling designs in studies where the fundamental unit is a function or image. Inference is based on functional quadratics and their relationship with the underlying covariance structure of the latent processes. A computationally fast and scalable estimation procedure is developed for high-dimensional data. Methods are used in applications including high-frequency accelerometer data for daily activity, pitch linguistic data for phonetic analysis, and EEG data for studying electrical brain activity during sleep. PMID:25327216

  18. Structural and Electrical Characterization of Protonic Acid Doped Polyaniline

    NASA Astrophysics Data System (ADS)

    Shaktawat, Vinodini; Saxena, Narendra S.; Sharma, Kananbala; Sharma, Thaneshwar P.

    2008-04-01

    Polyaniline doped with different protonic acids were chemically synthesized using ammonium persulfate (APS) as an oxidant. These samples were characterized through X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy, which confirms the amorphous nature and acid doping, respectively. Electrical conduction in these samples has been studied through the measurement of I-V characteristics at room temperature as well as in the temperature range from 313 K to 413 K. So obtained characteristic curves were found to be nonlinear. The conductivity of phosphoric acid doped polyaniline sample is higher as compared to HCl doped polyaniline and pure polyaniline. Temperature dependence of conductivity suggests a semiconducting nature with increase in temperature. Activation energies have been found to be 50.86, 25.74 and 21.05 meV for pure polyaniline (base), polyaniline doped with hydrochloric, phosphoric acid, respectively.

  19. Functional Insights from Structural Genomics

    SciTech Connect

    Forouhar,F.; Kuzin, A.; Seetharaman, J.; Lee, I.; Zhou, W.; Abashidze, M.; Chen, Y.; Montelione, G.; Tong, L.; et al

    2007-01-01

    Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNA methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF{_}0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP{_}1951), and a 12-stranded {beta}-barrel with a novel fold (V. parahaemolyticus VPA1032).

  20. Proton channel models

    PubMed Central

    Pupo, Amaury; Baez-Nieto, David; Martínez, Agustín; Latorre, Ramón; González, Carlos

    2014-01-01

    Voltage-gated proton channels are integral membrane proteins with the capacity to permeate elementary particles in a voltage and pH dependent manner. These proteins have been found in several species and are involved in various physiological processes. Although their primary topology is known, lack of details regarding their structures in the open conformation has limited analyses toward a deeper understanding of the molecular determinants of their function and regulation. Consequently, the function-structure relationships have been inferred based on homology models. In the present work, we review the existing proton channel models, their assumptions, predictions and the experimental facts that support them. Modeling proton channels is not a trivial task due to the lack of a close homolog template. Hence, there are important differences between published models. This work attempts to critically review existing proton channel models toward the aim of contributing to a better understanding of the structural features of these proteins. PMID:24755912

  1. Resonance Region Structure Functions and Parity Violating Deep Inelastic Scattering

    SciTech Connect

    Carl E. Carlson, Benjamin C. Rislow

    2012-04-01

    The primary motive of parity violating deep inelastic scattering experiments has been to test the standard model, particularly the axial couplings to the quarks, in the scaling region. The measurements can also test for the validity of models for the off-diagonal structure functions $F_{1,2,3}^{\\gamma Z}(x,Q^2)$ in the resonance region. The off-diagonal structure functions are important for the accurate calculation of the $\\gamma Z$-box correction to the weak charge of the proton. Currently, with no data to determine $F_{1,2,3}^{\\gamma Z}(x,Q^2)$ directly, models are constructed by modifying existing fits to electromagnetic data. We present the asymmetry value for deuteron and proton target predicted by several different $F_{1,2,3}^{\\gamma Z}(x,Q^2)$ models, and demonstrate that there are notable disagreements.

  2. Hydrogen-bonded proton transfer in the protonated guanine-cytosine (GC+H)+ base pair.

    PubMed

    Lin, Yuexia; Wang, Hongyan; Gao, Simin; Schaefer, Henry F

    2011-10-13

    The single proton transfer at the different sites of the Watson-Crick (WC) guanine-cytosine (GC) DNA base pair are studied here using density functional methods. The conventional protonated structures, transition state (TS) and proton-transferred product (PT) structures of every relevant species are optimized. Each transition state and proton-transferred product structure has been compared with the corresponding conventional protonated structure to demonstrate the process of proton transfer and the change of geometrical structures. The relative energies of the protonated tautomers and the proton-transfer energy profiles in gas and solvent are analyzed. The proton-transferred product structure G(+H(+))-H(+)C(N3)(-H(+))(PT) has the lowest relative energy for which only two hydrogen bonds exist. Almost all 14 isomers of the protonated GC base pair involve hydrogen-bonded proton transfer following the three pathways, with the exception of structure G-H(+)C(O2). When the positive charge is primarily "located" on the guanine moiety (H(+)G-C, G-H(+)C(C4), and G-H(+)C(C6)), the H(1) proton transfers from the N(1) site of guanine to the N(3) site of cytosine. The structures G-H(+)C(C5) and G-H(+)C(C4) involve H(4a) proton transfer from the N(4) of cytosine to the O(6) site of guanine. H(2a) proton transfer from the N(2) site of guanine to the O(2) site of cytosine is found only for the structure G-H(+)C(C4). The structures to which a proton is added on the six-centered sites adjoining the hydrogen bonds are more prone to proton transfer in the gas phase, whereas a proton added on the minor groove and the sites adjoining the hydrogen bonds is favorable to the proton transfer in energy in the aqueous phase.

  3. High energy proton-proton elastic scattering at the Large Hadron Collider and nucleon structure

    NASA Astrophysics Data System (ADS)

    Luddy, Richard Joseph

    To gain insight into the structure of the nucleon, we pursue the development of the phenomenological model of Islam et al. (IIFS model) for high energy elastic pp and p¯p scattering. We determine the energy dependence of the parameters of the IIFS model using the available elastic differential cross section data from SPS Collider and Tevatron and the known asymptotic behavior of sigmatot (s) and rho(s) from dispersion relation calculations and more recent analyses of Cudell et al. (COMPETE Collaboration). Next, we incorporate a high energy elastic valence quark-quark scattering amplitude into the model based on BFKL pomeron to describe small impact parameter (large | t|) pp collisions. Finally, we predict the pp elastic differential cross section at the unprecedented c.m. energy of s = 14.0 TeV at the Large Hadron Collider (LHC). This prediction assumes crucial significance---because of an approved experiment at LHC: TOTal and Elastic Measurement (TOTEM). The TOTEM group plans to measure pp elastic dsigma/dt at 14.0 TeV all the way from momentum transfer |t| = 0 to |t| ≃ 10 GeV 2. Their measurement will stringently test not only the diffraction and o-exchange descriptions of the original IIFS model, but also the additional valence quark-quark scattering contribution that we find to be dominant for large |t|. Successful quantitative verification of the predicted dsigma/dt will mean that our picture of the nucleon with an outer cloud of qq¯ condensed ground state, an inner core of topological baryonic charge, and a still smaller core of massless valence quarks provides a realistic description of nucleon structure.

  4. Water proton configurations in structures I, II, and H clathrate hydrate unit cells.

    PubMed

    Takeuchi, Fumihito; Hiratsuka, Masaki; Ohmura, Ryo; Alavi, Saman; Sum, Amadeu K; Yasuoka, Kenji

    2013-03-28

    Position and orientation of water protons need to be specified when the molecular simulation studies are performed for clathrate hydrates. Positions of oxygen atoms in water are experimentally determined by X-ray diffraction analysis of clathrate hydrate structures, but positions of water hydrogen atoms in the lattice are disordered. This study reports a determination of the water proton coordinates in unit cell of structure I (sI), II (sII), and H (sH) clathrate hydrates that satisfy the ice rules, have the lowest potential energy configuration for the protons, and give a net zero dipole moment. Possible proton coordinates in the unit cell were chosen by analyzing the symmetry of protons on the hexagonal or pentagonal faces in the hydrate cages and generating all possible proton distributions which satisfy the ice rules. We found that in the sI and sII unit cells, proton distributions with small net dipole moments have fairly narrow potential energy spreads of about 1 kJ∕mol. The total Coulomb potential on a test unit charge placed in the cage center for the minimum energy∕minimum dipole unit cell configurations was calculated. In the sI small cages, the Coulomb potential energy spread in each class of cage is less than 0.1 kJ∕mol, while the potential energy spread increases to values up to 6 kJ∕mol in sH and 15 kJ∕mol in the sII cages. The guest environments inside the cages can therefore be substantially different in the sII case. Cartesian coordinates for oxygen and hydrogen atoms in the sI, sII, and sH unit cells are reported for reference.

  5. Structure functions and parton distributions

    SciTech Connect

    Martin, A.D.; Stirling, W.J.; Roberts, R.G.

    1995-07-01

    The MRS parton distribution analysis is described. The latest sets are shown to give an excellent description of a wide range of deep-inelastic and other hard scattering data. Two important theoretical issues-the behavior of the distributions at small x and the flavor structure of the quark sea-are discussed in detail. A comparison with the new structure function data from HERA is made, and the outlook for the future is discussed.

  6. Single-proton resonant states and the isospin dependence investigated by Green’s function relativistic mean field theory

    NASA Astrophysics Data System (ADS)

    Sun, T. T.; Niu, Z. M.; Zhang, S. Q.

    2016-08-01

    The relativistic mean field theory formulated with Green’s function method (RMF-GF) is applied to investigate single-proton resonant states and isospin dependence. The calculated energies and widths for the single-proton resonant states in {}120{{Sn}} are in good agreement with previous investigations. The single-proton resonant states of the Sn isotopes and the N = 82 isotones are systematically studied and it is shown that the calculated energies and widths decrease monotonically with the increase of neutron number while increase monotonically with the increase of proton number. To further examine the evolutions of the single-proton resonant states, their dependence on the depth, radius and diffuseness of nuclear potential is investigated with the help of an analytic Woods-Saxon potential, and it is found that the increase of radius plays the most important role in the cross phenomenon appearing in the single-proton resonant states of the Sn isotopes.

  7. Structure functions and parton distributions

    SciTech Connect

    Olness, F.; Tung, Wu-Ki

    1991-04-01

    Activities of the structure functions and parton distributions group is summarized. The impact of scheme-dependence of parton distributions (especially sea-quarks and gluons) on the quantitative formulation of the QCD parton model is highlighted. Recent progress on the global analysis of parton distributions is summarized. Issues on the proper use of the next-to-leading parton distributions are stressed.

  8. Understanding the proton radius puzzle: Nuclear structure effects in light muonic atoms

    NASA Astrophysics Data System (ADS)

    Ji, Chen; Hernandez, Oscar Javier; Nevo Dinur, Nir; Bacca, Sonia; Barnea, Nir

    2016-03-01

    We present calculations of nuclear structure effects to the Lamb shift in light muonic atoms. We adopt a modern ab-initio approach by combining state-of-the-art nuclear potentials with the hyperspherical harmonics method. Our calculations are instrumental to the determination of nuclear charge radii in the Lamb shift measurements, which will shed light on the proton radius puzzle.

  9. Prospects for probing the structure of the proton with low-mass Drell-Yan events in ATLAS

    NASA Astrophysics Data System (ADS)

    Ince, Tayfun

    The biggest scientific experiment in history will begin taking data in late 2009 using the Large Hadron Collider (LHC) at CERN near Geneva, Switzerland. The LHC is designed to collide protons at an unprecedented 14 TeV centre of mass energy, enabling physicists to explore the constituents of matter at smaller scales than ever before. The Parton Distribution Functions (PDFs) are parametrizations of the proton structure and are best determined from experimental data. The PDFs are needed to calculate cross-sections or in other words the likelihood of observed physical processes, which are crucial in exploiting the discovery potential of the LHC. The prospects for measuring the Drell-Yan (DY) spectrum are assessed in the low invariant mass region below the Z boson resonance using e +e- pairs from the initial LHC data in order to probe the proton structure and further constrain the PDFs. The analysis is based on the full simulation of the ATLAS detector response to DY electrons and background processes. Assuming 100 pb-1 of LHC data, the total DY cross-section in the invariant mass range from 10 GeV to 60 GeV is expected to be measured as sigmaDY = 5.90+/-0.24(stat)+/-0.18(syst) nb. The result predicts an improvement over a current theoretical uncertainty of 7.6% and indicates that the PDF uncertainties can be reduced significantly with the early LHC data.

  10. New nanocomposite hybrid inorganic-organic proton-conducting membranes based on functionalized silica and PTFE.

    PubMed

    Di Noto, Vito; Piga, Matteo; Giffin, Guinevere A; Negro, Enrico; Furlan, Claudio; Vezzù, Keti

    2012-09-01

    Two types of new nanocomposite proton-exchange membranes, consisting of functionalized and pristine nanoparticles of silica and silicone rubber (SR) embedded in a polytetrafluoroethylene (PTFE) matrix, were prepared. The membrane precursor was obtained from a mechanical rolling process, and the SiO₂ nanoparticles were functionalized by soaking the membranes in a solution of 2-(4-chlorosulfonylphenyl)ethyl trichlorosilane (CSPhEtCS). The membranes exhibit a highly compact morphology and a lack of fibrous PTFE. At 125 °C, the membrane containing the functionalized nanoparticles has an elastic modulus (2.2 MPa) that is higher than that of pristine Nafion (1.28 MPa) and a conductivity of 3.6×10⁻³  S cm⁻¹ despite a low proton-exchange capacity (0.11 meq g⁻¹). The good thermal and mechanical stability and conductivity at T>100 °C make these membranes a promising low-cost material for application in proton-exchange membrane fuel cells operating at temperatures higher than 100 °C. PMID:22807005

  11. Protonation-induced change in the conformation, crystal structure and property of triarylmethyl carbocation radical

    NASA Astrophysics Data System (ADS)

    Zhang, Cong; Feng, Ya; Shen, Chen; Yong, Guoping

    2016-04-01

    We report a new triarylmethyl carbocation radical which was easily synthesized via "one-pot" approach. Interestingly, this "cis" triarylmethyl carbocation radical converted to the "trans" one upon protonation. Such an obviously conformational change is triggered by the intermolecular hydrogen bond interaction involving one exocyclic "keto" oxygen atom and the protonated pyridinium nitrogen atom. Two triarylmethyl carbocation radical crystals were characterized by the elemental analysis and single crystal X-ray diffraction. A change in conformation also brings about change in crystal structure, phosphorescence and magnetic susceptibility properties.

  12. Structural characterization of proton exchanged LiNbO3 optical waveguides

    NASA Astrophysics Data System (ADS)

    Canali, C.; Carnera, A.; Della Mea, G.; Mazzoldi, P.; Al Shukri, S. M.; Nutt, A. C. G.; De La Rue, R. M.

    1986-04-01

    This paper reports the results of structural analysis of proton-exchanged lithium niobate optical waveguides fabricated in Z-, X-, and Y-cut substrates immersed in pure benzoic acid. Rutherford backscattering spectrometry, nuclear reactions, secondary ion mass spectrometry, scanning electron microscopy, and x-ray diffraction were used to measure atomic composition profiles and the marked lattice distortion induced by the proton exchange process in the waveguiding layer. H and Li concentration measurements indicate an exchange of about 70% of the Li atoms are present in the virgin LiNbO3 crystal.

  13. Fine structure in proton radioactivity: An accurate tool to ascertain the breaking of axial symmetry in {sup 145}Tm

    SciTech Connect

    Arumugam, P.; Ferreira, L. S.; Maglione, E.

    2008-10-15

    With a proper formalism for proton emission from triaxially deformed nuclei, we perform exact calculations of decay widths for the decays to ground and first excited 2{sup +} states in the daughter nucleus. Our results for rotational spectrum, decay width and fine structure in the case of the nucleus {sup 145}Tm lead for the first time to an accurate identification of triaxial deformation using proton emission. This work also puts in evidence the advantage of proton emission over the conventional probes to study nuclear structure at the proton drip-line.

  14. Detonation wave structure studies in high explosives by means of proton radiography

    NASA Astrophysics Data System (ADS)

    Kolesnikov, Sergei; Dudin, Sergei; Mintsev, Victor; Utkin, Alexander; Demidov, Victor; Fertman, Alexander; Golubev, Alexander; Katz, Mark; Markov, Nikolai; Sharkov, Boris; Smirnov, Gennady; Turtikov, Vladimir

    2007-06-01

    Proton radiography is the unique experimental technique for obtaining direct information about important material characteristics of real solid objects under dynamic conditions. The aim of the present work is the application of this method to the investigation of evolution of density in shock and detonation waves in high explosives (HE). Obtained information will be very useful for the improvement of existing detonation models and equations of state of HE. For this purpose a proton radiography facility for dynamic experiments on the basis of TWAC-ITEP accelerator is being constructed. A special containment chamber for explosive experiments was built. Static experiments with imitators of detonating HE charges were performed; as a result the proton radiographic images of imitators with time resolution of up to 10 ns were obtained. Dynamic experiments on the registration of detonation wave structure in pressed TNT are underway.

  15. Color transparency and the structure of the proton in quantum chromodynamics

    SciTech Connect

    Brodsky, S.J.

    1989-06-01

    Many anomalies suggest that the proton itself is a much more complex object than suggested by simple non-relativistic quark models. Recent analyses of the proton distribution amplitude using QCD sum rules points to highly-nontrivial proton structure. Solutions to QCD in one-space and one-time dimension suggest that the momentum distributions of non-valence quarks in the hadrons have a non-trivial oscillatory structure. The data seems also to be suggesting that the intrinsic'' bound state structure of the proton has a non-negligible strange and charm quark content, in addition to the extrinsic'' sources of heavy quarks created in the collision itself. As we shall see in this lecture, the apparent discrepancies with experiment are not so much a failure of QCD, but rather symptoms of the complexity and richness of the theory. An important tool for analyzing this complexity is the light-cone Fock state representation of hadron wavefunctions, which provides a consistent but convenient framework for encoding the features of relativistic many-body systems in quantum field theory. 121 refs., 44 figs., 1 tab.

  16. Understanding structure, function, and mutations in the mitochondrial ATP synthase

    PubMed Central

    Xu, Ting; Pagadala, Vijayakanth; Mueller, David M.

    2015-01-01

    The mitochondrial ATP synthase is a multimeric enzyme complex with an overall molecular weight of about 600,000 Da. The ATP synthase is a molecular motor composed of two separable parts: F1 and Fo. The F1 portion contains the catalytic sites for ATP synthesis and protrudes into the mitochondrial matrix. Fo forms a proton turbine that is embedded in the inner membrane and connected to the rotor of F1. The flux of protons flowing down a potential gradient powers the rotation of the rotor driving the synthesis of ATP. Thus, the flow of protons though Fo is coupled to the synthesis of ATP. This review will discuss the structure/function relationship in the ATP synthase as determined by biochemical, crystallographic, and genetic studies. An emphasis will be placed on linking the structure/function relationship with understanding how disease causing mutations or putative single nucleotide polymorphisms (SNPs) in genes encoding the subunits of the ATP synthase, will affect the function of the enzyme and the health of the individual. The review will start by summarizing the current understanding of the subunit composition of the enzyme and the role of the subunits followed by a discussion on known mutations and their effect on the activity of the ATP synthase. The review will conclude with a summary of mutations in genes encoding subunits of the ATP synthase that are known to be responsible for human disease, and a brief discussion on SNPs. PMID:25938092

  17. Factor XIII: Structure and Function.

    PubMed

    Schroeder, Verena; Kohler, Hans P

    2016-06-01

    Over the last two decades, it became evident that factor XIII (FXIII) is not only a crucial determinant of clot characteristics but also has potentially important functions in many various fields such as bone biology, immunity, and adipogenesis. In this review, we aim to summarize the latest findings regarding structure and function of FXIII. In regard to FXIII structure, much progress has been made recently to understand how its subunits are held together. In the A subunit, the activation peptide has a crucial role in the formation of FXIII-A2 dimers. In the B subunit, Sushi domains that are involved in binding to the A subunit and in B2 dimer formation have been identified. In regard to FXIII function, interactions with immune cells and the complement system have been described. A novel function of FXIII-A in adipogenesis has been suggested. The role of FXIII-A in osteoblast differentiation has been further investigated; however, a novel double knockout mouse deficient in both FXIII-A and transglutaminase 2 showed normal bone formation. Thus, more research, in particular, into the cellular functions of FXIII-A is still required. PMID:27019464

  18. Structures of lithiated lysine and structural analogues in the gas phase: effects of water and proton affinity on zwitterionic stability.

    PubMed

    Lemoff, Andrew S; Bush, Matthew F; O'Brien, Jeremy T; Williams, Evan R

    2006-07-13

    The structures of lithiated lysine, ornithine, and related molecules, both with and without a water molecule, are investigated using both density functional theory and blackbody infrared radiative dissociation experiments. The lowest-energy structure of lithiated lysine without a water molecule is nonzwitterionic; the metal ion interacts with both nitrogen atoms and the carbonyl oxygen. Structures in which lysine is zwitterionic are higher in energy by more than 29 kJ/mol. In contrast, the singly hydrated clusters with the zwitterionic and nonzwitterionic forms of lysine are more similar in energy, with the nonzwitterionic form more stable by only approximately 7 kJ/mol. Thus, a single water molecule can substantially stabilize the zwitterionic form of an amino acid. Analogous molecules that have methyl groups attached to either the N-terminus (NMeLys) or the side-chain amine (Lys(Me)) have proton affinities greater than that of lysine. In the lithiated clusters with a water molecule attached, the zwitterionic forms of NMeLys and Lys(Me) are calculated to be approximately 4 and approximately 11 kJ/mol more stable than the nonzwitterionic forms, respectively. Calculations of the potential-energy pathway for interconversion between the different forms of lysine in the lithiated complex indicate multiple stable intermediates with an overall barrier height of approximately 83 kJ/mol between the lowest-energy nonzwitterionic form and the most accessible zwitterionic form. Experimentally determined binding energies of water are similar for all these complexes and range from 57 to 64 kJ/mol. These results suggest that loss of a water molecule from the lysine complexes is both energetically and entropically favored compared to interconversion between the nonzwitterionic and zwitterionic structures. Comparisons to calculated binding energies of water to the various structures show that the experimental results are most consistent with the nonzwitterionic forms. PMID

  19. Toward a chemical mechanism of proton pumping by the B-type cytochrome c oxidases: Application of Density Functional Theory to cytochrome ba3 of Thermus thermophilus

    PubMed Central

    Fee, James A.; Case, David A.; Noodleman, Louis

    2009-01-01

    A mechanism for proton pumping by the B-type cytochrome c oxidases is presented in which one proton is pumped in conjunction with the weakly-exergonic, two-electron reduction of Fe-bound O2 to the Fe-Cu bridging peroxodianion, and three protons are pumped in conjunction with the highly-exergonic, two-electron reduction of Fe(III)-−O-O−-Cu(II) to form water and the active oxidized enzyme, Fe(III)-−OH, Cu(II). The scheme is based on the active site structure of cytochrome ba3 from Thermus thermophilus, which is considered to be both necessary and sufficient for coupled O2 reduction and proton pumping when appropriate gates are in place (not included in the model). Fourteen detailed structures obtained from DFT geometry optimization are presented that are reasonably thought to occur during the four-electron reduction of O2. Each proton pumping step takes place when a proton resides on the imidazole ring of I-His376 and the large active site cluster has a net charge of +1 due to an uncompensated, positive charge formally associated with CuB. Density functional theory (DFT) of four types was applied to determine the energy of each intermediate, and standard thermochemical approaches were used to obtain the reaction free energies for each step in the catalytic cycle. This application of DFT generally conforms with previously suggested criteria for a valid model [P. E. M. Siegbahn & M. A. R. Blomberg (2000) 100 421 - 437] and, shows how the chemistry of O2-reduction in the heme a3-CuB dinuclear center can be harnessed to generate an electrochemical proton gradient across the lipid bilayer. PMID:18928258

  20. Structure and functions of angiotensinogen

    PubMed Central

    Lu, Hong; Cassis, Lisa A; Kooi, Craig W Vander; Daugherty, Alan

    2016-01-01

    Angiotensinogen (AGT) is the sole precursor of all angiotensin peptides. Although AGT is generally considered as a passive substrate of the renin–angiotensin system, there is accumulating evidence that the regulation and functions of AGT are intricate. Understanding the diversity of AGT properties has been enhanced by protein structural analysis and animal studies. In addition to whole-body genetic deletion, AGT can be regulated in vivo by cell-specific procedures, adeno-associated viral approaches and antisense oligonucleotides. Indeed, the availability of these multiple manipulations of AGT in vivo has provided new insights into the multifaceted roles of AGT. In this review, the combination of structural and functional studies is highlighted to focus on the increasing recognition that AGT exerts effects beyond being a sole provider of angiotensin peptides. PMID:26888118

  1. Structure and Function of Glucansucrases

    NASA Astrophysics Data System (ADS)

    Dijkstra, B. W.; Vujičić-Žagar, A.

    2008-03-01

    Glucansucrases are relatively large (~160 kDa) extracellular enzymes produced by lactic acid bacteria. Using sucrose as a substrate they synthesize high molecular mass glucose polymers, called α-glucans, which allow the bacteria to adhere to surfaces and create a biofilm. The glucan polymers are of importance for the food and dairy industry as thickening and jellying agents. An overview is given of the current insights into the structure and functioning of these and related enzymes.

  2. Structure of the c14 Rotor Ring of the Proton Translocating Chloroplast ATP Synthase*

    PubMed Central

    Vollmar, Melanie; Schlieper, Daniel; Winn, Martyn; Büchner, Claudia; Groth, Georg

    2009-01-01

    The structure of the membrane integral rotor ring of the proton translocating F1F0 ATP synthase from spinach chloroplasts was determined to 3.8 Å resolution by x-ray crystallography. The rotor ring consists of 14 identical protomers that are symmetrically arranged around a central pore. Comparisons with the c11 rotor ring of the sodium translocating ATPase from Ilyobacter tartaricus show that the conserved carboxylates involved in proton or sodium transport, respectively, are 10.6–10.8 Å apart in both c ring rotors. This finding suggests that both ATPases have the same gear distance despite their different stoichiometries. The putative proton-binding site at the conserved carboxylate Glu61 in the chloroplast ATP synthase differs from the sodium-binding site in Ilyobacter. Residues adjacent to the conserved carboxylate show increased hydrophobicity and reduced hydrogen bonding. The crystal structure reflects the protonated form of the chloroplast c ring rotor. We propose that upon deprotonation, the conformation of Glu61 is changed to another rotamer and becomes fully exposed to the periphery of the ring. Reprotonation of Glu61 by a conserved arginine in the adjacent a subunit returns the carboxylate to its initial conformation. PMID:19423706

  3. Role of the bound-state wave function in capture-loss rates: Slow proton in an electron gas

    SciTech Connect

    Alducin, M.; Nagy, I.

    2003-07-01

    Capture and loss rates for protons moving in an electron gas are calculated using many-body perturbation theory. The role of the form of the bound-state wave function for weakly bound states around the proton is analyzed. We find significant differences (up to a factor of 2 higher) in the values of Auger capture and loss rates when using Hulthen-type instead of hydrogenic wave functions. Its relevance in stopping power is briefly discussed.

  4. Alkali Metal Cation versus Proton and Methyl Cation Affinities: Structure and Bonding Mechanism

    PubMed Central

    Boughlala, Zakaria; Fonseca Guerra, Célia

    2016-01-01

    Abstract We have analyzed the structure and bonding of gas‐phase Cl−X and [HCl−X]+ complexes for X+= H+, CH3 +, Li+, and Na+, using relativistic density functional theory (DFT). We wish to establish a quantitative trend in affinities of the anionic and neutral Lewis bases Cl− and HCl for the various cations. The Cl−X bond becomes longer and weaker along X+ = H+, CH3 +, Li+, and Na+. Our main purpose is to understand the heterolytic bonding mechanism behind the intrinsic (i.e., in the absence of solvent) alkali metal cation affinities (AMCA) and how this compares with and differs from those of the proton affinity (PA) and methyl cation affinity (MCA). Our analyses are based on Kohn–Sham molecular orbital (KS‐MO) theory in combination with a quantitative energy decomposition analysis (EDA) that pinpoints the importance of the different features in the bonding mechanism. Orbital overlap appears to play an important role in determining the trend in cation affinities. PMID:27551660

  5. Diffusion tensor imaging and proton magnetic resonance spectroscopy in brain tumor: Correlation between structure and metabolism☆

    PubMed Central

    Min, Zhigang; Niu, Chen; Rana, Netra; Ji, Huanmei; Zhang, Ming

    2013-01-01

    Proton magnetic resonance spectroscopy and diffusion tensor imaging are non-invasive techniques used to detect metabolites and water diffusion in vivo. Previous studies have confirmed a positive correlation of individual fractional anisotropy values with N-acetylaspartate/creatine and N-acetylaspartate/choline ratios in tumors, edema, and normal white matter. This study divided the brain parenchyma into tumor, peritumoral edema, and normal-appearing white matter according to MRI data, and analyzed the correlation of metabolites with water molecular diffusion. Results demonstrated that in normal-appearing white matter, N-acetylaspartate/creatine ratios were positively correlated with fractional anisotropy values, negatively correlated with radial diffusivities, and positively correlated with maximum eigenvalues. Maximum eigenvalues and radial diffusivities in peritumoral edema showed a negative correlation with choline, N-acetylaspartate, and creatine. Radial diffusivities in tumor demonstrated a negative correlation with choline. These data suggest that the relationship between metabolism and structure is markedly changed from normal white matter to peritumoral edema and tumor. Neural metabolism in the peritumoral edema area decreased with expanding extracellular space. The normal relationship of neural function and microstructure disappeared in the tumor region. PMID:25206385

  6. Alkali Metal Cation versus Proton and Methyl Cation Affinities: Structure and Bonding Mechanism.

    PubMed

    Boughlala, Zakaria; Fonseca Guerra, Célia; Bickelhaupt, F Matthias

    2016-06-01

    We have analyzed the structure and bonding of gas-phase Cl-X and [HCl-X](+) complexes for X(+)= H(+), CH3 (+), Li(+), and Na(+), using relativistic density functional theory (DFT). We wish to establish a quantitative trend in affinities of the anionic and neutral Lewis bases Cl(-) and HCl for the various cations. The Cl-X bond becomes longer and weaker along X(+) = H(+), CH3 (+), Li(+), and Na(+). Our main purpose is to understand the heterolytic bonding mechanism behind the intrinsic (i.e., in the absence of solvent) alkali metal cation affinities (AMCA) and how this compares with and differs from those of the proton affinity (PA) and methyl cation affinity (MCA). Our analyses are based on Kohn-Sham molecular orbital (KS-MO) theory in combination with a quantitative energy decomposition analysis (EDA) that pinpoints the importance of the different features in the bonding mechanism. Orbital overlap appears to play an important role in determining the trend in cation affinities. PMID:27551660

  7. Protonation of Glu135 Facilitates the Outward-to-Inward Structural Transition of Fucose Transporter

    PubMed Central

    Liu, Yufeng; Ke, Meng; Gong, Haipeng

    2015-01-01

    Major facilitator superfamily (MFS) transporters typically need to alternatingly sample the outward-facing and inward-facing conformations, in order to transport the substrate across membrane. To understand the mechanism, in this work, we focused on one MFS member, the L-fucose/H+ symporter (FucP), whose crystal structure exhibits an outward-open conformation. Previous experiments imply several residues critical to the substrate/proton binding and structural transition of FucP, among which Glu135, located in the periplasm-accessible vestibule, is supposed as being involved in both proton translocation and conformational change of the protein. Here, the structural transition of FucP in presence of substrate was investigated using molecular-dynamics simulations. By combining the equilibrium and accelerated simulations as well as thermodynamic calculations, not only was the large-scale conformational change from the outward-facing to inward-facing state directly observed, but also the free energy change during the structural transition was calculated. The simulations confirm the critical role of Glu135, whose protonation facilitates the outward-to-inward structural transition both by energetically favoring the inward-facing conformation in thermodynamics and by reducing the free energy barrier along the reaction pathway in kinetics. Our results may help the mechanistic studies of both FucP and other MFS transporters. PMID:26244736

  8. Structural investigation of asymmetrical dimer radical cation system (H2O-H2S)+: proton-transferred or hemi-bonded?

    PubMed

    Joshi, Ravi; Ghanty, Tapan K; Naumov, Sergej; Mukherjee, Tulsi

    2007-03-29

    Ab initio molecular orbital and hybrid density functional methods have been employed to characterize the structure and bonding of (H2O-H2S)+, an asymmetrical dimer radical cation system. A comparison has been made between the two-center three-electron (2c-3e) hemi-bonded system and the proton-transferred hydrogen-bonded systems of (H2O-H2S)+. Geometry optimization of these systems was carried out using unrestricted Hartree Fock (HF), density functional theory with different functionals, and second-order Møller-Plesset perturbation (MP2) methods with 6-311++G(d,p) basis set. Hessian calculations have been done at the same level to check the nature of the equilibrium geometry. Energy data were further improved by calculating basis set superposition error for the structures optimized through MP2/6-311++G(d,p) calculations. The calculated results show that the dimer radical cation structure with H2O as proton acceptor is more stable than those structures in which H2O acts as a proton donor or the 2c-3e hemi-bonded (H2O thereforeSH2)+ system. This stability trend has been further confirmed by more accurate G3, G3B3, and CCSD(T) methods. On the basis of the present calculated results, the structure of H4OS+ can best be described as a hydrogen-bonded complex of H3O+ and SH with H2O as a proton acceptor. It is in contrast to the structure of neutral (H2O...H2S) dimer where H2O acts as a proton donor. The present work has been able to resolve the ambiguity in the nature of bonding between H2O and H2S in (H2O-H2S)+ asymmetrical dimer radical cation.

  9. Tracking the Structural and Electronic Configurations of a Cobalt Proton Reduction Catalyst in Water.

    PubMed

    Moonshiram, Dooshaye; Gimbert-Suriñach, Carolina; Guda, Alexander; Picon, Antonio; Lehmann, C Stefan; Zhang, Xiaoyi; Doumy, Gilles; March, Anne Marie; Benet-Buchholz, Jordi; Soldatov, Alexander; Llobet, Antoni; Southworth, Stephen H

    2016-08-24

    X-ray transient absorption spectroscopy (X-TAS) has been used to study the light-induced hydrogen evolution reaction catalyzed by a tetradentate macrocyclic cobalt complex with the formula [LCo(III)Cl2](+) (L = macrocyclic ligand), [Ru(bpy)3](2+) photosensitizer, and an equimolar mixture of sodium ascorbate/ascorbic acid electron donor in pure water. X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analysis of a binary mixture of the octahedral Co(III) precatalyst and [Ru(bpy)3](2+) after illumination revealed in situ formation of a Co(II) intermediate with significantly distorted geometry and electron-transfer kinetics of 51 ns. On the other hand, X-TAS experiments of the complete photocatalytic system in the presence of the electron donor showed the formation of a square planar Co(I) intermediate species within a few nanoseconds, followed by its decay in the microsecond time scale. The Co(I) structural assignment is supported by calculations based on density functional theory (DFT). At longer reaction times, we observe the formation of the initial Co(III) species concomitant to the decay of Co(I), thus closing the catalytic cycle. The experimental X-ray absorption spectra of the molecular species formed along the catalytic cycle are modeled using a combination of molecular orbital DFT calculations (DFT-MO) and finite difference method (FDM). These findings allowed us to assign the full mechanistic pathway, followed by the catalyst as well as to determine the rate-limiting step of the process, which consists in the protonation of the Co(I) species. This study provides a complete kinetics scheme for the hydrogen evolution reaction by a cobalt catalyst, revealing unique information for the development of better catalysts for the reductive side of hydrogen fuel cells. PMID:27452370

  10. Transport properties of proton-exchange membranes: Effect of supercritical-fluid processing and chemical functionality

    NASA Astrophysics Data System (ADS)

    Pulido Ayazo

    conductivity, even with blends of these and blends with Nafion membranes. Other alternative studied was the functionalization of the membranes SIBS with metallic cations, which decreased the methanol permeability in the membranes containing the cations Mg2+, Zn2+ and Al 3+, while the proton conductivity was maintained more or less constant. The permeation of methanol vapor was investigated and the behavior through the membranes studied followed a pattern of Fick's Law, while the pattern shown by the permeation in liquid phase was non-Fickian.

  11. Research of nanocomposite structure of boron nitride at proton radiation

    NASA Astrophysics Data System (ADS)

    Borodin, Y. V.; Ermolaev, D. S.; Pak, V.; Zhang, K.

    2016-02-01

    Using roentgen diffraction and electron microscopy, the influence of nanosecond irradiation by ion beams of high energy on forming of self-organized nanoblocks in near surface's layers of boron nitride (BN) has been studied. It was shown that low temperature transitions from hexagonal to wrutz boron nitrides is associated with changes of shape and sizes of self-organized particles consisting the nanoblocks. We have calculated the parameters of nanoblocks using the meanings of interplane distances and properties of subreflexes orders. The collective shifting deformations of layers in nanoblocks provides phase transition under the screen and forming the set of nanotubes with escaping of five order axes of symmetry. It has been realized that pentagons and stars arranged in points of entrance of five order axis of symmetry are associated with peculiarity of self-organization of the spiral-cyclic structures.

  12. Synthetic Models for the [FeFe]-Hydrogenase: Catalytic Proton Reduction and the Structure of the Doubly Protonated Intermediate

    PubMed Central

    Carroll, Maria E.; Barton, Bryan E.; Rauchfuss, Thomas B.; Carroll, Patrick J.

    2012-01-01

    This report compares biomimetic HER catalysts with and without the amine cofactor (adtNH): Fe2(adtNH)(CO)2(dppv)2 (1NH) and Fe2(pdt)(CO)2(dppv)2 (2; (adtNH)2− = (HN(CH2S)22−, pdt2− = 1,3-(CH2)3S22−). These compounds are spectroscopically, structurally, and stereodynamically very similar but exhibit very different catalytic properties. Protonation of 1NH and 2 each give three isomeric hydrides beginning with the kinetically favored terminal hydride, which converts sequentially to sym and unsym isomers of the bridging hydrides. In the case of the amine, the corresponding ammonium-hydrides are also observed. In the case of the terminal amine hydride [t-H1NH]BF4, the ammonium/amine-hydride equilibrium is sensitive to counteranions and solvent. The species [t-H1NH2](BF4)2 represents the first example of a crystallographically characterized terminal hydride produced by protonation. The NH--HFe distance of 1.88(7) Å indicates dihydrogen bonding. The bridging hydrides [µ-H1NH]+ and [µ-H2]+ reduce near −1.8 V, about 150 mV more negative than the reductions of the terminal hydride [t-H1NH]+ and [t-H2]+ at −1.65 V. Reductions of the amine hydrides [t-H1NH]+ and [t-H1NH2]2+ are irreversible. For the pdt analog, the [t-H2]+/0 couple is unaffected by weak acids (pKaMeCN 15.3) but exhibits catalysis with HBF4•Et2O, albeit with a TOF around 4 s−1 and an overpotential greater than 1 V. The voltammetry of [t-H1NH]+ is strongly affected by relatively weak acids and proceeds at 5000 s−1 with an overpotential of 0.7 V. The ammonium-hydride [t-H1NH2]2+ is a faster catalyst with an estimated TOF of 58,000 s−1 and an overpotential of 0.5 V. PMID:23126330

  13. An investigation of structure-property relationships in several categories of proton exchange membranes

    NASA Astrophysics Data System (ADS)

    Rodgers, Marianne Phelan

    The chemical and structural features of proton exchange membranes (PEMs) are related to their fuel cell relevant properties. The objective of this work is to understand structure-property relationships in PEMs through the fabrication and characterization of several classes of membranes. Incorporation of linear and angled monomers into the main chain of a polyimide permitted investigation of the effect of kinked versus linear polymers on membrane properties. The conductivity of angled sulfonated polyimide membranes is greater than those prepared from linear polymers, but water uptakes are lower. These differences are attributed to increased entanglements of angled polymers, which limit the degree of swelling and lead to increased proton concentration. Polyelectrolytes were incorporated into reinforcing materials to study the effect of incorporating and confining polyelectrolytes in the pores of reinforcing materials. The employment of reinforcing materials reduces conductivity, mobility, and permeance due to decreased ionomer content and connectivity of the ionomer. However, membranes are stronger and thinner, which compensates for these losses in terms of lower resistance and increased dimensional stability. Incorporating zirconium hydrogen phosphate (ZrP) and silicon dioxide (SiO2) into NafionRTM membranes permitted investigation of their effect on membrane properties. Data for NafionRTM/ZrP membranes support the theory that ZrP disrupts cohesive forces in Nafion RTM, causing it to absorb more water. The increased water content of the membranes does not result in increased conductivity because there is a concurrent decrease in proton concentration and mobility due to poorly conducting ZrP disrupting the conduction pathway and increased water content diluting protons and separating proton conduction sites. The decreasing density of the NafionRTM/SiO2 composite membranes with increasing SiO2 content and the increased dimensional stability of the membranes increasing

  14. Proton stopping using a full conserving dielectric function in plasmas at any degeneracy

    SciTech Connect

    Barriga-Carrasco, Manuel D.

    2010-10-15

    In this work, we present a dielectric function including the three conservation laws (density, momentum and energy) when we take into account electron-electron collisions in a plasma at any degeneracy. This full conserving dielectric function (FCDF) reproduces the random phase approximation (RPA) and Mermin ones, which confirms this outcome. The FCDF is applied to the determination of the proton stopping power. Differences among diverse dielectric functions in the proton stopping calculation are minimal if the plasma electron collision frequency is not high enough. These discrepancies can rise up to 2% between RPA values and the FCDF ones, and to 8% between the Mermin ones and FCDF ones. The similarity between RPA and FCDF results is not surprising, as all conservation laws are also considered in RPA dielectric function. Even for plasmas with low collision frequencies, those discrepancies follow the same behavior as for plasmas with higher frequencies. Then, discrepancies do not depend on the plasma degeneracy but essentially do on the value of the plasma collision frequency.

  15. The structure and function of fungal cells

    NASA Technical Reports Server (NTRS)

    Nozawa, Y.

    1984-01-01

    The structure and function of fungal cell walls were studied with particular emphasis on dermatophytes. Extraction, isolation, analysis, and observation of the cell wall structure and function were performed. The structure is described microscopically and chemically.

  16. How well do we know the neutron structure function?

    SciTech Connect

    J. Arrington, J. G. Rubin, W. Melnitchouk

    2012-06-01

    We present a detailed analysis of the uncertainty in the neutron F{sub 2}n structure function extracted from inclusive deuteron and proton deep-inelastic scattering data. The analysis includes experimental uncertainties as well as uncertainties associated with the deuteron wave function, nuclear smearing, and nucleon off-shell corrections. Consistently accounting for the Q{sup 2} dependence of the data and calculations, and restricting the nuclear corrections to microscopic models of the deuteron, we find significantly smaller uncertainty in the extracted F{sub 2}n/F{sub 2}p ratio than in previous analyses. In addition to yielding an improved extraction of the neutron structure function, this analysis also provides an important baseline that will allow future, model-independent extractions of neutron structure to be used to examine nuclear medium effects in the the deuteron.

  17. Investigation of the structure of light exotic nuclei by proton elastic scattering in inverse kinematics

    SciTech Connect

    Alkhazov, G. D.; Vorobyov, A. A.; Dobrovolsky, A. V. Inglessi, A. G.; Korolev, G. A.; Khanzadeev, A. V.

    2015-05-15

    In order to study the spatial structure of exotic nuclei, it was proposed at the Petersburg Nuclear Physics Institute (PNPI) to measure the differential cross section for small-angle proton elastic scattering in inverse kinematics. Several experiments in beams of 0.7-GeV/nucleon exotic nuclei were performed at the heavy-ion accelerator facility of GSI (Gesellschaft für Schwerionenforschung, Darmstadt, Germany) by using the IKAR ionization spectrometer developed at PNPI. The IKAR ionization chamber filled with hydrogen at a pressure of 10 bar served simultaneously as a target and as a recoil-proton detector, which measured the recoil-proton energy. The beam-particle scattering angle was also measured. The results obtained for the cross sections in question were analyzed on the basis of the Glauber-Sitenko theory using phenomenological nuclear-density distributions with two free parameters. Nuclear-matter distributions and root-mean-square radii were found for the nuclei under investigation. The size of the halo in the {sup 6}He, {sup 8}He, {sup 11}Li, and {sup 14}Be nuclei was determined among other things. Information about neutron distributions in nuclei was deduced by combining the data obtained here with the known values of the radii of proton distributions. A sizable neutron skin was revealed in the {sup 8}Li, {sup 9}Li, and {sup 12}Be nuclei.

  18. Investigation of the structure of light exotic nuclei by proton elastic scattering in inverse kinematics

    NASA Astrophysics Data System (ADS)

    Alkhazov, G. D.; Vorobyov, A. A.; Dobrovolsky, A. V.; Inglessi, A. G.; Korolev, G. A.; Khanzadeev, A. V.

    2015-05-01

    In order to study the spatial structure of exotic nuclei, it was proposed at the Petersburg Nuclear Physics Institute (PNPI) to measure the differential cross section for small-angle proton elastic scattering in inverse kinematics. Several experiments in beams of 0.7-GeV/nucleon exotic nuclei were performed at the heavy-ion accelerator facility of GSI (Gesellschaft für Schwerionenforschung, Darmstadt, Germany) by using the IKAR ionization spectrometer developed at PNPI. The IKAR ionization chamber filled with hydrogen at a pressure of 10 bar served simultaneously as a target and as a recoil-proton detector, which measured the recoil-proton energy. The beam-particle scattering angle was also measured. The results obtained for the cross sections in question were analyzed on the basis of the Glauber-Sitenko theory using phenomenological nuclear-density distributions with two free parameters. Nuclear-matter distributions and root-mean-square radii were found for the nuclei under investigation. The size of the halo in the 6He, 8He, 11Li, and 14Be nuclei was determined among other things. Information about neutron distributions in nuclei was deduced by combining the data obtained here with the known values of the radii of proton distributions. A sizable neutron skin was revealed in the 8Li, 9Li, and 12Be nuclei.

  19. Functional nanometer-scale structures

    NASA Astrophysics Data System (ADS)

    Chan, Tsz On Mario

    Nanometer-scale structures have properties that are fundamentally different from their bulk counterparts. Much research effort has been devoted in the past decades to explore new fabrication techniques, model the physical properties of these structures, and construct functional devices. The ability to manipulate and control the structure of matter at the nanoscale has made many new classes of materials available for the study of fundamental physical processes and potential applications. The interplay between fabrication techniques and physical understanding of the nanostructures and processes has revolutionized the physical and material sciences, providing far superior properties in materials for novel applications that benefit society. This thesis consists of two major aspects of my graduate research in nano-scale materials. In the first part (Chapters 3--6), a comprehensive study on the nanostructures based on electrospinning and thermal treatment is presented. Electrospinning is a well-established method for producing high-aspect-ratio fibrous structures, with fiber diameter ranging from 1 nm--1 microm. A polymeric solution is typically used as a precursor in electrospinning. In our study, the functionality of the nanostructure relies on both the nanostructure and material constituents. Metallic ions containing precursors were added to the polymeric precursor following a sol-gel process to prepare the solution suitable for electrospinning. A typical electrospinning process produces as-spun fibers containing both polymer and metallic salt precursors. Subsequent thermal treatments of the as-spun fibers were carried out in various conditions to produce desired structures. In most cases, polymer in the solution and the as-spun fibers acted as a backbone for the structure formation during the subsequent heat treatment, and were thermally removed in the final stage. Polymers were also designed to react with the metallic ion precursors during heat treatment in some

  20. Gompertz type dechanneling functions for protons in <1 0 0>, <1 1 0> and <1 1 1> Si crystal channels

    NASA Astrophysics Data System (ADS)

    Petrović, S.; Erić, M.; Kokkoris, M.; Nešković, N.

    2007-03-01

    In this work the energy dependences of the Gompertz type sigmoidal dechanneling function parameters for protons in <1 0 0>, <1 1 0> and <1 1 1> Si crystal channels is investigated theoretically. The proton energy range considered is between 1 and 10 MeV. The original dechanneling functions are generated using a realistic Monte Carlo computer simulation code. We show that the Gompertz type dechanneling function, having two parameters, lc and k, representing the dechanneling range and rate, respectively, approximate accurately the original dechanneling function. It is also shown that the energy dependences of parameters lc and k can be approximated by a linear function and a sum of two exponential functions, respectively. The results obtained can be used for accurate reproduction of experimental proton channeling spectra recorded in the backscattering geometry.

  1. Optimization of current modulation function for proton spread-out Bragg peak fields

    SciTech Connect

    Lu, H.-M.; Kooy, Hanne

    2006-05-15

    Proton treatments with spread-out Bragg peak (SOBP) fields often use a rotating modulation wheel of varying thickness to modulate the pristine Bragg peak in depth and intensity. The technique of modulating also the beam current independently over the wheel rotation provides an additional control over the intensities of the pulled-back Bragg peaks. As a result, a single wheel can be used over a large range of energies and SOBP parameters and field-specific wheels are no longer necessary. An essential task in commissioning a particular treatment depth is the determination of this current modulation function. We have developed a method for the optimization of the current modulation function. The basic idea is to treat the entire beam nozzle, housing the various beam scattering and modulating components, as a whole and to characterize its effect as a transformation from a modulating beam current to a depth-dose distribution. While this transformation is difficult to calculate theoretically due to the complex scattering paths in the nozzle and the phantom, it can, however, be determined by time-resolved dose measurements. Using this transformation, we can calculate SOBP depth-dose distributions for any current modulation function and optimize it by a simple numerical optimization. We have applied the new method to a number of proton beams with satisfactory results.

  2. Surface Protonation at the Rutile (110) Interface: Explicit Incorporation of Solvation Structure within the Refined MUSIC Model Framework

    SciTech Connect

    Machesky, Michael L.; Predota, M.; Wesolowski, David J

    2008-11-01

    The detailed solvation structure at the (110) surface of rutile ({alpha}-TiO{sub 2}) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 {angstrom} of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 C that agrees quantitatively with the experimentally determined value (5.4 {+-} 0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pH{sub znpc} values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pH{sub znpc} value of the rutile (110) surface at 25 C into quantitative agreement with the experimental value (4.8 {+-} 0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic

  3. Investigating Proton Spin Structure: A Measurement of g2p at Low Q2

    NASA Astrophysics Data System (ADS)

    Cummings, Melissa A.

    The g2p collaboration performed the first measurement of the reaction vec{p}(vec{ e},e')X in the kinematic range 0.02 < Q2 < 0.2 GeV2 in the resonance region. Experiment E08-027 took place in Hall A at the Thomas Jefferson National Accelerator Facility from March-May of 2012. Data was taken with a longitudinally polarized electron beam, using an NH3 target polarized in both parallel and perpendicular configurations. Very preliminary results for g1p and g2p are shown in this thesis. To extract the spin structure functions, asymmetries are calculated from data taken with a 2.2 GeV electron beam and a 5 T target field, and combined with the Bosted model proton cross section. Preliminary dilution factors and preliminary radiative corrections are included in the asymmetry analysis. Sum rules and chiPT allow us to test the Burkhardtt-Cottingham (BC) sum rule and obtain the spin polarizability quantities gamma0 and deltaLT. The BC sum rule, valid for all values of Q2 says that the integral of g 2 over all Bjorken x vanishes. The very preliminary result presented here shows the contribution to the integral from the measured kinematic region. Although the contribution from the resonance region is not consistent with the expected result of zero, an extrapolation to high and low x must be included to test whether the BC sum rule is satisfied. The difficulty in chiPT calculations of gamma0 and deltaLT is how to include the resonance contributions, particularly the Delta-resonance, which dominates. Recent developments have found better agreement with neutron experimental results, however this is little proton data to compare with the calculations, particularly at low Q 2. The very preliminary results shown here do not show agreement with any of the current chiPT predictions. However, as this is only the contribution from the measured kinematic region, it is necessary to include the extrapolation outside the resonance region to draw a stronger conclusion. Further analysis is

  4. Molecular hydrogen messengers can lead to structural infidelity: A cautionary tale of protonated glycine.

    PubMed

    Masson, Antoine; Williams, Evan R; Rizzo, Thomas R

    2015-09-14

    The effects of tagging protonated glycine with either He or between 1 and 14 H2 molecules on the infrared photodissociation spectra and the ion structure were investigated. Differences in the IR spectra with either a single He atom or H2 molecule attached indicate that even a single H2 molecule can affect the frequencies of some vibrational bands of this simple ion. The protonation site is the preferred location of the tag with He and with up to two H2 molecules, but evidence for H2 attachment to the hydrogen atom of the uncharged carboxylic acid is observed for ions tagged with three or more H2 molecules. This results in a 55 cm(-1) red shift in the carboxylic acid OH stretch, and evidence for some structural isomers where the hydrogen bond between the protonated nitrogen and the carbonyl oxygen is partially broken; as a result H2 molecules attached to this site are observed. These results are supported by theory, which indicates that H2 molecules can effectively break this weak hydrogen bond with three or more H2 molecules. These results indicate that large spectral shifts as a result of H2 molecules attaching to sites remote from the charge can occur and affect stretching frequencies as a result of charge transfer, and that tagging with multiple H2 molecules can change the structure of the ion itself.

  5. Molecular hydrogen messengers can lead to structural infidelity: A cautionary tale of protonated glycine

    NASA Astrophysics Data System (ADS)

    Masson, Antoine; Williams, Evan R.; Rizzo, Thomas R.

    2015-09-01

    The effects of tagging protonated glycine with either He or between 1 and 14 H2 molecules on the infrared photodissociation spectra and the ion structure were investigated. Differences in the IR spectra with either a single He atom or H2 molecule attached indicate that even a single H2 molecule can affect the frequencies of some vibrational bands of this simple ion. The protonation site is the preferred location of the tag with He and with up to two H2 molecules, but evidence for H2 attachment to the hydrogen atom of the uncharged carboxylic acid is observed for ions tagged with three or more H2 molecules. This results in a 55 cm-1 red shift in the carboxylic acid OH stretch, and evidence for some structural isomers where the hydrogen bond between the protonated nitrogen and the carbonyl oxygen is partially broken; as a result H2 molecules attached to this site are observed. These results are supported by theory, which indicates that H2 molecules can effectively break this weak hydrogen bond with three or more H2 molecules. These results indicate that large spectral shifts as a result of H2 molecules attaching to sites remote from the charge can occur and affect stretching frequencies as a result of charge transfer, and that tagging with multiple H2 molecules can change the structure of the ion itself.

  6. Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers.

    PubMed

    Wong, Richard L; Williams, Evan R; Counterman, Anne E; Clemmer, David E

    2005-07-01

    The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs.

  7. Density functional investigation of photo induced Intramolecular Proton Transfer (IPT) in Indole-7-carboxaldehyde and its experimental verification

    NASA Astrophysics Data System (ADS)

    Singla, Nidhi; Chowdhury, Papia

    2013-08-01

    A detail theoretical study has been performed using Density functional theory (DFT) and Time dependent DFT (TDDFT) to investigate the Intramolecular Proton Transfer (IPT) mechanism in Indole-7-carboxaldehyde (I7C) from its normal (I*) to zwitterion (II*) form. B3LYP/6-311++G (d, p) basis set has been used to obtain structural parameters and relative energies in the ground state (S0) and excited state (S1). Atoms in Molecules (AIMs), Mulliken and Natural bond orbitals (NBOs) analysis proves the existence of intramolecular hydrogen bonding (IHB). The electron density (ρ) at Bond critical points (BCPs) on a hydrogen bridge (N15sbnd H12⋯O18) certify IHB and possibility of IPT from acidic (N15sbnd H12) to basic (lbond2 C16dbnd O18) group and creation of II*. Transition state (TS) with dual minima in the Potential energy surface (PES) confirms the I* → TS → II* transition due to excited state Intramolecular Proton Transfer (ESIPT). Photo-physical pathway from I* → II* agrees well with computed/experimental emission peaks.

  8. Effects of proton and electron irradiation on the structural and tribological properties of MoS 2/polyimide

    NASA Astrophysics Data System (ADS)

    Liu, Baixing; Pei, Xianqiang; Wang, Qihua; Sun, Xiaojun; Wang, Tingmei

    2011-11-01

    To study the structural and tribological properties of MoS2/polyimide (MoS2/PI) composite under the irradiation environment of proton and electron, the MoS2/PI composites were investigated in a ground-based simulation facility, in which the energy of proton and electron was 25 keV and the flux was 2.5 × 1014 cm-2 s-1. The experimental results revealed that the simplex and combined irradiation of proton and electron induced bond break and cross-link, proton irradiation can break the PI bond easier than electron irradiation and then formed the graphite-like structure at surface area of the samples. Irradiation decreased the friction coefficient and wear rate remarkably of the composites comparing with the pristine one. The wear rate increased with the increasing of the proton and combined radiation time, and decreased with the electron radiation conditions.

  9. A divergent route to core- and peripherally functionalized diazacoronenes that act as colorimetric and fluorescence proton sensors

    SciTech Connect

    He, Bo; Dai, Jing; Zherebetskyy, Danylo; Chen, Teresa L.; Zhang, Benjamin A.; Teat, Simon J.; Zhang, Qichun; Wang, Linwang; Liu, Yi

    2015-03-31

    Combining core annulation and peripheral group modification, we have demonstrated a divergent synthesis of a family of highly functionalized coronene derivatives from a readily accessible dichlorodiazaperylene intermediate. Various reactions, such as aromatic nucleophilic substitution, Kumada coupling and Suzuki coupling proceed effectively on α-positions of the pyridine sites, giving rise to alkoxy, thioalkyl, alkyl or aryl substituted polycyclic aromatic hydrocarbons. In addition to peripheral group modulation, the aromatic core structures can be altered by annulation with thiophene or benzene ring systems. Corresponding single crystal X-ray diffraction and optical studies indicate that the heteroatom linkages not only impact the solid state packing, but also significantly influence the optoelectronic properties. Moreover, these azacoronene derivatives display significant acid-induced spectroscopic changes, suggesting their great potential as colorimetric and fluorescence proton sensors.

  10. A divergent route to core- and peripherally functionalized diazacoronenes that act as colorimetric and fluorescence proton sensors

    DOE PAGES

    He, Bo; Dai, Jing; Zherebetskyy, Danylo; Chen, Teresa L.; Zhang, Benjamin A.; Teat, Simon J.; Zhang, Qichun; Wang, Linwang; Liu, Yi

    2015-03-31

    Combining core annulation and peripheral group modification, we have demonstrated a divergent synthesis of a family of highly functionalized coronene derivatives from a readily accessible dichlorodiazaperylene intermediate. Various reactions, such as aromatic nucleophilic substitution, Kumada coupling and Suzuki coupling proceed effectively on α-positions of the pyridine sites, giving rise to alkoxy, thioalkyl, alkyl or aryl substituted polycyclic aromatic hydrocarbons. In addition to peripheral group modulation, the aromatic core structures can be altered by annulation with thiophene or benzene ring systems. Corresponding single crystal X-ray diffraction and optical studies indicate that the heteroatom linkages not only impact the solid state packing,more » but also significantly influence the optoelectronic properties. Moreover, these azacoronene derivatives display significant acid-induced spectroscopic changes, suggesting their great potential as colorimetric and fluorescence proton sensors.« less

  11. Unprecedented χ isomers of single-side triol-functionalized Anderson polyoxometalates and their proton-controlled isomer transformation.

    PubMed

    Zhang, Jiangwei; Liu, Zhenhua; Huang, Yichao; zhang, Jin; Hao, Jian; Wei, Yongge

    2015-06-01

    The μ2-O atom in Anderson polyoxometalates was regioselectively activated by the introduction of protons, which, upon functionalization with triol ligands, could afford a series of unique χ isomers of the organically-derived Anderson cluster {[RCC(CH2O)3]MMo6O18(OH)3}(3-). Herein proton-controlled isomer transformation between the δ and χ isomer was observed by using the fingerprint region in the IR spectra and (13)C NMR spectra.

  12. Computer Modeling of the Earliest Cellular Structures and Functions

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Chipot, Christophe; Schweighofer, Karl

    2000-01-01

    In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells). the most direct way to test our understanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform proto-cellular functions. Many of these functions, such as import of nutrients, capture and storage of energy. and response to changes in the environment are carried out by proteins bound to membrane< We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (eg. channels), and (c) by what mechanisms such aggregates perform essential proto-cellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each item in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10(exp 6)-10(exp 8) time steps.

  13. A-dependence of weak nuclear structure functions

    SciTech Connect

    Haider, H.; Athar, M. Sajjad; Simo, I. Ruiz

    2015-05-15

    Effect of nuclear medium on the weak structure functions F{sub 2}{sup A}(x, Q{sup 2}) and F{sub 3}{sup A}(x, Q{sup 2}) have been studied using charged current (anti)neutrino deep inelastic scattering on various nuclear targets. Relativistic nuclear spectral function which incorporate Fermi motion, binding and nucleon correlations are used for the calculations. We also consider the pion and rho meson cloud contributions calculated from a microscopic model for meson-nucleus self-energies. Using these structure functions, F{sub i}{sup A}/F{sub i}{sup proton} and F{sub i}{sup A}/F{sub i}{sup deuteron}(i=2,3, A={sup 12}C, {sup 16}O, CH and H{sub 2}O) are obtained.

  14. Structures and Functions of Oligosaccharins

    SciTech Connect

    Albersheim, Peter

    1995-12-01

    We have made considerable progress during the 2.5 year funding period just ending in our studies of the structures and functions of oligosaccharide signal molecules (oligosaccharins). We have emphasized studies of the enzymes that solubilize, process, and degrade oligosaccharins and of the proteins that inhibit those enzymes. We have been especially interested in elucidating how oligosaccharins and their processing enzymes participate in determining the outcome of challenges to plants by pathogenic microbes. We have studied, to a lesser extent, the roles of oligosaccharins in plant growth and development. Abstracts of papers describing results acquired with support from this grant that have been published, submitted, or in preparation are presented to summarize the progress made during the last two and one half years. The report highlights the most important contributions made in our oiigosaccharin research during this time period, and the corresponding abstract is referenced. Results of work in progress are described primarily in conjunction with our application for continued support.

  15. Functional evolution of nuclear structure

    PubMed Central

    Dawson, Scott C.

    2011-01-01

    The evolution of the nucleus, the defining feature of eukaryotic cells, was long shrouded in speculation and mystery. There is now strong evidence that nuclear pore complexes (NPCs) and nuclear membranes coevolved with the endomembrane system, and that the last eukaryotic common ancestor (LECA) had fully functional NPCs. Recent studies have identified many components of the nuclear envelope in living Opisthokonts, the eukaryotic supergroup that includes fungi and metazoan animals. These components include diverse chromatin-binding membrane proteins, and membrane proteins with adhesive lumenal domains that may have contributed to the evolution of nuclear membrane architecture. Further discoveries about the nucleoskeleton suggest that the evolution of nuclear structure was tightly coupled to genome partitioning during mitosis. PMID:22006947

  16. Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus.

    PubMed

    Acharya, Rudresh; Carnevale, Vincenzo; Fiorin, Giacomo; Levine, Benjamin G; Polishchuk, Alexei L; Balannik, Victoria; Samish, Ilan; Lamb, Robert A; Pinto, Lawrence H; DeGrado, William F; Klein, Michael L

    2010-08-24

    The M2 proton channel from influenza A virus is an essential protein that mediates transport of protons across the viral envelope. This protein has a single transmembrane helix, which tetramerizes into the active channel. At the heart of the conduction mechanism is the exchange of protons between the His37 imidazole moieties of M2 and waters confined to the M2 bundle interior. Protons are conducted as the total charge of the four His37 side chains passes through 2(+) and 3(+) with a pK(a) near 6. A 1.65 A resolution X-ray structure of the transmembrane protein (residues 25-46), crystallized at pH 6.5, reveals a pore that is lined by alternating layers of sidechains and well-ordered water clusters, which offer a pathway for proton conduction. The His37 residues form a box-like structure, bounded on either side by water clusters with well-ordered oxygen atoms at close distance. The conformation of the protein, which is intermediate between structures previously solved at higher and lower pH, suggests a mechanism by which conformational changes might facilitate asymmetric diffusion through the channel in the presence of a proton gradient. Moreover, protons diffusing through the channel need not be localized to a single His37 imidazole, but instead may be delocalized over the entire His-box and associated water clusters. Thus, the new crystal structure provides a possible unification of the discrete site versus continuum conduction models.

  17. Next-to leading order analysis of target mass corrections to structure functions and asymmetries

    SciTech Connect

    L. T. Brady, A. Accardi, T. J. Hobbs, W. Melnitchouk

    2011-10-01

    We perform a comprehensive analysis of target mass corrections (TMCs) to spin-averaged structure functions and asymmetries at next-to-leading order. Several different prescriptions for TMCs are considered, including the operator product expansion, and various approximations to it, collinear factorization, and xi-scaling. We assess the impact of each of these on a number of observables, such as the neutron to proton F{sub 2} structure function ratio, and parity-violating electron scattering asymmetries for protons and deuterons which are sensitive to gamma-Z interference effects. The corrections from higher order radiative and nuclear effects on the parity-violating deuteron asymmetry are also quantified.

  18. Study of the proton structure by measurements of polarization transfers in real Compton scattering at Jlab

    SciTech Connect

    Fanelli, Cristiano Fanelli; Cisbani, Evarostp; Hamilton, David; Salme, G.; Wojtsekhowski, Bogdan B.

    2014-03-01

    A preliminary analysis of polarization-transfer data at large scattering angle (70°), obtained in an experiment of real Compton scattering on proton, performed in Hall-C of Jefferson Lab, is presented. It is also discussed the relevance of this kind of experiments for shedding light on the non-perturbative structure of the proton, at low energy, and on the transition from the non-perturbative regime to the perturbative one, that occurs at high energy. Moreover, the possibility to extract Compton form factors and the Generalized Parton Distributions, one of the most promising theoretical tool to determine the total angular momentum contribution of quarks and gluons to nucleon spin, is emphasized.

  19. Spherical proton-neutron structure of isomeric states in {sup 128}Cd

    SciTech Connect

    Caceres, L.; Gorska, M.; Grawe, H.; Sieja, K.; Geissel, H.; Gerl, J.; Kojouharov, I.; Kurz, N.; Montes, F.; Martinez-Pinedo, G.; Prokopowicz, W.; Schaffner, H.; Tashenov, S.; Wollersheim, H. J.; Jungclaus, A.; Pfuetzner, M.; Werner-Malento, E.; Nowacki, F.

    2009-01-15

    The {gamma}-ray decay of isomeric states in the even-even nucleus {sup 128}Cd has been observed. The nucleus of interest was produced both by the fragmentation of {sup 136}Xe and the fission of {sup 238}U primary beams. The level scheme was unambiguously constructed based on {gamma}{gamma} coincidence relations in conjunction with detailed lifetime analysis employed for the first time on this nucleus. Large-scale shell-model calculations, without consideration of excitations across the N=82 shell closure, were performed and provide a consistent description of the experimental level scheme. The structure of the isomeric states and their decays exhibit coexistence of proton, neutron, and strongly mixed configurations due to {pi}{nu} interaction in overlapping orbitals for both proton and neutron holes.

  20. Excited-state proton coupled charge transfer modulated by molecular structure and media polarization.

    PubMed

    Demchenko, Alexander P; Tang, Kuo-Chun; Chou, Pi-Tai

    2013-02-01

    Charge and proton transfer reactions in the excited states of organic dyes can be coupled in many different ways. Despite the complementarity of charges, they can occur on different time scales and in different directions of the molecular framework. In certain cases, excited-state equilibrium can be established between the charge-transfer and proton-transfer species. The interplay of these reactions can be modulated and even reversed by variations in dye molecular structures and changes of the surrounding media. With knowledge of the mechanisms of these processes, desired rates and directions can be achieved, and thus the multiple emission spectral features can be harnessed. These features have found versatile applications in a number of cutting-edge technological areas, particularly in fluorescence sensing and imaging.

  1. STAS Domain Structure and Function

    PubMed Central

    Sharma, Alok K.; Rigby, Alan C.; Alper, Seth L.

    2011-01-01

    Pendrin shares with nearly all SLC26/SulP anion transporters a carboxy-terminal cytoplasmic segment organized around a Sulfate Transporter and Anti-Sigma factor antagonist (STAS) domain. STAS domains of divergent amino acid sequence exhibit a conserved fold of 4 β strands interspersed among 5 α helices. The first STAS domain proteins studied were single-domain anti-sigma factor antagonists (anti-anti-σ). These anti-anti-σ indirectly stimulate bacterial RNA polymerase by inactivating inhibitory anti-σ kinases, liberating σ factors to direct specific transcription of target genes or operons. Some STAS domains are nucleotide-binding phosphoproteins or nucleotidases. Others are interaction/transduction modules within multidomain sensors of light, oxygen and other gasotransmitters, cyclic nucleotides, inositol phosphates, and G proteins. Additional multidomain STAS protein sequences suggest functions in sensing, metabolism, or transport of nutrients such as sugars, amino acids, lipids, anions, vitamins, or hydrocarbons. Still other multidomain STAS polypeptides include histidine and serine/threonine kinase domains and ligand-activated transcription factor domains. SulP/SLC26 STAS domains and adjacent sequences interact with other transporters, cytoskeletal scaffolds, and with enzymes metabolizing transported anion substrates, forming putative metabolons. STAS domains are central to membrane targeting of many SulP/SLC26 anion transporters, and STAS domain mutations are associated with at least three human recessive diseases. This review summarizes STAS domain structure and function. PMID:22116355

  2. Characteristics of velocity distribution functions and entry mechanisms of protons in the near-lunar wake from SWIM/SARA on Chandrayaan-1

    NASA Astrophysics Data System (ADS)

    Dhanya, M. B.; Barabash, Stas; Wieser, Martin; Holmström, Mats; Bhardwaj, Anil; Wurz, Peter; Alok, Abhinaw; Futaana, Yoshifumi

    2016-07-01

    Moon is an airless body with no global magnetic field, although regions of crustal magnetic fields known as magnetic anomalies exist on Moon. Solar wind, the magnetized plasma flow from the Sun, continuously impinges on Moon. Due to the high absorption of solar wind plasma on the lunar dayside, a large scale wake structure is formed downstream of the Moon. However, recent in-situ observations have revealed the presence of protons in the near-lunar wake (100 km to 200 km from the surface). The source of these protons have been found to be the solar wind that enter the wake either directly or after interaction with the lunar surface or with the magnetic anomalies. Using the entire data from the SWIM sensor, which was an ion-mass analyzer, of the SARA experiment onboard Chandrayaan-1, the characteristics of velocity distribution of these protons were investigated to understand the entry mechanisms to near lunar wake. The velocity distribution functions were computed in the two dimensional velocity space, namely in the directions parallel and perpendicular to the IMF (v_allel and v_perp) in the solar wind rest frame. Several proton populations were identified from the velocity distribution and their possible entry mechanism were inferred based on the characteristics of the velocity distribution. These entry mechanisms include (i) diffusion of solar wind protons into the wake along IMF, (ii) the solar wind protons with finite gyro-radii that are aided by the wake boundary electric field, (iii) solar wind protons with gyro-radii larger than lunar radii from the tail of the solar wind velocity distribution, and (iv) scattering of solar wind protons from the dayside lunar surface or from magnetic anomalies. In order to gain more insight into the entry mechanisms associated with different populations, the trajectories of the protons were computed backward in time (backtracing) for each of these populations. For most of the populations, the source mechanism obtained from

  3. Pickup protons and pressure-balanced structures: Voyager 2 observations in merged interaction regions near 35 AU

    NASA Technical Reports Server (NTRS)

    Burlaga, L. F.; Ness, N. F.; Belcher, J. W.; Szabo, A.; Isenberg, P. A.; Lee, M. A.

    1994-01-01

    Five pressure-balanced structures, each with a scale of the order of a few hundredths of an astonomical unit (AU), were identified in two merged interaction regions (MIRs) near 35 AU in the Voyager 2 plasma and magnetic field data. They include a tangential discountinuity, simple and complex magnetic holes, slow correlated variations among the plasma and magnetic field parameters, and complex uncorrelated variations among the parameters. The changes in the magnetic pressure in these events are balanced by changes in the pressure of interstellar pickup protons. Thus the pickup protons probably play a major role in the dynamics of the MIRs. The solar wind proton and electron pressures are relatively unimportant in the MIRs at 35 AU and beyond. The region near 35 AU is transition region: the Sun is the source of the magnetic field, but the interstellar medium in source of pickups protons. Relative to the solar wind proton guyroadius, the thicknesses of the discontinuities and simple magnetic holes observed near 35 AU are at least an order of magnitude greater than those observed at 1 AU. However, the thicknesses of the tangential discontinuity and simple magnetic holes observed near 35 AU (in units of the pickup proton Larmor radius) are comparable to those observed at 1 AU (in units of the solar wind proton gyroradius). Thus the gyroradius of interstellar pickup protons controls the thickness of current sheets near 35 AU. We determine the interstellar pickup proton pressure in the PBSs. Using a model for the pickup proton temperature, we estimate that the average interstellar pickup proton pressure, temperature, and density in the MIRs at 35 AU are (0.53 +/- 0.14) x 10(exp -12) erg/cu cm, (5.8 +/- 0.4) x 10(exp 6) K and (7 +/- 2) x 10(exp -4)/cu cm.

  4. Structure Function Estimated From Histological Tissue Sections.

    PubMed

    Han, Aiguo; O'Brien, William D

    2016-09-01

    Ultrasonic scattering is determined by not only the properties of individual scatterers but also the correlation among scatterer positions. The role of scatterer spatial correlation is significant for dense medium, but has not been fully understood. The effect of scatterer spatial correlation may be modeled by the structure function as a frequency-dependent factor in the backscatter coefficient (BSC) expression. The structure function has been previously estimated from the BSC data. The aim of this study is to estimate the structure function from histology to test if the acoustically estimated structure function is indeed caused by the scatterer spatial distribution. Hematoxylin and eosin stained histological sections from dense cell pellet biophantoms were digitized. The scatterer positions were determined manually from the histological images. The structure function was calculated from the extracted scatterer positions. The structure function obtained from histology showed reasonable agreement in the shape but not in the amplitude, compared with the structure function previously estimated from the backscattered data. Fitting a polydisperse structure function model to the histologically estimated structure function yielded relatively accurate cell radius estimates ([Formula: see text]). Furthermore, two types of mouse tumors that have similar cell size and shape but distinct cell spatial distributions were studied, where the backscattered data were shown to be related to the cell spatial distribution through the structure function estimated from histology. In conclusion, the agreement between acoustically estimated and histologically estimated structure functions suggests that the acoustically estimated structure function is related to the scatterer spatial distribution.

  5. Structure and functions of fungal cell surfaces

    NASA Technical Reports Server (NTRS)

    Nozawa, Y.

    1984-01-01

    A review with 24 references on the biochemistry, molecular structure, and function of cell surfaces of fungi, especially dermatophytes: the chemistry and structure of the cell wall, the effect of polyene antibiotics on the morphology and function of cytoplasmic membranes, and the chemical structure and function of pigments produced by various fungi are discussed.

  6. A proton current associated with sour taste: distribution and functional properties.

    PubMed

    Bushman, Jeremy D; Ye, Wenlei; Liman, Emily R

    2015-07-01

    Sour taste is detected by taste receptor cells that respond to acids through yet poorly understood mechanisms. The cells that detect sour express the protein PKD2L1, which is not the sour receptor but nonetheless serves as a useful marker for sour cells. By use of mice in which the PKD2L1 promoter drives expression of yellow fluorescent protein, we previously reported that sour taste cells from circumvallate papillae in the posterior tongue express a proton current. To establish a correlation between this current and sour transduction, we examined its distribution by patch-clamp recording. We find that the current is present in PKD2L1-expressing taste cells from mouse circumvallate, foliate, and fungiform papillae but not in a variety of other cells, including spinal cord neurons that express PKD2L1. We describe biophysical properties of the current, including pH-dependent Zn(2+) inhibition, lack of voltage-dependent gating, and activation at modest pH values (6.5) that elicit action potentials in isolated cells. Consistent with a channel that is constitutively open, the cytosol of sour taste cells is acidified. These data define a functional signature for the taste cell proton current and indicate that its expression is mostly restricted to the subset of taste cells that detect sour.

  7. The potential utility of predicted one bond carbon-proton coupling constants in the structure elucidation of small organic molecules by NMR spectroscopy.

    PubMed

    Venkata, Chandrasekhar; Forster, Mark J; Howe, Peter W A; Steinbeck, Christoph

    2014-01-01

    NMR spectroscopy is the most popular technique used for structure elucidation of small organic molecules in solution, but incorrect structures are regularly reported. One-bond proton-carbon J-couplings provide additional information about chemical structure because they are determined by different features of molecular structure than are proton and carbon chemical shifts. However, these couplings are not routinely used to validate proposed structures because few software tools exist to predict them. This study assesses the accuracy of Density Functional Theory for predicting them using 396 published experimental observations from a diverse range of small organic molecules. With the B3LYP functional and the TZVP basis set, Density Functional Theory calculations using the open-source software package NWChem can predict one-bond CH J-couplings with good accuracy for most classes of small organic molecule. The root-mean-square deviation after correction is 1.5 Hz for most sp3 CH pairs and 1.9 Hz for sp2 pairs; larger errors are observed for sp3 pairs with multiple electronegative substituents and for sp pairs. These results suggest that prediction of one-bond CH J-couplings by Density Functional Theory is sufficiently accurate for structure validation. This will be of particular use in strained ring systems and heterocycles which have characteristic couplings and which pose challenges for structure elucidation.

  8. The Potential Utility of Predicted One Bond Carbon-Proton Coupling Constants in the Structure Elucidation of Small Organic Molecules by NMR Spectroscopy

    PubMed Central

    Venkata, Chandrasekhar; Forster, Mark J.; Howe, Peter W. A.; Steinbeck, Christoph

    2014-01-01

    NMR spectroscopy is the most popular technique used for structure elucidation of small organic molecules in solution, but incorrect structures are regularly reported. One-bond proton-carbon J-couplings provide additional information about chemical structure because they are determined by different features of molecular structure than are proton and carbon chemical shifts. However, these couplings are not routinely used to validate proposed structures because few software tools exist to predict them. This study assesses the accuracy of Density Functional Theory for predicting them using 396 published experimental observations from a diverse range of small organic molecules. With the B3LYP functional and the TZVP basis set, Density Functional Theory calculations using the open-source software package NWChem can predict one-bond CH J-couplings with good accuracy for most classes of small organic molecule. The root-mean-square deviation after correction is 1.5 Hz for most sp3 CH pairs and 1.9 Hz for sp2 pairs; larger errors are observed for sp3 pairs with multiple electronegative substituents and for sp pairs. These results suggest that prediction of one-bond CH J-couplings by Density Functional Theory is sufficiently accurate for structure validation. This will be of particular use in strained ring systems and heterocycles which have characteristic couplings and which pose challenges for structure elucidation. PMID:25365289

  9. [Effect of proton irradiation of the hypophysis on its gonadotropic and thyrotropic functions in patients with prolactinoma].

    PubMed

    Isakov, A V; Konnov, B A; Potin, V V; Svechnikova, F A; Tkachenko, N N

    1988-01-01

    In order to study the effect of proton beam irradiation on prolactinoma cells and hypophyseal intact cells tests with i.v. administration of TRH (200 micrograms) and LH-RH (100 micrograms) were performed in 16 women with prolactin-secreting adenomas before and in 2 mos.-2 years after irradiation of the pituitary body with a high energy narrow proton beam (1000 MeV) at a dose of 40-120 Gy. A curative therapeutic effect of proton therapy which was low with respect to reproductive function recovery, was combined with lowered functional reserves of hypophyseal thyrotrophs and gonadotrophs. The informative value of the tests with the releasing hormones was shown for the determination of damage of hypophyseal intact cells. The results suggest refractivity of adenomatous lactotrophs to radiation exposure and the hypothalamic level of disorder of ovarian function regulation in this pathology.

  10. Structure and Mechanism of the M2 Proton Channel of Influenza A Virus

    PubMed Central

    Schnell, Jason R.; Chou, James J.

    2011-01-01

    The integral membrane protein, M2, of influenza virus forms pH-gated proton channels in the viral lipid envelope1. The low pH of an endosome activates the M2 channel prior to hemagglutinin-mediated fusion. Conductance of protons acidifies the viral interior and thereby facilitates dissociation of the matrix protein from the viral nucleoproteins – a required process for unpacking of the viral genome2. In addition to its role in release of viral nucleoproteins, M2 in the trans-Golgi network (TGN) membrane prevents premature conformational rearrangement of newly synthesized hemagglutinin during transport to the cell surface by equilibrating the pH of the TGN with that of the host cell cytoplasm3. Inhibitng the proton conductance of M2 with the anti-viral drug amantadine or rimantadine inhibits viral replication4–7. We have determined by NMR the structure of the tetrameric M2 channel in complex with rimantadine. In the closed state, four tightly packed transmembrane (TM) helices define a narrow channel, in which a “tryptophan gate” is locked by inter-molecular interactions with aspartic acid. A C-terminal, amphipathic (AP) helix oriented nearly perpendicular to the TM helix, forms an inward facing base. Lowering the pH destabilizes the TM helical packing and unlocks the gate, admitting water to conduct protons, while the C-terminal base remains intact, preventing dissociation of the tetramer. Rimantadine binds at four equivalent sites near the gate on the lipid facing side of the channel and stabilizes the closed conformation of the pore. Drug-resistance mutations are predicted to counter the effect of drug binding by either increasing the hydrophilicity of the pore or weakening helix-helix packing, thus facilitating channel opening. PMID:18235503

  11. Soft nanotechnology: "structure" vs. "function".

    PubMed

    Whitesides, George M; Lipomi, Darren J

    2009-01-01

    This paper offers a perspective on "soft nanotechnology"; that is, the branch of nanotechnology concerned with the synthesis and properties of organic and organometallic nanostructures, and with nanofabrication using techniques in which soft components play key roles. It begins with a brief history of soft nanotechnology. This history has followed a path involving a gradual shift from the promise of revolutionary electronics, nanorobotics, and other futuristic concepts, to the realization of evolutionary improvements in the technology for current challenges in information technology, medicine, and sustainability. Soft nanoscience is an area that is occupied principally by chemists, and is in many ways indistinguishable from "nanochemistry". The paper identifies the natural tendency of its practitioners--exemplified by the speakers at this Faraday Discussion--to focus on synthesis and structure, rather than on function and application, of nanostructures. Soft nanotechnology has the potential to apply to a wide variety of large-scale applied (information technology, healthcare cost reduction, sustainability, energy) and fundamental (molecular biochemistry, cell biology, charge transport in organic matter) problems. PMID:20334113

  12. Soft nanotechnology: "structure" vs. "function".

    PubMed

    Whitesides, George M; Lipomi, Darren J

    2009-01-01

    This paper offers a perspective on "soft nanotechnology"; that is, the branch of nanotechnology concerned with the synthesis and properties of organic and organometallic nanostructures, and with nanofabrication using techniques in which soft components play key roles. It begins with a brief history of soft nanotechnology. This history has followed a path involving a gradual shift from the promise of revolutionary electronics, nanorobotics, and other futuristic concepts, to the realization of evolutionary improvements in the technology for current challenges in information technology, medicine, and sustainability. Soft nanoscience is an area that is occupied principally by chemists, and is in many ways indistinguishable from "nanochemistry". The paper identifies the natural tendency of its practitioners--exemplified by the speakers at this Faraday Discussion--to focus on synthesis and structure, rather than on function and application, of nanostructures. Soft nanotechnology has the potential to apply to a wide variety of large-scale applied (information technology, healthcare cost reduction, sustainability, energy) and fundamental (molecular biochemistry, cell biology, charge transport in organic matter) problems.

  13. Molecular hydrogen messengers can lead to structural infidelity: A cautionary tale of protonated glycine

    SciTech Connect

    Masson, Antoine Rizzo, Thomas R. E-mail: thomas.rizzo@epfl.ch; Williams, Evan R. E-mail: thomas.rizzo@epfl.ch

    2015-09-14

    The effects of tagging protonated glycine with either He or between 1 and 14 H{sub 2} molecules on the infrared photodissociation spectra and the ion structure were investigated. Differences in the IR spectra with either a single He atom or H{sub 2} molecule attached indicate that even a single H{sub 2} molecule can affect the frequencies of some vibrational bands of this simple ion. The protonation site is the preferred location of the tag with He and with up to two H{sub 2} molecules, but evidence for H{sub 2} attachment to the hydrogen atom of the uncharged carboxylic acid is observed for ions tagged with three or more H{sub 2} molecules. This results in a 55 cm{sup −1} red shift in the carboxylic acid OH stretch, and evidence for some structural isomers where the hydrogen bond between the protonated nitrogen and the carbonyl oxygen is partially broken; as a result H{sub 2} molecules attached to this site are observed. These results are supported by theory, which indicates that H{sub 2} molecules can effectively break this weak hydrogen bond with three or more H{sub 2} molecules. These results indicate that large spectral shifts as a result of H{sub 2} molecules attaching to sites remote from the charge can occur and affect stretching frequencies as a result of charge transfer, and that tagging with multiple H{sub 2} molecules can change the structure of the ion itself.

  14. X-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and O2-reduction states.

    PubMed

    Serrano-Posada, Hugo; Centeno-Leija, Sara; Rojas-Trejo, Sonia Patricia; Rodríguez-Almazán, Claudia; Stojanoff, Vivian; Rudiño-Piñera, Enrique

    2015-12-01

    During X-ray data collection from a multicopper oxidase (MCO) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the X-ray-induced reduction of O2 to 2H2O at the trinuclear copper cluster (TNC) of the enzyme. In this work, 12 crystallographic structures of Thermus thermophilus HB27 multicopper oxidase (Tth-MCO) in holo, apo and Hg-bound forms and with different X-ray absorbed doses have been determined. In holo Tth-MCO structures with four Cu atoms, the proton-donor residue Glu451 involved in O2 reduction was found in a double conformation: Glu451a (∼7 Å from the TNC) and Glu451b (∼4.5 Å from the TNC). A positive peak of electron density above 3.5σ in an Fo - Fc map for Glu451a O(ℇ2) indicates the presence of a carboxyl functional group at the side chain, while its significant absence in Glu451b strongly suggests a carboxylate functional group. In contrast, for apo Tth-MCO and in Hg-bound structures neither the positive peak nor double conformations were observed. Together, these observations provide the first structural evidence for a proton-relay mechanism in the MCO family and also support previous studies indicating that Asp106 does not provide protons for this mechanism. In addition, eight composite structures (Tth-MCO-C1-8) with different X-ray-absorbed doses allowed the observation of different O2-reduction states, and a total depletion of T2Cu at doses higher than 0.2 MGy showed the high susceptibility of this Cu atom to radiation damage, highlighting the importance of taking radiation effects into account in biochemical interpretations of an MCO structure.

  15. Density functional theory of tautomerism and water-assisted proton transfer of glycoluril

    NASA Astrophysics Data System (ADS)

    Beni, Alireza Salimi; Aazari, Masumeh; Chermahini, Alireza Najafi; Zarandi, Maryam

    2016-09-01

    Density functional theory and MP2 methods have been employed to study of proton transfer reaction in annular tautomerization of tetrahydroimidazo[4,5-d]imidazole-2,5(1H,3H)-dione (glycoluril). Ten different tautomers are possible for the tetrahydroimidazo[4,5-d]imidazole-2,5(1H,3H)-dione. For all molecules, the Gibbs free energy at 0 and 298 K was estimated. In addition variation of dipole moments and charges on atoms are studied in the gas phase and solution, the specific solvent effects with addition of one molecule of water near the electrophilic centers of tautomer and the NBO charges of atoms were investigated. NBO analysis shows that there is a strong interaction between nitrogen lone pairs and double bonds.

  16. Response functions of Fuji imaging plates to monoenergetic protons in the energy range 0.6-3.2 MeV

    SciTech Connect

    Bonnet, T.; Denis-Petit, D.; Gobet, F.; Hannachi, F.; Tarisien, M.; Versteegen, M.; Aleonard, M. M.

    2013-01-15

    We have measured the responses of Fuji MS, SR, and TR imaging plates (IPs) to protons with energies ranging from 0.6 to 3.2 MeV. Monoenergetic protons were produced with the 3.5 MV AIFIRA (Applications Interdisciplinaires de Faisceaux d'Ions en Region Aquitaine) accelerator at the Centre d'Etudes Nucleaires de Bordeaux Gradignan (CENBG). The IPs were irradiated with protons backscattered off a tantalum target. We present the photo-stimulated luminescence response of the IPs together with the fading measurements for these IPs. A method is applied to allow correction of fading effects for variable proton irradiation duration. Using the IP fading corrections, a model of the IP response function to protons was developed. The model enables extrapolation of the IP response to protons up to proton energies of 10 MeV. Our work is finally compared to previous works conducted on Fuji TR IP response to protons.

  17. Structural tuning intra- versus inter-molecular proton transfer reaction in the excited state.

    PubMed

    Chung, Min-Wen; Liao, Jia-Ling; Tang, Kuo-Chun; Hsieh, Cheng-Chih; Lin, Tsung-Yi; Liu, Chun; Lee, Gene-Hsiang; Chi, Yun; Chou, Pi-Tai

    2012-07-01

    A series of 2-pyridyl-pyrazole derivatives 1-4 possessing five-membered ring hydrogen bonding configuration are synthesized, the structural flexibility of which is strategically tuned to be in the order of 1 > 2 > 3 > 4. This system then serves as an ideal chemical model to investigate the correlation between excited-state intramolecular proton transfer (ESIPT) reaction and molecular skeleton motion associated with hydrogen bonds. The resulting luminescence data reveal that the rate of ESIPT decreases upon increasing the structural constraint. At sufficiently low concentration where negligible dimerization is observed, ESIPT takes place in 1 and 2 but is prohibited in 3 and 4, for which high geometry constraint is imposed. The results imply that certain structural bending motions associated with hydrogen bonding angle/distance play a key role in ESIPT. This trend is also well supported by the DFT computational approach, in which the barrier associated with ESIPT is in the order of 1 < 2 < 3 < 4. Upon increasing the concentration in cyclohexane, except for 2, the rest of the title compounds undergo ground-state dimerization, from which the double proton transfer takes place in the excited state, resulting in a relatively blue shifted dimeric tautomer emission (cf. the monomer tautomer emission). The lack of dimerization in 2 is rationalized by substantial energy required to adjust the angle of hydrogen bond via twisting the propylene bridge prior to dimerization. PMID:22618273

  18. Weak-coupling structure of proton resonant states in 23Al studied with RI beam at CNS

    NASA Astrophysics Data System (ADS)

    He, J. J.; Kubono, S.; Teranishi, T.; Notani, M.; Michimasa, S.; Baba, H.; Nishimura, S.; Nishimura, M.; Yanagisawa, Y.; Hokoiwa, N.; Kibe, M.; Gono, Y.; Moon, J. Y.; Lee, J. H.; Lee, C. S.; Iwasaki, H.; Kato, S.

    2006-07-01

    Proton resonances in 23Al have been investigated for the first time by the resonant elastic and inelastic scattering of 22Mg+p by using a 4.38 MeV/nucleon 22Mg beam bombarding a thick Hydrogen target. The low-energy 22Mg beam was separated by the CNS radioactive ion beam separator (CRIB). A new resonant state due to elastic scattering was observed at Ex = 3.00 MeV with a Jπ = (3/2+) assignment. Other three excited states due to resonant inelastic scattering at 3.14, 3.26 and 3.95 MeV were identified and all mainly decay to the first excited state in 22Mg by the proton emissions. The newly observed 3.95-MeV state probably has a spin-parity of Jπ = (7/2+). The resonant properties were determined from an R-matrix analysis of the excitation functions. The weak-coupling structure in 23Al is discussed in conjunction with a shell-model calculation.

  19. Fabrication of sulfonated poly(ether ether ketone)-based hybrid proton-conducting membranes containing carboxyl or amino acid-functionalized titania by in situ sol-gel process

    NASA Astrophysics Data System (ADS)

    Yin, Yongheng; Xu, Tao; He, Guangwei; Jiang, Zhongyi; Wu, Hong

    2015-02-01

    Functionalized titania are used as fillers to modify the sulfonated poly(ether ether ketone) (SPEEK) membrane for improved proton conductivity and methanol barrier property. The functionalized titania sol which contains proton conductive carboxylic acid groups or amino acid groups are derived from a facile chelation method using different functional additives. Then the novel SPEEK/carboxylic acid-functionalized titania (SPEEK/TC) and SPEEK/amino acid-functionalized titania (SPEEK/TNC) hybrid membranes are fabricated via in situ sol-gel method. The anti-swelling property and thermal stability of hybrid membranes are enhanced owing to the formation of electrostatic force between SPEEK and titania nanoparticles. The hybrid membranes exhibit higher proton conductivity than plain SPEEK membrane because more proton transfer sites are provided by the functionalized titania nanoparticles. Particularly, the proton conductivity of SPEEK/TNC membrane with 15% filler content reaches up to 6.24 × 10-2 S cm-1, which is 3.5 times higher than that of the pure SPEEK membrane. For methanol permeability, the SPEEK/TNC membranes possess the lowest values because the acid-base interaction between sulfonic acid groups in SPEEK and amino groups in functionalized titania leads to a more compact membrane structure.

  20. Disgust: Evolved Function and Structure

    ERIC Educational Resources Information Center

    Tybur, Joshua M.; Lieberman, Debra; Kurzban, Robert; DeScioli, Peter

    2013-01-01

    Interest in and research on disgust has surged over the past few decades. The field, however, still lacks a coherent theoretical framework for understanding the evolved function or functions of disgust. Here we present such a framework, emphasizing 2 levels of analysis: that of evolved function and that of information processing. Although there is…

  1. Study of proton resonance structure in 27P via resonant elastic scattering of 26Si+p

    NASA Astrophysics Data System (ADS)

    Jung, H. S.; Lee, C. S.; Kwon, Y. K.; Moon, J. Y.; Lee, J. H.; Yun, C. C.; Kubono, S.; Yamaguchi, H.; Hashimoto, T.; Kahl, D.; Hayakawa, S.; Choi, Seonho; Kim, M. J.; Kim, Y. H.; Kim, Y. K.; Park, J. S.; Kim, E. J.; Moon, C.-B.; Teranishi, T.; Wakabayashi, Y.; Iwasa, N.; Yamada, T.; Togano, Y.; Kato, S.; Cherubini, S.; Rapisarda, G. G.

    2012-11-01

    A measurement of resonant elastic scattering of 26Si+p was performed with a thick target using a 26Si radioactive ion beam at the CRIB (CNS Radioactive Ion Beam separator) of the Center for Nuclear Study (CNS), the University of Tokyo. The excitation function of 27P was measured successfully with the inverse kinematics method through a covered the range of excitation energies from Ex ~ 2.3 to 3.8 MeV, providing information about the resonance structure of this nucleus. The properties of these resonances are important to better determine the production rates of 26Si(p,g)27P reaction, which is one of the astrophysically important nuclear reactions to understand the production of the 26Al. Some new resonant states have been investigated, and determined their resonance parameters, such as excitation energies, proton partial widths, and spin-parities by R-matrix calculation.

  2. Hydrogen bonding and collective proton modes in clusters and periodic layers of squaric acid: A density functional study

    NASA Astrophysics Data System (ADS)

    Rovira, Carme; Novoa, Juan J.; Ballone, Pietro

    2001-10-01

    Hydrogen bonding in clusters and extended layers of squaric acid molecules has been investigated by density functional computations. Equilibrium geometries, harmonic vibrational frequencies, and energy barriers for proton transfer along hydrogen bonds have been determined using the Car-Parrinello method. The results provide crucial parameters for a first principles modeling of the potential energy surface, and highlight the role of collective modes in the low-energy proton dynamics. The importance of quantum effects in condensed squaric acid systems has been investigated, and shown to be negligible for the lowest-energy collective proton modes. This information provides a quantitative basis for improved atomistic models of the order-disorder and displacive transitions undergone by squaric acid crystals as a function of temperature and pressure.

  3. Molecular Mechanism of Biological Proton Transport

    SciTech Connect

    Pomes, R.

    1998-09-01

    Proton transport across lipid membranes is a fundamental aspect of biological energy transduction (metabolism). This function is mediated by a Grotthuss mechanism involving proton hopping along hydrogen-bonded networks embedded in membrane-spanning proteins. Using molecular simulations, the authors have explored the structural, dynamic, and thermodynamic properties giving rise to long-range proton translocation in hydrogen-bonded networks involving water molecules, or water wires, which are emerging as ubiquitous H{sup +}-transport devices in biological systems.

  4. Evidence for a spin-aligned neutron-proton paired phase from the level structure of (92)Pd.

    PubMed

    Cederwall, B; Moradi, F Ghazi; Bäck, T; Johnson, A; Blomqvist, J; Clément, E; de France, G; Wadsworth, R; Andgren, K; Lagergren, K; Dijon, A; Jaworski, G; Liotta, R; Qi, C; Nyakó, B M; Nyberg, J; Palacz, M; Al-Azri, H; Algora, A; de Angelis, G; Ataç, A; Bhattacharyya, S; Brock, T; Brown, J R; Davies, P; Di Nitto, A; Dombrádi, Zs; Gadea, A; Gál, J; Hadinia, B; Johnston-Theasby, F; Joshi, P; Juhász, K; Julin, R; Jungclaus, A; Kalinka, G; Kara, S O; Khaplanov, A; Kownacki, J; La Rana, G; Lenzi, S M; Molnár, J; Moro, R; Napoli, D R; Singh, B S Nara; Persson, A; Recchia, F; Sandzelius, M; Scheurer, J-N; Sletten, G; Sohler, D; Söderström, P-A; Taylor, M J; Timár, J; Valiente-Dobón, J J; Vardaci, E; Williams, S

    2011-01-01

    Shell structure and magic numbers in atomic nuclei were generally explained by pioneering work that introduced a strong spin-orbit interaction to the nuclear shell model potential. However, knowledge of nuclear forces and the mechanisms governing the structure of nuclei, in particular far from stability, is still incomplete. In nuclei with equal neutron and proton numbers (N = Z), enhanced correlations arise between neutrons and protons (two distinct types of fermions) that occupy orbitals with the same quantum numbers. Such correlations have been predicted to favour an unusual type of nuclear superfluidity, termed isoscalar neutron-proton pairing, in addition to normal isovector pairing. Despite many experimental efforts, these predictions have not been confirmed. Here we report the experimental observation of excited states in the N = Z = 46 nucleus (92)Pd. Gamma rays emitted following the (58)Ni((36)Ar,2n)(92)Pd fusion-evaporation reaction were identified using a combination of state-of-the-art high-resolution γ-ray, charged-particle and neutron detector systems. Our results reveal evidence for a spin-aligned, isoscalar neutron-proton coupling scheme, different from the previous prediction. We suggest that this coupling scheme replaces normal superfluidity (characterized by seniority coupling) in the ground and low-lying excited states of the heaviest N = Z nuclei. Such strong, isoscalar neutron-proton correlations would have a considerable impact on the nuclear level structure and possibly influence the dynamics of rapid proton capture in stellar nucleosynthesis. PMID:21179086

  5. Reactions of acids with naphthyridine-functionalized ferrocenes: protonation and metal extrusion.

    PubMed

    Sadhukhan, Nabanita; Sarkar, Mithun; Ghatak, Tapas; Rahaman, S M Wahidur; Barbour, Leonard J; Bera, Jitendra K

    2013-02-01

    Reaction of 1,8-naphthyrid-2-yl-ferrocene (FcNP) with a variety of acids affords protonated salts at first, whereas longer reaction time leads to partial demetalation of FcNP resulting in a series of Fe complexes. The corresponding salts [FcNP·H][X] (X = BF(4) or CF(3)SO(3) (1)) are isolated for HBF(4) and CF(3)SO(3)H. Reaction of FcNP with equimolar amount of CF(3)CO(2)H for 12 h affords a neutral complex [Fe(FcNP)(2)(O(2)CCF(3))(2)(OH(2))(2)] (2). Use of excess acid gave a trinuclear Fe(II) complex [Fe(3)(H(2)O)(2)(O(2)CCF(3))(8)(FcNP·H)(2)] (3). Three linear iron atoms are held together by four bridging trifluoroacetates and two aqua ligands in a symmetric fashion. Reaction with ethereal solution of HCl afforded [(FcNP·H)(3)(Cl)][FeCl(4)](2) (4) irrespective of the amount of the acid used. Even the picric acid (HPic) led to metal extrusion giving rise to [Fe(2)(Cl)(2)(FcNP)(2)(Pic)(2)] (5) when crystallized from dichloromethane. Metal extrusion was also observed for CF(3)SO(3)H, but an analytically pure compound could not be isolated. The demetalation reaction proceeds with an initial proton attack to the distal nitrogen of the NP unit. Subsequently, coordination of the conjugate base to the electrophilic Fe facilitates the release of Cp rings from metal. The conjugate base plays an important role in the demetalation process and favors the isolation of the Fe complex as well. The 1,1'-bis(1,8-naphthyrid-2-yl)ferrocene (FcNP(2)) does not undergo demetalation under identical conditions. Two NP units share one positive charge causing the Fe-Cp bonds weakened to an extent that is not sufficient for demetalation. X-ray structure of the monoprotonated FcNP(2) reveals a discrete dimer [(FcNP(2)·H)](2)[OTf](2) (6) supported by two N-H···N hydrogen bonds. Crystal packing and dispersive forces associated with intra- and intermolecular π-π stacking interactions (NP···NP and Cp···NP) allow the formation of the dimer in the solid-state. The protonation and

  6. Structure and Dynamics of Proton-Conducting Azoles Confined within Metal-Organic Frameworks

    NASA Astrophysics Data System (ADS)

    Ford, Jamie; Simmons, Jason; Yildirim, Taner

    2011-03-01

    Efficient polymer electrolyte membrane (PEM) fuel cells are one of the most promising candidates to power our vehicles of the future. Hydrated sulfonated polymers are currently the preferred membrane material because of their excellent conductivity and gas diffusion characteristics. The intrinsic water dependence in these systems limits the operating temperature to 100 C, leading to reduced electrode kinetics and increased CO poisoning. If water can be replaced by a small molecule with a higher boiling point, the overall efficiency of the system can be improved. To this end, we have investigated a set of new host/guest materials based on metal-organic frameworks (MOFs) loaded with a variety of azoles. The thermally and chemically stable frameworks provide a well-defined porous structure that accommodates the proton conduction pathways formed by the azole networks. We will present the structure of the azole networks as well as insight into the proton motion dynamics as a result of a variety of neutron scattering experiments.

  7. Proton NMR assignments and secondary structure of the snake venom protein echistatin

    SciTech Connect

    Yuan Chen; Baum, J. ); Pitzenberger, S.M.; Garsky, V.M.; Lumma, P.K.; Sanyal, G. )

    1991-12-17

    The snake venom protein echistatin is a potent inhibitor of platelet aggregation. The inhibitory properties of echistatin have been attributed to the Arg-Gly-Asp sequence at residues 24-26. In this paper, sequence-specific nuclear magnetic resonance assignments are presented for the proton resonances of echistatin in water. The single-chain protein contains 49 amino acids and 4 cystine bridges. All of the backbone amide, C{sub alpha}H, and side-chain resonances, except for the {eta}-NH of the arginines, have been assigned. The secondary structure of the protein was characterized from the pattern of nuclear Overhauser enhancements, from the identification of slowly exchanging amide protons, from {sup 3}J{sub c{alpha}H-NH} coupling constants, and from circular dichroism studies. The data suggest that the secondary structure consists of a type I {beta}-turn, a short {beta}-hairpin, and a short-, irregular, antiparallel {beta}-sheet and that the Arg-Gly-Asp sequence is in a flexible loop connecting two strands of the distorted antiparallel {beta}-sheet.

  8. Structure of a prokaryotic virtual proton pump at 3.2 Å resolution

    SciTech Connect

    Fang, Yiling; Jayaram, Hariharan; Shane, Tania; Kolmakova-Partensky, Ludmila; Wu, Fang; Williams, Carole; Xiong, Yong; Miller, Christopher

    2009-09-15

    To reach the mammalian gut, enteric bacteria must pass through the stomach. Many such organisms survive exposure to the harsh gastric environment (pH 1.5-4) by mounting extreme acid-resistance responses, one of which, the arginine-dependent system of Escherichia coli, has been studied at levels of cellular physiology, molecular genetics and protein biochemistry. This multiprotein system keeps the cytoplasm above pH 5 during acid challenge by continually pumping protons out of the cell using the free energy of arginine decarboxylation. At the heart of the process is a 'virtual proton pump' in the inner membrane, called AdiC, that imports L-arginine from the gastric juice and exports its decarboxylation product agmatine. AdiC belongs to the APC superfamily of membrane proteins, which transports amino acids, polyamines and organic cations in a multitude of biological roles, including delivery of arginine for nitric oxide synthesis, facilitation of insulin release from pancreatic {beta}-cells, and, when inappropriately overexpressed, provisioning of certain fast-growing neoplastic cells with amino acids. High-resolution structures and detailed transport mechanisms of APC transporters are currently unknown. Here we describe a crystal structure of AdiC at 3.2 {angstrom} resolution. The protein is captured in an outward-open, substrate-free conformation with transmembrane architecture remarkably similar to that seen in four other families of apparently unrelated transport proteins.

  9. Structure of a Prokaryotic Virtual Proton Pump at 3.2 Astroms Resolution

    SciTech Connect

    Fang, Y.; Jayaram, H; Shane, T; Partensky, L; Wu, F; williams, C; Xiong, Y; Miller, C

    2009-01-01

    To reach the mammalian gut, enteric bacteria must pass through the stomach. Many such organisms survive exposure to the harsh gastric environment (pH 1.5-4) by mounting extreme acid-resistance responses, one of which, the arginine-dependent system of Escherichia coli, has been studied at levels of cellular physiology, molecular genetics and protein biochemistry. This multiprotein system keeps the cytoplasm above pH 5 during acid challenge by continually pumping protons out of the cell using the free energy of arginine decarboxylation. At the heart of the process is a 'virtual proton pump' in the inner membrane, called AdiC, that imports L-arginine from the gastric juice and exports its decarboxylation product agmatine. AdiC belongs to the APC superfamily of membrane proteins, which transports amino acids, polyamines and organic cations in a multitude of biological roles, including delivery of arginine for nitric oxide synthesis, facilitation of insulin release from pancreatic beta-cells, and, when inappropriately overexpressed, provisioning of certain fast-growing neoplastic cells with amino acids. High-resolution structures and detailed transport mechanisms of APC transporters are currently unknown. Here we describe a crystal structure of AdiC at 3.2 A resolution. The protein is captured in an outward-open, substrate-free conformation with transmembrane architecture remarkably similar to that seen in four other families of apparently unrelated transport proteins.

  10. Structure and transport mechanism of the sodium/proton antiporter MjNhaP1

    PubMed Central

    Paulino, Cristina; Wöhlert, David; Kapotova, Ekaterina; Yildiz, Özkan; Kühlbrandt, Werner

    2014-01-01

    Sodium/proton antiporters are essential for sodium and pH homeostasis and play a major role in human health and disease. We determined the structures of the archaeal sodium/proton antiporter MjNhaP1 in two complementary states. The inward-open state was obtained by x-ray crystallography in the presence of sodium at pH 8, where the transporter is highly active. The outward-open state was obtained by electron crystallography without sodium at pH 4, where MjNhaP1 is inactive. Comparison of both structures reveals a 7° tilt of the 6 helix bundle. 22Na+ uptake measurements indicate non-cooperative transport with an activity maximum at pH 7.5. We conclude that binding of a Na+ ion from the outside induces helix movements that close the extracellular cavity, open the cytoplasmic funnel, and result in a ∼5 Å vertical relocation of the ion binding site to release the substrate ion into the cytoplasm. DOI: http://dx.doi.org/10.7554/eLife.03583.001 PMID:25426803

  11. Proton transport by halorhodopsin

    SciTech Connect

    Varo, G.; Brown, L.S.; Needleman, R.

    1996-05-28

    In halorhodopsin from Natronobacterium pharaonis, a light-driven chloride pump, the chloride binding site also binds azide. When azide is bound at this location the retinal Schiff base transiently deprotonates after photoexcitation with light >530 nm, like in the light-driven proton pump bacteriorhodopsin. As in the photocycle of bacteriorhodopsin, pyranine detects the release of protons to the bulk. The subsequent reprotonation of the Schiff base is also dependent on azide, but with different kinetics that suggest a shuttling of protons from the surface as described earlier for halorhodopsin from Halobacterium salinarium. The azide-dependent, bacteriorhodopsin-like photocycle results in active electrogenic proton transport in the cytoplasmic to extracellular direction, detected in cell envelope vesicle suspensions both with a potential-sensitive electrode and by measuring light-dependent pH change. We conclude that in halorhodopsin an azide bound to the extracellular side of the Schiff base, and another azide shuttling between the Schiff base and the cytoplasmic surface, fulfill the functions of Asp-85 and Asp-96, respectively, in bacteriorhodopsin. Thus, although halorhodopsin is normally a chloride ion pump, it evidently contains all structural requirements, except an internal proton acceptor and a donor, of a proton pump. This observation complements our earlier finding that when a chloride binding site was created in bacteriorhodopsin through replacement of Asp-85 with a threonine, that protein became a chloride ion pump. 52 refs., 9 figs.

  12. Endocrine function following high dose proton therapy for tumors of the upper clivus

    SciTech Connect

    Slater, J.D.; Austin-Seymour, M.; Munzenrider, J.; Birnbaum, S.; Carroll, R.; Klibanski, A.; Riskind, P.; Urie, M.; Verhey, L.; Goitein, M.

    1988-09-01

    The endocrine status of patients receiving proton radiation for tumors of the upper clivus was reviewed to evaluate the effect of high dose treatment on the pituitary gland. The fourteen patients had chordomas or low grade chondrosarcomas and were all treated by the same techniques. The median tumor dose was 69.7 Cobalt Gray Equivalent (CGE) with a range from 66.6 to 74.4 CGE. (CGE is used because modulated protons have an RBE of 1.1 compared to 60Co). The daily fraction size was 1.8-2.1 CGE. The median follow-up time is 48 months, ranging from 30 to 68 months. All treatments were planned using a computerized multi-dimensional system with the position of the pituitary outlined on the planning CT scan. Review of the dose distribution indicated that the dose to the pituitary ranged from 60.5 to 72.3 CGE, with a median of 67.6 CGE. One female patient had decreased thyroid and gonadotropin function at the time of diagnosis and has been on hormone replacement since that time. The other three females were all pre-menopausal at the time of radiotherapy. At this time four patients (3 males and 1 female) have developed endocrine abnormalities 14 to 45 months after irradiation. All four had evidence of hypothyroidism and two have also developed corticotropin deficiency. The three males had decreased testosterone levels; the female patient developed amenorrhea and hyperprolactinemia. All four are asymptomatic with ongoing hormone replacement.

  13. Functional keratin as structural platforms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wool with up to 95% keratin by weight is a rich and pure source of proteinous biomaterial. As polymeric polyamide it exhibits high functionality through amide, carboxyl, sulfoxide, sulfide, and thiosulfide functions. Solubilized wool was transformed into keratin morphologies with the unique characte...

  14. Stories: The Function of Structure.

    ERIC Educational Resources Information Center

    Mandler, Jean M.

    The differences between story grammar and story schema are outlined and discussed based on research on story understanding by children and adults. The contention of all story grammars is that stories have a relatively invariant structure despite great differences in story content. The importance of structure within folk tales, and the ways in…

  15. Influence of 5-HALOGENATION on the Structure of Protonated Uridine: Irmpd Action Spectroscopy and Theoretical Studies of the Protonated 5-HALOURIDINES

    NASA Astrophysics Data System (ADS)

    Roy, Harrison; Hamlow, Lucas; Lee, Justin; Rodgers, M. T.; Berden, Giel; Oomens, Jos

    2016-06-01

    The chemical and structural diversity and the extent of post-transcriptional modification of RNA is remarkable! Presently, there are 142 different naturally-occurring and many more synthetically modified nucleosides known. Uridine (Urd) is the most commonly modified nucleoside among those that occur naturally, but has also been an important target for synthesis and development of modified nucleosides for pharmaceutical applications. Indeed, modified nucleosides are of pharmaceutical interest due to their bioactivities. In particular, 5-bromouridine (br5Urd) has been shown to exhibit antiviral activity to human immunodeficiency virus and has been used in RNA labeling studies. Halogenation is a common modification employed in pharmaceutical studies that enables systematic variation is the electronic properties of the molecule of interest due to the availability of halogen substituents that vary in size, dipole moment, polarizability, and electron withdrawing properties. In order to elucidate the influence of 5-halogenation on the intrinsic gas-phase structure and stability on the protonated form of Urd, synergistic spectroscopic and theoretical studies of the protonated forms of the 5-halouridines are performed here, where x5Urd = 5-fluorouridine (f5Urd), 5-chlorouridine (cl5Urd), br5Urd, and 5-iodouridine (i5Urd). Infrared multiple photon dissociation (IRMPD) action spectra of the protonated forms of the 5-halouridines, [x5Urd+H]+, are measured over the IR fingerprint region using the FELIX free electron laser and the hydrogen stretching region using an OPO/OPA laser from 3300-3800 wn. Complementary electronic structure calculations are performed to determine the stable low-energy conformations available to these species and to predict their IR spectra. Comparative analyses of the measured IRMPD spectra and predicted IR spectra are performed to elucidate the preferred sites of protonation, and the low-energy tautomeric conformations that are populated by

  16. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving.

    PubMed

    Pauli, Guido F; Niemitz, Matthias; Bisson, Jonathan; Lodewyk, Michael W; Soldi, Cristian; Shaw, Jared T; Tantillo, Dean J; Saya, Jordy M; Vos, Klaas; Kleinnijenhuis, Roel A; Hiemstra, Henk; Chen, Shao-Nong; McAlpine, James B; Lankin, David C; Friesen, J Brent

    2016-02-01

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of "structural correctness" depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D (1)H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D (1)H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by (1)H iterative full spin analysis (HiFSA). Fully characterized 1D (1)H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication. PMID:26812443

  17. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving

    PubMed Central

    2016-01-01

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of “structural correctness” depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D 1H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D 1H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by 1H iterative full spin analysis (HiFSA). Fully characterized 1D 1H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication. PMID:26812443

  18. Interaction of ring current and radiation belt protons with ducted plasmaspheric hiss. 2. Time evolution of the distribution function

    NASA Astrophysics Data System (ADS)

    Kozyra, J. U.; Rasmussen, C. E.; Miller, R. H.; Villalon, E.

    1995-11-01

    The evolution of the bounce-averaged ring current/radiation belt proton distribution is simulated during resonant interactions with ducted plasmaspheric hiss. The plasmaspheric hiss is assumed to be generated by ring current electrons and to be damped by the energetic protons. Thus energy is transferred between energetic electrons and protons using the plasmaspheric hiss as a mediary. The problem is not solved self-consistently. During the simulation period, interactions with ring current electrons (not represented in the model) are assumed to maintain the wave amplitudes in the presence of damping by the energetic protons, allowing the wave spectrum to be held fixed. Diffusion coefficients in pitch angle, cross pitch angle/energy, and energy were previously calculated by Kozyra et al. (1994) and are adopted for the present study. The simulation treats the energy range, E>=80 keV, within which the wave diffusion operates on a shorter timescale than other proton loss processes (i.e., Coulomb drag and charge exchange). These other loss processes are not included in the simulation. An interesting result of the simulation is that energy diffusion maximizes at moderate pitch angles near the edge of the atmospheric loss cone. Over the simulation period, diffusion in energy creates an order of magnitude enhancement in the bounce-averaged proton distribution function at moderate pitch angles. The loss cone is nearly empty because scattering of particles at small pitch angles is weak. The bounce-averaged flux distribution, mapped to ionospheric heights, results in elevated locally mirroring proton fluxes. OGO 5 observed order of magnitude enhancements in locally mirroring energetic protons at altitudes between 350 and 1300 km and invariant latitudes between 50° and 60° (Lundblad and Soraas, 1978). The proton distributions were highly anisotropic in pitch angle with nearly empty loss cones. The similarity between the observed distributions and those resulting from this

  19. Low energy proton bidirectional anisotropies and their relation to transient interplanetary magnetic structures: ISEE-3 observations

    NASA Technical Reports Server (NTRS)

    Marsden, R. G.; Sanderson, T. R.; Wenzel, K. P.; Smith, E. J.

    1985-01-01

    It is known that the interplanetary medium in the period approaching solar maximum is characterized by an enhancement in the occurrence of transient solar wind streams and shocks and that such systems are often associated with looplike magnetic structures or clouds. There is observational evidence that bidirectional, field aligned flows of low energy particles could be a signature of such looplike structures, although detailed models for the magnetic field configuration and injection mechanisms do not exist at the current time. Preliminary results of a survey of low energy proton bidirectional anisotropies measured on ISEE-3 in the interplanetary medium between August 1978 and May 1982, together with magnetic field data from the same spacecraft are presented.

  20. Jet and underlying event properties as a function of charged-particle multiplicity in proton-proton collisions at sqrt(s) = 7 TeV

    SciTech Connect

    Chatrchyan, Serguei; et al.,

    2013-12-17

    Characteristics of multi-particle production in proton-proton collisions at sqrt(s) = 7 TeV are studied as a function of the charged-particle multiplicity, N[ch]. The produced particles are separated into two classes: those belonging to jets and those belonging to the underlying event. Charged particles are measured with pseudorapidity abs(eta) < 2.4 and transverse momentum pt > 0.25 GeV. Jets are reconstructed from charged-particles only and required to have pt > 5 GeV. The distributions of jet pt, average pt of charged particles belonging to the underlying event or to jets, jet rates, and jet shapes are presented as functions of N[ch] and compared to the predictions of the PYTHIA and HERWIG event generators. Predictions without multi-parton interactions fail completely to describe the N[ch]-dependence observed in the data. For increasing N[ch], PYTHIA systematically predicts higher jet rates and harder pt spectra than seen in the data, whereas HERWIG shows the opposite trends. At the highest multiplicity, the data-model agreement is worse for most observables, indicating the need for further tuning and/or new model ingredients.

  1. Differential Velocity between Solar Wind Protons and Alpha Particles in Pressure Balance Structures

    NASA Technical Reports Server (NTRS)

    Yamauchi, Yohei; Suess, Steven T.; Steinberg, John T.; Sakurai, Takashi

    2004-01-01

    Pressure balance structures (PBSs) are a common high-plasma beta feature in high-latitude, high-speed solar wind. They have been proposed as remnants of coronal plumes. If true, they should reflect the observation that plumes are rooted in unipolar magnetic flux concentrations in the photosphere and are heated as oppositely directed flux is advected into and reconnects with the flux concentration. A minimum variance analysis (MVA) of magnetic discontinuities in PBSs showed there is a larger proportion of tangential discontinuities than in the surrounding high-speed wind, supporting the hypothesis that plasmoids or extended current sheets are formed during reconnection at the base of plumes. To further evaluate the character of magnetic field discontinuities in PBSs, differential streaming between alpha particles and protons is analyzed here for the same sample of PBSs used in the MVA. Alpha particles in high-speed wind generally have a higher radial flow speed than protons. However, if the magnetic field is folded back on itself, as in a large-amplitude Alfven wave, alpha particles will locally have a radial flow speed less than protons. This characteristic is used here to distinguish between folded back magnetic fields (which would contain rotational discontinuities) and tangential discontinuities using Ulysses high-latitude, high-speed solar wind data. The analysis indicates that almost all reversals in the radial magnetic field in PBSs are folded back field lines. This is found to also be true outside PBSs, supporting existing results for typical high-speed, high-latitude wind. There remains a small number of cases that appear not to be folds in the magnetic field and which may be flux tubes with both ends rooted in the Sun. The distinct difference in MVA results inside and outside PBSs remains unexplained.

  2. Measurement of the strange quark contribution to the vector structure of the proton

    SciTech Connect

    Phillips, Sarah

    2007-11-30

    The goal of the G0 experiment is to determine the contribution of the strange quarks in the quark-antiquark sea to the structure of the nucleon. To this end, the experiment measured parityviolating asymmetries from elastic electron-proton scattering from 0.12 ≤ Q2 ≤ 1.0 (GeV/c)2 at Thomas Jefferson National Accelerator Facility. These asymmetries come from the interference of the electromagnetic and neutral weak interactions, and are sensitive to the strange quark contributions in the proton. The results from the forward-angle measurement, the linear combination of the strange electric and magnetic form factors GsE +ηGsM, suggest possible non-zero, Q2 dependent, strange quark contributions and provide new information to understand the magnitude of the contributions. This dissertation presents the analysis and results of the forward-angle measurement. In addition, the G0 experiment measured the beam-normal single-spin asymmetry in the elastic scattering of transversely polarized 3 GeV electrons from unpolarized protons at Q2 = 0.15, 0.25 (GeV/c)2 as part of the forward-angle measurement. The transverse asymmetry provides a direct probe of the imaginary component of the two-photon exchange amplitude, the complete description of which is important in the interpretation of data from precision electron-scattering experiments. The results of the measurement indicate that calculations using solely the elastic nucleon intermediate state are insufficient and generally agree with calculations that include significant inelastic hadronic intermediate state contributions. This dissertation presents the analysis and results of this measurement.

  3. The energy spectra of solar energetic protons in the large energy range: their functional form and parameters.

    NASA Astrophysics Data System (ADS)

    Nymmik, Rikho; Pervaia, Taisia

    2016-07-01

    Experimental data on the fluxes of protons of solar energetic particles (SEP) are analyzed. It is known that above energies of 2-45 MeV (averaging 27-30 MeV), the proton spectra are a power-law function of the energy (at relativistic energies - from the momentum) of the particles. At lower energies, the spectra become harder, with the high-energy part of the spectra forming the "knee". This report is devoted to the determination of the parameters of the SEP spectra, having the form of a "double power-law shape", to ascertain the reliability of the parameters of the approximations of the experimental data.

  4. Proton Transport

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    channel is large enough to contain water molecules. and is normally filled with water. In analogy to the mechanism of proton transfer in some other channels, it has been postulated that protons are translocated along the network of water molecules filling the pore of the channel. This mechanism, however, must involve an additional important step because the channel contains four histidine amino acid residues, one from each of the helices, which are sufficiently large to occlude the pore and interrupt the water network. The histidine residues ensure channel selectivity by blocking transport of small ions, such as sodium or potassium. They have been also implicated in gating protons due to the ability of each histidine to become positively charged by accepting an additional proton. Two mechanisms of gating have been proposed. In one mechanism, all four histidines acquire an additional proton and, due to repulsion between their positive charges, move away from one another, thus opening the channel. The alternative mechanism relies of the ability of protons to move between different atoms in a molecule (tautomerization). Thus, a proton is captured on one side of the gate while another proton is released from the opposite side, and the molecule returns to the initial state through tautomerization. The simulations were designed to test these two mechanisms. Large-scale, atomic-level molecular dynamics simulations of the channel with the histidine residues in different protonation states revealed that all intermediate states of the system involved in the tautomerization mechanism are structurally stable and the arrangement of water molecules in the channel is conducive to the proton transport. In contrast, in the four-protonated state, postulated to exist in the gate-opening mechanism, the electrostatic repulsion between the histidine residues appears to be so large that the channel loses its structural integrity and one helix moves away from the remaining three. Additional

  5. The self-consistent charge density functional tight binding method applied to liquid water and the hydrated excess proton: benchmark simulations.

    PubMed

    Maupin, C Mark; Aradi, Bálint; Voth, Gregory A

    2010-05-27

    The self-consistent charge density functional tight binding (SCC-DFTB) method is a relatively new approximate electronic structure method that is increasingly used to study biologically relevant systems in aqueous environments. There have been several gas phase cluster calculations that indicate, in some instances, an ability to predict geometries, energies, and vibrational frequencies in reasonable agreement with high level ab initio calculations. However, to date, there has been little validation of the method for bulk water properties, and no validation for the properties of the hydrated excess proton in water. Presented here is a detailed SCC-DFTB analysis of the latter two systems. This work focuses on the ability of the original SCC-DFTB method, and a modified version that includes a hydrogen bonding damping function (HBD-SCC-DFTB), to describe the structural, energetic, and dynamical nature of these aqueous systems. The SCC-DFTB and HBD-SCC-DFTB results are compared to experimental data and Car-Parrinello molecular dynamics (CPMD) simulations using the HCTH/120 gradient-corrected exchange-correlation energy functional. All simulations for these systems contained 128 water molecules, plus one additional proton in the case of the excess proton system, and were carried out in a periodic simulation box with Ewald long-range electrostatics. The liquid water structure for the original SCC-DFTB is shown to poorly reproduce bulk water properties, while the HBD-SCC-DFTB somewhat more closely represents bulk water due to an improved ability to describe hydrogen bonding energies. Both SCC-DFTB methods are found to underestimate the water dimer interaction energy, resulting in a low heat of vaporization and a significantly elevated water oxygen diffusion coefficient as compared to experiment. The addition of an excess hydrated proton to the bulk water resulted in the Zundel cation (H(5)O(2)(+)) stabilized species being the stable form of the charge defect, which

  6. Electrochemical model of the function of the cytochrome c oxidase proton pump

    NASA Astrophysics Data System (ADS)

    Stojković, Branko P.; McMahon, Benjamin H.; Martin, R. L.; Gennis, Robert B.

    2000-03-01

    We combine quantum chemical calculations with an electrostatic model of the oxidase protein (in which the protein is seen as a non-uniform dielectric) to quantify the potential energy changes as the protein cycles through the four electron reduction of molecular oxygen to water. We find that the electric fields obtained directly from the quantum chemical calculations are adequate to explain the active translocation of four protons and joining of four protons and electrons at the oxygen, all against a 200 mV potential. The source of energy is the 500 mV per electron of redox energy released by bringing an electron from cytochrome c to the active binuclear site of the oxidase protein. Each electron entering the active site is accompanied by a proton taken up rapidly through the D channel. Two protons are pumped by the protons entering via the K channel, which are slower than D channel protons, but chemically stabilized at the active site, thus pushing the D channel protons ahead of them. Two other protons are forced out the high potential side of the oxidase when electrons move from the copper ligands and the heme onto the oxygen molecule during the 0=0 bond cleavage step.

  7. 3D-structures with arbitrary shapes created in negative resists by grayscale proton beam writing

    NASA Astrophysics Data System (ADS)

    Menzel, F.; Spemann, D.; Koal, T.; Butz, T.

    2011-10-01

    The direct and maskless technique of proton beam writing (PBW) was used for grayscale lithography which allows to create 3D microstructures with arbitrary surface topographies. For this purpose, several micrometer thick layers of the negative resists ma-N and SU-8 were irradiated with 2.25 MeV H+ and 1.125 MeV H2+ in arbitrary shapes using different fluences on different areas with values smaller than the threshold fluence for complete exposure. These irradiations result in multilevel microstructures, whose heights increase with increasing fluence. However, the comparison of the measured structure height with calculated predictions from SRIM simulations disproves the assumption that the structure height is proportional to the linear energy transfer (LET). In fact, the fluence reduction below the threshold for sufficient exposure is responsible for grayscale structuring due to reduced etching of the insufficiently exposed regions. The artifacts obtained with the first grayscale structures created by PBW in ma-N and strongly affecting the structure quality could be reduced by optimizing the scanning procedure, e.g. reducing the pixel distance. Therewith, a micro-Fresnel-lens could be fabricated in ma-N. The first PBW grayscale structures in SU-8 exhibited very strong mechanical instabilities which could be reduced by the use of a post exposure bake step, normally omitted for PBW with SU-8.

  8. Energy dependent track structure parametrisations for protons and carbon ions based on nanometric simulations

    NASA Astrophysics Data System (ADS)

    Alexander, Frauke; Villagrasa, Carmen; Rabus, Hans; Wilkens, Jan J.

    2015-09-01

    The BioQuaRT project within the European Metrology Research Programme aims at correlating ion track structure characteristics with the biological effects of radiation and develops measurement and simulation techniques for determining ion track structure on different length scales from about 2 nm to about 10 μm. Within this framework, we investigate methods to translate track-structure quantities derived on a nanometre scale to macroscopic dimensions. Input data sets were generated by simulations of ion tracks of protons and carbon ions in liquid water using the Geant 4 Monte Carlo toolkit with the Geant4-DNA processes. Based on the energy transfer points - recorded with nanometre resolution - we investigated parametrisations of overall properties of ion track structure. Three different track structure parametrisations have been developed using the distances to the 10 next neighbouring ionisations, the radial energy distribution and ionisation cluster size distributions. These parametrisations of nanometric track structure build a basis for deriving biologically relevant mean values which are essential in the clinical situation where each voxel is exposed to a mixed radiation field. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

  9. Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus

    PubMed Central

    Acharya, Rudresh; Carnevale, Vincenzo; Fiorin, Giacomo; Levine, Benjamin G.; Polishchuk, Alexei L.; Balannik, Victoria; Samish, Ilan; Lamb, Robert A.; Pinto, Lawrence H.; DeGrado, William F.; Klein, Michael L.

    2010-01-01

    The M2 proton channel from influenza A virus is an essential protein that mediates transport of protons across the viral envelope. This protein has a single transmembrane helix, which tetramerizes into the active channel. At the heart of the conduction mechanism is the exchange of protons between the His37 imidazole moieties of M2 and waters confined to the M2 bundle interior. Protons are conducted as the total charge of the four His37 side chains passes through 2+ and 3+ with a pKa near 6. A 1.65 Å resolution X-ray structure of the transmembrane protein (residues 25–46), crystallized at pH 6.5, reveals a pore that is lined by alternating layers of sidechains and well-ordered water clusters, which offer a pathway for proton conduction. The His37 residues form a box-like structure, bounded on either side by water clusters with well-ordered oxygen atoms at close distance. The conformation of the protein, which is intermediate between structures previously solved at higher and lower pH, suggests a mechanism by which conformational changes might facilitate asymmetric diffusion through the channel in the presence of a proton gradient. Moreover, protons diffusing through the channel need not be localized to a single His37 imidazole, but instead may be delocalized over the entire His-box and associated water clusters. Thus, the new crystal structure provides a possible unification of the discrete site versus continuum conduction models. PMID:20689043

  10. Structure and Mechanism of Proton Transport Through the Transmembrane Tetrameric M2 Protein Bundle of the Influenza A Virus

    SciTech Connect

    R Acharya; V Carnevale; G Fiorin; B Levine; A Polishchuk; V Balannick; I Samish; R Lamb; L Pinto; et al.

    2011-12-31

    The M2 proton channel from influenza A virus is an essential protein that mediates transport of protons across the viral envelope. This protein has a single transmembrane helix, which tetramerizes into the active channel. At the heart of the conduction mechanism is the exchange of protons between the His37 imidazole moieties of M2 and waters confined to the M2 bundle interior. Protons are conducted as the total charge of the four His37 side chains passes through 2{sup +} and 3{sup +} with a pK{sub a} near 6. A 1.65 {angstrom} resolution X-ray structure of the transmembrane protein (residues 25-46), crystallized at pH 6.5, reveals a pore that is lined by alternating layers of sidechains and well-ordered water clusters, which offer a pathway for proton conduction. The His37 residues form a box-like structure, bounded on either side by water clusters with well-ordered oxygen atoms at close distance. The conformation of the protein, which is intermediate between structures previously solved at higher and lower pH, suggests a mechanism by which conformational changes might facilitate asymmetric diffusion through the channel in the presence of a proton gradient. Moreover, protons diffusing through the channel need not be localized to a single His37 imidazole, but instead may be delocalized over the entire His-box and associated water clusters. Thus, the new crystal structure provides a possible unification of the discrete site versus continuum conduction models.

  11. Electromagnetic structure of the proton within the CP-violation hypothesis

    SciTech Connect

    Krutov, A. F. Kudinov, M. Yu.

    2013-11-15

    The so-called non-Rosenbluth behavior of the proton electromagnetic form factors can be explained within the hypothesis of CP violation in electromagnetic processes involving composite systems of strongly interacting particles. It is shown that this hypothesis leads to the appearance of an additional, anapole, form factor of the proton. The proton electromagnetic form factors, including the anapole form factor, are estimated on the basis of experimental data on elastic electron-proton scattering.

  12. Eukaryotic V-ATPase: novel structural findings and functional insights.

    PubMed

    Marshansky, Vladimir; Rubinstein, John L; Grüber, Gerhard

    2014-06-01

    The eukaryotic V-type adenosine triphosphatase (V-ATPase) is a multi-subunit membrane protein complex that is evolutionarily related to F-type adenosine triphosphate (ATP) synthases and A-ATP synthases. These ATPases/ATP synthases are functionally conserved and operate as rotary proton-pumping nano-motors, invented by Nature billions of years ago. In the first part of this review we will focus on recent structural findings of eukaryotic V-ATPases and discuss the role of different subunits in the function of the V-ATPase holocomplex. Despite structural and functional similarities between rotary ATPases, the eukaryotic V-ATPases are the most complex enzymes that have acquired some unconventional cellular functions during evolution. In particular, the novel roles of V-ATPases in the regulation of cellular receptors and their trafficking via endocytotic and exocytotic pathways were recently uncovered. In the second part of this review we will discuss these unique roles of V-ATPases in modulation of function of cellular receptors, involved in the development and progression of diseases such as cancer and diabetes as well as neurodegenerative and kidney disorders. Moreover, it was recently revealed that the V-ATPase itself functions as an evolutionarily conserved pH sensor and receptor for cytohesin-2/Arf-family GTP-binding proteins. Thus, in the third part of the review we will evaluate the structural basis for and functional insights into this novel concept, followed by the analysis of the potentially essential role of V-ATPase in the regulation of this signaling pathway in health and disease. Finally, future prospects for structural and functional studies of the eukaryotic V-ATPase will be discussed.

  13. Structure of olefin-imidacloprid and gas-phase fragmentation chemistry of its protonated form.

    PubMed

    Fusetto, Roberto; White, Jonathan M; Hutton, Craig A; O'Hair, Richard A J

    2016-02-01

    One of the major insect metabolites of the widely used neonicotinoid insecticide imidacloprid, 1 (1-[(6-chloro-3-pyridinyl)methyl]-N-nitro-1H-imidazol-2-amine), is the olefin 2. To better understand how the structure of olefin 2 relates to the gas-phase fragmentation of its protonated form, 2H(+), X-ray crystallography, tandem mass spectrometry experiments and DFT calculations were carried out. Olefin 2 was found to be in a tautomeric form where the proton is on the N(1) position of the imidazole ring and forms a hydrogen bond to one of the oxygen atoms of the coplanar nitroamine group. Under conditions of low-energy collision-induced dissociation (CID) in a linear ion trap, 2H(+), formed via electrospray ionization (ESI), fragments via a major loss of water, together with minor competing losses of HNO2 and NO2•.This contrasts with 1H+, which mainly undergoes bond homolysis via NO2• loss. Thus, installation of the double bond in 2 plays a key role in facilitating the loss of water. DFT calculations, carried out using the B3LYP/6-311G++(d,p) level of theory, revealed that loss of water was energetically more favourable compared to HNO2 and NO2• loss. Three multistep, energetically accessible mechanisms were identified for loss of water from 2H(+), and these have the following barriers: (I) direct proton transfer from N(5) of the pyridine to O(1) on the NO2 group (119 kJ mol(-1)); (II) rotation of the N(2)-N(4) bond (117 kJ mol(-1)); (III) 1,3-intramolecular proton transfer between the two oxygen atoms of the NO2 group (145 kJ mol(-1)). Given that the lowest barrier for the losses of HNO2 and NO2• is 156 kJ mol(-1), it is likely that all three water loss mechanisms occur concurrently.

  14. Observations of defect structure evolution in proton and Ni ion irradiated Ni-Cr binary alloys

    NASA Astrophysics Data System (ADS)

    Briggs, Samuel A.; Barr, Christopher M.; Pakarinen, Janne; Mamivand, Mahmood; Hattar, Khalid; Morgan, Dane D.; Taheri, Mitra; Sridharan, Kumar

    2016-10-01

    Two binary Ni-Cr model alloys with 5 wt% Cr and 18 wt% Cr were irradiated using 2 MeV protons at 400 and 500 °C and 20 MeV Ni4+ ions at 500 °C to investigate microstructural evolution as a function of composition, irradiation temperature, and irradiating ion species. Transmission electron microscopy (TEM) was applied to study irradiation-induced void and faulted Frank loops microstructures. Irradiations at 500 °C were shown to generate decreased densities of larger defects, likely due to increased barriers to defect nucleation as compared to 400 °C irradiations. Heavy ion irradiation resulted in a larger density of smaller voids when compared to proton irradiations, indicating in-cascade clustering of point defects. Cluster dynamics simulations were in good agreement with the experimental findings, suggesting that increases in Cr content lead to an increase in interstitial binding energy, leading to higher densities of smaller dislocation loops in the Ni-18Cr alloy as compared to the Ni-5Cr alloy.

  15. From structure to function, via dynamics

    NASA Astrophysics Data System (ADS)

    Stetter, O.; Soriano, J.; Geisel, T.; Battaglia, D.

    2013-01-01

    Neurons in the brain are wired into a synaptic network that spans multiple scales, from local circuits within cortical columns to fiber tracts interconnecting distant areas. However, brain function require the dynamic control of inter-circuit interactions on time-scales faster than synaptic changes. In particular, strength and direction of causal influences between neural populations (described by the so-called directed functional connectivity) must be reconfigurable even when the underlying structural connectivity is fixed. Such directed functional influences can be quantified resorting to causal analysis of time-series based on tools like Granger Causality or Transfer Entropy. The ability to quickly reorganize inter-areal interactions is a chief requirement for performance in a changing natural environment. But how can manifold functional networks stem "on demand" from an essentially fixed structure? We explore the hypothesis that the self-organization of neuronal synchronous activity underlies the control of brain functional connectivity. Based on simulated and real recordings of critical neuronal cultures in vitro, as well as on mean-field and spiking network models of interacting brain areas, we have found that "function follows dynamics", rather than structure. Different dynamic states of a same structural network, characterized by different synchronization properties, are indeed associated to different functional digraphs (functional multiplicity). We also highlight the crucial role of dynamics in establishing a structure-to-function link, by showing that whenever different structural topologies lead to similar dynamical states, than the associated functional connectivities are also very similar (structural degeneracy).

  16. Binding Energies of Protonated Betaine Complexes: A Probe of Zwitterion Structure in the Gas Phase

    PubMed Central

    Price, William D.; Jockusch, Rebecca A.

    2005-01-01

    The dissociation kinetics of proton-bound dimers of betaine with molecules of comparable gas-phase basicity were investigated using blackbody infrared radiative dissociation (BIRD). Threshold dissociation energies were obtained from these data using master equation modeling. For bases that have comparable or higher gas-phase basicity, the binding energy of the protonated base·betaine complex is ~1.4 eV. For molecules that are ~2 kcal/mol or more less basic, the dissociation energy of the complexes is ~1.2 eV. The higher binding energy of the former is attributed to an ion–zwitterion structure which has a much larger ion–dipole interaction. The lower binding energy for molecules that are ~2 kcal/mol or more less basic indicates that an ion–molecule structure is more favored. Semiempirical calculations at both the AM1 and PM3 levels indicate the most stable ion–molecule structure is one in which the base interacts with the charged quaternary ammonium end of betaine. These results indicate that the measurement of binding energies of neutral molecules to biological ions could provide a useful probe for the presence of zwitterions and salt bridges in the gas phase. From the BIRD data, the gas-phase basicity of betaine obtained from the kinetic method is found to be 239.2 ± 1.0 kcal/mol. This value is in excellent agreement with the value of 239.3 kcal/mol (298 K) from ab initio calculations at the MP2/6-31+g** level. The measured value is slightly higher than those reported previously. This difference is attributed to entropy effects. The lower ion internal energy and longer time frame of BIRD experiments should provide values closer to those at standard temperature. PMID:16543945

  17. Structure-function investigations of bacterial photosynthetic reaction centers.

    PubMed

    Leonova, M M; Fufina, T Yu; Vasilieva, L G; Shuvalov, V A

    2011-12-01

    During photosynthesis light energy is converted into energy of chemical bonds through a series of electron and proton transfer reactions. Over the first ultrafast steps of photosynthesis that take place in the reaction center (RC) the quantum efficiency of the light energy transduction is nearly 100%. Compared to the plant and cyanobacterial photosystems, bacterial RCs are well studied and have relatively simple structure. Therefore they represent a useful model system both for manipulating of the electron transfer parameters to study detailed mechanisms of its separate steps as well as to investigate the common principles of the photosynthetic RC structure, function, and evolution. This review is focused on the research papers devoted to chemical and genetic modifications of the RCs of purple bacteria in order to study principles and mechanisms of their functioning. Investigations of the last two decades show that the maximal rates of the electron transfer reactions in the RC depend on a number of parameters. Chemical structure of the cofactors, distances between them, their relative orientation, and interactions to each other are of great importance for this process. By means of genetic and spectral methods, it was demonstrated that RC protein is also an essential factor affecting the efficiency of the photochemical charge separation. Finally, some of conservative water molecules found in RC not only contribute to stability of the protein structure, but are directly involved in the functioning of the complex.

  18. Proton beam writing of long, arbitrary structures for micro/nano photonics and fluidics applications

    NASA Astrophysics Data System (ADS)

    Udalagama, Chammika; Teo, E. J.; Chan, S. F.; Kumar, V. S.; Bettiol, A. A.; Watt, F.

    2011-10-01

    The last decade has seen proton beam writing maturing into a versatile lithographic technique able to produce sub-100 nm, high aspect ratio structures with smooth side walls. However, many applications in the fields of photonics and fluidics require the fabrication of structures with high spatial resolution that extends over several centimetres. This cannot be achieved by purely magnetic or electrostatic beam scanning due to the large off-axis beam aberrations in high demagnification systems. As a result, this has limited us to producing long straight structures using a combination of beam and stage scanning. In this work we have: (1) developed an algorithm to include any arbitrary pattern into the writing process by using a more versatile combination of beam and stage scanning while (2) incorporating the use of the ubiquitous AutoCAD DXF (drawing exchange format) into the design process. We demonstrate the capability of this approach in fabricating structures such as Y-splitters, Mach-Zehnder modulators and microfluidic channels that are over several centimetres in length, in polymer. We also present optimisation of such parameters as scanning speed and scanning loops to improve on the surface roughness of the structures. This work opens up new possibilities of using CAD software in PBW for microphotonics and fluidics device fabrication.

  19. Proton pump inhibitors and vascular function: A prospective cross-over pilot study

    PubMed Central

    Ghebremariam, Yohannes T.; Cooke, John P.; Khan, Fouzia; Thakker, Rahul N.; Chang, Peter; Shah, Nigam H.; Nead, Kevin T.; Leeper, Nicholas J.

    2015-01-01

    Background Proton pump inhibitors (PPIs) are commonly used drugs for the treatment of gastric reflux. Recent retrospective cohorts and large database studies have raised concern that the use of PPIs is associated with increased cardiovascular (CV) risk. However, there is no prospective clinical study evaluating whether the use of PPIs directly causes CV harm. Methods We conducted a controlled open-label cross-over pilot study among 21 adults aged 18 and older who are healthy (n = 11) or have established clinical cardiovascular disease (n = 10). Study subjects were assigned to receive a PPI (Prevacid; 30 mg) or a placebo pill once daily for 4 weeks. After a 2 week washout period, participants were crossed-over to receive the alternate treatment for the ensuing 4 weeks. Subjects underwent evaluation of vascular function (by the EndoPAT technique) and had plasma levels of asymmetric dimethylarginine (ADMA, an endogenous inhibitor of endothelial function previously implicated in PPI-mediated risk) measured prior to and after each treatment interval. Results We observed a marginal inverse correlation between the EndoPAT score and plasma levels of ADMA (r = −0.364). Subjects experienced a greater worsening in plasma ADMA levels while on PPI than on placebo, and this trend was more pronounced amongst those subjects with a history of vascular disease. However, these trends did not reach statistical significance, and PPI use was also not associated with an impairment in flow mediated vasodilation during the course of this study. Conclusions In this open-label, cross-over pilot study conducted among healthy subjects and coronary disease patients, PPI use did not significantly influence vascular endothelial function. Larger, long-term and blinded trials are needed to mechanistically explain the correlation between PPI use and adverse clinical outcomes, which has recently been reported in retrospective cohort studies. PMID:25835348

  20. Evaluation of Liver Function After Proton Beam Therapy for Hepatocellular Carcinoma

    SciTech Connect

    Mizumoto, Masashi; Okumura, Toshiyuki; Hashimoto, Takayuki; Fukuda, Kuniaki; Oshiro, Yoshiko; Fukumitsu, Nobuyoshi; Abei, Masato; Kawaguchi, Atsushi; Hayashi, Yasutaka; Ohkawa, Ayako; Hashii, Haruko; Kanemoto, Ayae; Moritake, Takashi; Tohno, Eriko; Tsuboi, Koji; Sakae, Takeji; Sakurai, Hideyuki

    2012-03-01

    Purpose: Our previous results for treatment of hepatocellular carcinoma with proton beam therapy (PBT) revealed excellent local control. In this study, we focused on the impact of PBT on normal liver function. Methods and Materials: The subjects were 259 patients treated with PBT at University of Tsukuba between January 2001 and December 2007. We evaluated the Child-Pugh score pretreatment, on the final day of PBT, and 6, 12, and 24 months after treatment with PBT. Patients who had disease progression or who died with tumor progression at each evaluation point were excluded from the analysis to rule out an effect of tumor progression. An increase in the Child-Pugh score of 1 or more was defined as an adverse event. Results: Of the 259 patients, 241 had no disease progression on the final day of PBT, and 91 had no progression within 12 months after PBT. In univariate analysis, the percentage volumes of normal liver receiving at least 0, 10, 20, and 30 GyE in PBT (V0, 10, 20, and 30) were significantly associated with an increase of Child-Pugh score at 12 months after PBT. Of the 91 patients evaluated at 12 months, 66 had no increase of Child-Pugh score, 15 had a 1-point increase, and 10 had an increase of {>=}2 points. For the Youden index, the optimal cut-offs for V0, V10, V20, and V30 were 30%, 20%, 26%, and 18%, respectively. Conclusion: Our findings indicate that liver function after PBT is significantly related to the percentage volume of normal liver that is not irradiated. This suggests that further study of the relationship between liver function and PBT is required.

  1. Organically functionalized titanium oxide/Nafion composite proton exchange membranes for fuel cells applications

    NASA Astrophysics Data System (ADS)

    Cozzi, Dafne; de Bonis, Catia; D'Epifanio, Alessandra; Mecheri, Barbara; Tavares, Ana C.; Licoccia, Silvia

    2014-02-01

    An organically-modified ceramic material (TiO2-RSO3H) to be used as filler in Nafion-based composite membranes was synthesized by covalently grafting propylsulfonic acid groups on the surface of TiO2 nanoparticles. Higher ion exchange capacity (IEC) and proton conductivity of the hybrid material (one order of magnitude higher for the functionalized filler) reflected in superior performance of Nafion/TiO2-RSO3H composite membranes compared to Nafion. The highest conductivity value was obtained for the composite membrane containing 10 wt. % TiO2-RSO3H (σ = 0.08 S cm-1 at 140 °C). The membranes were tested in a DMFC single cell. The presence of the filler resulted in a general enhancement in the cell response, in terms of both higher power density (PD) delivered and lower methanol crossover with respect to unfilled Nafion membrane. The DMFC containing N_10TiO2-RSO3H membrane showed the best performance at 110 °C with a PD of 64 mW cm-2, corresponding to a PD improvement of about 40% with respect to that of Nafion membrane.

  2. The structure and function of catalytic RNAs.

    PubMed

    Wu, QiJia; Huang, Lin; Zhang, Yi

    2009-03-01

    Before the discovery of ribozymes, RNA had been proposed to function as a catalyst, based on the discovery that RNA folded into high-ordered structures as protein did. This hypothesis was confirmed in the 1980s, after the discovery of Tetrahymena group I intron and RNase P ribozyme. There have been about ten ribozymes identified during the past thirty years, as well as the fact that ribosomes function as ribozymes. Advances have been made in understanding the structures and functions of ribozymes, with numerous crystal structures resolved in the past years. Here we review the structure-function relationship of both small and large ribozymes, especially the structural basis of their catalysis. ribozyme, structure, catalysis. PMID:19294348

  3. Nuclear Structure of 8B Studied by Proton Resonance Scatterings on 7Be

    NASA Astrophysics Data System (ADS)

    Yamaguchi, H.; Wakabayashi, Y.; Hayakawa, S.; Amadio, G.; Kubono, S.; Fujikawa, H.; Saito, A.; He, J. J.; Teranishi, T.; Kwon, Y. K.; Nishimura, S.; Togano, Y.; Iwasa, N.; Inafuku, K.; Niikura, M.; Binh, D. N.; Khiem, L. H.

    2008-05-01

    A new measurement of the proton resonance scattering on 7Be was performed up to the excitation energy of 6.8 MeV using the low-energy RI beam facility CRIB (CNS Radioactive Ion Beam separator) at the Center for Nuclear Study (CNS) of the University of Tokyo. The excitation function of 8B above 3.5 MeV was successfully measured for the first time, providing important information about the reaction rate of 7Be(p,γ)8B, which is the key reaction in the solar 8B neutrino production. For more intensive experimental studies with RI beams, the development of a cryogenic gas target system is ongoing at CNS. In this paper a preliminary result of the 7Be experiment and the present status of the development of the target system are presented.

  4. Nuclear Structure of {sup 8}B Studied by Proton Resonance Scatterings on {sup 7}Be

    SciTech Connect

    Yamaguchi, H.; Wakabayashi, Y.; Hayakawa, S.; Amadio, G.; Kubono, S.; Fujikawa, H.; Niikura, M.; Binh, D. N.; Saito, A.; He, J. J.; Teranishi, T.; Kwon, Y. K.; Nishimura, S.; Togano, Y.; Iwasa, N.; Inafuku, K.; Khiem, L. H.

    2008-05-21

    A new measurement of the proton resonance scattering on {sup 7}Be was performed up to the excitation energy of 6.8 MeV using the low-energy RI beam facility CRIB (CNS Radioactive Ion Beam separator) at the Center for Nuclear Study (CNS) of the University of Tokyo. The excitation function of {sup 8}B above 3.5 MeV was successfully measured for the first time, providing important information about the reaction rate of {sup 7}Be(p,{gamma}){sup 8}B, which is the key reaction in the solar {sup 8}B neutrino production. For more intensive experimental studies with RI beams, the development of a cryogenic gas target system is ongoing at CNS. In this paper a preliminary result of the {sup 7}Be experiment and the present status of the development of the target system are presented.

  5. Proton NMR assignments and regular backbone structure of bovine pancreatic ribonuclease A in aqueous solution

    SciTech Connect

    Robertson, A.D. ); Purisima, E.O. Cornell Univ., Ithaca, NY ); Eastman, M.A.; Scheraga, H.A. )

    1989-07-11

    Proton NMR assignments have been made for 121 of the 124 residues of bovine pancreatic ribonuclease A (RNase A). During the first stage of assignment, COSY and relayed COSY data were used to identify 40 amino acid spin systems belonging to alanine, valine, threonine, isoleucine, and serine residues. Approximately 60 other NH-{alpha}CH-{beta}CH systems were also identified but not assigned to specific amino acid type. NOESY data then were used to connect sequentially neighboring spin systems; approximately 475 of the possible 700 resonances in RNase A were assigned in this way. The authors' assignments agree with those for 20 residues assigned previously. NOESY correlations were used to identify regular backbone structure elements in RNase A, which are very similar to those observed in X-ray crystallographic studies.

  6. Advances in structural and functional analysis of membrane proteins by electron crystallography.

    PubMed

    Wisedchaisri, Goragot; Reichow, Steve L; Gonen, Tamir

    2011-10-12

    Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography.

  7. Structure and Function of the Mitochondrial Ribosome.

    PubMed

    Greber, Basil J; Ban, Nenad

    2016-06-01

    Mitochondrial ribosomes (mitoribosomes) perform protein synthesis inside mitochondria, the organelles responsible for energy conversion and adenosine triphosphate production in eukaryotic cells. Throughout evolution, mitoribosomes have become functionally specialized for synthesizing mitochondrial membrane proteins, and this has been accompanied by large changes to their structure and composition. We review recent high-resolution structural data that have provided unprecedented insight into the structure and function of mitoribosomes in mammals and fungi. PMID:27023846

  8. Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori.

    PubMed

    Strugatsky, David; McNulty, Reginald; Munson, Keith; Chen, Chiung-Kuang; Soltis, S Michael; Sachs, George; Luecke, Hartmut

    2013-01-10

    Half the world's population is chronically infected with Helicobacter pylori, causing gastritis, gastric ulcers and an increased incidence of gastric adenocarcinoma. Its proton-gated inner-membrane urea channel, HpUreI, is essential for survival in the acidic environment of the stomach. The channel is closed at neutral pH and opens at acidic pH to allow the rapid access of urea to cytoplasmic urease. Urease produces NH(3) and CO(2), neutralizing entering protons and thus buffering the periplasm to a pH of roughly 6.1 even in gastric juice at a pH below 2.0. Here we report the structure of HpUreI, revealing six protomers assembled in a hexameric ring surrounding a central bilayer plug of ordered lipids. Each protomer encloses a channel formed by a twisted bundle of six transmembrane helices. The bundle defines a previously unobserved fold comprising a two-helix hairpin motif repeated three times around the central axis of the channel, without the inverted repeat of mammalian-type urea transporters. Both the channel and the protomer interface contain residues conserved in the AmiS/UreI superfamily, suggesting the preservation of channel architecture and oligomeric state in this superfamily. Predominantly aromatic or aliphatic side chains line the entire channel and define two consecutive constriction sites in the middle of the channel. Mutation of Trp 153 in the cytoplasmic constriction site to Ala or Phe decreases the selectivity for urea in comparison with thiourea, suggesting that solute interaction with Trp 153 contributes specificity. The previously unobserved hexameric channel structure described here provides a new model for the permeation of urea and other small amide solutes in prokaryotes and archaea.

  9. Structure-Derived Proton-Transfer Mechanism of Action Human Pyruvate Dehydrogenase

    NASA Technical Reports Server (NTRS)

    Ciszak, Ewa; Dominiak, Paulina

    2003-01-01

    The derivative of vitamin B1 thiamin pyrophosphate (TPP) is a cofactor of pyruvate dehydrogenase (E1p) that is involved in decarboxylation of pyruvate followed by reductive acetylation of lipoic acid covalently bound to a lysine residue of dihydrolipoamide acetyltransferase. The structure of E1p recently determined in our laboratory revealed patterns of association of foul subunits and specifics of two TPP binding sites. The mechanism of action in part includes a conserved hydrogen bond between the N1' atom of the aminopyrimidine ring of the cofactor and the carboxylate group of Glu59 from the beta subunits, and a V-conformation of the cofactor that brings the N4' atom of the aminopyrimidine ring to the distance of the intramolecular hydrogen bond formed with the C2-atom of the thiazolium moiety. The carboxylate group of Glu59 is the local proton acceptor that enables proton translocation within the aminopyrimidine ring and stabilization of the rare N4' - iminopyrimidine tautomer. Based on the analysis of E1p structure, we postulate that the protein environment drives N4' - amino/N4' - imino dynamics resulting in a concerted shuttle-like movement of the subunits. We also propose that this movement of the subunits is strictly coordinated with the two enzymatic reactions carried out in E1p by each of the two cofactor sites. It is proposed that these reactions are in alternating phases such that when one active site is involved in decarboxylation, the other is involved in acetylation of lipoyl noiety.

  10. Reconstruction of Helio-Latitudinal Structure of the Solar Wind Proton Speed and Density

    NASA Astrophysics Data System (ADS)

    Sokół, Justyna M.; Swaczyna, Paweł; Bzowski, Maciej; Tokumaru, Munetoshi

    2015-09-01

    The modeling of the heliosphere requires continuous three-dimensional solar wind data. The in-situ out-of-ecliptic measurements are very rare, so that other methods of solar wind detection are needed. We use the remote-sensing data of the solar wind speed from observations of interplanetary scintillation (IPS) to reconstruct spatial and temporal structures of the solar wind proton speed from 1985 to 2013. We developed a method of filling the data gaps in the IPS observations to obtain continuous and homogeneous solar wind speed records. We also present a method to retrieve the solar wind density from the solar wind speed, utilizing the invariance of the solar wind dynamic pressure and energy flux with latitude. To construct the synoptic maps of the solar wind speed we use the decomposition into spherical harmonics of each of the Carrington rotation map. To fill the gaps in time we apply the singular spectrum analysis to the time series of the coefficients of spherical harmonics. We obtained helio-latitudinal profiles of the solar wind proton speed and density over almost three recent solar cycles. The accuracy in the reconstruction is, due to computational limitations, about 20 %. The proposed methods allow us to improve the spatial and temporal resolution of the model of the solar wind parameters presented in our previous paper (Sokół et al., Solar Phys. 285, 167, 2013) and give a better insight into the time variations of the solar wind structure. Additionally, the solar wind density is reconstructed more accurately and it fits better to the in-situ measurements from Ulysses.

  11. Oxide-ion and proton conducting electrolyte materials for clean energy applications: structural and mechanistic features.

    PubMed

    Malavasi, Lorenzo; Fisher, Craig A J; Islam, M Saiful

    2010-11-01

    This critical review presents an overview of the various classes of oxide materials exhibiting fast oxide-ion or proton conductivity for use as solid electrolytes in clean energy applications such as solid oxide fuel cells. Emphasis is placed on the relationship between structural and mechanistic features of the crystalline materials and their ion conduction properties. After describing well-established classes such as fluorite- and perovskite-based oxides, new materials and structure-types are presented. These include a variety of molybdate, gallate, apatite silicate/germanate and niobate systems, many of which contain flexible structural networks, and exhibit different defect properties and transport mechanisms to the conventional materials. It is concluded that the rich chemistry of these important systems provides diverse possibilities for developing superior ionic conductors for use as solid electrolytes in fuel cells and related applications. In most cases, a greater atomic-level understanding of the structures, defects and conduction mechanisms is achieved through a combination of experimental and computational techniques (217 references). PMID:20848015

  12. Oxide-ion and proton conducting electrolyte materials for clean energy applications: structural and mechanistic features.

    PubMed

    Malavasi, Lorenzo; Fisher, Craig A J; Islam, M Saiful

    2010-11-01

    This critical review presents an overview of the various classes of oxide materials exhibiting fast oxide-ion or proton conductivity for use as solid electrolytes in clean energy applications such as solid oxide fuel cells. Emphasis is placed on the relationship between structural and mechanistic features of the crystalline materials and their ion conduction properties. After describing well-established classes such as fluorite- and perovskite-based oxides, new materials and structure-types are presented. These include a variety of molybdate, gallate, apatite silicate/germanate and niobate systems, many of which contain flexible structural networks, and exhibit different defect properties and transport mechanisms to the conventional materials. It is concluded that the rich chemistry of these important systems provides diverse possibilities for developing superior ionic conductors for use as solid electrolytes in fuel cells and related applications. In most cases, a greater atomic-level understanding of the structures, defects and conduction mechanisms is achieved through a combination of experimental and computational techniques (217 references).

  13. Tear Lipocalin: Structure and Function

    PubMed Central

    Dartt, Darlene A.

    2014-01-01

    Lipocalins are a family of diverse low molecular weight proteins that act extracellularly. They use multiple recognition properties that include: 1) ligand binding to small hydrophobic molecules, 2) macromolecular complexation with other soluble macromolecules, and 3) binding to specific cell surface receptors to deliver cargo. Tear lipocalin (TLC) is a major protein in tears and has a large ligand binding cavity that allows the lipocalin to bind an extensive and diverse set of lipophilic molecules. TLC can also bind to macromolecules including the tear proteins lactoferin and lysozyme. The receptor to which TLC binds is termed tear lipocalin interacting membrane receptor (LIMR). LIMR appears to work by endocytosis. TLC has a variety of suggested functions in tears including regulation of tear viscosity, binding and release of lipids, endonuclease inactivation of viral DNA, binding of microbial siderophores (iron chelators used to deliver essential iron to bacteria), use as a biomarker for dry eye, and possession of anti-inflammatory activity. Additional research is warranted to determine the actual functions of TLC in tears and the presence of its receptor on the ocular surface. PMID:21791187

  14. [Interferons: between structure and function].

    PubMed

    Bandurska, Katarzyna; Król, Izabela; Myga-Nowak, Magdalena

    2014-01-01

    Interferons are a family of proteins that are released by a variety of cells in response to infections caused by viruses. Currently, we distinguish three types of interferons. They are classified based on the nucleotide sequence, interaction with specific receptors, chromosomal location, structure and physicochemical properties. The following interferons are classified as type I: α, β, ω, κ, ε, ζ, τ, δ, ν. They are recognized and bound by a receptor formed by two peptides, IFN-αR1 and IFN-αR2. Representative of type II interferons is interferon-γ. It binds to a receptor composed of chains IFNGR-1 and IFNGR-2. The recently classified type III interferons comprise IFN-λ1, IFN-λ2, and IFN-λ3. They act on receptors formed by λR1 IFN-and IL-10R2 subunits. A high level of antiviral protection is achieved by IFN-α, IFN-β and IFN-λ. Antiviral activity of interferons is based on the induction and regulation of innate and acquired immune mechanisms. By binding to transmembrane receptors, IFN interacts with target cells mainly by activating the JAK/STAT, but also other signaling pathways. This leads to induction and activation of many antiviral agents, such as protein kinase RNA-activated (PKR), ribonuclease 2-5A pathway, and Mx proteins, as well as numerous apoptotic pathways. As a result of the protective effect of interferons, the virus binding to cells and viral particles penetration into cells is stopped, and the release of the nucleocapsid from an envelope is suppressed. Disruption of transcription and translation processes of the structural proteins prevents the formation of virions or budding of viruses, and as a result degradation of the viral mRNA; the started processes inhibit the chain synthesis of viral proteins and therefore further stimulate the immune system cells.

  15. Confirmation of quark-hadron duality in the neutron F_2 structure function

    SciTech Connect

    Simona Malace, Yonatan Kahn, Wolodymyr Melnitchouk, Cynthia Keppel

    2010-03-01

    Using a recently developed technique we extract the neutron F_2^n structure function from new inclusive proton and deuteron data in the large-x region, and test the validity of quark-hadron duality in the neutron. We establish for the first time the accuracy of duality in the low-lying neutron resonance regions over a range of Q^2, and compare with the corresponding results on the proton. Our findings open the possibility of using averaged resonance region data to constrain parton distributions at large x.

  16. Polarization effects in hadron structure functions and in quark and gluon fragmentation

    SciTech Connect

    Einhorn, M.B.

    1986-07-20

    The predictions of QCD for the evolution of the quark and gluon structure functions of a polarized proton are discussed. In fact, the parton polarizations increase with energy, for fixed Feynman x. Thus, polarized protons may be useful for the discovery or investigation of new physical phenomena at very high energy, especially if there are new interactions or particles whose behavior violates one of the natural symmetries of QCD, such as parity. The mean gluon asymmetry grows as l-scriptnQ/sup 2/, which implies that the orbital angular momentum of the gluons grows similarly.

  17. The pathway for serial proton supply to the active site of nitrogenase: enhanced density functional modeling of the Grotthuss mechanism.

    PubMed

    Dance, Ian

    2015-11-01

    Nitrogenase contains a well defined and conserved chain of water molecules leading to the FeMo cofactor (FeMo-co, an [Fe7MoCS9] cluster with bidentate chelation of Mo by homocitrate) that is the active site where N2 and other substrates are sequentially hydrogenated using multiple protons and electrons. The function of this chain is proposed to be a proton wire, serially translocating protons to triply-bridging S3B of FeMo-co, where, concomitant with electron transfer to FeMo-co, an H atom is generated on S3B. Density functional simulations of this proton translocation mechanism are reported here, using a large 269-atom model that includes all residues hydrogen bonded to and surrounding the water chain, and likely to influence proton transfer: three carboxylate O atoms of obligatory homocitrate are essential. The mechanism involves the standard two components of the Grotthuss mechanism, namely H atom slides that shift H3O(+) from one water site to the next, and HOH molecular rotations that convert backward (posterior) OH bonds in the water chain to forward (anterior) OH bonds. The topography of the potential energy surface for each of these steps has been mapped. H atom slides pass through very short (ca. 2.5 Å) O-H-O hydrogen bonds, while HOH rotations involve the breaking of O-HO hydrogen bonds, and the occurrence of long (up to 3.6 Å) separations between contiguous water molecules. Both steps involve low potential energy barriers, <7 kcal mol(-1). During operation of the Grotthuss mechanism in nitrogenase there are substantial displacements of water molecules along the chain, occurring as ripples. These characteristics of the 'Grotthuss two-step', coupled with a buffering ability of two carboxylate O atoms of homocitrate, and combined with density functional characterisation of the final proton slide from the ultimate water molecule to S3B (including electron addition), have been choreographed into a complete mechanism for serial hydrogenation of FeMo-co. The

  18. Changes in gastrointestinal tract function and structure in functional dyspepsia.

    PubMed

    Vanheel, Hanne; Farré, Ricard

    2013-03-01

    Functional dyspepsia is an extremely common disorder of gastrointestinal function. The disorder is thought to be heterogeneous, with different pathophysiological mechanisms underlying varied symptom patterns. A diversity of changes in gastrointestinal tract function and structure has been described in functional dyspepsia. These involve alterations in the stomach, such as impaired accommodation, delayed gastric emptying and hypersensitivity, and alterations in the duodenum, such as increased sensitivity to duodenal acid and/or lipids and low-grade inflammation. In this Review, we summarize all these abnormalities in an attempt to provide an integrated overview of the pathophysiological mechanisms in functional dyspepsia. PMID:23318268

  19. Structural stability of anhydrous proton conducting SrZr0.9Er0.1O3-δ perovskite ceramic vs. protonation/deprotonation cycling: Neutron diffraction and Raman studies

    NASA Astrophysics Data System (ADS)

    Slodczyk, Aneta; Colomban, Philippe; Upasen, Settakorn; Grasset, Frédéric; André, Gilles

    2015-08-01

    Long-term chemical and structural stability of an ion conducting ceramic is one of the main criteria for its selection as an electrolytic membrane in energy plant devices. Consequently, medium density SrZr0.9Er0.1O3-δ (SZE) anhydrous proton conducting ceramic - a potential electrolyte of SOFC/PCFC, was analysed by neutron diffraction between room temperature and 900 °C. After the first heating/cooling cycle, the ceramic pieces were exposed to water vapour pressure in an autoclave (500 °C, 40 bar, 7 days) in order to incorporate protonic species; the protonated compound was then again analysed by neutron diffraction. This procedure was repeated two times. At each step, the sample was also controlled by TGA and Raman spectroscopy. These studies allow the first comprehensive comparison of structural and chemical stability during the protonation/deprotonation cycling. The results reveal good structural stability, although an irreversible small contraction of the unit-cell volume and local structure modifications near Zr/ErO5[] octahedra are detected after the first protonation. After the second protonation easy ceramic crumbling under a stress is observed because of the presence of secondary phases (SrCO3, Sr(OH)2) well detected by Raman scattering and TGA. The role of crystallographic purity, substituting element and residual porosity in the proton conducting perovskite electrolyte stability is discussed.

  20. Test of structure functions using leptons with CDF

    SciTech Connect

    Dickson, M.; CDF Collaboration

    1993-11-01

    The charge asymmetry as a function of lepton rapidity, A(yl), has been measured at {radical}s = 1.8 TeV for {vert_bar}yl{vert_bar} < 1.8, using the W decays to electrons and muons recorded by CDF during the 1992--1993 run of the Tevatron Collider. The luminosity used, approximately 20 pb{sup {minus}1}, and detector improvements have lead to a six fold increase in statistics making discrimination between sets of parton distributions possible. Our data favors the most recent parton distributions and demonstrates the value of collider data in the measurement of the proton`s structure. In addition, the Drell-Yan cross section has been measured using 4.13 pb{sup {minus}1} of dielectron and 2.77 pb{sup {minus}1} of dimuon data taken during the 1988--1989 run. These measurements probe the quark distributions to x < 0.01 at high Q{sup 2} where nonperturbative effects are minimal.

  1. Crystal structure of the pristine peroxidase ferryl center and its relevance to proton-coupled electron transfer.

    PubMed

    Chreifi, Georges; Baxter, Elizabeth L; Doukov, Tzanko; Cohen, Aina E; McPhillips, Scott E; Song, Jinhu; Meharenna, Yergalem T; Soltis, S Michael; Poulos, Thomas L

    2016-02-01

    The reaction of peroxides with peroxidases oxidizes the heme iron from Fe(III) to Fe(IV)=O and a porphyrin or aromatic side chain to a cationic radical. X-ray-generated hydrated electrons rapidly reduce Fe(IV), thereby requiring very short exposures using many crystals, and, even then, some reduction cannot be avoided. The new generation of X-ray free electron lasers capable of generating intense X-rays on the tenths of femtosecond time scale enables structure determination with no reduction or X-ray damage. Here, we report the 1.5-Å crystal structure of cytochrome c peroxidase (CCP) compound I (CmpI) using data obtained with the Stanford Linear Coherent Light Source (LCLS). This structure is consistent with previous structures. Of particular importance is the active site water structure that can mediate the proton transfer reactions required for both CmpI formation and reduction of Fe(IV)=O to Fe(III)-OH. The structures indicate that a water molecule is ideally positioned to shuttle protons between an iron-linked oxygen and the active site catalytic His. We therefore have carried out both computational and kinetic studies to probe the reduction of Fe(IV)=O. Kinetic solvent isotope experiments show that the transfer of a single proton is critical in the peroxidase rate-limiting step, which is very likely the proton-coupled reduction of Fe(IV)=O to Fe(III)-OH. We also find that the pKa of the catalytic His substantially increases in CmpI, indicating that this active site His is the source of the proton required in the reduction of Fe(IV)=O to Fe(IV)-OH.

  2. Crystal structure of the pristine peroxidase ferryl center and its relevance to proton-coupled electron transfer

    PubMed Central

    Chreifi, Georges; Baxter, Elizabeth L.; Doukov, Tzanko; Cohen, Aina E.; McPhillips, Scott E.; Song, Jinhu; Meharenna, Yergalem T.; Soltis, S. Michael; Poulos, Thomas L.

    2016-01-01

    The reaction of peroxides with peroxidases oxidizes the heme iron from Fe(III) to Fe(IV)=O and a porphyrin or aromatic side chain to a cationic radical. X-ray–generated hydrated electrons rapidly reduce Fe(IV), thereby requiring very short exposures using many crystals, and, even then, some reduction cannot be avoided. The new generation of X-ray free electron lasers capable of generating intense X-rays on the tenths of femtosecond time scale enables structure determination with no reduction or X-ray damage. Here, we report the 1.5-Å crystal structure of cytochrome c peroxidase (CCP) compound I (CmpI) using data obtained with the Stanford Linear Coherent Light Source (LCLS). This structure is consistent with previous structures. Of particular importance is the active site water structure that can mediate the proton transfer reactions required for both CmpI formation and reduction of Fe(IV)=O to Fe(III)-OH. The structures indicate that a water molecule is ideally positioned to shuttle protons between an iron-linked oxygen and the active site catalytic His. We therefore have carried out both computational and kinetic studies to probe the reduction of Fe(IV)=O. Kinetic solvent isotope experiments show that the transfer of a single proton is critical in the peroxidase rate-limiting step, which is very likely the proton-coupled reduction of Fe(IV)=O to Fe(III)-OH. We also find that the pKa of the catalytic His substantially increases in CmpI, indicating that this active site His is the source of the proton required in the reduction of Fe(IV)=O to Fe(IV)-OH. PMID:26787871

  3. Textbook Error, 138: The Singly Protonated Structure of Thiamine: Basicity of the Heterocyclic Nitrogen versus NH2 Nitrogen.

    ERIC Educational Resources Information Center

    Panijpan, Bhinyo

    1979-01-01

    Spectroscopic studies on solutions and x-ray diffraction work on crystals lead to the conclusion that the Metrogen of the pyrimidine ring is preferentially protonated. The correct monoprotonated structures of thiamine and its 4-amino-pyrimidine synthetic precursor are presented. (BT)

  4. Enhanced Spectral Anisotropies Near the Proton-Cyclotron Scale: Possible Two-Component Structure in Hall-FLR MHD Turbulence Simulations

    NASA Technical Reports Server (NTRS)

    Ghosh, Sanjoy; Goldstein, Melvyn L.

    2011-01-01

    Recent analysis of the magnetic correlation function of solar wind fluctuations at 1 AU suggests the existence of two-component structure near the proton-cyclotron scale. Here we use two-and-one-half dimensional and three-dimensional compressible MHD models to look for two-component structure adjacent the proton-cyclotron scale. Our MHD system incorporates both Hall and Finite Larmor Radius (FLR) terms. We find that strong spectral anisotropies appear adjacent the proton-cyclotron scales depending on selections of initial condition and plasma beta. These anisotropies are enhancements on top of related anisotropies that appear in standard MHD turbulence in the presence of a mean magnetic field and are suggestive of one turbulence component along the inertial scales and another component adjacent the dissipative scales. We compute the relative strengths of linear and nonlinear accelerations on the velocity and magnetic fields to gauge the relative influence of terms that drive the system with wave-like (linear) versus turbulent (nonlinear) dynamics.

  5. Mechanisms of proton pumping in bacteriorhodopsin

    SciTech Connect

    Ebrey, T.G.

    1991-01-01

    The purple membrane of Halobacterium halobium probably represents the simplest biological solar energy conversion system. Light absorbed by bacteriorhodopsin directly leads to the transport of protons across the cell membrane. The resulting chemosmotic potential can be used to make ATP. An additional feature of the purple membrane is its ability to pump protons over a wide variety of salt concentration including in extreme saline environments. This project investigates the relationship between the transport of protons across the membrane and structure and conformation of bacteriorhodospin. We have proposed experiments to study the pH dependence of proton pumping. Secondly, we are examining the role of divalent cations and the effect of the large surface potential of the purple membrane on the proton pumping function of this membrane using the photocurrents associated with the pumping process. Finally we are studying the role of proteinatable amino acids in proton transport. 16 refs.

  6. Four RNA families with functional transient structures

    PubMed Central

    Zhu, Jing Yun A; Meyer, Irmtraud M

    2015-01-01

    Protein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since Rfam annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing Rfam families or introduce a new RNA family to Rfam. For each of the four RNA families, we compile a multiple-sequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance model and manual curation. The first alignment is the Trp operon leader which regulates the operon transcription in response to tryptophan abundance through alternative structures. The second alignment is the HDV ribozyme which we extend to the 5′ flanking sequence. This flanking sequence is involved in the regulation of the transcript's self-cleavage activity. The third alignment is the 5′ UTR of the maturation protein from Levivirus which contains a transient structure that temporarily postpones the formation of the final inhibitory structure to allow translation of maturation protein. The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM

  7. Four RNA families with functional transient structures.

    PubMed

    Zhu, Jing Yun A; Meyer, Irmtraud M

    2015-01-01

    Protein-coding and non-coding RNA transcripts perform a wide variety of cellular functions in diverse organisms. Several of their functional roles are expressed and modulated via RNA structure. A given transcript, however, can have more than a single functional RNA structure throughout its life, a fact which has been previously overlooked. Transient RNA structures, for example, are only present during specific time intervals and cellular conditions. We here introduce four RNA families with transient RNA structures that play distinct and diverse functional roles. Moreover, we show that these transient RNA structures are structurally well-defined and evolutionarily conserved. Since Rfam annotates one structure for each family, there is either no annotation for these transient structures or no such family. Thus, our alignments either significantly update and extend the existing Rfam families or introduce a new RNA family to Rfam. For each of the four RNA families, we compile a multiple-sequence alignment based on experimentally verified transient and dominant (dominant in terms of either the thermodynamic stability and/or attention received so far) RNA secondary structures using a combination of automated search via covariance model and manual curation. The first alignment is the Trp operon leader which regulates the operon transcription in response to tryptophan abundance through alternative structures. The second alignment is the HDV ribozyme which we extend to the 5' flanking sequence. This flanking sequence is involved in the regulation of the transcript's self-cleavage activity. The third alignment is the 5' UTR of the maturation protein from Levivirus which contains a transient structure that temporarily postpones the formation of the final inhibitory structure to allow translation of maturation protein. The fourth and last alignment is the SAM riboswitch which regulates the downstream gene expression by assuming alternative structures upon binding of SAM. All

  8. Dipole rescattering and the nuclear structure function

    SciTech Connect

    Carvalho, F.; Goncalves, V. P.; Navarra, F. S.; Oliveira, E. G.

    2013-03-25

    In the framework of the dipole model, we study the effects of the dipole multiple scatterings in a nuclear target and compute the nuclear structure function. We compare different unitarization schemes and confront our results with the E665 data.

  9. Function and structure of GFP-like proteins in the protein data bank.

    PubMed

    Ong, Wayne J-H; Alvarez, Samuel; Leroux, Ivan E; Shahid, Ramza S; Samma, Alex A; Peshkepija, Paola; Morgan, Alicia L; Mulcahy, Shawn; Zimmer, Marc

    2011-04-01

    The RCSB protein databank contains 266 crystal structures of green fluorescent proteins (GFP) and GFP-like proteins. This is the first systematic analysis of all the GFP-like structures in the pdb. We have used the pdb to examine the function of fluorescent proteins (FP) in nature, aspects of excited state proton transfer (ESPT) in FPs, deformation from planarity of the chromophore and chromophore maturation. The conclusions reached in this review are that (1) The lid residues are highly conserved, particularly those on the "top" of the β-barrel. They are important to the function of GFP-like proteins, perhaps in protecting the chromophore or in β-barrel formation. (2) The primary/ancestral function of GFP-like proteins may well be to aid in light induced electron transfer. (3) The structural prerequisites for light activated proton pumps exist in many structures and it's possible that like bioluminescence, proton pumps are secondary functions of GFP-like proteins. (4) In most GFP-like proteins the protein matrix exerts a significant strain on planar chromophores forcing most GFP-like proteins to adopt non-planar chromophores. These chromophoric deviations from planarity play an important role in determining the fluorescence quantum yield. (5) The chemospatial characteristics of the chromophore cavity determine the isomerization state of the chromophore. The cavities of highlighter proteins that can undergo cis/trans isomerization have chemospatial properties that are common to both cis and trans GFP-like proteins.

  10. Structure functions of electroweak boson and leptons

    SciTech Connect

    Slominski, W; Szwed, J. |

    1996-04-02

    The QCD structure of the electroweak bosons is reviewed and the lepton structure function is defined and calculated. The leading order splitting functions of electron into quarks are extracted, showing an important contribution from {gamma}-Z interference. Leading logarithmic QCD evolution equations are constructed and solved in the asymptotic region where log{sup 2} behavior of the Parton densities is observed. Possible applications with clear manifestation of ``resolved`` photon and weak bosons are discussed. 8 refs., 3 figs.

  11. Tensor-polarized structure functions: Tensor structure of deuteron in 2020's

    NASA Astrophysics Data System (ADS)

    Kumano, S.

    2014-10-01

    We explain spin structure for a spin-one hadron, in which there are new structure functions, in addition to the ones (F1, F2, g1, g2) which exist for the spin-1/2 nucleon, associated with its tensor structure. The new structure functions are b1, b2, b3, and b4 in deep inelastic scattering of a charged-lepton from a spin-one hadron such as the deuteron. Among them, twist- two functions are related by the Callan-Gross type relation b2 = 2xb1 in the Bjorken scaling limit. First, these new structure functions are introduced, and useful formulae are derived for projection operators of b1-4 from a hadron tensor Wμν. Second, a sum rule is explained for b1, and possible tensor-polarized distributions are discussed by using HERMES data in order to propose future experimental measurements and to compare them with theoretical models. A proposal was approved to measure b1 at the Thomas Jefferson National Accelerator Facility (JLab), so that much progress is expected for b1 in the near future. Third, formalisms of polarized proton-deuteron Drell-Yan processes are explained for probing especially tensor- polarized antiquark distributions, which were suggested by the HERMES data. The studies of the tensor-polarized structure functions will open a new era in 2020's for tensor-structure studies in terms of quark and gluon degrees of freedom, which are very different from ordinary descriptions in terms of nucleons and mesons.

  12. 2004 Structural, Function and Evolutionary Genomics

    SciTech Connect

    Douglas L. Brutlag Nancy Ryan Gray

    2005-03-23

    This Gordon conference will cover the areas of structural, functional and evolutionary genomics. It will take a systematic approach to genomics, examining the evolution of proteins, protein functional sites, protein-protein interactions, regulatory networks, and metabolic networks. Emphasis will be placed on what we can learn from comparative genomics and entire genomes and proteomes.

  13. Functional structure of the human X chromosome

    SciTech Connect

    1993-12-31

    Chapter 23, describes the functional structure of the human X chromosome. It provides a functional map of the human X chromosome, discussing in depth the inactivation center, always-active regions, and critical region. Finally, it provides a summary of X inactivation. 34 refs., 4 figs.

  14. Feminine Faces of Leadership: Beyond Structural- Functionalism?

    ERIC Educational Resources Information Center

    Fennell, Hope-Arlene

    1999-01-01

    Reviews four philosophical leadership perspectives: structural-functionalism, constructivism, critical theory, and feminism. Explores the leadership phenomenon through the eyes of six women principals. Although the behaviors of all six fall within a structural-functionalist perspective, each is attempting to construct inclusive, positive, and…

  15. Voltage Gated Ion Channel Function: Gating, Conduction, and the Role of Water and Protons

    PubMed Central

    Kariev, Alisher M.; Green, Michael E.

    2012-01-01

    Ion channels, which are found in every biological cell, regulate the concentration of electrolytes, and are responsible for multiple biological functions, including in particular the propagation of nerve impulses. The channels with the latter function are gated (opened) by a voltage signal, which allows Na+ into the cell and K+ out. These channels have several positively charged amino acids on a transmembrane domain of their voltage sensor, and it is generally considered, based primarily on two lines of experimental evidence, that these charges move with respect to the membrane to open the channel. At least three forms of motion, with greatly differing extents and mechanisms of motion, have been proposed. There is a “gating current”, a capacitative current preceding the channel opening, that corresponds to several charges (for one class of channel typically 12–13) crossing the membrane field, which may not require protein physically crossing a large fraction of the membrane. The coupling to the opening of the channel would in these models depend on the motion. The conduction itself is usually assumed to require the “gate” of the channel to be pulled apart to allow ions to enter as a section of the protein partially crosses the membrane, and a selectivity filter at the opposite end of the channel determines the ion which is allowed to pass through. We will here primarily consider K+ channels, although Na+ channels are similar. We propose that the mechanism of gating differs from that which is generally accepted, in that the positively charged residues need not move (there may be some motion, but not as gating current). Instead, protons may constitute the gating current, causing the gate to open; opening consists of only increasing the diameter at the gate from approximately 6 Å to approximately 12 Å. We propose in addition that the gate oscillates rather than simply opens, and the ion experiences a barrier to its motion across the channel that is tuned

  16. Voltage gated ion channel function: gating, conduction, and the role of water and protons.

    PubMed

    Kariev, Alisher M; Green, Michael E

    2012-01-01

    Ion channels, which are found in every biological cell, regulate the concentration of electrolytes, and are responsible for multiple biological functions, including in particular the propagation of nerve impulses. The channels with the latter function are gated (opened) by a voltage signal, which allows Na(+) into the cell and K(+) out. These channels have several positively charged amino acids on a transmembrane domain of their voltage sensor, and it is generally considered, based primarily on two lines of experimental evidence, that these charges move with respect to the membrane to open the channel. At least three forms of motion, with greatly differing extents and mechanisms of motion, have been proposed. There is a "gating current", a capacitative current preceding the channel opening, that corresponds to several charges (for one class of channel typically 12-13) crossing the membrane field, which may not require protein physically crossing a large fraction of the membrane. The coupling to the opening of the channel would in these models depend on the motion. The conduction itself is usually assumed to require the "gate" of the channel to be pulled apart to allow ions to enter as a section of the protein partially crosses the membrane, and a selectivity filter at the opposite end of the channel determines the ion which is allowed to pass through. We will here primarily consider K(+) channels, although Na(+) channels are similar. We propose that the mechanism of gating differs from that which is generally accepted, in that the positively charged residues need not move (there may be some motion, but not as gating current). Instead, protons may constitute the gating current, causing the gate to open; opening consists of only increasing the diameter at the gate from approximately 6 Å to approximately 12 Å. We propose in addition that the gate oscillates rather than simply opens, and the ion experiences a barrier to its motion across the channel that is tuned by

  17. Precision measurement of the neutron spin dependent structure functions

    SciTech Connect

    Kolomensky, Y.G.

    1997-02-01

    In experiment E154 at the Stanford Linear Accelerator Center the spin dependent structure function g{sub 1}{sup n} (x, Q{sup 2}) of the neutron was measured by scattering longitudinally polarized 48.3 GeV electrons off a longitudinally polarized {sup 3}He target. The high beam energy allowed the author to extend the kinematic coverage compared to the previous SLAC experiments to 0.014 {le} x {le} 0.7 with an average Q{sup 2} of 5 GeV{sup 2}. The author reports the integral of the spin dependent structure function in the measured range to be {integral}{sub 0.014}{sup 0.7} dx g{sub 1}{sup n}(x, 5 GeV{sup 2}) = {minus}0.036 {+-} 0.004(stat.) {+-} 0.005(syst.). The author observes relatively large values of g{sub 1}{sup n} at low x that call into question the reliability of data extrapolation to x {r_arrow} 0. Such divergent behavior disagrees with predictions of the conventional Regge theory, but is qualitatively explained by perturbative QCD. The author performs a Next-to-Leading Order perturbative QCD analysis of the world data on the nucleon spin dependent structure functions g{sub 1}{sup p} and g{sub 1}{sup n} paying careful attention to the experimental and theoretical uncertainties. Using the parameterizations of the helicity-dependent parton distributions obtained in the analysis, the author evolves the data to Q{sup 2} = 5 GeV{sup 2}, determines the first moments of the polarized structure functions of the proton and neutron, and finds agreement with the Bjorken sum rule.

  18. Maintenance of Functionality during Earthquakes: Structural and Non Structural Aspects

    SciTech Connect

    Di Donato, Enrico

    2008-07-08

    The necessity to maintain functionality during and after an earthquake, means that we have to protect not only structures but also functional elements that are inside each building, in particular for strategic constructions, like hospitals, schools. Fortunately, modern solutions to prevent the possibility of failure exist and, very important, are available.

  19. The Proton

    NASA Astrophysics Data System (ADS)

    Canal, Carlos Garcia; Sassot, Rodolfo

    2003-10-01

    In this talk we present a collection of selected topics concerning the structure of the proton and the fundamental interactions as seen inside it. These topics have been thoroughly covered by high energy experiments with ever increasing precision in recent years and beautifully illustrate our present knowledge of the standard model.

  20. Spin models of the proton

    SciTech Connect

    Ramsey, G.P.

    1988-10-20

    We have constructed a model of the proton spin based on a broken SU(6) parameterization for the spin-weighted valence quark distributions in a longitudinally polarized proton. The polarized sea and gluon distributions are assumed to have simple relations to the corresponding unpolarized structure functions. The sum rules, which involve the non-singlet components of the structure function xg/sub 1/, imply that the valence quarks carry about 78% of the proton spin, while the spin carried by sea quarks is negative. Recent EMC data suggest a model in which the sea quarks carry a large negative polarization, whereas certain theoretical arguments favor a model with a smaller negatively polarized sea. These models are discussed with reference to the sum rules. Experiments are suggested which will discriminate between these models. 24 refs., 4 figs.

  1. [Structure and function of the eukaryotic ribosome].

    PubMed

    Bakowska-Zywicka, Kamilla; Twardowski, Tomasz

    2008-01-01

    The protein biosynthesis is a complicated process and not fully understood yet. According to smaller size and less complicated structure, understanding of prokaryotic 70S ribosomes is much more advanced. Eucaryotic 80S ribosomes are more complex and generate more difficulties in research. The morphology of 80S ribosome has been pretty well resolved and we know a lot about mechanism of functioning. Determination of the interactions between the ribosomes and the factors taking part in protein biosynthesis is still a great challenge. Dynamic changes of these interactions during particular steps of elongation cycle are quite difficult to understand. Conformational changes of the ribosome are of great functional and regulatory importance during protein biosynthesis. They are essential for the whole gene expression process. Only further research of the structure and function of the ribosome will lead us to knowledge about specificity of the mechanism of their action. In this article we present current opinions concerning structure and function of the eukaryotic ribosomes.

  2. The proteome: structure, function and evolution.

    PubMed

    Fleming, Keiran; Kelley, Lawrence A; Islam, Suhail A; MacCallum, Robert M; Muller, Arne; Pazos, Florencio; Sternberg, Michael J E

    2006-03-29

    This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family.

  3. Dramatic improvement in water retention and proton conductivity in electrically aligned functionalized CNT/SPEEK nanohybrid PEM.

    PubMed

    Gahlot, Swati; Kulshrestha, Vaibhav

    2015-01-14

    Nanohybrid membranes of electrically aligned functionalized carbon nanotube f CNT with sulfonated poly ether ether ketone (SPEEK) have been successfully prepared by solution casting. Functionalization of CNTs was done through a carboxylation and sulfonation route. Further, a constant electric field (500 V·cm(-2)) has been applied to align CNTs in the same direction during the membrane drying process. All the membranes are characterized chemically, thermally, and mechanically by the means of FTIR, DSC, DMA, UTM, SEM, TEM, and AFM techniques. Intermolecular interactions between the components in hybrid membranes are established by FTIR. Physicochemical measurements were done to analyze membrane stability. Membranes are evaluated for proton conductivity (30-90 °C) and methanol crossover resistance to reveal their potential for direct methanol fuel cell application. Incorporation of f CNT reasonably increases the ion-exchange capacity, water retention, and proton conductivity while it reduces the methanol permeability. The maximum proton conductivity has been found in the S-sCNT-5 nanohybrid PEM with higher methanol crossover resistance. The prepared membranes can be also used for electrode material for fuel cells and batteries.

  4. A NEW METHOD FOR EXTRACTING SPIN-DEPENDENT NEUTRON STRUCTURE FUNCTIONS FROM NUCLEAR DATA

    SciTech Connect

    Kahn, Y.F.; Melnitchouk, W.

    2009-01-01

    High-energy electrons are currently the best probes of the internal structure of nucleons (protons and neutrons). By collecting data on electrons scattering off light nuclei, such as deuterium and helium, one can extract structure functions (SFs), which encode information about the quarks that make up the nucleon. Spin-dependent SFs, which depend on the relative polarization of the electron beam and the target nucleus, encode quark spins. Proton SFs can be measured directly from electron-proton scattering, but those of the neutron must be extracted from proton data and deuterium or helium-3 data because free neutron targets do not exist. At present, there is no reliable method for accurately determining spin-dependent neutron SFs in the low-momentum-transfer regime, where nucleon resonances are prominent and the functions are not smooth. The focus of this study was to develop a new method for extracting spin-dependent neutron SFs from nuclear data. An approximate convolution formula for nuclear SFs reduces the problem to an integral equation, for which a recursive solution method was designed. The method was then applied to recent data from proton and deuterium scattering experiments to perform a preliminary extraction of spin-dependent neutron SFs in the resonance region. The extraction method was found to reliably converge for arbitrary test functions, and the validity of the extraction from data was verifi ed using a Bjorken integral, which relates integrals of SFs to a known quantity. This new information on neutron structure could be used to assess quark-hadron duality for the neutron, which requires detailed knowledge of SFs in all kinematic regimes.

  5. Effect of wave function on the proton induced L XRP cross sections for {sub 62}Sm and {sub 74}W

    SciTech Connect

    Shehla,; Kaur, Rajnish; Kumar, Anil; Puri, Sanjiv

    2015-08-28

    The L{sub k}(k= 1, α, β, γ) X-ray production cross sections have been calculated for {sub 74}W and {sub 62}Sm at different incident proton energies ranging 1-5 MeV using theoretical data sets of different physical parameters, namely, the Li(i=1-3) sub-shell X-ray emission rates based on the Dirac-Fork (DF) model, the fluorescence and Coster Kronig yields based on the Dirac- Hartree-Slater (DHS) model and two sets the proton ionization cross sections based on the DHS model and the ECPSSR in order to assess the influence of the wave function on the XRP cross sections. The calculated cross sections have been compared with the measured cross sections reported in the recent compilation to check the reliability of the calculated values.

  6. Effect of wave function on the proton induced L XRP cross sections for 62Sm and 74W

    NASA Astrophysics Data System (ADS)

    Shehla, Kaur, Rajnish; Kumar, Anil; Puri, Sanjiv

    2015-08-01

    The Lk(k= 1, α, β, γ) X-ray production cross sections have been calculated for 74W and 62Sm at different incident proton energies ranging 1-5 MeV using theoretical data sets of different physical parameters, namely, the Li(i=1-3) sub-shell X-ray emission rates based on the Dirac-Fork (DF) model, the fluorescence and Coster Kronig yields based on the Dirac- Hartree-Slater (DHS) model and two sets the proton ionization cross sections based on the DHS model and the ECPSSR in order to assess the influence of the wave function on the XRP cross sections. The calculated cross sections have been compared with the measured cross sections reported in the recent compilation to check the reliability of the calculated values.

  7. DESIGN OF SUPERCONDUCTING COMBINED FUNCTION MAGNETS FOR THE 50 GEV PROTON BEAM LINE FOR THE J-PARC NEUTRINO EXPERIMENT.

    SciTech Connect

    WANDERER,P.; ET AL.

    2003-06-15

    Superconducting combined function magnets will be utilized for the 50GeV-750kW proton beam line for the J-PARC neutrino experiment and an R and D program has been launched at KEK. The magnet is designed to provide a combined function with a dipole field of 2.59 T and a quadrupole field of 18.7 T/m in a coil aperture of 173.4 mm. A single layer coil is proposed to reduce the fabrication cost and the coil arrangement in the 2-D cross-section results in left-right asymmetry. This paper reports the design study of the magnet.

  8. Calculation of excitation functions of proton, alpha and deuteron induced reactions for production of medical radioisotopes 122-125I

    NASA Astrophysics Data System (ADS)

    Artun, Ozan; Aytekin, Hüseyin

    2015-02-01

    In this work, the excitation functions for production of medical radioisotopes 122-125I with proton, alpha, and deuteron induced reactions were calculated by two different level density models. For the nuclear model calculations, the Talys 1.6 code were used, which is the latest version of Talys code series. Calculations of excitation functions for production of the 122-125I isotopes were carried out by using the generalized superfluid model (GSM) and Fermi-gas model (FGM). The results have shown that generalized superfluid model is more successful than Fermi-gas model in explaining the experimental results.

  9. Superbasic alkyl-substituted bisphosphazene proton sponges: synthesis, structural features, thermodynamic and kinetic basicity, nucleophilicity and coordination chemistry.

    PubMed

    Kögel, Julius F; Xie, Xiulan; Baal, Eduard; Gesevičius, Donatas; Oelkers, Benjamin; Kovačević, Borislav; Sundermeyer, Jörg

    2014-06-16

    Herein we describe an easily accessible class of superbasic proton sponges based on the 1,8-bisphosphazenylnaphthalene (PN) proton pincer motif and P-alkyl substituents ranging from methyl (TMPN) to n-butyl (TBPN), isopropyl (TiPrPN) and cyclopentyl (TcyPPN). These neutral bases with a pK(BH)(+) value (MeCN) of ~30 were accessible via a Kirsanov condensation using commercially available 1,8-diaminonaphthalene, and in case of TMPN and TBPN, simple one-pot procedures starting from trisalkylphosphanes can be performed. Furthermore, the known pyrrolidinyl-substituted superbase TPPN previously synthesized via a Staudinger reaction could also be prepared by the Kirsanov strategy allowing its preparation in a larger scale. The four alkyl-substituted proton sponges were structurally characterized in their protonated form; molecular XRD structures were also obtained for unprotonated TiPrPN and TcyPPN. Moreover, we present a detailed description of spectroscopic features of chelating bisphosphazenes including TPPN and its hyperbasic homologue P2-TPPN on which we reported recently. The four alkyl-substituted superbases were investigated with respect to their basic features by computational means and by NMR titration experiments revealing unexpectedly high experimental pK(BH)(+) values in acetonitrile between 29.3 for TMPN and 30.9 for TBPN. Besides their thermodynamic basicity, we exemplarily studied the kinetic basicity of TMPN and TPPN by means of NMR-spectroscopic methods. Furthermore, the competing nucleophilic versus basic properties were examined by reacting the proton sponges with ethyl iodide. Insight into the coordination chemistry of chelating superbases was provided by reacting TMPN with trimethylaluminum and trimethylgallium to give cationic complexes of Group XIII metal alkyls that were structurally characterized.

  10. Crystal structure of the eukaryotic light-driven proton-pumping rhodopsin, Acetabularia rhodopsin II, from marine alga.

    PubMed

    Wada, Takashi; Shimono, Kazumi; Kikukawa, Takashi; Hato, Masakatsu; Shinya, Naoko; Kim, So Young; Kimura-Someya, Tomomi; Shirouzu, Mikako; Tamogami, Jun; Miyauchi, Seiji; Jung, Kwang-Hwan; Kamo, Naoki; Yokoyama, Shigeyuki

    2011-09-01

    Acetabularia rhodopsin (AR) is a rhodopsin from the marine plant Acetabularia acetabulum. The opsin-encoding gene from A. acetabulum, ARII, was cloned and found to be novel but homologous to that reported previously. ARII is a light-driven proton pump, as demonstrated by the existence of a photo-induced current through Xenopus oocytes expressing ARII. The photochemical reaction of ARII prepared by cell-free protein synthesis was similar to that of bacteriorhodopsin (BR), except for the lack of light-dark adaptation and the different proton release and uptake sequence. The crystal structure determined at 3.2 Å resolution is the first structure of a eukaryotic member of the microbial rhodopsin family. The structure of ARII is similar to that of BR. From the cytoplasmic side to the extracellular side of the proton transfer pathway in ARII, Asp92, a Schiff base, Asp207, Asp81, Arg78, Glu199, and Ser189 are arranged in positions similar to those of the corresponding residues directly involved in proton transfer by BR. The side-chain carboxyl group of Asp92 appears to interact with the sulfhydryl group of Cys218, which is unique to ARII and corresponds to Leu223 of BR and to Asp217 of Anabaena sensory rhodopsin. The orientation of the Arg78 side chain is opposite to the corresponding Arg82 of BR. The putative absence of water molecules around Glu199 and Arg78 may disrupt the formation of the low-barrier hydrogen bond at Glu199, resulting in the "late proton release".

  11. Study of proton resonance structure in {sup 27}P via resonant elastic scattering of {sup 26}Si+p

    SciTech Connect

    Jung, H. S.; Lee, C. S.; Kwon, Y. K.; Moon, J. Y.; Lee, J. H.; Yun, C. C.; Kubono, S.; Yamaguchi, H.; Hashimoto, T.; Kahl, D.; Hayakawa, S.; Choi, Seonho; Kim, M. J.; Kim, Y. H.; Kim, Y. K.; Park, J. S.; Kim, E. J.; Moon, C.-B.; Teranishi, T.; Wakabayashi, Y.; and others

    2012-11-12

    A measurement of resonant elastic scattering of {sup 26}Si+p was performed with a thick target using a {sup 26}Si radioactive ion beam at the CRIB (CNS Radioactive Ion Beam separator) of the Center for Nuclear Study (CNS), the University of Tokyo. The excitation function of {sup 27}P was measured successfully with the inverse kinematics method through a covered the range of excitation energies from E{sub x}{approx} 2.3 to 3.8 MeV, providing information about the resonance structure of this nucleus. The properties of these resonances are important to better determine the production rates of {sup 26}Si(p,g){sup 27}P reaction, which is one of the astrophysically important nuclear reactions to understand the production of the {sup 26}Al. Some new resonant states have been investigated, and determined their resonance parameters, such as excitation energies, proton partial widths, and spin-parities by R-matrix calculation.

  12. Investigation of structure in Al23 via resonant proton scattering of Mg22+p and the 22Mg(p,γ) Al23 astrophysical reaction rate

    NASA Astrophysics Data System (ADS)

    He, J. J.; Kubono, S.; Teranishi, T.; Notani, M.; Baba, H.; Nishimura, S.; Moon, J. Y.; Nishimura, M.; Iwasaki, H.; Yanagisawa, Y.; Hokoiwa, N.; Kibe, M.; Lee, J. H.; Kato, S.; Gono, Y.; Lee, C. S.

    2007-11-01

    Proton resonant states in Al23 have been investigated for the first time by the resonant elastic and inelastic scattering of Mg22+p with a Mg22 beam at 4.38 MeV/nucleon bombarding a thick (CH2)n target. The low-energy Mg22 beam was separated by the CNS radioactive ion beam separator (CRIB). The energy spectra of recoiled protons were measured at average scattering angles of θlab≈4°,17° and 23°. A new state has been observed at Ex=3.00 MeV with a spin-parity assignment of (3/2+). In addition, resonant inelastic scattering has populated three more states at excitation energies of 3.14, 3.26, and 3.95 MeV, with proton decay to the first excited state in Mg22 being observed. The new state at 3.95 MeV has been assigned a spin-parity of Jπ=(7/2+). The resonant parameters were determined by an R-matrix analysis of the excitation functions with a SAMMY-M6-BETA code. The core-excited structure of Al23 is discussed within a shell-model picture. The stellar reaction rate of the Mg22(p,γ)Al23 reaction has been reevaluated, and the revised total reaction rate is about 40% greater than the previous result for temperatures beyond T9=0.3.

  13. Expression cloning and functional characterization of the kidney cortex high-affinity proton-coupled peptide transporter.

    PubMed Central

    Boll, M; Herget, M; Wagener, M; Weber, W M; Markovich, D; Biber, J; Clauss, W; Murer, H; Daniel, H

    1996-01-01

    The presence of a proton-coupled electrogenic high-affinity peptide transporter in the apical membrane of tubular cells has been demonstrated by microperfusion studies and by use of brush border membrane vesicles. The transporter mediates tubular uptake of filtered di- and tripeptides and aminocephalosporin antibiotics. We have used expression cloning in Xenopus laevis oocytes for identification and characterization of the renal high-affinity peptide transporter. Injection of poly(A)+ RNA isolated from rabbit kidney cortex into oocytes resulted in expression of a pH-dependent transport activity for the aminocephalosporin antibiotic cefadroxil. After size fractionation of poly(A)+ RNA the transport activity was identified in the 3.0- to 5.0-kb fractions, which were used for construction of a cDNA library. The library was screened for expression of cefadroxil transport after injection of complementary RNA synthesized in vitro from different pools of clones. A single clone (rPepT2) was isolated that stimulated cefadroxil uptake into oocytes approximately 70-fold at a pH of 6.0. Kinetic analysis of cefadroxil uptake expressed by the transporter's complementary RNA showed a single saturable high-affinity transport system shared by dipeptides, tripeptides, and selected amino-beta-lactam antibiotics. Electrophysiological studies established that the transport activity is electrogenic and affected by membrane potential. Sequencing of the cDNA predicts a protein of 729 amino acids with 12 membrane-spanning domains. Although there is a significant amino acid sequence identity (47%) to the recently cloned peptide transporters from rabbit and human small intestine, the renal transporter shows distinct structural and functional differences. Images Fig. 7 PMID:8552623

  14. GRASPs in Golgi Structure and Function

    PubMed Central

    Zhang, Xiaoyan; Wang, Yanzhuang

    2016-01-01

    The Golgi apparatus is a central intracellular membrane organelle for trafficking and modification of proteins and lipids. Its basic structure is a stack of tightly aligned flat cisternae. In mammalian cells, dozens of stacks are concentrated in the pericentriolar region and laterally connected to form a ribbon. Despite extensive research in the last decades, how this unique structure is formed and why its formation is important for proper Golgi functioning remain largely unknown. The Golgi ReAssembly Stacking Proteins, GRASP65, and GRASP55, are so far the only proteins shown to function in Golgi stacking. They are peripheral membrane proteins on the cytoplasmic face of the Golgi cisternae that form trans-oligomers through their N-terminal GRASP domain, and thereby function as the “glue” to stick adjacent cisternae together into a stack and to link Golgi stacks into a ribbon. Depletion of GRASPs in cells disrupts the Golgi structure and results in accelerated protein trafficking and defective glycosylation. In this minireview we summarize our current knowledge on how GRASPs function in Golgi structure formation and discuss why Golgi structure formation is important for its function. PMID:26779480

  15. Theoretical study of the structure and electronic spectra of fully protonated emeraldine oligomers

    NASA Astrophysics Data System (ADS)

    Zhekova, H.; Tadjer, A.; Ivanova, A.; Petrova, J.; Gospodinova, N.

    Polyaniline (PANI) is one of the most studied conducting polymers. Obtained in its conducting form (known as ?emeraldine salt?) by chemical or electrochemical oxidation of aniline in aqueous acidic medium, this polymer manifests an array of attractive properties. Nevertheless, these properties still need to be described at the molecular level. Intense theoretical investigations during the past few years aim at explaining the chain organization, conductivity mechanism, and other structural and spectral characteristics. Most studies adopt simplified models in which hydration effect is underestimated, since all simulations are performed either in vacuum or in the presence of a limited number of water molecules. The present computational study sheds light on the molecular organization of a number of model PANI hydrated clusters with different alignment and multiplicity, which can explain the experimentally recorded UV/VIS spectra. The influence of hydration and interaction with adjacent oligomers is estimated. Short-chain doubly protonated emeraldine oligomers are used as model systems. The calculations are performed at the semi-empirical (AM1) and/or molecular mechanics (AMBER96) level. Proper configurations of the clusters are selected using Monte Carlo simulations. Electron correlation (CIS) is accounted for upon evaluation of the absorption spectra of the clusters. The relative strength of the interchain coupling is estimated by simulation of PANI clusters consisting of two PANI tetramers in water. Comparison to experimental results is made.

  16. The role of charge transfer in the structure and dynamics of the hydrated proton

    PubMed Central

    Swanson, Jessica M.J.; Simons, Jack

    2009-01-01

    Although it has long been recognized that multiple water molecules strongly associate with an extra proton in bulk water, some models and conceptual frameworks continue to utilize the classical hydronium ion (H3O+) as a fundamental building block. In this work, the nature of the hydronium ion in aqueous systems is examined using an ab initio energy decomposition analysis (EDA) that evaluates both the magnitude of and energetic stabilization due to charge transfer among H3O+ and the surrounding water molecules. The EDA is performed on structures extracted from dynamical bulk-phase simulations, and used to determine how frequently the pure hydronium ion, where the excess charge is primarily localized on H3O+, occurs under dynamic conditions. The answer is essentially never. The energetic stabilization of H3O+ due to charge delocalization to neighboring water molecules is found to be much larger (16 to 49 kcal/mol) than for other ions (even Li+) and to constitute a substantial portion (20% to 52%) of the complex's binding energy. The charge defect is also shown to have intrinsic dynamical asymmetry and to display dynamical signatures that can be related to features appearing in IR spectra. PMID:19309128

  17. Fabrication and evaluation of flexible Mach–Zehnder waveguide structure embedded in a poly(dimethylsiloxane) thin film using a proton microbeam

    NASA Astrophysics Data System (ADS)

    Parajuli, Raj Kumar; Saruya, Ryota; Akutzu, Naoki; Miura, Satoshi; Kada, Wataru; Kawabata, Shunsuke; Matsubara, Yoshinori; Satoh, Takahiro; Koka, Masashi; Yamada, Naoto; Kamiya, Tomihiro; Miura, Kenta; Hanaizumi, Osamu

    2016-06-01

    A flexible Mach–Zehnder (MZ) optical waveguide was fabricated in a poly(dimethylsiloxane) (PDMS) film by proton beam writing (PBW). A focused 750 keV proton microbeam was used to fabricate a 40 × 20 mm2 MZ optical waveguide structure with a width of 8 µm embedded in a PDMS film for the single-mode light propagation of infrared (IR) laser light. The structure was measured by ion-beam-induced luminescence (IBIL) analysis and the beam fluence was optimized according to the IBIL intensity obtained from the waveguide structure. The entire structure of the MZ waveguide functioned well, confirmed by observing the near-field pattern (NFP) with a tunable IR laser (1.55 µm) for different PDMS film conditions. The optical throughput measurements for different sample configurations were obtained under continuous mechanical stress and a relatively low optical loss was observed at an inclination angle of 16°. Our results suggest that the MZ waveguide can be used for optical interlink connections under continuous mechanical stress.

  18. Fabrication and evaluation of flexible Mach-Zehnder waveguide structure embedded in a poly(dimethylsiloxane) thin film using a proton microbeam

    NASA Astrophysics Data System (ADS)

    Parajuli, Raj Kumar; Saruya, Ryota; Akutzu, Naoki; Miura, Satoshi; Kada, Wataru; Kawabata, Shunsuke; Matsubara, Yoshinori; Satoh, Takahiro; Koka, Masashi; Yamada, Naoto; Kamiya, Tomihiro; Miura, Kenta; Hanaizumi, Osamu

    2016-06-01

    A flexible Mach-Zehnder (MZ) optical waveguide was fabricated in a poly(dimethylsiloxane) (PDMS) film by proton beam writing (PBW). A focused 750 keV proton microbeam was used to fabricate a 40 × 20 mm2 MZ optical waveguide structure with a width of 8 µm embedded in a PDMS film for the single-mode light propagation of infrared (IR) laser light. The structure was measured by ion-beam-induced luminescence (IBIL) analysis and the beam fluence was optimized according to the IBIL intensity obtained from the waveguide structure. The entire structure of the MZ waveguide functioned well, confirmed by observing the near-field pattern (NFP) with a tunable IR laser (1.55 µm) for different PDMS film conditions. The optical throughput measurements for different sample configurations were obtained under continuous mechanical stress and a relatively low optical loss was observed at an inclination angle of 16°. Our results suggest that the MZ waveguide can be used for optical interlink connections under continuous mechanical stress.

  19. Density functional study of the proton transfer effect on vibrations of strong (short) intermolecular O-H...N/O-...H-N+ hydrogen bonds in aprotic solvents.

    PubMed

    Kong, Shushu; Shenderovich, Ilja G; Vener, Mikhail V

    2010-02-18

    The structure and spectroscopic properties of the 1:1 complexes of substituted pyridines with benzoic acid and phenol derivatives in aprotic solvents are studied using B3LYP functional combined with the polarizable continuum model approximation. Two extreme structures are investigated: the state without (HB) and with proton transfer (PT). In the presence of an external electric field the O...N distance is contracted and the PT state does appear. The PT state of both the pyridine-benzoic and the pyridine-phenol complexes displays the only IR-active band in the 2800-1800 frequency region, which is located around 2000 cm(-1). However, the nature of the band is different for these two complexes. In the pyridine-benzoic acid complex it is practically a pure stretching vibration of the HN(+) group, while in the pyridine-phenol complex it is the mixed vibration of the bridging proton. A specific feature of the PT state in the pyridine-phenol complex is an IR-intensive band near 600 cm(-1), associated with the asymmetric stretching vibrations of the O(-)...HN(+) fragment. Its intensity is reciprocally proportional to the O...N distance. The appearance of this band provides an efficient criterion to differentiate between the HB and PT states of the 1:1 complexes of phenols with pyridines in aprotic solvents. PMID:20104882

  20. Proton Therapy

    MedlinePlus

    ... nucleus is surrounded by electrons. In proton therapy, beams of fast-moving protons are used to destroy ... atoms to release proton, neutron, and helium ion beams. In this highly specialized form of radiosurgery , proton ...

  1. Optimized Structures and Proton Affinities of Fluorinated Dimethyl Ethers: An Ab Initio Study

    NASA Technical Reports Server (NTRS)

    Orgel, Victoria B.; Ball, David W.; Zehe, Michael J.

    1996-01-01

    Ab initio methods have been used to investigate the proton affinity and the geometry changes upon protonation for the molecules (CH3)2O, (CH2F)2O, (CHF2)2O, and (CF3)2O. Geometry optimizations were performed at the MP2/3-2 I G level, and the resulting geometries were used for single-point energy MP2/6-31G calculations. The proton affinity calculated for (CH3)2O was 7 Kjoule/mole from the experimental value, within the desired variance of +/- 8Kjoule/mole for G2 theory, suggesting that the methodology used in this study is adequate for energy difference considerations. For (CF3)20, the calculated proton affinity of 602 Kjoule/mole suggests that perfluorinated ether molecules do not act as Lewis bases under normal circumstances; e.g. degradation of commercial lubricants in tribological applications.

  2. Bound-state field-theory approach to proton-structure effects in muonic hydrogen

    NASA Astrophysics Data System (ADS)

    Mohr, Peter J.; Griffith, J.; Sapirstein, J.

    2013-05-01

    A bound-state field-theory approach to muonic hydrogen is set up using a variant of the Furry representation in which the lowest-order Hamiltonian describes a muon in the presence of a point Coulomb field, but the origin of the binding field is taken to be three charged quarks in the proton, which are modeled as Dirac particles that move freely within a spherical well. Bound-state field-theory techniques are used to evaluate one- and two-photon effects. Particular attention is paid to two-photon-exchange diagrams, which include the effect of proton polarizability. In addition, the modification of the electromagnetic self energy of the proton by the electric field of the muon is examined. Finally, the model is used to carry out a calculation of the static electric polarizability of the proton.

  3. Structural Analysis of Cytochrome bc1 Complexes: Implications to the Mechanism of Function

    PubMed Central

    Xia, Di; Esser, Lothar; Tang, Wai-Kwan; Zhou, Fei; Zhou, Yihui; Yu, Linda; Yu, Chang-An

    2012-01-01

    Summary The cytochrome bc1 complex (bc1) is the mid-segment of the cellular respiratory chain of mitochondria and many aerobic prokaryotic organisms; it is also part of the photosynthetic apparatus of non-oxygenic purple bacteria. The bc1 complex catalyzes the reaction of transferring electrons from the low potential substrate ubiquinol to high potential cytochrome c. Concomitantly, bc1 translocates protons across the membrane, contributing to the proton-motive force essential for a variety of cellular activities such as ATP synthesis. Structural investigations of bc1 have been exceedingly successful, yielding atomic resolution structures of bc1 from various organisms and trapped in different reaction intermediates. These structures have confirmed and unified results of decades of experiments and have contributed to our understanding of the mechanism of bc1 functions as well as its inactivation by respiratory inhibitors. PMID:23201476

  4. The rhodopsins: structure and function. Introduction

    NASA Technical Reports Server (NTRS)

    Lanyi, J. K.

    1992-01-01

    Nature makes use of the propensity of retinal for light-dependent double-bond isomerization in a number of systems and in a variety of ways. The common theme for light receptors based on this kind of chemistry is that (1) the retinal is bound in most cases to a small membrane protein via a protonated lysine-retinal Schiff base, (2) the absorption maximum in the visible is tuned to a suitable wavelength largely by electrostatic interaction with polar protein residues, and (3) the light-induced bond rotations and strains in the retinal set off reaction chains during which at least part of the excess free energy acquired is transferred to the protein and causes pK shifts of acidic residues and/or backbone conformational changes. The physiological consequence of the process initiated by absorption of light is either the activation of an information transfer chain (sensory and visual rhodopsins) or energy transduction which drives the electrogenic movement of ions across the membrane (ion-motive rhodopsins). Rhodopsins with these functions occur in bacteria and in higher organisms; from an evolutionary standpoint they are not related to one another. Nevertheless, all of these proteins are remarkably similar and form a distinct family.

  5. Quark-hadron duality in structure functions

    SciTech Connect

    Wally Melnitchouk

    2011-09-01

    We review recent progress in the study of quark-hadron duality in electron–nucleon structure functions. New developments include insights into the local aspects of duality obtained using truncated moments of structure functions, which allow duality-violating higher-twist contributions to be identified in individual resonance regions. Preliminary studies of pion electropro-duction have also showed the first glimpses of duality in semi-inclusive cross sections, which if confirmed would greatly expand the scope of constraining the flavor and spin dependence of parton distributions.

  6. Track structure model for damage to mammalian cell cultures during solar proton events

    NASA Technical Reports Server (NTRS)

    Cucinotta, F. A.; Wilson, J. W.; Townsend, L. W.; Shinn, J. L.; Katz, R.

    1992-01-01

    Solar proton events (SPEs) occur infrequently and unpredictably, thus representing a potential hazard to interplanetary space missions. Biological damage from SPEs will be produced principally through secondary electron production in tissue, including important contributions due to delta rays from nuclear reaction products. We review methods for estimating the biological effectiveness of SPEs using a high energy proton model and the parametric cellular track model. Results of the model are presented for several of the historically largest flares using typical levels and body shielding.

  7. Structural methods for studying IRES function.

    PubMed

    Kieft, Jeffrey S; Costantino, David A; Filbin, Megan E; Hammond, John; Pfingsten, Jennifer S

    2007-01-01

    Internal ribosome entry sites (IRESs) substitute RNA sequences for some or all of the canonical translation initiation protein factors. Therefore, an important component of understanding IRES function is a description of the three-dimensional structure of the IRES RNA underlying this mechanism. This includes determining the degree to which the RNA folds, the global RNA architecture, and higher resolution information when warranted. Knowledge of the RNA structural features guides ongoing mechanistic and functional studies. In this chapter, we present a roadmap to structurally characterize a folded RNA, beginning from initial studies to define the overall architecture and leading to high-resolution structural studies. The experimental strategy presented here is not unique to IRES RNAs but is adaptable to virtually any RNA of interest, although characterization of RNA-protein interactions requires additional methods. Because IRES RNAs have a specific function, we present specific ways in which the data are interpreted to gain insight into that function. We provide protocols for key experiments that are particularly useful for studying IRES RNA structure and that provide a framework onto which additional approaches are integrated. The protocols we present are solution hydroxyl radical probing, RNase T1 probing, native gel electrophoresis, sedimentation velocity analytical ultracentrifugation, and strategies to engineer RNA for crystallization and to obtain initial crystals. PMID:17913644

  8. Singularity of proton transport in salts of orthoperiodic and orthotellurium acids: theoretical modeling using density functional calculations.

    PubMed

    Zyubina, Tatiana S; Shilov, Gennady V; Dobrovolsky, Yury A; Leonova, Ludmila S; Mebel, Alexander M

    2004-07-21

    Density functional B3LYP calculations have been performed to investigate proton transport in orthoperiodic and orthotellurium acids, their salts MIO(6)H(4)(M = Li, Rb, Cs) and CsH(5)TeO(6), dimers of the salt*acid type MIO(6)H(4)*H(5)IO(6)(M = Rb, Cs), CsIO(6)H(4)*H(6)TeO(6), CsHSO(4)*H(6)TeO(6), Cs(2)SO(4)*H(6)TeO(6), and also in double-substituted and binary salts Rb(2)H(3)IO(6) and Rb(4)H(2)I(2)O(10). It has been shown that the energy of salt dimerization is 33-35 kcal mol(-1) and the activation barrier for proton migration between the neighboring octahedrons of the salt*acid --> acid*salt type is calculated to be 3-13 kcal mol(-1). The activation energy of the proton migration along the octahedron, 20-30 kcal mol(-1), is comparable with the barrier for water molecule separation. Quantum-chemical calculations correlate with the results of X-ray and electrochemical studies.

  9. Multifactorial Resistance of Bacillus subtilis Spores to High-Energy Proton Radiation: Role of Spore Structural Components and the Homologous Recombination and Non-Homologous End Joining DNA Repair Pathways

    PubMed Central

    Reitz, Günther; Li, Zuofeng; Klein, Stuart; Nicholson, Wayne L.

    2012-01-01

    Abstract The space environment contains high-energy charged particles (e.g., protons, neutrons, electrons, α-particles, heavy ions) emitted by the Sun and galactic sources or trapped in the radiation belts. Protons constitute the majority (87%) of high-energy charged particles. Spores of Bacillus species are one of the model systems used for astro- and radiobiological studies. In this study, spores of different Bacillus subtilis strains were used to study the effects of high energetic proton irradiation on spore survival. Spores of the wild-type B. subtilis strain [mutants deficient in the homologous recombination (HR) and non-homologous end joining (NHEJ) DNA repair pathways and mutants deficient in various spore structural components such as dipicolinic acid (DPA), α/β-type small, acid-soluble spore protein (SASP) formation, spore coats, pigmentation, or spore core water content] were irradiated as air-dried multilayers on spacecraft-qualified aluminum coupons with 218 MeV protons [with a linear energy transfer (LET) of 0.4 keV/μm] to various final doses up to 2500 Gy. Spores deficient in NHEJ- and HR-mediated DNA repair were significantly more sensitive to proton radiation than wild-type spores, indicating that both HR and NHEJ DNA repair pathways are needed for spore survival. Spores lacking DPA, α/β-type SASP, or with increased core water content were also significantly more sensitive to proton radiation, whereas the resistance of spores lacking pigmentation or spore coats was essentially identical to that of the wild-type spores. Our results indicate that α/β-type SASP, core water content, and DPA play an important role in spore resistance to high-energy proton irradiation, suggesting their essential function as radioprotectants of the spore interior. Key Words: Bacillus—Spores—DNA repair—Protection—High-energy proton radiation. Astrobiology 12, 1069–1077. PMID:23088412

  10. Possibilities of studying the structure of halo nuclei in reactions of quasifree proton scattering at low energies

    SciTech Connect

    Zuyev, S. V. Kasparov, A. A.; Konobeevski, E. S.

    2015-07-15

    The possibility of experimentally studying the structure of halo nuclei in reactions induced by quasifree proton scattering on clusters of these nuclei is considered. Quasifree proton scattering on {sup 6}He, {sup 4}He, {sup 4}n, {sup 2}n, and n clusters in inverse kinematics is considered for the example of the {sup 8}He nucleus. Angular and energy distributions of secondaries are obtained for various representations of the cluster structure of the {sup 8}He nucleus. It is clearly shown that, in the angular and energy distributions of secondaries, one can single out regions that receive dominant contributions from reactions on specific clusters and which correspond to concrete cluster configurations of halo nuclei. Possible relevant experiments are proposed.

  11. Development of embedded Mach-Zehnder optical waveguide structures in polydimethylsiloxane thin films by proton beam writing

    NASA Astrophysics Data System (ADS)

    Kada, W.; Miura, K.; Kato, H.; Saruya, R.; Kubota, A.; Satoh, T.; Koka, M.; Ishii, Y.; Kamiya, T.; Nishikawa, H.; Hanaizumi, O.

    2015-04-01

    A focused 750 keV proton microbeam was used to fabricate an embedded Mach-Zehnder (MZ) optical waveguide in a polydimethylsiloxane (PDMS) film for interferometer application. The sample position was precisely controlled by a mechanical stage together with scanning microbeam to form an embedded MZ waveguide structure within an area of 0.3 mm × 40 mm. The MZ waveguides with core size of 8 μm was successfully embedded in PDMS film at a depth of 18 μm by 750 keV proton microbeam with fluences from 10 to 100 nC/mm2. The MZ waveguides were coupled with an IR fiber-laser with a center wavelength of 1550 nm and evaluated by using the transmitted intensity images from an IR vidicon camera. The results indicate that the embedded MZ waveguide structure in PDMS achieved single spot light propagation, which is necessary for building optical switching circuits based on polymer MZ waveguides.

  12. Synthesis of an extra-large molecular sieve using proton sponges as organic structure-directing agents

    PubMed Central

    Martínez-Franco, Raquel; Moliner, Manuel; Yun, Yifeng; Sun, Junliang; Wan, Wei; Zou, Xiaodong; Corma, Avelino

    2013-01-01

    The synthesis of crystalline microporous materials containing large pores is in high demand by industry, especially for the use of these materials as catalysts in chemical processes involving bulky molecules. An extra-large–pore silicoaluminophosphate with 16-ring openings, ITQ-51, has been synthesized by the use of bulky aromatic proton sponges as organic structure-directing agents. Proton sponges show exceptional properties for directing extra-large zeolites because of their unusually high basicity combined with their large size and rigidity. This extra-large–pore material is stable after calcination, being one of the very few examples of hydrothermally stable molecular sieves containing extra-large pores. The structure of ITQ-51 was solved from submicrometer-sized crystals using the rotation electron diffraction method. Finally, several hypothetical zeolites related to ITQ-51 have been proposed. PMID:23431186

  13. Molecular structure and protonation trends in 6-methoxy- and 8-methoxy-2,4,5-tris(dimethylamino)quinolines

    NASA Astrophysics Data System (ADS)

    Dyablo, O. V.; Pozharskii, A. F.; Shmoilova, E. A.; Ozeryanskii, V. A.; Fedik, N. S.; Suponitsky, K. Yu.

    2016-03-01

    Molecular structure and protonation trends of 6-methoxy- 7 and 8-methoxy- 8 derivatives of 2,4,5-tris(dimethylamino)quinoline were studied using X-ray measurements, NMR spectra and theoretical calculations. It has been found that while 8 in the solid state forms protic salts of a quinolinium type, its isomer 7 behaves as a typical proton sponge giving the anilinium cation with a proton chelated by peri-NMe2 groups. In solution, both compounds are simultaneously monoprotonated at two possible centers but again a tendency of 7 to form anilinium cation is much higher if compared to 8. It has been also shown that basicity of 7 is the largest among all known derivatives of 4,5-bis(dimethylamino)quinoline and even slightly exceeds that of 1,8-bis(dimethylamino)naphthalene (parent proton sponge). This was attributed to the "buttressing effect" exhibited by the 6-MeO group. Stable double salts of 7 with picrate and perchlorate anions unprecedented for azines with conjugated aza and NMe2 groups were obtained and thoroughly studied.

  14. Clustering aspects in nuclear structure functions

    SciTech Connect

    Hirai, M.; Saito, K.; Watanabe, T.; Kumano, S.

    2011-03-15

    For understanding an anomalous nuclear effect experimentally observed for the beryllium-9 nucleus at the Thomas Jefferson National Accelerator Facility, clustering aspects are studied in structure functions of deep inelastic lepton-nucleus scattering by using momentum distributions calculated in antisymmetrized (or fermionic) molecular dynamics (AMD) and also in a simple shell model for comparison. According to AMD, the {sup 9}Be nucleus consists of two {alpha}-like clusters with a surrounding neutron. The clustering produces high-momentum components in nuclear wave functions, which affects nuclear modifications of the structure functions. We investigated whether clustering features could appear in the structure function F{sub 2} of {sup 9}Be along with studies for other light nuclei. We found that nuclear modifications of F{sub 2} are similar in both AMD and shell models within our simple convolution description although there are slight differences in {sup 9}Be. It indicates that the anomalous {sup 9}Be result should be explained by a different mechanism from the nuclear binding and Fermi motion. If nuclear-modification slopes d(F{sub 2}{sup A}/F{sub 2}{sup D})/dx are shown by the maximum local densities, the {sup 9}Be anomaly can be explained by the AMD picture, namely by the clustering structure, whereas it certainly cannot be described in the simple shell model. This fact suggests that the large nuclear modification in {sup 9}Be should be explained by large densities in the clusters. For example, internal nucleon structure could be modified in the high-density clusters. The clustering aspect of nuclear structure functions is an unexplored topic which is interesting for future investigations.

  15. Characterization of the microbunch time structure of proton pencil beams at a clinical treatment facility.

    PubMed

    Petzoldt, J; Roemer, K E; Enghardt, W; Fiedler, F; Golnik, C; Hueso-González, F; Helmbrecht, S; Kormoll, T; Rohling, H; Smeets, J; Werner, T; Pausch, G

    2016-03-21

    Proton therapy is an advantageous treatment modality compared to conventional radiotherapy. In contrast to photons, charged particles have a finite range and can thus spare organs at risk. Additionally, the increased ionization density in the so-called Bragg peak close to the particle range can be utilized for maximum dose deposition in the tumour volume. Unfortunately, the accuracy of the therapy can be affected by range uncertainties, which have to be covered by additional safety margins around the treatment volume. A real-time range and dose verification is therefore highly desired and would be key to exploit the major advantages of proton therapy. Prompt gamma rays, produced in nuclear reactions between projectile and target nuclei, can be used to measure the proton's range. The prompt gamma-ray timing (PGT) method aims at obtaining this information by determining the gamma-ray emission time along the proton path using a conventional time-of-flight detector setup. First tests at a clinical accelerator have shown the feasibility to observe range shifts of about 5 mm at clinically relevant doses. However, PGT spectra are smeared out by the bunch time spread. Additionally, accelerator related proton bunch drifts against the radio frequency have been detected, preventing a potential range verification. At OncoRay, first experiments using a proton bunch monitor (PBM) at a clinical pencil beam have been conducted. Elastic proton scattering at a hydrogen-containing foil could be utilized to create a coincident proton-proton signal in two identical PBMs. The selection of coincident events helped to suppress uncorrelated background. The PBM setup was used as time reference for a PGT detector to correct for potential bunch drifts. Furthermore, the corrected PGT data were used to image an inhomogeneous phantom. In a further systematic measurement campaign, the bunch time spread and the proton transmission rate were measured for several beam energies between 69 and 225 Me

  16. Characterization of the microbunch time structure of proton pencil beams at a clinical treatment facility.

    PubMed

    Petzoldt, J; Roemer, K E; Enghardt, W; Fiedler, F; Golnik, C; Hueso-González, F; Helmbrecht, S; Kormoll, T; Rohling, H; Smeets, J; Werner, T; Pausch, G

    2016-03-21

    Proton therapy is an advantageous treatment modality compared to conventional radiotherapy. In contrast to photons, charged particles have a finite range and can thus spare organs at risk. Additionally, the increased ionization density in the so-called Bragg peak close to the particle range can be utilized for maximum dose deposition in the tumour volume. Unfortunately, the accuracy of the therapy can be affected by range uncertainties, which have to be covered by additional safety margins around the treatment volume. A real-time range and dose verification is therefore highly desired and would be key to exploit the major advantages of proton therapy. Prompt gamma rays, produced in nuclear reactions between projectile and target nuclei, can be used to measure the proton's range. The prompt gamma-ray timing (PGT) method aims at obtaining this information by determining the gamma-ray emission time along the proton path using a conventional time-of-flight detector setup. First tests at a clinical accelerator have shown the feasibility to observe range shifts of about 5 mm at clinically relevant doses. However, PGT spectra are smeared out by the bunch time spread. Additionally, accelerator related proton bunch drifts against the radio frequency have been detected, preventing a potential range verification. At OncoRay, first experiments using a proton bunch monitor (PBM) at a clinical pencil beam have been conducted. Elastic proton scattering at a hydrogen-containing foil could be utilized to create a coincident proton-proton signal in two identical PBMs. The selection of coincident events helped to suppress uncorrelated background. The PBM setup was used as time reference for a PGT detector to correct for potential bunch drifts. Furthermore, the corrected PGT data were used to image an inhomogeneous phantom. In a further systematic measurement campaign, the bunch time spread and the proton transmission rate were measured for several beam energies between 69 and 225 Me

  17. Comparison of x ray computed tomography number to proton relative linear stopping power conversion functions using a standard phantom

    SciTech Connect

    Moyers, M. F.

    2014-06-15

    Purpose: Adequate evaluation of the results from multi-institutional trials involving light ion beam treatments requires consideration of the planning margins applied to both targets and organs at risk. A major uncertainty that affects the size of these margins is the conversion of x ray computed tomography numbers (XCTNs) to relative linear stopping powers (RLSPs). Various facilities engaged in multi-institutional clinical trials involving proton beams have been applying significantly different margins in their patient planning. This study was performed to determine the variance in the conversion functions used at proton facilities in the U.S.A. wishing to participate in National Cancer Institute sponsored clinical trials. Methods: A simplified method of determining the conversion function was developed using a standard phantom containing only water and aluminum. The new method was based on the premise that all scanners have their XCTNs for air and water calibrated daily to constant values but that the XCTNs for high density/high atomic number materials are variable with different scanning conditions. The standard phantom was taken to 10 different proton facilities and scanned with the local protocols resulting in 14 derived conversion functions which were compared to the conversion functions used at the local facilities. Results: For tissues within ±300 XCTN of water, all facility functions produced converted RLSP values within ±6% of the values produced by the standard function and within 8% of the values from any other facility's function. For XCTNs corresponding to lung tissue, converted RLSP values differed by as great as ±8% from the standard and up to 16% from the values of other facilities. For XCTNs corresponding to low-density immobilization foam, the maximum to minimum values differed by as much as 40%. Conclusions: The new method greatly simplifies determination of the conversion function, reduces ambiguity, and in the future could promote

  18. Controlling the conductivity and stability of azoles: Proton and hydroxide exchange functionalities

    NASA Astrophysics Data System (ADS)

    Chaloux, Brian Leonard

    For low temperature hydrogen fuel cells to achieve widespread adoption in transport applications, it is necessary to both decrease their cost and improve the range of environmental conditions under which they effectively operate. These problems can be addressed, respectively, by either switching the catalyst from platinum to a less expensive metal, or by reducing the polymer exchange membrane's reliance upon water for proton conduction. This work focuses on understanding the chemistry and physics that limit cation stability in alkaline environments and that enable high proton conductivity in anhydrous polymer exchange membranes. Polystyrenic 1H-azoles (including 1H-tetrazole, 1H-1,2,3-triazole, and 1H-imidazoline) were synthesized to investigate whether pKa and pKb of an amophoteric, proton-conductive group have a systematic effect on anhydrous proton conductivity. It was discovered that the 1H-tetrazole (PS-Tet) exhibited distinct phase separation not seen in its carboxylic acid analog (PSHA) or reported for other 1 H-azole--containing homopolymers in literature. The resulting microstructured polymer, hypothesized to be the result of regions of high and low clustering of azoles, analogous to the multiplet-cluster model of ionomer microstructure, resulted in proton conductivity coupled with simultaneous rubbery behavior of the polymer well above its glass transition (Tg). Phase separation was similarly observed in PS-Tri and PS-ImH2 (the triazole- and imidazoline-containing polymers); soft phases with similar Tgs and hard phases with varying Tgs lend support to this hypothesis of aggregation-driven phase separation. Electrode polarization exhibited in the impedance spectra of PS-Tet and PS-HA was modeled to determine the extent of proton dissociation in undoped 1H-tetrazoles and carboxylic acids. Dry polymers (0% relative humidity) retained ~1% by weight residual water, which was observed to act as the proton acceptor in both cases. Despite doping by residual water

  19. Body Structure and Function. Teacher Edition.

    ERIC Educational Resources Information Center

    Oklahoma State Dept. of Vocational and Technical Education, Stillwater. Curriculum and Instructional Materials Center.

    This curriculum guide contains the materials required to teach a course in body structure and function. The following topics are covered in the course's 17 instructional units: basic concepts of physical and life sciences; microbiology and bacteriology; the integumentary, skeletal, muscular, digestive, circulatory, respiratory, urinary, central…

  20. Structural Functionalism as a Heuristic Device.

    ERIC Educational Resources Information Center

    Chilcott, John H.

    1998-01-01

    Argues that structural functionalism as a method for conducting fieldwork and as a format for the analysis of ethnographic data remains a powerful model, one that is easily understood by professional educators. As a heuristic device, functionalist theory can help in the solution of a problem that is otherwise incapable of theoretical…

  1. Photon structure function at small x

    SciTech Connect

    Gluck, M.; Reya, E.; Schienbein, I.

    2001-07-01

    It is shown that recent small-x measurements of the photon structure function F{sub 2}{sup {gamma}}(x,Q{sup 2}) by the CERN LEP OPAL Collaboration are consistent with parameter-free QCD predictions at all presently accessible values of Q{sup 2}.

  2. Structures and Functions of Selective Attention.

    ERIC Educational Resources Information Center

    Posner, Michael I.

    While neuropsychology relates the neural structures damaged in traumatic brain injury with their cognitive functions in daily life, this report reviews evidence that elementary operations of cognition as defined by cognitive studies are the level at which the brain localizes its computations. Orienting of visual attention is used as a model task.…

  3. [Structure and functions of glutathione transferases].

    PubMed

    Fedets, O M

    2014-01-01

    Data about classification, nomenclature, structure, substrate specificity and role of many glutathione transferase's isoenzymes in cell functions have been summarised. The enzyme has been discovered more than 50 years ago. This family of proteins is updated continuously. It has very different composition and will have demand for system analysis for many years.

  4. DEVELOPMENT OF SUPERCONDUCTING COMBINED FUNCTION MAGNETS FOR THE PROTON TRANSPORT LINE FOR THE J-PARC NEUTRINO EXPERIMENT.

    SciTech Connect

    NAKAMOTO, T.; AJIMA, Y.; FUJII, Y.; HIGASHI, N.; ICHIKAWA, A.; KIMURA, N.; KOBAYASHI, T.; MAKIDA, Y.; OGITSU, T.; OHHATA, H.; OKAMURA, T.; SASAKI, K.; ET AL.

    2005-05-16

    Superconducting combined function magnets will be utilized for the 50 GeV, 750 kW proton beam line for the J-PARC neutrino experiment. The magnet is designed to provide a dipole field of 2.6 T combined with a quadrupole field of 19 T/m in a coil aperture of 173.4 mm at a nominal current of 7345 A. Two full-scale prototype magnets to verify the magnet performance were successfully developed. The first prototype experienced no training quench during the excitation test and good field quality was confirmed.

  5. Structure and function of complex brain networks.

    PubMed

    Sporns, Olaf

    2013-09-01

    An increasing number of theoretical and empirical studies approach the function of the human brain from a network perspective. The analysis of brain networks is made feasible by the development of new imaging acquisition methods as well as new tools from graph theory and dynamical systems. This review surveys some of these methodological advances and summarizes recent findings on the architecture of structural and functional brain networks. Studies of the structural connectome reveal several modules or network communities that are interlinked by hub regions mediating communication processes between modules. Recent network analyses have shown that network hubs form a densely linked collective called a "rich club," centrally positioned for attracting and dispersing signal traffic. In parallel, recordings of resting and task-evoked neural activity have revealed distinct resting-state networks that contribute to functions in distinct cognitive domains. Network methods are increasingly applied in a clinical context, and their promise for elucidating neural substrates of brain and mental disorders is discussed.

  6. [Structural-functional organization of Golgi apparatus].

    PubMed

    Snigirevskaia, E S; Sokolova, Iu Ia; Komissarchik, Ia Iu

    2006-01-01

    This review is dedicated to the structure and function of Golgi apparatus (GA). It summarizes contemporary data published in numerous experimental papers and in several reviews. Possible ways of intra-Golgi transport of proteins, existent models of structural and functional organization of Golgi organelle, as well as the issues of its biogenesis, posttranslational modification and sorting of proteins and lipids, and mechanisms of their traffic-king are discussed. Special attention is paid to the role of coatomer proteins (COPI, COPII and clathrin), fusion proteins (SNAREs), and small GTPases (ARF, SARI) in the secretory pathway. In addition, the phenomena of ultrastructural alterations of GA due to various functional conditions and physiological stimuli are specifically accented. We included in this review our original data on a probable involvement of GA in water transport, and on the organization of atypical GA in microsporidia--intracellular parasitic protists.

  7. [Structural-functional organization of Golgi apparatus].

    PubMed

    Snigirevskaia, E S; Sokolova, Iu Ia; Komissarchik, Ia Iu

    2006-01-01

    This review is dedicated to the structure and function of Golgi apparatus (GA). It summarizes contemporary data published in numerous experimental papers and in several reviews. Possible ways of intra-Golgi transport of proteins, existent models of structural and functional organization of Golgi organelle, as well as the issues of its biogenesis, posttranslational modification and sorting of proteins and lipids, and mechanisms of their trafficking are discussed. Special attention is paid to the role of coatomer proteins (COPI, COPII and clathrin), fusion proteins (SNAREs), and small GTPases (ARF, SARI) in the secretory pathway. In addition, the phenomena of ultrastructural alterations of GA due to various functional conditions and physiological stimuli are specifically accented. We included in this review our original data on a probable involvement of GA in water transport, and on the organization of atypical GA in microsporidia--intracellular parasitic protists.

  8. Crystal structure of acetanilide at 15 and 295 K by neutron diffraction. Lack of evidence for proton transfer along the N-H...O hydrogen bond

    SciTech Connect

    Johnson, S.W.; Eckert, J.; Barthes, M.; McMullan, R.K.; Muller, M.

    1995-11-02

    The crystal structure of acetanilide C{sub 8}H{sub 9}NO, M{sub r} = 135.17, orthorhombic, space group Pbca, Z=8, has been determined from neutron diffraction data at 15 and 295 K. The crystal data obtained are presented. This new investigation of the structure of acetanilide has been undertaken in order to assess a recent suggestion that confirmational substates in the amide proton position may be responsible for the vibrational anomalies. We found no evidence for multiple conformations or transfer along the N-H...O hydrogen bond of the amide proton at either temperature. However the intramolecular O...H6 distance from O to the nearest phenyl ring proton is unusually short and the amide proton has relatively close contacts with one of the phenyl and one of the methyl protons, which may well affect the vibrational parameters of the respective molecular groups. 44 refs., 6 figs., 5 tabs.

  9. Structure and function of echinoderm telomerase RNA.

    PubMed

    Podlevsky, Joshua D; Li, Yang; Chen, Julian J-L

    2016-02-01

    Telomerase is a ribonucleoprotein (RNP) enzyme that requires an integral telomerase RNA (TR) subunit, in addition to the catalytic telomerase reverse transcriptase (TERT), for enzymatic function. The secondary structures of TRs from the three major groups of species, ciliates, fungi, and vertebrates, have been studied extensively and demonstrate dramatic diversity. Herein, we report the first comprehensive secondary structure of TR from echinoderms-marine invertebrates closely related to vertebrates-determined by phylogenetic comparative analysis of 16 TR sequences from three separate echinoderm classes. Similar to vertebrate TR, echinoderm TR contains the highly conserved template/pseudoknot and H/ACA domains. However, echinoderm TR lacks the ancestral CR4/5 structural domain found throughout vertebrate and fungal TRs. Instead, echinoderm TR contains a distinct simple helical region, termed eCR4/5, that is functionally equivalent to the CR4/5 domain. The urchin and brittle star eCR4/5 domains bind specifically to their respective TERT proteins and stimulate telomerase activity. Distinct from vertebrate telomerase, the echinoderm TR template/pseudoknot domain with the TERT protein is sufficient to reconstitute significant telomerase activity. This gain-of-function of the echinoderm template/pseudoknot domain for conferring telomerase activity presumably facilitated the rapid structural evolution of the eCR4/5 domain throughout the echinoderm lineage. Additionally, echinoderm TR utilizes the template-adjacent P1.1 helix as a physical template boundary element to prevent nontelomeric DNA synthesis, a mechanism used by ciliate and fungal TRs. Thus, the chimeric and eccentric structural features of echinoderm TR provide unparalleled insights into the rapid evolution of telomerase RNP structure and function.

  10. Structure and function of echinoderm telomerase RNA.

    PubMed

    Podlevsky, Joshua D; Li, Yang; Chen, Julian J-L

    2016-02-01

    Telomerase is a ribonucleoprotein (RNP) enzyme that requires an integral telomerase RNA (TR) subunit, in addition to the catalytic telomerase reverse transcriptase (TERT), for enzymatic function. The secondary structures of TRs from the three major groups of species, ciliates, fungi, and vertebrates, have been studied extensively and demonstrate dramatic diversity. Herein, we report the first comprehensive secondary structure of TR from echinoderms-marine invertebrates closely related to vertebrates-determined by phylogenetic comparative analysis of 16 TR sequences from three separate echinoderm classes. Similar to vertebrate TR, echinoderm TR contains the highly conserved template/pseudoknot and H/ACA domains. However, echinoderm TR lacks the ancestral CR4/5 structural domain found throughout vertebrate and fungal TRs. Instead, echinoderm TR contains a distinct simple helical region, termed eCR4/5, that is functionally equivalent to the CR4/5 domain. The urchin and brittle star eCR4/5 domains bind specifically to their respective TERT proteins and stimulate telomerase activity. Distinct from vertebrate telomerase, the echinoderm TR template/pseudoknot domain with the TERT protein is sufficient to reconstitute significant telomerase activity. This gain-of-function of the echinoderm template/pseudoknot domain for conferring telomerase activity presumably facilitated the rapid structural evolution of the eCR4/5 domain throughout the echinoderm lineage. Additionally, echinoderm TR utilizes the template-adjacent P1.1 helix as a physical template boundary element to prevent nontelomeric DNA synthesis, a mechanism used by ciliate and fungal TRs. Thus, the chimeric and eccentric structural features of echinoderm TR provide unparalleled insights into the rapid evolution of telomerase RNP structure and function. PMID:26598712

  11. Mechanism of adenylate kinase. Demonstration of a functional relationship between aspartate 93 and Mg2+ by site-directed mutagenesis and proton, phosphorus-31, and magnesium-25 NMR.

    PubMed

    Yan, H G; Tsai, M D

    1991-06-01

    Earlier magnetic resonance studies suggested no direct interaction between Mg2+ ions and adenylate kinase (AK) in the AK.MgATP (adenosine 5'-triphosphate) complex. However, recent NMR studies concluded that the carboxylate of aspartate 119 accepts a hydrogen bond from a water ligand of the bound Mg2+ ion in the muscle AK.MgATP complex [Fry, D.C., Kuby, S.A., & Mildvan, A.S. (1985) Biochemistry 24, 4680-4694]. On the other hand, in the 2.6-A crystal structure of the yeast AK.MgAP5A [P1,P5-bis(5'-adenosyl)pentaphosphate] complex, the Mg2+ ion is in proximity to aspartate 93 [Egner, U., Tomasselli, A.G., & Schulz, G.E. (1987) J. Mol. Biol. 195, 649-658]. Substitution of Asp-93 with alanine resulted in no change in dissociation constants, 4-fold increases in Km, and a 650-fold decrease in kcat. Notable changes have been observed in the chemical shifts of the aromatic protons of histidine 36 and a few other aromatic residues. However, the results of detailed analyses of the free enzymes and the AK.MgAP5A complexes by one- and two-dimensional NMR suggested that the changes are due to localized perturbations. Thus it is concluded that Asp-93 stabilizes the transition state by ca. 3.9 kcal/mol. The next question is how. Since proton NMR results indicated that binding of Mg2+ to the AK.AP5A complex induces some changes in the proton NMR signals of WT but not those of D93A, the functional role of Asp-93 should be in binding to Mg2+.(ABSTRACT TRUNCATED AT 250 WORDS)

  12. Sequence, structure, function, immunity: structural genomics of costimulation

    PubMed Central

    Chattopadhyay, Kausik; Lazar-Molnar, Eszter; Yan, Qingrong; Rubinstein, Rotem; Zhan, Chenyang; Vigdorovich, Vladimir; Ramagopal, Udupi A.; Bonanno, Jeffrey; Nathenson, Stanley G.; Almo, Steven C.

    2010-01-01

    Summary Costimulatory receptors and ligands trigger the signaling pathways that are responsible for modulating the strength, course and duration of an immune response. High-resolution structures have provided invaluable mechanistic insights by defining the chemical and physical features underlying costimulatory receptor/ligand specificity, affinity, oligomeric state, and valency. Furthermore, these structures revealed general architectural features that are important for the integration of these interactions and their associated signaling pathways into overall cellular physiology. Recent technological advances in structural biology promise unprecedented opportunities for furthering our understanding of the structural features and mechanisms that govern costimulation. In this review we highlight unique insights that have been revealed by structures of costimulatory molecules from the immunoglobulin and tumor necrosis factor superfamilies, and describe a vision for future structural and mechanistic analysis of costimulation. This vision includes simple strategies for the selection of candidate molecules for structure determination and highlights the critical role of structure in the design of mutant costimulatory molecules for the generation of in vivo structure-function correlations in a mammalian model system. This integrated ‘atoms-to-animals’ paradigm provides a comprehensive approach for defining atomic and molecular mechanisms. PMID:19426233

  13. Characterization of the microbunch time structure of proton pencil beams at a clinical treatment facility

    NASA Astrophysics Data System (ADS)

    Petzoldt, J.; Roemer, K. E.; Enghardt, W.; Fiedler, F.; Golnik, C.; Hueso-González, F.; Helmbrecht, S.; Kormoll, T.; Rohling, H.; Smeets, J.; Werner, T.; Pausch, G.

    2016-03-01

    Proton therapy is an advantageous treatment modality compared to conventional radiotherapy. In contrast to photons, charged particles have a finite range and can thus spare organs at risk. Additionally, the increased ionization density in the so-called Bragg peak close to the particle range can be utilized for maximum dose deposition in the tumour volume. Unfortunately, the accuracy of the therapy can be affected by range uncertainties, which have to be covered by additional safety margins around the treatment volume. A real-time range and dose verification is therefore highly desired and would be key to exploit the major advantages of proton therapy. Prompt gamma rays, produced in nuclear reactions between projectile and target nuclei, can be used to measure the proton’s range. The prompt gamma-ray timing (PGT) method aims at obtaining this information by determining the gamma-ray emission time along the proton path using a conventional time-of-flight detector setup. First tests at a clinical accelerator have shown the feasibility to observe range shifts of about 5 mm at clinically relevant doses. However, PGT spectra are smeared out by the bunch time spread. Additionally, accelerator related proton bunch drifts against the radio frequency have been detected, preventing a potential range verification. At OncoRay, first experiments using a proton bunch monitor (PBM) at a clinical pencil beam have been conducted. Elastic proton scattering at a hydrogen-containing foil could be utilized to create a coincident proton-proton signal in two identical PBMs. The selection of coincident events helped to suppress uncorrelated background. The PBM setup was used as time reference for a PGT detector to correct for potential bunch drifts. Furthermore, the corrected PGT data were used to image an inhomogeneous phantom. In a further systematic measurement campaign, the bunch time spread and the proton transmission rate were measured for several beam energies between 69 and 225

  14. Structure-Function Analysis of Yeast Tubulin

    PubMed Central

    Luchniak, Anna; Fukuda, Yusuke; Gupta, Mohan L.

    2014-01-01

    Microtubules play essential roles in a wide variety of cellular processes including cell division, motility, and vesicular transport. Microtubule function depends on the polymerization dynamics of tubulin, and specific interactions between tubulin and diverse microtubule-associated proteins. To date, investigation of the structural and functional properties of tubulin and tubulin mutants has been limited by the inability to obtain functional protein from overexpression systems, and by the heterogeneous mixture of tubulin isotypes typically isolated from higher eukaryotes. The budding yeast, Saccharomyces cerevisiae, has emerged as a leading system for tubulin structure-function analysis. Yeast cells encode a single beta-tubulin gene and can be engineered to express just one, of two, alpha isotypes. Moreover, yeast allows site-directed modification of tubulin genes at the endogenous loci expressed under the native promoter and regulatory elements. These advantageous features provide a homogeneous and controlled environment for analysis of the functional consequences of specific mutations. Here we present techniques to generate site-specific tubulin mutations in diploid and haploid cells, assess the ability of the mutated protein to support cell viability, measure overall microtubule stability, and define changes in the specific parameters of microtubule dynamic instability. We also outline strategies to determine whether mutations disrupt interactions with microtubule-associated proteins. Microtubule-based functions in yeast are well defined, which allows the observed changes in microtubule properties to be related to the role of microtubules in specific cellular processes. PMID:23973083

  15. A Functional EXXEK Motif is Essential for Proton Coupling and Active Glucosinolate Transport by NPF2.11.

    PubMed

    Jørgensen, Morten Egevang; Olsen, Carl Erik; Geiger, Dietmar; Mirza, Osman; Halkier, Barbara Ann; Nour-Eldin, Hussam Hassan

    2015-12-01

    The proton-dependent oligopeptide transporter (POT/PTR) family shares a highly conserved E1X1X2E2RFXYY (E1X1X2E2R) motif across all kingdoms of life. This motif is suggested to have a role in proton coupling and active transport in bacterial homologs. For the plant POT/PTR family, also known as the NRT1/PTR family (NPF), little is known about the role of the E1X1X2E2R motif. Moreover, nothing is known about the role of the X1 and X2 residues within the E1X1X2E2R motif. We used NPF2.11-a proton-coupled glucosinolate (GLS) symporter from Arabidopsis thaliana-to investigate the role of the E1X1X2E2K motif variant in a plant NPF transporter. Using liquid chromatography-mass spectrometry (LC-MS)-based uptake assays and two-electrode voltage clamp (TEVC) electrophysiology, we demonstrate an essential role for the E1X1X2E2K motif for accumulation of substrate by NPF2.11. Our data suggest that the highly conserved E1, E2 and K residues are involved in translocation of protons, as has been proposed for the E1X1X2E2R motif in bacteria. Furthermore, we show that the two residues X1 and X2 in the E1X1X2E2[K/R] motif are conserved as uncharged amino acids in POT/PTRs from bacteria to mammals and that introducing a positive or negative charge in either position hampers the ability to overaccumulate substrate relative to the assay medium. We hypothesize that introducing a charge at X1 and X2 interferes with the function of the conserved glutamate and lysine residues of the E1X1X2E2K motif and affects the mechanism behind proton coupling. PMID:26443378

  16. A Functional EXXEK Motif is Essential for Proton Coupling and Active Glucosinolate Transport by NPF2.11.

    PubMed

    Jørgensen, Morten Egevang; Olsen, Carl Erik; Geiger, Dietmar; Mirza, Osman; Halkier, Barbara Ann; Nour-Eldin, Hussam Hassan

    2015-12-01

    The proton-dependent oligopeptide transporter (POT/PTR) family shares a highly conserved E1X1X2E2RFXYY (E1X1X2E2R) motif across all kingdoms of life. This motif is suggested to have a role in proton coupling and active transport in bacterial homologs. For the plant POT/PTR family, also known as the NRT1/PTR family (NPF), little is known about the role of the E1X1X2E2R motif. Moreover, nothing is known about the role of the X1 and X2 residues within the E1X1X2E2R motif. We used NPF2.11-a proton-coupled glucosinolate (GLS) symporter from Arabidopsis thaliana-to investigate the role of the E1X1X2E2K motif variant in a plant NPF transporter. Using liquid chromatography-mass spectrometry (LC-MS)-based uptake assays and two-electrode voltage clamp (TEVC) electrophysiology, we demonstrate an essential role for the E1X1X2E2K motif for accumulation of substrate by NPF2.11. Our data suggest that the highly conserved E1, E2 and K residues are involved in translocation of protons, as has been proposed for the E1X1X2E2R motif in bacteria. Furthermore, we show that the two residues X1 and X2 in the E1X1X2E2[K/R] motif are conserved as uncharged amino acids in POT/PTRs from bacteria to mammals and that introducing a positive or negative charge in either position hampers the ability to overaccumulate substrate relative to the assay medium. We hypothesize that introducing a charge at X1 and X2 interferes with the function of the conserved glutamate and lysine residues of the E1X1X2E2K motif and affects the mechanism behind proton coupling.

  17. Simplified Solar Modulation Model of Inner Trapped Belt Proton Flux As a Function of Atmospheric Density

    NASA Technical Reports Server (NTRS)

    Wilson, Thomas L.; Lodhi, M. A. K.; Diaz, Abel B.

    2005-01-01

    No simple algorithm seems to exist for calculating proton fluxes and lifetimes in the Earth's inner, trapped radiation belt throughout the solar cycle. Most models of the inner trapped belt in use depend upon AP8 which only describes the radiation environment at solar maximum and solar minimum in Cycle 20. One exception is NOAAPRO which incorporates flight data from the TIROS/NOAA polar orbiting spacecraft. The present study discloses yet another, simple formulation for approximating proton fluxes at any time in a given solar cycle, in particular between solar maximum and solar minimum. It is derived from AP8 using a regression algorithm technique from nuclear physics. From flux and its time integral fluence, one can then approximate dose rate and its time integral dose. It has already been published in this journal that the absorbed dose rate, D, in the trapped belts exhibits a power law relationship, D = A(rho)(sup -n), where A is a constant, rho is the atmospheric density, and the index n is weakly dependent upon shielding. However, that method does not work for flux and fluence. Instead, we extend this idea by showing that the power law approximation for flux J is actually bivariant in energy E as well as density rho. The resulting relation is J(E,rho)approx.(sum of)A(E(sup n))rho(sup -n), with A itself a power law in E. This provides another method for calculating approximate proton flux and lifetime at any time in the solar cycle. These in turn can be used to predict the associated dose and dose rate.

  18. Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers.

    PubMed

    Boschmans, Jasper; Jacobs, Sam; Williams, Jonathan P; Palmer, Martin; Richardson, Keith; Giles, Kevin; Lapthorn, Cris; Herrebout, Wouter A; Lemière, Filip; Sobott, Frank

    2016-06-20

    Electrospray ion mobility-mass spectrometry (IM-MS) data show that for some small molecules, two (or even more) ions with identical sum formula and mass, but distinct drift times are observed. In spite of showing their own unique and characteristic fragmentation spectra in MS/MS, no configurational or constitutional isomers are found to be present in solution. Instead the observation and separation of such ions appears to be inherent to their gas-phase behaviour during ion mobility experiments. The origin of multiple drift times is thought to be the result of protonation site isomers ('protomers'). Although some important properties of protomers have been highlighted by other studies, correlating the experimental collision cross-sections (CCSs) with calculated values has proven to be a major difficulty. As a model, this study uses the pharmaceutical compound melphalan and a number of related molecules with alternative (gas-phase) protonation sites. Our study combines density functional theory (DFT) calculations with modified MobCal methods (e.g. nitrogen-based Trajectory Method algorithm) for the calculation of theoretical CCS values. Calculated structures can be linked to experimentally observed signals, and a strong correlation is found between the difference of the calculated dipole moments of the protomer pairs and their experimental CCS separation.

  19. Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers.

    PubMed

    Boschmans, Jasper; Jacobs, Sam; Williams, Jonathan P; Palmer, Martin; Richardson, Keith; Giles, Kevin; Lapthorn, Cris; Herrebout, Wouter A; Lemière, Filip; Sobott, Frank

    2016-06-20

    Electrospray ion mobility-mass spectrometry (IM-MS) data show that for some small molecules, two (or even more) ions with identical sum formula and mass, but distinct drift times are observed. In spite of showing their own unique and characteristic fragmentation spectra in MS/MS, no configurational or constitutional isomers are found to be present in solution. Instead the observation and separation of such ions appears to be inherent to their gas-phase behaviour during ion mobility experiments. The origin of multiple drift times is thought to be the result of protonation site isomers ('protomers'). Although some important properties of protomers have been highlighted by other studies, correlating the experimental collision cross-sections (CCSs) with calculated values has proven to be a major difficulty. As a model, this study uses the pharmaceutical compound melphalan and a number of related molecules with alternative (gas-phase) protonation sites. Our study combines density functional theory (DFT) calculations with modified MobCal methods (e.g. nitrogen-based Trajectory Method algorithm) for the calculation of theoretical CCS values. Calculated structures can be linked to experimentally observed signals, and a strong correlation is found between the difference of the calculated dipole moments of the protomer pairs and their experimental CCS separation. PMID:27264846

  20. Proton Therapy - Accelerating Protons to Save Lives

    SciTech Connect

    Keppel, Cynthia

    2011-10-25

    In 1946, physicist Robert Wilson first suggested that protons could be used as a form of radiation therapy in the treatment of cancer because of the sharp drop-off that occurs on the distal edge of the radiation dose. Research soon confirmed that high-energy protons were particularly suitable for treating tumors near critical structures, such as the heart and spinal column. The precision with which protons can be delivered means that more radiation can be deposited into the tumor while the surrounding healthy tissue receives substantially less or, in some cases, no radiation. Since these times, particle accelerators have continuously been used in cancer therapy and today new facilities specifically designed for proton therapy are being built in many countries. Proton therapy has been hailed as a revolutionary cancer treatment, with higher cure rates and fewer side effects than traditional X-ray photon radiation therapy. Proton therapy is the modality of choice for treating certain small tumors of the eye, head or neck. Because it exposes less of the tissue surrounding a tumor to the dosage, proton therapy lowers the risk of secondary cancers later in life - especially important for young children. To date, over 80,000 patients worldwide have been treated with protons. Currently, there are nine proton radiation therapy facilities operating in the United States, one at the Hampton University Proton Therapy Institute. An overview of the treatment technology and this new center will be presented.

  1. Nuclear excitation functions from 40 to 200 MeV proton irradiation of terbium

    NASA Astrophysics Data System (ADS)

    Engle, Jonathan W.; Mashnik, Stepan G.; Parker, Lauren A.; Jackman, Kevin R.; Bitteker, Leo J.; Ullmann, John L.; Gulley, Mark S.; Pillai, Chandra; John, Kevin D.; Birnbaum, Eva R.; Nortier, Francois M.

    2016-01-01

    Nuclear formation cross sections are reported for 26 radionuclides, measured with 40-200 MeV proton irradiations of terbium foils. These data provide the basis for the production of medically relevant radionuclides (e.g., 152Tb, 155Tb, 155Eu, and 156Eu) and 153Gd, a potential source used in ongoing efforts to characterize stellar nucleosynthesis routes. Computational predictions from the ALICE2011, CEM03.03, Bertini, and INCL + ABLA codes are compared with newly measured data to contribute to the ongoing process of code development, and yields are calculated for selected radionuclides using measured data.

  2. Synthesis, crystal structure, and protonation behaviour in solution of the recently-discovered drug metabolite, N1,N10-diacetyltriethylenetetramine

    NASA Astrophysics Data System (ADS)

    Wichmann, Kathrin A.; Söhnel, Tilo; Cooper, Garth J. S.

    2012-03-01

    N1,N10-diacetyltriethylenetetramine (DAT) is a recently-discovered major in vivo metabolite of triethylenetetramine (TETA), a highly-selective CuII chelator currently under clinical development as a novel first-in-class therapeutic for the cardiovascular, renal and retinal complications of diabetes mellitus. Characterisation of DAT is an integral aspect of the pharmacological work-up required to support this clinical development programme and, to our knowledge, no previous synthesis for it has been published. Here we report the synthesis of DAT dihydrochloride (DAT·2 HCl); its crystal structure as determined by X-ray single-crystal (XRD) and powder diffraction (XRPD); and protonation constants and species distribution in aqueous solution, which represents the different protonation states of DAT at different pH values. The crystal structure of DAT·2 HCl reveals 3D-assemblies of alternating 2D-layers comprising di-protonated DAT strands and anionic species, which form an extensive hydrogen-bond network between amine groups, acetyl groups, and chloride anions. Potentiometric titrations show that HDAT+ is the physiologically relevant state of DAT in solution. These findings contribute to the understanding of TETA's pharmacology and to its development for the experimental therapeutics of the diabetic complications.

  3. Cross-shell excitation in two-proton knockout: Structure of {sup 52}Ca

    SciTech Connect

    Gade, A.; Brown, B. A.; Campbell, C. M.; Cook, J. M.; Dinca, D.-C.; Glasmacher, T.; Hansen, P. G.; Terry, J. R.; Janssens, R. V. F.; Carpenter, M. P.; Zhu, S.; Bazin, D.; Mueller, W. F.; Broda, R.; Fornal, B.; Deacon, A. N.; Freeman, S. J.; Kay, B. P.; Mantica, P. F.; Tostevin, J. A.

    2006-08-15

    The two-proton knockout reaction {sup 9}Be({sup 54}Ti,{sup 52}Ca+{gamma}) has been studied at 72 MeV/nucleon. Besides the strong feeding of the {sup 52}Ca ground state, the only other sizeable cross section proceeds to a 3{sup -} level at 3.9 MeV. There is no measurable direct yield to the first excited 2{sup +} state at 2.6 MeV. The results illustrate the potential of such direct reactions for exploring cross-shell proton excitations in neutron-rich nuclei and confirms the doubly-magic nature of {sup 52}Ca.

  4. Surface Structure of Protonated R-Sapphire (1$\\bar{1}$02) Studied by Sum-Frequency Vibrational Spectroscopy

    SciTech Connect

    Sung, Jaeho; Zhang, Luning; Tian, Chuanshan; Waychunas, Glenn A.; Shen, Y. Ron

    2011-03-23

    Sum frequency vibrational spectroscopy was used to study the protonated R-plane (1$\\bar{1}$02 ) sapphire surface. The OH stretch vibrational spectra show that the surface is terminated with three hydroxyl moieties, two from AlOH2 and one from Al2OH functional groups. The observed polarization dependence allows determination of the orientations of the three OH species. The results suggest that the protonated sapphire (1$\\bar{1}$02 ) surface differs from an ideal stoichimetric termination in a manner consistent with previous X-ray surface diffraction (crystal truncation rod) studies. However, in order to best explain the observed hydrogenbonding arrangement, surface oxygen spacing determined from the X-ray diffraction study requires modification.

  5. Ab initio study of the molecular structure and vibrational spectrum of nitric acid and its protonated forms

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Rice, Julia E.

    1992-01-01

    The equilibrium structures, harmonic vibrational frequencies, IR intensities, and relative energetics of HNO3 and its protonated form H2NO3+ were investigated using double-zeta plus polarization and triple-zeta plus polarization basis sets in conjunction with high-level ab initio methods. The latter include second-order Moller-Plesset perturbation theory, the single and double excitation coupled cluster (CCSD) methods, a perturbational estimate of the effects of connected triple excitations (CCSD(T)), and the self-consistent field. To determine accurate energy differences CCSD(T) energies were computed using large atomic natural orbital basis sets. Four different isomers of H2NO3+ were considered. The lowest energy form of protonated nitric acid was found to correspond to a complex between H2O and NO2+, which is consistent with earlier theoretical and experimental studies.

  6. Perinatal choline influences brain structure and function.

    PubMed

    Zeisel, Steven H; Niculescu, Mihai D

    2006-04-01

    Choline is derived not only from the diet, but also from de novo synthesis. It is important for methyl-group metabolism, the formation of membranes, kidney function, and neurotransmission. When deprived of dietary choline, most adult men and postmenopausal women develop signs of organ dysfunction (fatty liver or muscle damage) and have a decreased capacity to convert homocysteine to methionine. Choline is critical during fetal development, when it influences stem cell proliferation and apoptosis, thereby altering brain structure and function (memory is permanently enhanced in rodents exposed to choline during the latter part of gestation). PMID:16673755

  7. A statistical mechanical theory of proton transport kinetics in hydrogen-bonded networks based on population correlation functions with applications to acids and bases.

    PubMed

    Tuckerman, Mark E; Chandra, Amalendu; Marx, Dominik

    2010-09-28

    Extraction of relaxation times, lifetimes, and rates associated with the transport of topological charge defects in hydrogen-bonded networks from molecular dynamics simulations is a challenge because proton transfer reactions continually change the identity of the defect core. In this paper, we present a statistical mechanical theory that allows these quantities to be computed in an unbiased manner. The theory employs a set of suitably defined indicator or population functions for locating a defect structure and their associated correlation functions. These functions are then used to develop a chemical master equation framework from which the rates and lifetimes can be determined. Furthermore, we develop an integral equation formalism for connecting various types of population correlation functions and derive an iterative solution to the equation, which is given a graphical interpretation. The chemical master equation framework is applied to the problems of both hydronium and hydroxide transport in bulk water. For each case it is shown that the theory establishes direct links between the defect's dominant solvation structures, the kinetics of charge transfer, and the mechanism of structural diffusion. A detailed analysis is presented for aqueous hydroxide, examining both reorientational time scales and relaxation of the rotational anisotropy, which is correlated with recent experimental results for these quantities. Finally, for OH(-)(aq) it is demonstrated that the "dynamical hypercoordination mechanism" is consistent with available experimental data while other mechanistic proposals are shown to fail. As a means of going beyond the linear rate theory valid from short up to intermediate time scales, a fractional kinetic model is introduced in the Appendix in order to describe the nonexponential long-time behavior of time-correlation functions. Within the mathematical framework of fractional calculus the power law decay ∼t(-σ), where σ is a parameter of the

  8. Expression and functioning of retinal-based proton pumps in a saltern crystallizer brine.

    PubMed

    Oren, Aharon; Abu-Ghosh, Said; Argov, Tal; Kara-Ivanov, Eliahu; Shitrit, Dror; Volpert, Adi; Horwitz, Rael

    2016-01-01

    We examined the presence of bacteriorhodopsin and other retinal protein pigments in the microbial community of the saltern crystallizer ponds in Eilat, Israel, and assessed the effect of the retinal-based proton pumps on the metabolic activity. The biota of the hypersaline (~309 g salts l(-1)) brine consisted of ~2200 β-carotene-rich Dunaliella cells and ~3.5 × 10(7) prokaryotes ml(-1), most of which were flat, square or rectangular Haloquadratum-like archaea. No indications were obtained for massive presence of Salinibacter. We estimated a concentration of bacteriorhodopsin and bacteriorhodopsin-like pigments of 3.6 nmol l(-1). When illuminated, the community respiration activity of the brine samples in which oxygenic photosynthesis was inhibited by 3-(3-4-dichlorophenyl)-1,1-dimethylurea, decreased by 40-43 %. This effect was interpreted to be the result of competition between two energy yielding systems: the bacteriorhodopsin proton pump and the respiratory chain. The results presented have important implications for the interpretation of many published data on photosynthetic and respiratory activities in hypersaline environments. PMID:26507954

  9. Characterizing the proton loading site in cytochrome c oxidase.

    PubMed

    Lu, Jianxun; Gunner, M R

    2014-08-26

    Cytochrome c oxidase (CcO) uses the energy released by reduction of O2 to H2O to drive eight charges from the high pH to low pH side of the membrane, increasing the electrochemical gradient. Four electrons and protons are used for chemistry, while four more protons are pumped. Proton pumping requires that residues on a pathway change proton affinity through the reaction cycle to load and then release protons. The protonation states of all residues in CcO are determined in MultiConformational Continuum Electrostatics simulations with the protonation and redox states of heme a, a3, Cu(B), Y288, and E286 used to define the catalytic cycle. One proton is found to be loaded and released from residues identified as the proton loading site (PLS) on the P-side of the protein in each of the four CcO redox states. Thus, the same proton pumping mechanism can be used each time CcO is reduced. Calculations with structures of Rhodobacter sphaeroides, Paracoccus denitrificans, and bovine CcO derived by crystallography and molecular dynamics show the PLS functions similarly in different CcO species. The PLS is a cluster rather than a single residue, as different structures show 1-4 residues load and release protons. However, the proton affinity of the heme a3 propionic acids primarily determines the number of protons loaded into the PLS; if their proton affinity is too low, less than one proton is loaded.

  10. Proteins with Novel Structure, Function and Dynamics

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew

    2014-01-01

    Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

  11. Structure, function, and regulation of adrenergic receptors.

    PubMed Central

    Strosberg, A. D.

    1993-01-01

    Adrenergic receptors for adrenaline and noradrenaline belong to the large multigenic family of receptors coupled to GTP-binding proteins. Three pharmacologic types have been identified: alpha 1-, alpha 2-, and beta-adrenergic receptors. Each of these has three subtypes, characterized by both structural and functional differences. The alpha 2 and beta receptors are coupled negatively and positively, respectively, to adenylyl cyclase via Gi or Gs regulatory proteins, and the alpha 1 receptors modulate phospholipase C via the Go protein. Subtype expression is regulated at the level of the gene, the mRNA, and the protein through various transcriptional and postsynthetic mechanisms. Adrenergic receptors constitute, after rhodopsin, one of the best studied models for the other receptors coupled to G proteins that are likely to display similar structural and functional properties. PMID:8401205

  12. Phosphatidylinositol 4-kinases: Function, structure, and inhibition

    SciTech Connect

    Boura, Evzen Nencka, Radim

    2015-10-01

    The phosphatidylinositol 4-kinases (PI4Ks) synthesize phosphatidylinositol 4-phosphate (PI4P), a key member of the phosphoinositide family. PI4P defines the membranes of Golgi and trans-Golgi network (TGN) and regulates trafficking to and from the Golgi. Humans have two type II PI4Ks (α and β) and two type III enzymes (α and β). Recently, the crystal structures were solved for both type II and type III kinase revealing atomic details of their function. Importantly, the type III PI4Ks are hijacked by +RNA viruses to create so-called membranous web, an extensively phosphorylated and modified membrane system dedicated to their replication. Therefore, selective and potent inhibitors of PI4Ks have been developed as potential antiviral agents. Here we focus on the structure and function of PI4Ks and their potential in human medicine.

  13. Truncated Moment Analysis of Nucleon Structure Functions

    SciTech Connect

    A. Psaker; W. Melnitchouk; M. E. Christy; C. E. Keppel

    2007-11-16

    We employ a novel new approach using "truncated" moments, or integrals of structure functions over restricted regions of x, to study local quark-hadron duality, and the degree to which individual resonance regions are dominated by leading twists. Because truncated moments obey the same Q^2 evolution equations as the leading twist parton distributions, this approach makes possible for the first time a description of resonance region data and the phenomenon of quark-hadron duality directly from QCD.

  14. Residues in the Polar Loop of Subunit c in Escherichia coli ATP Synthase Function in Gating Proton Transport to the Cytoplasm*

    PubMed Central

    Steed, P. Ryan; Fillingame, Robert H.

    2014-01-01

    Rotary catalysis in F1F0 ATP synthase is powered by proton translocation through the membrane-embedded F0 sector. Proton binding and release occur in the middle of the membrane at Asp-61 on the second transmembrane helix (TMH) of subunit c, which folds in a hairpin-like structure with two TMHs. Previously, the aqueous accessibility of Cys substitutions in the transmembrane regions of subunit c was probed by testing the inhibitory effects of Ag+ or Cd2+ on function, which revealed extensive aqueous access in the region around Asp-61 and on the half of TMH2 extending to the cytoplasm. In the current study, we surveyed the Ag+ and Cd2+ sensitivity of Cys substitutions in the loop of the helical hairpin and used a variety of assays to categorize the mechanisms by which Ag+ or Cd2+ chelation with the Cys thiolates caused inhibition. We identified two distinct metal-sensitive regions in the cytoplasmic loop where function was inhibited by different mechanisms. Metal binding to Cys substitutions in the N-terminal half of the loop resulted in an uncoupling of F1 from F0 with release of F1 from the membrane. In contrast, substitutions in the C-terminal half of the loop retained membrane-bound F1 after metal treatment. In several of these cases, inhibition was shown to be due to blockage of passive H+ translocation through F0 as assayed with F0 reconstituted into liposomes. The results suggest that the C-terminal domain of the cytoplasmic loop may function in gating H+ translocation to the cytoplasm. PMID:24297166

  15. The structure and shape of exotic nuclei beyond the proton drip-line

    SciTech Connect

    Ferreira, L. S.; Arumugam, P.; Maglione, E.

    2008-11-11

    Proton emission from deformed nuclei with triaxial symmetry is discussed within the non-adiabatic quasi-particle approach. As an example, we consider decay from {sup 161}Re, where we were able to reproduce the experimental half-life with a noticeable {gamma} deformation.

  16. The Mass Function of Cosmic Structures

    NASA Astrophysics Data System (ADS)

    Audit, E.; Teyssier, R.; Alimi, J.-M.

    We investigate some modifications to the Press and Schechter (1974) (PS) prescription resulting from shear and tidal effects. These modifications rely on more realistic treatments of the collapse process than the standard approach based on the spherical model. First, we show that the mass function resulting from a new approximate Lagrangian dynamic (Audit and Alimi, A&A 1996), contains more objects at high mass, than the classical PS mass function and is well fitted by a PS-like function with a threshold density of deltac ≍ 1.4. However, such a Lagrangian description can underestimate the epoch of structure formation since it defines it as the collapse of the first principal axis. We therefore suggest some analytical prescriptions, for computing the collapse time along the second and third principal axes, and we deduce the corresponding mass functions. The collapse along the third axis is delayed by the shear and the number of objects of high mass then decreases. Finally, we show that the shear also strongly affects the formation of low-mass halos. This dynamical effect implies a modification of the low-mass slope of the mass function and allows the reproduction of the observed luminosity function of field galaxies.

  17. Excitation functions of (nat)Zn(p,x) nuclear reactions with proton beam energy below 18 MeV.

    PubMed

    Asad, Ali H; Chan, Sun; Morandeau, Laurence; Cryer, David; Smith, Suzanne V; Price, Roger I

    2014-12-01

    We measured the excitation functions of (nat)Zn (p,x) reactions up to 17.6MeV, using the stacked-foils activation technique. High-purity natural zinc (and copper) foils were irradiated with proton beams generated by an 18MeV isochronous cyclotron. Activated foils were measured using high-purity Ge gamma spectroscopy to quantify the radionuclides (61)Cu, (66)Ga, (67)Ga, and (65)Zn produced from the reactions. Thick-target integral yields were also deduced from the measured excitation functions of the produced radioisotopes. These results were compared with the published literature and were found to be in good agreement with most reports, particularly those most recently compiled.

  18. Functional cavitands: Chemical reactivity in structured environments

    PubMed Central

    Purse, Byron W.; Rebek, Julius

    2005-01-01

    Container-shaped molecules provide structured environments that impart geometric bounds on the motions and conformations of smaller molecular occupants. Moreover, they provide “solvation” that is constrained in time and space. When inwardly directed functional groups are present, they can interact chemically with the occupants. Additionally, the potential for reactivity and catalysis is greatly enhanced. Deep cavitands, derived from resorcinarenes, nearly surround smaller molecules and have been one of the most successful platforms for elaboration with functional groups. Derivatives bearing organic and metal-binding functional groups have been shown to affect recognition properties and selectively accelerate diverse reactions. In this review, we examine recent examples of these systems with an emphasis on how and why ordered nanoenvironments impart changes in the properties and reactivity of their occupants. PMID:16043720

  19. Structural and regulatory functions of keratins

    SciTech Connect

    Magin, Thomas M. . E-mail: t.magin@uni-bonn.de; Vijayaraj, Preethi; Leube, Rudolf E. . E-mail: leube@uni-mainz.de

    2007-06-10

    The diversity of epithelial functions is reflected by the expression of distinct keratin pairs that are responsible to protect epithelial cells against mechanical stress and to act as signaling platforms. The keratin cytoskeleton integrates these functions by forming a supracellular scaffold that connects at desmosomal cell-cell adhesions. Multiple human diseases and murine knockouts in which the integrity of this system is destroyed testify to its importance as a mechanical stabilizer in certain epithelia. Yet, surprisingly little is known about the precise mechanisms responsible for assembly and disease pathology. In addition to these structural aspects of keratin function, experimental evidence accumulating in recent years has led to a much more complex view of the keratin cytoskeleton. Distinct keratins emerge as highly dynamic scaffolds in different settings and contribute to cell size determination, translation control, proliferation, cell type-specific organelle transport, malignant transformation and various stress responses. All of these properties are controlled by highly complex patterns of phosphorylation and molecular associations.

  20. Cardiac Na Channels: Structure to Function.

    PubMed

    DeMarco, K R; Clancy, C E

    2016-01-01

    Heart rhythms arise from electrical activity generated by precisely timed opening and closing of ion channels in individual cardiac myocytes. Opening of the primary cardiac voltage-gated sodium (NaV1.5) channel initiates cellular depolarization and the propagation of an electrical action potential that promotes coordinated contraction of the heart. The regularity of these contractile waves is critically important since it drives the primary function of the heart: to act as a pump that delivers blood to the brain and vital organs. When electrical activity goes awry during a cardiac arrhythmia, the pump does not function, the brain does not receive oxygenated blood, and death ensues. Perturbations to NaV1.5 may alter the structure, and hence the function, of the ion channel and are associated downstream with a wide variety of cardiac conduction pathologies, such as arrhythmias. PMID:27586288

  1. Structure, mechanism and function of prenyltransferases.

    PubMed

    Liang, Po-Huang; Ko, Tzu-Ping; Wang, Andrew H-J

    2002-07-01

    In this review, we summarize recent progress in studying three main classes of prenyltransferases: (a) isoprenyl pyrophosphate synthases (IPPSs), which catalyze chain elongation of allylic pyrophosphate substrates via consecutive condensation reactions with isopentenyl pyrophosphate (IPP) to generate linear polymers with defined chain lengths; (b) protein prenyltransferases, which catalyze the transfer of an isoprenyl pyrophosphate (e.g. farnesyl pyrophosphate) to a protein or a peptide; (c) prenyltransferases, which catalyze the cyclization of isoprenyl pyrophosphates. The prenyltransferase products are widely distributed in nature and serve a variety of important biological functions. The catalytic mechanism deduced from the 3D structure and other biochemical studies of these prenyltransferases as well as how the protein functions are related to their reaction mechanism and structure are discussed. In the IPPS reaction, we focus on the mechanism that controls product chain length and the reaction kinetics of IPP condensation in the cis-type and trans-type enzymes. For protein prenyltransferases, the structures of Ras farnesyltransferase and Rab geranylgeranyltransferase are used to elucidate the reaction mechanism of this group of enzymes. For the enzymes involved in cyclic terpene biosynthesis, the structures and mechanisms of squalene cyclase, 5-epi-aristolochene synthase, pentalenene synthase, and trichodiene synthase are summarized. PMID:12135472

  2. Structure, mechanism and function of prenyltransferases.

    PubMed

    Liang, Po-Huang; Ko, Tzu-Ping; Wang, Andrew H-J

    2002-07-01

    In this review, we summarize recent progress in studying three main classes of prenyltransferases: (a) isoprenyl pyrophosphate synthases (IPPSs), which catalyze chain elongation of allylic pyrophosphate substrates via consecutive condensation reactions with isopentenyl pyrophosphate (IPP) to generate linear polymers with defined chain lengths; (b) protein prenyltransferases, which catalyze the transfer of an isoprenyl pyrophosphate (e.g. farnesyl pyrophosphate) to a protein or a peptide; (c) prenyltransferases, which catalyze the cyclization of isoprenyl pyrophosphates. The prenyltransferase products are widely distributed in nature and serve a variety of important biological functions. The catalytic mechanism deduced from the 3D structure and other biochemical studies of these prenyltransferases as well as how the protein functions are related to their reaction mechanism and structure are discussed. In the IPPS reaction, we focus on the mechanism that controls product chain length and the reaction kinetics of IPP condensation in the cis-type and trans-type enzymes. For protein prenyltransferases, the structures of Ras farnesyltransferase and Rab geranylgeranyltransferase are used to elucidate the reaction mechanism of this group of enzymes. For the enzymes involved in cyclic terpene biosynthesis, the structures and mechanisms of squalene cyclase, 5-epi-aristolochene synthase, pentalenene synthase, and trichodiene synthase are summarized.

  3. Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness.

    PubMed Central

    Paula, S; Volkov, A G; Van Hoek, A N; Haines, T H; Deamer, D W

    1996-01-01

    Two mechanisms have been proposed to account for solute permeation of lipid bilayers. Partitioning into the hydrophobic phase of the bilayer, followed by diffusion, is accepted by many for the permeation of water and other small neutral solutes, but transient pores have also been proposed to account for both water and ionic solute permeation. These two mechanisms make distinctively different predictions about the permeability coefficient as a function of bilayer thickness. Whereas the solubility-diffusion mechanism predicts only a modest variation related to bilayer thickness, the pore model predicts an exponential relationship. To test these models, we measured the permeability of phospholipid bilayers to protons, potassium ions, water, urea, and glycerol. Bilayers were prepared as liposomes, and thickness was varied systematically by using unsaturated lipids with chain lengths ranging from 14 to 24 carbon atoms. The permeability coefficient of water and neutral polar solutes displayed a modest dependence on bilayer thickness, with an approximately linear fivefold decrease as the carbon number varied from 14 to 24 atoms. In contrast, the permeability to protons and potassium ions decreased sharply by two orders of magnitude between 14 and 18 carbon atoms, and leveled off, when the chain length was further extended to 24 carbon atoms. The results for water and the neutral permeating solutes are best explained by the solubility-diffusion mechanism. The results for protons and potassium ions in shorter-chain lipids are consistent with the transient pore model, but better fit the theoretical line predicted by the solubility-diffusion model at longer chain lengths. PMID:8770210

  4. Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness

    NASA Technical Reports Server (NTRS)

    Paula, S.; Volkov, A. G.; Van Hoek, A. N.; Haines, T. H.; Deamer, D. W.

    1996-01-01

    Two mechanisms have been proposed to account for solute permeation of lipid bilayers. Partitioning into the hydrophobic phase of the bilayer, followed by diffusion, is accepted by many for the permeation of water and other small neutral solutes, but transient pores have also been proposed to account for both water and ionic solute permeation. These two mechanisms make distinctively different predictions about the permeability coefficient as a function of bilayer thickness. Whereas the solubility-diffusion mechanism predicts only a modest variation related to bilayer thickness, the pore model predicts an exponential relationship. To test these models, we measured the permeability of phospholipid bilayers to protons, potassium ions, water, urea, and glycerol. Bilayers were prepared as liposomes, and thickness was varied systematically by using unsaturated lipids with chain lengths ranging from 14 to 24 carbon atoms. The permeability coefficient of water and neutral polar solutes displayed a modest dependence on bilayer thickness, with an approximately linear fivefold decrease as the carbon number varied from 14 to 24 atoms. In contrast, the permeability to protons and potassium ions decreased sharply by two orders of magnitude between 14 and 18 carbon atoms, and leveled off, when the chain length was further extended to 24 carbon atoms. The results for water and the neutral permeating solutes are best explained by the solubility-diffusion mechanism. The results for protons and potassium ions in shorter-chain lipids are consistent with the transient pore model, but better fit the theoretical line predicted by the solubility-diffusion model at longer chain lengths.

  5. Multifactorial resistance of Bacillus subtilis spores to high-energy proton radiation: role of spore structural components and the homologous recombination and non-homologous end joining DNA repair pathways.

    PubMed

    Moeller, Ralf; Reitz, Günther; Li, Zuofeng; Klein, Stuart; Nicholson, Wayne L

    2012-11-01

    The space environment contains high-energy charged particles (e.g., protons, neutrons, electrons, α-particles, heavy ions) emitted by the Sun and galactic sources or trapped in the radiation belts. Protons constitute the majority (87%) of high-energy charged particles. Spores of Bacillus species are one of the model systems used for astro- and radiobiological studies. In this study, spores of different Bacillus subtilis strains were used to study the effects of high energetic proton irradiation on spore survival. Spores of the wild-type B. subtilis strain [mutants deficient in the homologous recombination (HR) and non-homologous end joining (NHEJ) DNA repair pathways and mutants deficient in various spore structural components such as dipicolinic acid (DPA), α/β-type small, acid-soluble spore protein (SASP) formation, spore coats, pigmentation, or spore core water content] were irradiated as air-dried multilayers on spacecraft-qualified aluminum coupons with 218 MeV protons [with a linear energy transfer (LET) of 0.4 keV/μm] to various final doses up to 2500 Gy. Spores deficient in NHEJ- and HR-mediated DNA repair were significantly more sensitive to proton radiation than wild-type spores, indicating that both HR and NHEJ DNA repair pathways are needed for spore survival. Spores lacking DPA, α/β-type SASP, or with increased core water content were also significantly more sensitive to proton radiation, whereas the resistance of spores lacking pigmentation or spore coats was essentially identical to that of the wild-type spores. Our results indicate that α/β-type SASP, core water content, and DPA play an important role in spore resistance to high-energy proton irradiation, suggesting their essential function as radioprotectants of the spore interior. PMID:23088412

  6. Multifactorial resistance of Bacillus subtilis spores to high-energy proton radiation: role of spore structural components and the homologous recombination and non-homologous end joining DNA repair pathways.

    PubMed

    Moeller, Ralf; Reitz, Günther; Li, Zuofeng; Klein, Stuart; Nicholson, Wayne L

    2012-11-01

    The space environment contains high-energy charged particles (e.g., protons, neutrons, electrons, α-particles, heavy ions) emitted by the Sun and galactic sources or trapped in the radiation belts. Protons constitute the majority (87%) of high-energy charged particles. Spores of Bacillus species are one of the model systems used for astro- and radiobiological studies. In this study, spores of different Bacillus subtilis strains were used to study the effects of high energetic proton irradiation on spore survival. Spores of the wild-type B. subtilis strain [mutants deficient in the homologous recombination (HR) and non-homologous end joining (NHEJ) DNA repair pathways and mutants deficient in various spore structural components such as dipicolinic acid (DPA), α/β-type small, acid-soluble spore protein (SASP) formation, spore coats, pigmentation, or spore core water content] were irradiated as air-dried multilayers on spacecraft-qualified aluminum coupons with 218 MeV protons [with a linear energy transfer (LET) of 0.4 keV/μm] to various final doses up to 2500 Gy. Spores deficient in NHEJ- and HR-mediated DNA repair were significantly more sensitive to proton radiation than wild-type spores, indicating that both HR and NHEJ DNA repair pathways are needed for spore survival. Spores lacking DPA, α/β-type SASP, or with increased core water content were also significantly more sensitive to proton radiation, whereas the resistance of spores lacking pigmentation or spore coats was essentially identical to that of the wild-type spores. Our results indicate that α/β-type SASP, core water content, and DPA play an important role in spore resistance to high-energy proton irradiation, suggesting their essential function as radioprotectants of the spore interior.

  7. Three order state space modeling of proton exchange membrane fuel cell with energy function definition

    NASA Astrophysics Data System (ADS)

    Becherif, M.; Hissel, D.; Gaagat, S.; Wack, M.

    The fuel cell is a complex system which is the centre of a lot of multidisciplinary research activities since it involves intricate application of various fields of study. The operation of a fuel cell depends on a wide range of parameters. The effect of one cannot be studied in isolation without disturbing the system which makes it very difficult to comprehend, analyze and predict various phenomena occurring in the fuel cell. In the current work, we present an equivalent electrical circuit of the pneumatics and fluidics in a fuel cell stack. The proposed model is based on the physical phenomena occurring inside fuel cell stack where we define the fluidic-electrical and pneumatic-electrical analogy. The effect of variation in temperature and relative humidity on the cell are considered in this model. The proposed model, according to the considered hypothesis, is a simple three order state space model which is suitable for the control purpose where a desired control structure can be formulated for high-end applications of the fuel cell as a subpart of a larger system, for instance, in hybrid propulsion of vehicles coupled with batteries and supercapacitors. Another key point of our work is the definition of the natural fuel cell stack energy function. The circuit analysis equations are presented and the simulated model is validated using the experimental data obtained using the fuel cell test bench available in Fuel Cell Laboratory, France.

  8. Structural origin of proton mobility in a protic ionic liquid/imidazole mixture: insights from computational and experimental results.

    PubMed

    Yaghini, Negin; Gómez-González, Víctor; Varela, Luis M; Martinelli, Anna

    2016-08-17

    The structure, dynamics, and phase behavior of a binary mixture based on the protic ionic liquid 1-ethylimidazolium bis(trifluoromethanesulfonyl)imide (C2HImTFSI) and imidazole are investigated by (1)H NMR spectroscopy, vibrational spectroscopy, diffusion NMR, calorimetric measurements, and molecular dynamics simulations. Particular attention is given to the nature of the H-bonds established and the consequent occurrence of the Grotthuss mechanism of proton transfer. We find that due to their structural similarity, the imidazolium cation and the imidazole molecule behave as interchangeable and competing sites of interaction for the TFSI anion. All investigated properties, that is the phase behavior, strength of ion-ion and ion-imidazole interactions, number of specific H-bonds, density, and self-diffusivity, are composition dependent and show trend changes at mole fractions of imidazole (χ) approximately equal to 0.2 and 0.5. Beyond χ = 0.8 imidazole is not miscible in C2HImTFSI at room temperature. We find that at the equimolar composition (χ ≈ 0.5) a structural transition occurs from an ionic network mainly stabilized by coulombic forces to a mixed phase held together by site specific H-bonds. The same composition also marks a steeper decrease in density and increase in diffusivity, resulting from the preference of imidazole molecules to H-bond to each other in a chain-like manner. As a result of these structural features the Grotthuss mechanism of proton transfer is less favored at the equimolar composition where H-bonds are too stable. By contrast, the Grotthuss mechanism is more pronounced in the low concentration range where imidazole acts as a base pulling the proton of the imidazolium cation. At high imidazole concentrations the contribution from the vehicular mechanism dominates. PMID:27499376

  9. Structural origin of proton mobility in a protic ionic liquid/imidazole mixture: insights from computational and experimental results.

    PubMed

    Yaghini, Negin; Gómez-González, Víctor; Varela, Luis M; Martinelli, Anna

    2016-08-17

    The structure, dynamics, and phase behavior of a binary mixture based on the protic ionic liquid 1-ethylimidazolium bis(trifluoromethanesulfonyl)imide (C2HImTFSI) and imidazole are investigated by (1)H NMR spectroscopy, vibrational spectroscopy, diffusion NMR, calorimetric measurements, and molecular dynamics simulations. Particular attention is given to the nature of the H-bonds established and the consequent occurrence of the Grotthuss mechanism of proton transfer. We find that due to their structural similarity, the imidazolium cation and the imidazole molecule behave as interchangeable and competing sites of interaction for the TFSI anion. All investigated properties, that is the phase behavior, strength of ion-ion and ion-imidazole interactions, number of specific H-bonds, density, and self-diffusivity, are composition dependent and show trend changes at mole fractions of imidazole (χ) approximately equal to 0.2 and 0.5. Beyond χ = 0.8 imidazole is not miscible in C2HImTFSI at room temperature. We find that at the equimolar composition (χ ≈ 0.5) a structural transition occurs from an ionic network mainly stabilized by coulombic forces to a mixed phase held together by site specific H-bonds. The same composition also marks a steeper decrease in density and increase in diffusivity, resulting from the preference of imidazole molecules to H-bond to each other in a chain-like manner. As a result of these structural features the Grotthuss mechanism of proton transfer is less favored at the equimolar composition where H-bonds are too stable. By contrast, the Grotthuss mechanism is more pronounced in the low concentration range where imidazole acts as a base pulling the proton of the imidazolium cation. At high imidazole concentrations the contribution from the vehicular mechanism dominates.

  10. Structure and Function of the Bi-Directional Bacterial Flagellar Motor

    PubMed Central

    Morimoto, Yusuke V.; Minamino, Tohru

    2014-01-01

    The bacterial flagellum is a locomotive organelle that propels the bacterial cell body in liquid environments. The flagellum is a supramolecular complex composed of about 30 different proteins and consists of at least three parts: a rotary motor, a universal joint, and a helical filament. The flagellar motor of Escherichia coli and Salmonella enterica is powered by an inward-directed electrochemical potential difference of protons across the cytoplasmic membrane. The flagellar motor consists of a rotor made of FliF, FliG, FliM and FliN and a dozen stators consisting of MotA and MotB. FliG, FliM and FliN also act as a molecular switch, enabling the motor to spin in both counterclockwise and clockwise directions. Each stator is anchored to the peptidoglycan layer through the C-terminal periplasmic domain of MotB and acts as a proton channel to couple the proton flow through the channel with torque generation. Highly conserved charged residues at the rotor–stator interface are required not only for torque generation but also for stator assembly around the rotor. In this review, we will summarize our current understanding of the structure and function of the proton-driven bacterial flagellar motor. PMID:24970213

  11. Proton Affinities of Anionic Bases:  Trends Across the Periodic Table, Structural Effects, and DFT Validation.

    PubMed

    Swart, Marcel; Bickelhaupt, F Matthias

    2006-03-01

    We have carried out an extensive exploration of the gas-phase basicity of archetypal anionic bases across the periodic system using the generalized gradient approximation of density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities:  BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 1.6 kcal/mol for the proton affinity at 0 K with respect to high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the anionic conjugate bases of all main-group-element hydrides of groups 14-17 and periods 2-6. We have also studied the effect of stepwise methylation of the protophilic center of the second- and third-period bases.

  12. Proton affinities of maingroup-element hydrides and noble gases: trends across the periodic table, structural effects, and DFT validation.

    PubMed

    Swart, Marcel; Rösler, Ernst; Bickelhaupt, F Matthias

    2006-10-01

    We have carried out an extensive exploration of the gas-phase basicity of archetypal neutral bases across the periodic system using the generalized gradient approximation (GGA) of the density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities: BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 2.0 kcal/mol for the proton affinity at 298 K with respect to experiment, and 1.2 kcal/mol with high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the neutral bases constituted by all maingroup-element hydrides of groups 15-17 and the noble gases, that is, group 18, and periods 1-6. We have also studied the effect of step-wise methylation of the protophilic center of the second- and third-period bases.

  13. Proton affinities of maingroup-element hydrides and noble gases: trends across the periodic table, structural effects, and DFT validation.

    PubMed

    Swart, Marcel; Rösler, Ernst; Bickelhaupt, F Matthias

    2006-10-01

    We have carried out an extensive exploration of the gas-phase basicity of archetypal neutral bases across the periodic system using the generalized gradient approximation (GGA) of the density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities: BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 2.0 kcal/mol for the proton affinity at 298 K with respect to experiment, and 1.2 kcal/mol with high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the neutral bases constituted by all maingroup-element hydrides of groups 15-17 and the noble gases, that is, group 18, and periods 1-6. We have also studied the effect of step-wise methylation of the protophilic center of the second- and third-period bases. PMID:16823810

  14. Local Atomic Structure of Semiconductor Alloys Using Pair Distribution Function Analysis

    SciTech Connect

    Billinge, S.J.L.; Thorpe, M.F.

    2002-06-24

    We have been taking advantage of recent experimental developments, which involve utilizing diffraction data from x-rays or neutrons out to very large wave-vectors, to obtain a detailed structural characterization of semiconductor alloys. This approach allows an accurate Pair Distribution Function (PDF) to be obtained to 20A and beyond and reveals the local structure of the alloy directly. These data can be modeled explicitly to learn about local correlations and short-range order in materials. We are combining theory, modeling and experiments to study a range of materials from semiconductors to thermoelectrics and proton conductors.

  15. Meiotic chromosome structure and function in plants.

    PubMed

    Mainiero, Samantha; Pawlowski, Wojciech P

    2014-01-01

    Chromosome structure is important for many meiotic processes. Here, we outline 3 main determinants of chromosome structure and their effects on meiotic processes in plants. Cohesins are necessary to hold sister chromatids together until the first meiotic division, ensuring that homologous chromosomes and not sister chromatids separate during anaphase I. During meiosis in maize, Arabidopsis, and rice, cohesins are needed for establishing early prophase chromosome structure and recombination and for aligning bivalents at the metaphase plate. Condensin complexes play pivotal roles in controlling the packaging of chromatin into chromosomes through chromatin compaction and chromosome individualization. In animals and fungi, these complexes establish a meiotic chromosome structure that allows for proper recombination, pairing, and synapsis of homologous chromosomes. In plants, information on the role of condensins in meiosis is limited, but they are known to be required for successful completion of reproductive development. Therefore, we speculate that they play roles similar to animal and fungal condensins during meiosis. Plants generally have large and complex genomes due to frequent polyploidy events, and likely, condensins and cohesins organize chromosomes in such a way as to ensure genome stability. Hexaploid wheat has evolved a unique mechanism using a Ph1 locus-controlled chromosome organization to ensure proper chromosome pairing in meiosis. Altogether, studies on meiotic chromosome structure indicate that chromosome organization is not only important for chromatin packaging but also fulfills specific functions in facilitating chromosome interactions during meiosis, including pairing and recombination. PMID:25096046

  16. Polymer nanocomposites: structure, interaction, and functionality.

    PubMed

    Keledi, Gergely; Hári, József; Pukánszky, Béla

    2012-03-21

    This feature article discusses the main factors determining the properties of polymer nanocomposites with special attention paid to structure and interactions. Usually more complicated structure develops in nanocomposites than in traditional particulate filled polymers, and that is especially valid for composites prepared from plate-like nanofillers. Besides the usually assumed exfoliated/intercalated morphology, i.e. individual platelets and tactoids, such nanocomposites often contain large particles, and a network structure developing at large extent of exfoliation. Aggregation and orientation are the most important structural phenomena in nanotube or nanofiber reinforced composites, and ag-gregation is a major problem also in composites prepared with spherical particles. The surface characteristics of nanofillers and interactions are rarely determined or known; the related problems are discussed in the paper in detail. The surface of these reinforcements is modified practically always. The goal of the modification is to improve dispersion and/or adhesion in nanotube and spherical particle reinforced composites, and to help exfoliation in nanocomposites containing platelets. However, modification decreases surface energy often leading to decreased interaction with the matrix. Very limited information exists about interphase formation and the properties of the interphase in nanocomposites, although they must influence properties considerably. The properties of nanocomposites are usually far from the expectations, the main reason being insufficient homogeneity, undefined structure and improper adhesion. In spite of considerable difficulties nanocomposites have great potentials especially in functional applications. Several nanocomposite products are already used in industrial practice demonstrated by a few examples in the article. PMID:22349033

  17. Crystal structures of nitric oxide reductases provide key insights into functional conversion of respiratory enzymes.

    PubMed

    Tosha, Takehiko; Shiro, Yoshitsugu

    2013-03-01

    Respiration is an essential biological process to get bioenergy, ATP, for all kingdoms of life. Cytochrome c oxidase (COX) plays central role in aerobic respiration, catalyzing the reduction of O(2) coupled with pumping proton across the biological membrane. Nitric oxide reductase (NOR) involved in anaerobic nitrate respiration is suggested to be evolutionary related to COX and share the same progenitor with COX, on the basis of the amino acid sequence homology. Contrary to COX, NOR catalyzes the reduction of nitric oxide and shows no proton pumping ability. Thus, the respiratory enzyme acquires (or loses) proton pumping ability in addition to the conversion of the catalytic property along with the environmental change on earth. Recently, we solved the structures of two types of NORs, which provides novel insights into the functional conversion of the respiratory enzymes. In this review, we focus on the structural similarities and differences between COXs and NORs and discuss possible mechanism for the functional conversion of these enzymes during molecular evolution.

  18. Measurement of the neutron F2 structure function via spectator tagging with CLAS

    SciTech Connect

    Baillie, N.; Tkachenko, S.; Zhang, J.; Bosted, P.; Bültmann, S.; Christy, M. E.; Fenker, H.; Griffioen, K. A.; Keppel, C. E.; Kuhn, S. E.; Melnitchouk, W.; Tvaskis, V.; Adhikari, K. P.; Adikaram, D.; Aghasyan, M.; Amaryan, M. J.; Anghinolfi, M.; Arrington, J.; Avakian, H.; Baghdasaryan, H.; Battaglieri, M.; Biselli, A. S.; Branford, D.; Briscoe, W. J.; Brooks, W. K.; Burkert, V. D.; Carman, D. S.; Celentano, A.; Chandavar, S.; Charles, G.; Cole, P. L.; Contalbrigo, M.; Crede, V.; D’Angelo, A.; Daniel, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Deur, A.; Dey, B.; Djalali, C.; Dodge, G.; Domingo, J.; Doughty, D.; Dupre, R.; Dutta, D.; Ent, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Elouadrhiri, L.; Eugenio, P.; Fedotov, G.; Fegan, S.; Fradi, A.; Gabrielyan, M. Y.; Gevorgyan, N.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Gohn, W.; Golovatch, E.; Gothe, R. W.; Graham, L.; Guegan, B.; Guidal, M.; Guler, N.; Guo, L.; Hafidi, K.; Heddle, D.; Hicks, K.; Holtrop, M.; Hungerford, E.; Hyde, C. E.; Ilieva, Y.; Ireland, D. G.; Ispiryan, M.; Isupov, E. L.; Jawalkar, S. S.; Jo, H. S.; Kalantarians, N.; Khandaker, M.; Khetarpal, P.; Kim, A.; Kim, W.; King, P. M.; Klein, A.; Klein, F. J.; Klimenko, A.; Kubarovsky, V.; Kuleshov, S. V.; Kvaltine, N. D.; Livingston, K.; Lu, H. Y.; MacGregor, I. J. D.; Mao, Y.; Markov, N.; McKinnon, B.; Mineeva, T.; Morrison, B.; Moutarde, H.; Munevar, E.; Nadel-Turonski, P.; Ni, A.; Niccolai, S.; Niculescu, I.; Niculescu, G.; Osipenko, M.; Ostrovidov, A. I.; Pappalardo, L.; Park, K.; Park, S.; Pasyuk, E.; Anefalos Pereira, S.; Pisano, S.; Pozdniakov, S.; Price, J. W.; Procureur, S.; Prok, Y.; Protopopescu, D.; Raue, B. A.; Ricco, G.; Rimal, D.; Ripani, M.; Rosner, G.; Rossi, P.; Sabatié, F.; Saini, M. S.; Salgado, C.; Schott, D.; Schumacher, R. A.; Seder, E.; Sharabian, Y. G.; Sober, D. I.; Sokhan, D.; Stepanyan, S.; Stepanyan, S. S.; Stoler, P.; Strauch, S.; Taiuti, M.; Tang, W.; Ungaro, M.; Vineyard, M. F.; Voutier, E.; Watts, D. P.; Weinstein, L. B.; Weygand, D. P.; Wood, M. H.; Zana, L.; Zhao, B.

    2012-04-01

    We report on the first measurement of the F2 structure function of the neutron from semi-inclusive scattering of electrons from deuterium, with low-momentum protons detected in the backward hemisphere. Restricting the momentum of the spectator protons to ≈< 100 MeV and their angles to ≈> 100 degrees relative to the momentum transfer allows an interpretation of the process in terms of scattering from nearly on-shell neutrons. The F2n data collected cover the nucleon resonance and deep-inelastic regions over a wide range of x for 0.65 < Q2 < 4.52 GeV2, with uncertainties from nuclear corrections estimated to be less than a few percent. These measurements provide the first determination of the neutron to proton structure function ratio F2n/F2p at 0.2 ≈< x ≈< 0.8, essentially free of nuclear corrections.

  19. Measurement of the neutron F2 structure function via spectator tagging with CLAS

    DOE PAGES

    Baillie, N.; Tkachenko, S.; Zhang, J.; Bosted, P.; Bültmann, S.; Christy, M. E.; Fenker, H.; Griffioen, K. A.; Keppel, C. E.; Kuhn, S. E.; et al

    2012-04-01

    We report on the first measurement of the F2 structure function of the neutron from semi-inclusive scattering of electrons from deuterium, with low-momentum protons detected in the backward hemisphere. Restricting the momentum of the spectator protons to ≈< 100 MeV and their angles to ≈> 100 degrees relative to the momentum transfer allows an interpretation of the process in terms of scattering from nearly on-shell neutrons. The F2n data collected cover the nucleon resonance and deep-inelastic regions over a wide range of x for 0.65 < Q2 < 4.52 GeV2, with uncertainties from nuclear corrections estimated to be less thanmore » a few percent. These measurements provide the first determination of the neutron to proton structure function ratio F2n/F2p at 0.2 ≈< x ≈< 0.8, essentially free of nuclear corrections.« less

  20. Measurement of the neutron F2 structure function via spectator tagging with CLAS.

    PubMed

    Baillie, N; Tkachenko, S; Zhang, J; Bosted, P; Bültmann, S; Christy, M E; Fenker, H; Griffioen, K A; Keppel, C E; Kuhn, S E; Melnitchouk, W; Tvaskis, V; Adhikari, K P; Adikaram, D; Aghasyan, M; Amaryan, M J; Anghinolfi, M; Arrington, J; Avakian, H; Baghdasaryan, H; Battaglieri, M; Biselli, A S; Branford, D; Briscoe, W J; Brooks, W K; Burkert, V D; Carman, D S; Celentano, A; Chandavar, S; Charles, G; Cole, P L; Contalbrigo, M; Crede, V; D'Angelo, A; Daniel, A; Dashyan, N; De Vita, R; De Sanctis, E; Deur, A; Dey, B; Djalali, C; Dodge, G; Domingo, J; Doughty, D; Dupre, R; Dutta, D; Ent, R; Egiyan, H; El Alaoui, A; El Fassi, L; Elouadrhiri, L; Eugenio, P; Fedotov, G; Fegan, S; Fradi, A; Gabrielyan, M Y; Gevorgyan, N; Gilfoyle, G P; Giovanetti, K L; Girod, F X; Gohn, W; Golovatch, E; Gothe, R W; Graham, L; Guegan, B; Guidal, M; Guler, N; Guo, L; Hafidi, K; Heddle, D; Hicks, K; Holtrop, M; Hungerford, E; Hyde, C E; Ilieva, Y; Ireland, D G; Ispiryan, M; Isupov, E L; Jawalkar, S S; Jo, H S; Kalantarians, N; Khandaker, M; Khetarpal, P; Kim, A; Kim, W; King, P M; Klein, A; Klein, F J; Klimenko, A; Kubarovsky, V; Kuleshov, S V; Kvaltine, N D; Livingston, K; Lu, H Y; MacGregor, I J D; Mao, Y; Markov, N; McKinnon, B; Mineeva, T; Morrison, B; Moutarde, H; Munevar, E; Nadel-Turonski, P; Ni, A; Niccolai, S; Niculescu, I; Niculescu, G; Osipenko, M; Ostrovidov, A I; Pappalardo, L; Park, K; Park, S; Pasyuk, E; Anefalos Pereira, S; Pisano, S; Pozdniakov, S; Price, J W; Procureur, S; Prok, Y; Protopopescu, D; Raue, B A; Ricco, G; Rimal, D; Ripani, M; Rosner, G; Rossi, P; Sabatié, F; Saini, M S; Salgado, C; Schott, D; Schumacher, R A; Seder, E; Sharabian, Y G; Sober, D I; Sokhan, D; Stepanyan, S; Stepanyan, S S; Stoler, P; Strauch, S; Taiuti, M; Tang, W; Ungaro, M; Vineyard, M F; Voutier, E; Watts, D P; Weinstein, L B; Weygand, D P; Wood, M H; Zana, L; Zhao, B

    2012-04-01

    We report on the first measurement of the F(2) structure function of the neutron from the semi-inclusive scattering of electrons from deuterium, with low-momentum protons detected in the backward hemisphere. Restricting the momentum of the spectator protons to ≲100 MeV/c and their angles to ≳100° relative to the momentum transfer allows an interpretation of the process in terms of scattering from nearly on-shell neutrons. The F(2)(n) data collected cover the nucleon-resonance and deep-inelastic regions over a wide range of Bjorken x for 0.65proton structure function ratio F(2)(n)/F(2)(p) at 0.2≲x≲0.8 with little uncertainty due to nuclear effects. PMID:22540786

  1. Pion structure function from leading neutron electroproduction and SU(2) flavor asymmetry

    DOE PAGES

    McKenney, Joshua R.; Sato, Nobuo; Melnitchouk, Wally; Ji, Chueng-Ryong

    2016-03-07

    In this paper, we examine the efficacy of pion exchange models to simultaneously describe leading neutron electroproduction at HERA and themore » $$\\bar{d}-\\bar{u}$$ flavor asymmetry in the proton. A detailed $$\\chi^2$$ analysis of the ZEUS and H1 cross sections, when combined with constraints on the pion flux from Drell-Yan data, allows regions of applicability of one-pion exchange to be delineated. The analysis disfavors several models of the pion flux used in the literature, and yields an improved extraction of the pion structure function and its uncertainties at parton momentum fractions in the pion of $$4 \\times 10^{-4} \\lesssim x_\\pi \\lesssim 0.05$$ at a scale of $Q^2$=10 GeV$^2$. Also, we provide estimates for leading proton structure functions in upcoming tagged deep-inelastic scattering experiments on the deuteron with forward protons, based on the fit results, at Jefferson Lab.« less

  2. Catchment Classification: Connecting Climate, Structure and Function

    NASA Astrophysics Data System (ADS)

    Sawicz, K. A.; Wagener, T.; Sivapalan, M.; Troch, P. A.; Carrillo, G. A.

    2010-12-01

    Hydrology does not yet possess a generally accepted catchment classification framework. Such a classification framework needs to: [1] give names to things, i.e. the main classification step, [2] permit transfer of information, i.e. regionalization of information, [3] permit development of generalizations, i.e. to develop new theory, and [4] provide a first order environmental change impact assessment, i.e., the hydrologic implications of climate, land use and land cover change. One strategy is to create a catchment classification framework based on the notion of catchment functions (partitioning, storage, and release). Results of an empirical study presented here connects climate and structure to catchment function (in the form of select hydrologic signatures), based on analyzing over 300 US catchments. Initial results indicate a wide assortment of signature relationships with properties of climate, geology, and vegetation. The uncertainty in the different regionalized signatures varies widely, and therefore there is variability in the robustness of classifying ungauged basins. This research provides insight into the controls of hydrologic behavior of a catchment, and enables a classification framework applicable to gauged and ungauged across the study domain. This study sheds light on what we can expect to achieve in mapping climate, structure and function in a top-down manner. Results of this study complement work done using a bottom-up physically-based modeling framework to generalize this approach (Carrillo et al., this session).

  3. The structure and function of presynaptic endosomes.

    PubMed

    Jähne, Sebastian; Rizzoli, Silvio O; Helm, Martin S

    2015-07-15

    The function of endosomes and of endosome-like structures in the presynaptic compartment is still controversial. This is in part due to the absence of a consensus on definitions and markers for these compartments. Synaptic endosomes are sometimes seen as stable organelles, permanently present in the synapse. Alternatively, they are seen as short-lived intermediates in synaptic vesicle recycling, arising from the endocytosis of large vesicles from the plasma membrane, or from homotypic fusion of small vesicles. In addition, the potential function of the endosome is largely unknown in the synapse. Some groups have proposed that the endosome is involved in the sorting of synaptic vesicle proteins, albeit others have produced data that deny this possibility. In this review, we present the existing evidence for synaptic endosomes, we discuss their potential functions, and we highlight frequent technical pitfalls in the analysis of this elusive compartment. We also sketch a roadmap to definitely determine the role of synaptic endosomes for the synaptic vesicle cycle. Finally, we propose a common definition of synaptic endosome-like structures. PMID:25939282

  4. The structure and function of presynaptic endosomes

    SciTech Connect

    Jähne, Sebastian; Rizzoli, Silvio O.; Helm, Martin S.

    2015-07-15

    The function of endosomes and of endosome-like structures in the presynaptic compartment is still controversial. This is in part due to the absence of a consensus on definitions and markers for these compartments. Synaptic endosomes are sometimes seen as stable organelles, permanently present in the synapse. Alternatively, they are seen as short-lived intermediates in synaptic vesicle recycling, arising from the endocytosis of large vesicles from the plasma membrane, or from homotypic fusion of small vesicles. In addition, the potential function of the endosome is largely unknown in the synapse. Some groups have proposed that the endosome is involved in the sorting of synaptic vesicle proteins, albeit others have produced data that deny this possibility. In this review, we present the existing evidence for synaptic endosomes, we discuss their potential functions, and we highlight frequent technical pitfalls in the analysis of this elusive compartment. We also sketch a roadmap to definitely determine the role of synaptic endosomes for the synaptic vesicle cycle. Finally, we propose a common definition of synaptic endosome-like structures.

  5. Structural and functional brain imaging in schizophrenia.

    PubMed Central

    Cleghorn, J M; Zipursky, R B; List, S J

    1991-01-01

    We present an evaluation of the contribution of structural and functional brain imaging to our understanding of schizophrenia. Methodological influences on the validity of the data generated by these new technologies include problems with measurement and clinical and anatomic heterogeneity. These considerations greatly affect the interpretation of the data generated by these technologies. Work in these fields to date, however, has produced strong evidence which suggests that schizophrenia is a disease which involves abnormalities in the structure and function of many brain areas. Structural brain imaging studies of schizophrenia using computed tomography (CT) and magnetic resonance imaging (MRI) are reviewed and their contribution to current theories of the pathogenesis of schizophrenia are discussed. Positron emission tomography (PET) studies of brain metabolic activity and dopamine receptor binding in schizophrenia are summarized and the critical questions raised by these studies are outlined. Future studies in these fields have the potential to yield critical insights into the pathophysiology of schizophrenia; new directions for studies of schizophrenia using these technologies are identified. PMID:1911736

  6. Structure and function of C1-inhibitor.

    PubMed

    Wagenaar-Bos, Ineke G A; Hack, C Erik

    2006-11-01

    C1-INH belongs to the family of serpins. Structural studies have yielded a clear understanding of the biochemical principle underlying the functional activities of these proteins. Although the crystal structure of C1-INH has yet to be revealed, homology modeling has provided a three-dimensional model of the serpin part of C1-INH. This model has helped us understand the biochemical consequences of mutations of the C1-INH gene as they occur in patients who have HAE. The structure of the N-terminal domain of C1-INH remains unknown; however, this part of the molecule is unlikely to be important in the inhibitory activity of C1-INH toward its target proteases. Mutations in this part have not been described in patients who have HAE, except for a deletion containing two cysteine residues involved in the stabilization of the serpin domain. Recent studies suggest some anti-inflammatory functions for this N-terminal part, possibly explaining the effects of C1-INH in diseases other than HAE.

  7. Egg yolk: structures, functionalities and processes.

    PubMed

    Anton, Marc

    2013-09-01

    Hen egg yolk is an ideal example of natural supramolecular assemblies of lipids and proteins with different organization levels. These assemblies are mainly due to interactions between proteins and phospholipids, and these interactions are essential in understanding and controlling the production of food made with yolk, and particularly emulsions. Furthermore, these assemblies can be modulated by external constraints among which thermo-mechanical and high-pressure treatments. This review focuses on multi-scale structures present in egg yolk, and their modulation by processes, in relation with their emulsifying properties. Egg yolk is mainly composed of two fractions-plasma and granules-which are natural nano- and micro-assemblies. These two fractions possess different composition, structures and functionalities and exhibit specific behaviour under treatments such as high pressure and temperature. Plasma contains a large quantity of lipids structured as lipoproteins (low-density lipoproteins), whereas granules are mainly composed of proteins aggregated in micrometric assemblies. If plasma is responsible for the important emulsifying properties of yolk, granules bring interesting emulsifying properties when assemblies are in the form of micelles in presence of salts. High-pressure or thermal treatments, applied before or after emulsion fabrication, alter their functionalities and could be used to commercially exploit these fractions.

  8. Phenylalanine hydroxylase: function, structure, and regulation.

    PubMed

    Flydal, Marte I; Martinez, Aurora

    2013-04-01

    Mammalian phenylalanine hydroxylase (PAH) catalyzes the rate-limiting step in the phenylalanine catabolism, consuming about 75% of the phenylalanine input from the diet and protein catabolism under physiological conditions. In humans, mutations in the PAH gene lead to phenylketonuria (PKU), and most mutations are mainly associated with PAH misfolding and instability. The established treatment for PKU is a phenylalanine-restricted diet and, recently, supplementation with preparations of the natural tetrahydrobiopterin cofactor also shows effectiveness for some patients. Since 1997 there has been a significant increase in the understanding of the structure, catalytic mechanism, and regulation of PAH by its substrate and cofactor, in addition to improved correlations between genotype and phenotype in PKU. Importantly, there has also been an increased number of studies on the structure and function of PAH from bacteria and lower eukaryote organisms, revealing an additional anabolic role of the enzyme in the synthesis of melanin-like pigments. In this review, we discuss these recent studies, which contribute to define the evolutionary adaptation of the PAH structure and function leading to sophisticated regulation for effective catabolic processing of phenylalanine in mammalian organisms.

  9. Water versus DNA: new insights into proton track-structure modelling in radiobiology and radiotherapy.

    PubMed

    Champion, C; Quinto, M A; Monti, J M; Galassi, M E; Weck, P F; Fojón, O A; Hanssen, J; Rivarola, R D

    2015-10-21

    Water is a common surrogate of DNA for modelling the charged particle-induced ionizing processes in living tissue exposed to radiations. The present study aims at scrutinizing the validity of this approximation and then revealing new insights into proton-induced energy transfers by a comparative analysis between water and realistic biological medium. In this context, a self-consistent quantum mechanical modelling of the ionization and electron capture processes is reported within the continuum distorted wave-eikonal initial state framework for both isolated water molecules and DNA components impacted by proton beams. Their respective probability of occurrence-expressed in terms of total cross sections-as well as their energetic signature (potential and kinetic) are assessed in order to clearly emphasize the differences existing between realistic building blocks of living matter and the controverted water-medium surrogate. Consequences in radiobiology and radiotherapy will be discussed in particular in view of treatment planning refinement aiming at better radiotherapy strategies.

  10. Water versus DNA: new insights into proton track-structure modelling in radiobiology and radiotherapy

    NASA Astrophysics Data System (ADS)

    Champion, C.; Quinto, M. A.; Monti, J. M.; Galassi, M. E.; Weck, P. F.; Fojón, O. A.; Hanssen, J.; Rivarola, R. D.

    2015-10-01

    Water is a common surrogate of DNA for modelling the charged particle-induced ionizing processes in living tissue exposed to radiations. The present study aims at scrutinizing the validity of this approximation and then revealing new insights into proton-induced energy transfers by a comparative analysis between water and realistic biological medium. In this context, a self-consistent quantum mechanical modelling of the ionization and electron capture processes is reported within the continuum distorted wave-eikonal initial state framework for both isolated water molecules and DNA components impacted by proton beams. Their respective probability of occurrence—expressed in terms of total cross sections—as well as their energetic signature (potential and kinetic) are assessed in order to clearly emphasize the differences existing between realistic building blocks of living matter and the controverted water-medium surrogate. Consequences in radiobiology and radiotherapy will be discussed in particular in view of treatment planning refinement aiming at better radiotherapy strategies.

  11. Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: A theoretical analysis of structural elements

    SciTech Connect

    Bondar, A.N.; Suhai, Sandor; Fischer, S.; Smith, Jeremy C; Elstner, Marcus

    2006-10-01

    The transfer of a proton from the retinal Schiff base to the nearby Asp85 protein group is an essential step in the directional proton-pumping by bacteriorhodopsin. To avoid the wasteful back reprotonation of the Schiff base from Asp85, the protein must ensure that, following Schiff base deprotonation, the energy barrier for back proton-transfer from Asp85 to the Schiff base is larger than that for proton-transfer from the Schiff base to Asp85. Here, three structural elements that may contribute to suppressing the back proton-transfer from Asp85 to the Schiff base are investigated: (1) retinal twisting; (2) hydrogen-bonding distances in the active site; and (3) the number and location of internal water molecules. The impact of the pattern of bond twisting on the retinal deprotonation energy is dissected by performing an extensive set of quantum-mechanical calculations. Structural rearrangements in the active site, such as changes of the Thr89:Asp85 distance and relocation of water molecules hydrogen-bonding to the Asp85 acceptor group, may participate in the mechanism which ensures that following the transfer of the Schiff base proton to Asp85 the protein proceeds with the subsequent photocycle steps, and not with back proton transfer from Asp85 to the Schiff base.

  12. Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: A theoretical analysis of structural elements

    SciTech Connect

    Bondar, A.N.; Suhai, Sandor; Fischer, S.; Smith, Jeremy C; Elstner, Marcus

    2007-03-01

    The transfer of a proton from the retinal Schiff base to the nearby Asp85 protein group is an essential step in the directional proton-pumping by bacteriorhodopsin. To avoid the wasteful back reprotonation of the Schiff base from Asp85, the protein must ensure that, following Schiff base deprotonation, the energy barrier for back proton-transfer from Asp85 to the Schiff base is larger than that for proton-transfer from the Schiff base to Asp85. Here, three structural elements that may contribute to suppressing the back proton-transfer from Asp85 to the Schiff base are investigated: (i) retinal twisting; (ii) hydrogen-bonding distances in the active site; and (iii) the number and location of internal water molecules. The impact of the pattern of bond twisting on the retinal deprotonation energy is dissected by performing an extensive set of quantum-mechanical calculations. Structural rearrangements in the active site, such as changes of the Thr89:Asp85 distance and relocation of water molecules hydrogen-bonding to the Asp85 acceptor group, may participate in the mechanism which ensures that following the transfer of the Schiff base proton to Asp85 the protein proceeds with the subsequent photocycle steps, and not with back proton transfer from Asp85 to the Schiff base.

  13. Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: A theoretical analysis of structural elements.

    SciTech Connect

    Bondar, A.N.; Suhai, Sandor; Fischer, S.; Smith, Jeremy C; Elstner, Marcus

    2007-03-01

    The transfer of a proton from the retinal Schiff base to the nearby Asp85 protein group is an essential step in the directional proton-pumping by bacteriorhodopsin. To avoid the wasteful back reprotonation of the Schiff base from Asp85, the protein must ensure that, following Schiff base deprotonation, the energy barrier for back proton-transfer from Asp85 to the Schiff base is larger than that for proton-transfer from the Schiff base to Asp85. Here, three structural elements that may contribute to suppressing the back proton-transfer from Asp85 to the Schiff base are investigated: (1) retinal twisting; (2) hydrogen-bonding distances in the active site; and (3) the number and location of internal water molecules. The impact of the pattern of bond twisting on the retinal deprotonation energy is dissected by performing an extensive set of quantum-mechanical calculations. Structural rearrangements in the active site, such as changes of the Thr89:Asp85 distance and relocation of water molecules hydrogen-bonding to the Asp85 acceptor group, may participate in the mechanism which ensures that following the transfer of the Schiff base proton to Asp85 the protein proceeds with the subsequent photocycle steps, and not with back proton transfer from Asp85 to the Schiff base.

  14. Persistent changes in neuronal structure and synaptic plasticity caused by proton irradiation

    PubMed Central

    Parihar, Vipan K.; Pasha, Junaid; Tran, Katherine K.; Craver, Brianna M.; Acharya, Munjal M.; Limoli, Charles L.

    2014-01-01

    Cranial radiotherapy is used routinely to control the growth of primary and secondary brain tumors, but often results in serious and debilitating cognitive dysfunction. In part due to the beneficial dose depth distributions that may spare normal tissue damage, the use of protons to treat CNS and other tumor types is rapidly gaining popularity. Astronauts exposed to lower doses of protons in the space radiation environment are also at risk for developing adverse CNS complications. To explore the consequences of whole body proton irradiation, mice were subjected to 0.1 and 1 Gy and analyzed for morphometric changes in hippocampal neurons 10 and 30 days following exposure. Significant dose-dependent reductions (~33%) in dendritic complexity were found, when dendritic length, branching and area were analyzed 30 days after exposure. At equivalent doses and times, significant reductions in the number (~30%) and density (50–75%) of dendritic spines along hippocampal neurons of the dentate gyrus were also observed. Immature spines (filopodia, long) exhibited the greatest sensitivity (1.5–3 fold) to irradiation, while more mature spines (mushroom) were more resistant to changes over a 1-month post-irradiation timeframe. Irradiated granule cell neurons spanning the subfields of the dentate gyrus showed significant and dose-responsive reductions in synaptophysin expression, while the expression of postsynaptic density protein (PSD-95) was increased significantly. These findings corroborate our past work using photon irradiation, and demonstrate for the first time, dose-responsive changes in dendritic complexity, spine density and morphology and synaptic protein levels following exposure to low dose whole body proton irradiation. PMID:24446074

  15. The effect of proton disorder on the structure of ice-Ih: a theoretical study.

    PubMed

    Kuo, Jer-Lai; Klein, Michael L; Kuhs, Werner F

    2005-10-01

    A precise and accurate measurement of the crystal structure of ice-Ih is hindered by its disordered H-bond network. In this work, we carried out first-principle calculations to study the effects of H-bond topology on the structure of ice-Ih with emphasis on the molecular geometry of water and the distortion in oxygen lattice. An analytic algorithm based on group and graph theory is employed to enumerate all possible configurations in a given unit cell and to select a set of structures for detailed examinations. In total we have studied more than 60 ice-Ih structures in a hexagonal unit cell of 48 water molecules by quantum-chemical methods and found a significant amount of static distortion in the oxygen positions from their crystallographic positions which is in good agreements with highly significant higher-order terms obtained from both x-ray and neutron-diffraction data. Much debated structural information such as H-O-H angle and O-H bond length is found to be 106.34+/-0.36 degrees and 0.9997+/-0.0008 A, compared to experimental value of 106.6+/-1.5 degrees and 0.986+/-0.005 A. Detailed benchmarking calculations were carried out to gauge the influence of using different exchange and correlation functionals, pseudopotentials, and unit-cell sizes. Our results have proven that first-principle methods are useful complementary tools to experiments, especially for cases in which experimental accuracy is limited by intrinsic orientational disorder.

  16. Exotic Protonated Species Produced by UV-Induced Photofragmentation of a Protonated Dimer: Metastable Protonated Cinchonidine.

    PubMed

    Alata, Ivan; Scuderi, Debora; Lepere, Valeria; Steinmetz, Vincent; Gobert, Fabrice; Thiao-Layel, Loïc; Le Barbu-Debus, Katia; Zehnacker-Rentien, Anne

    2015-10-01

    A metastable protonated cinchona alkaloid was produced in the gas phase by UV-induced photodissociation (UVPD) of its protonated dimer in a Paul ion trap. The infrared multiple photon dissociation (IRMPD) spectrum of the molecular ion formed by UVPD was obtained and compared to DFT calculations to characterize its structure. The protonation site obtained thereby is not accessible by classical protonation ways. The protonated monomer directly formed in the ESI source or by collision-induced dissociation (CID) of the dimer undergoes protonation at the most basic alkaloid nitrogen. In contrast, protonation occurs at the quinoline aromatic ring nitrogen in the UVPD-formed monomer. PMID:26347997

  17. Exotic Protonated Species Produced by UV-Induced Photofragmentation of a Protonated Dimer: Metastable Protonated Cinchonidine.

    PubMed

    Alata, Ivan; Scuderi, Debora; Lepere, Valeria; Steinmetz, Vincent; Gobert, Fabrice; Thiao-Layel, Loïc; Le Barbu-Debus, Katia; Zehnacker-Rentien, Anne

    2015-10-01

    A metastable protonated cinchona alkaloid was produced in the gas phase by UV-induced photodissociation (UVPD) of its protonated dimer in a Paul ion trap. The infrared multiple photon dissociation (IRMPD) spectrum of the molecular ion formed by UVPD was obtained and compared to DFT calculations to characterize its structure. The protonation site obtained thereby is not accessible by classical protonation ways. The protonated monomer directly formed in the ESI source or by collision-induced dissociation (CID) of the dimer undergoes protonation at the most basic alkaloid nitrogen. In contrast, protonation occurs at the quinoline aromatic ring nitrogen in the UVPD-formed monomer.

  18. Connexinopathies: a structural and functional glimpse.

    PubMed

    García, Isaac E; Prado, Pavel; Pupo, Amaury; Jara, Oscar; Rojas-Gómez, Diana; Mujica, Paula; Flores-Muñoz, Carolina; González-Casanova, Jorge; Soto-Riveros, Carolina; Pinto, Bernardo I; Retamal, Mauricio A; González, Carlos; Martínez, Agustín D

    2016-01-01

    Mutations in human connexin (Cx) genes have been related to diseases, which we termed connexinopathies. Such hereditary disorders include nonsyndromic or syndromic deafness (Cx26, Cx30), Charcot Marie Tooth disease (Cx32), occulodentodigital dysplasia and cardiopathies (Cx43), and cataracts (Cx46, Cx50). Despite the clinical phenotypes of connexinopathies have been well documented, their pathogenic molecular determinants remain elusive. The purpose of this work is to identify common/uncommon patterns in channels function among Cx mutations linked to human diseases. To this end, we compiled and discussed the effect of mutations associated to Cx26, Cx32, Cx43, and Cx50 over gap junction channels and hemichannels, highlighting the function of the structural channel domains in which mutations are located and their possible role affecting oligomerization, gating and perm/selectivity processes.

  19. Connexinopathies: a structural and functional glimpse.

    PubMed

    García, Isaac E; Prado, Pavel; Pupo, Amaury; Jara, Oscar; Rojas-Gómez, Diana; Mujica, Paula; Flores-Muñoz, Carolina; González-Casanova, Jorge; Soto-Riveros, Carolina; Pinto, Bernardo I; Retamal, Mauricio A; González, Carlos; Martínez, Agustín D

    2016-01-01

    Mutations in human connexin (Cx) genes have been related to diseases, which we termed connexinopathies. Such hereditary disorders include nonsyndromic or syndromic deafness (Cx26, Cx30), Charcot Marie Tooth disease (Cx32), occulodentodigital dysplasia and cardiopathies (Cx43), and cataracts (Cx46, Cx50). Despite the clinical phenotypes of connexinopathies have been well documented, their pathogenic molecular determinants remain elusive. The purpose of this work is to identify common/uncommon patterns in channels function among Cx mutations linked to human diseases. To this end, we compiled and discussed the effect of mutations associated to Cx26, Cx32, Cx43, and Cx50 over gap junction channels and hemichannels, highlighting the function of the structural channel domains in which mutations are located and their possible role affecting oligomerization, gating and perm/selectivity processes. PMID:27228968

  20. Versatile hemidesmosomal linker proteins: structure and function.

    PubMed

    Chaudhari, Pratik R; Vaidya, Milind M

    2015-04-01

    Hemidesmosomes are anchoring junctions which connect basal epidermal cells to the extracellular matrix. In complex epithelia like skin, hemidesmosomes are composed of transmembrane proteins like α6β4 integrin, BP180, CD151 and cytoplasmic proteins like BPAG1e and plectin. BPAG1e and plectin are plakin family cytolinker proteins which anchor intermediate filament proteins i.e. keratins to the hemidesmosomal transmembrane proteins. Mutations in BPAG1e and plectin lead to severe skin blistering disorders. Recent reports indicate that these hemidesmosomal linker proteins play a role in various cellular processes like cell motility and cytoskeleton dynamics apart from their known anchoring function. In this review, we will discuss their role in structural and signaling functions.

  1. Androgen Modulation of Hippocampal Structure and Function

    PubMed Central

    Atwi, Sarah; McMahon, Dallan; Scharfman, Helen; MacLusky, Neil J.

    2016-01-01

    Androgens have profound effects on hippocampal structure and function, including induction of spines and spine synapses on the dendrites of CA1 pyramidal neurons, as well as alterations in long-term synaptic plasticity (LTP) and hippocampally dependent cognitive behaviors. How these effects occur remains largely unknown. Emerging evidence, however, suggests that one of the key elements in the response mechanism may be modulation of brain-derived neurotrophic factor (BDNF) in the mossy fiber (MF) system. In male rats, orchidectomy increases synaptic transmission and excitability in the MF pathway. Testosterone reverses these effects, suggesting that testosterone exerts tonic suppression on MF BDNF levels. These findings suggest that changes in hippocampal function resulting from declining androgen levels may reflect the outcome of responses mediated through normally balanced, but opposing, mechanisms: loss of androgen effects on the hippocampal circuitry may be compensated, at least in part, by an increase in BDNF-dependent MF plasticity. PMID:25416742

  2. Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif.

    PubMed

    Kim, Kuglae; Kwon, Soon-Kyeong; Jun, Sung-Hoon; Cha, Jeong Seok; Kim, Hoyoung; Lee, Weontae; Kim, Jihyun F; Cho, Hyun-Soo

    2016-01-01

    A novel light-driven chloride-pumping rhodopsin (ClR) containing an 'NTQ motif' in its putative ion conduction pathway has been discovered and functionally characterized in a genomic analysis study of a marine bacterium. Here we report the crystal structure of ClR from the flavobacterium Nonlabens marinus S1-08(T) determined under two conditions at 2.0 and 1.56 Å resolutions. The structures reveal two chloride-binding sites, one around the protonated Schiff base and the other on a cytoplasmic loop. We identify a '3 omega motif' formed by three non-consecutive aromatic amino acids that is correlated with the B-C loop orientation. Detailed ClR structural analyses with functional studies in E. coli reveal the chloride ion transduction pathway. Our results help understand the molecular mechanism and physiological role of ClR and provide a structural basis for optogenetic applications. PMID:27554809

  3. Structure, function and regulation of pyruvate carboxylase.

    PubMed Central

    Jitrapakdee, S; Wallace, J C

    1999-01-01

    Pyruvate carboxylase (PC; EC 6.4.1.1), a member of the biotin-dependent enzyme family, catalyses the ATP-dependent carboxylation of pyruvate to oxaloacetate. PC has been found in a wide variety of prokaryotes and eukaryotes. In mammals, PC plays a crucial role in gluconeogenesis and lipogenesis, in the biosynthesis of neurotransmitter substances, and in glucose-induced insulin secretion by pancreatic islets. The reaction catalysed by PC and the physical properties of the enzyme have been studied extensively. Although no high-resolution three-dimensional structure has yet been determined by X-ray crystallography, structural studies of PC have been conducted by electron microscopy, by limited proteolysis, and by cloning and sequencing of genes and cDNA encoding the enzyme. Most well characterized forms of active PC consist of four identical subunits arranged in a tetrahedron-like structure. Each subunit contains three functional domains: the biotin carboxylation domain, the transcarboxylation domain and the biotin carboxyl carrier domain. Different physiological conditions, including diabetes, hyperthyroidism, genetic obesity and postnatal development, increase the level of PC expression through transcriptional and translational mechanisms, whereas insulin inhibits PC expression. Glucocorticoids, glucagon and catecholamines cause an increase in PC activity or in the rate of pyruvate carboxylation in the short term. Molecular defects of PC in humans have recently been associated with four point mutations within the structural region of the PC gene, namely Val145-->Ala, Arg451-->Cys, Ala610-->Thr and Met743-->Thr. PMID:10229653

  4. Hot-embossing replication of self-centering optical fiber alignment structures prototyped by deep proton writing

    NASA Astrophysics Data System (ADS)

    Ebraert, Evert; Wissmann, Markus; Guttmann, Markus; Kolew, Alexander; Worgull, Matthias; Barié, Nicole; Schneider, Marc; Hofmann, Andreas; Beri, Stefano; Watté, Jan; Thienpont, Hugo; Van Erps, Jürgen

    2016-07-01

    This paper presents the hot-embossing replication of self-centering fiber alignment structures for high-precision, single-mode optical fiber connectors. To this end, a metal mold insert was fabricated by electroforming a polymer prototype patterned by means of deep proton writing (DPW). To achieve through-hole structures, we developed a postembossing process step to remove the residual layer inherently present in hot-embossed structures. The geometrical characteristics of the hot-embossed replicas are compared, before and after removal of the residual layer, with the DPW prototypes. Initial measurements on the optical performance of the replicas are performed. The successful replication of these components paves the way toward low-cost mass replication of DPW-fabricated prototypes in a variety of high-tech plastics.

  5. Sulfonic acid-functionalized hybrid organic-inorganic proton exchange membranes synthesized by sol-gel using 3-mercaptopropyl trimethoxysilane (MPTMS)

    NASA Astrophysics Data System (ADS)

    Mosa, J.; Durán, A.; Aparicio, M.

    2015-11-01

    Organic/inorganic hybrid membranes based on (3-glycidoxypropyl) trimethoxysilane (GPTMS) and 3-mercaptopropyl trimethoxysilane (MPTMS) have been prepared by sol-gel method and organic polymerisation, as candidate materials for proton exchange membranes in direct alcohol fuel cell (DMFC) applications. The -SH groups of MPTMS are oxidized to sulfonic acid groups, which are attributed to enhance the proton conductivity of hybrid membranes. FTIR, XPS and contact angle were used to characterize and confirm the hybrid structure and oxidation reaction progress. Membranes characterization also includes ion exchange capacity, water uptake, methanol permeability and proton conductivity to confirm their applicability in fuel cells. All the membranes were homogeneous and thermally and chemically resistant. In particular, the hybrid membranes demonstrated proton conductivities as high as 0.16 S cm-1 at high temperature, while exhibiting a low methanol permeability as compared to Nafion®. These results are associated with proton conducting paths through the silica pseudo-PEO network in which sulfonic acid groups work as proton donor.

  6. Protonated polynucleotides structures - 22.CD study of the acid-base titration of poly(dG).poly(dC).

    PubMed

    Marck, C; Thiele, D; Schneider, C; Guschlbauer, W

    1978-06-01

    The acid-base titration (pH 8 --> pH 2.5 --> pH 8) of eleven mixing curve samples of the poly(dG) plus poly(dC) system has been performed in 0.15 M NaCl. Upon protonation, poly(dG).poly(dC) gives rise to an acid complex, in various amounts according to the origin of the sample. We have established that the hysteresis of the acid-base titration is due to the non-reversible formation of an acid complex, and the liberation of the homopolymers at the end of the acid titration and during the base titration: the homopolymer mixtures remain stable up to pH 7. A 1G:1C stoichiometry appears to be the most probable for the acid complex, a 1G:2C stoichiometry, as found in poly(C(+)).poly(I).poly(C) or poly(C(+)).poly(G).poly(C), cannot be rejected. In the course of this study, evidence has been found that the structural consequences of protonation could be similar for both double stranded poly(dG).poly(dC) and G-C rich DNA's: 1) protonation starts near pH 6, dissociation of the acid complex of poly(dG).poly(dC) and of protonated DNA take place at pH 3; 2) the CD spectrum computed for the acid polymer complex displays a positive peak at 255 nm as found in the acid spectra of DNA's; 3) double stranded poly(dG).poly(dC) embedded in triple-stranded poly(dG).poly(dG).poly(dC) should be in the A-form and appears to be prevented from the proton induced conformational change. The neutral triple stranded poly(dG).poly(dG).poly(dC) appears therefore responsible, although indirectly, for the complexity and variability of the acid titration of poly(dG).poly(dC) samples.

  7. Models of protocellular structures, functions and evolution

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; New, Michael H.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    The central step in the origin of life was the emergence of organized structures from organic molecules available on the early earth. These predecessors to modern cells, called 'proto-cells,' were simple, membrane bounded structures able to maintain themselves, grow, divide, and evolve. Since there is no fossil record of these earliest of life forms, it is a scientific challenge to discover plausible mechanisms for how these entities formed and functioned. To meet this challenge, it is essential to create laboratory models of protocells that capture the main attributes associated with living systems, while remaining consistent with known, or inferred, protobiological conditions. This report provides an overview of a project which has focused on protocellular metabolism and the coupling of metabolism to energy transduction. We have assumed that the emergence of systems endowed with genomes and capable of Darwinian evolution was preceded by a pre-genomic phase, in which protocells functioned and evolved using mostly proteins, without self-replicating nucleic acids such as RNA.

  8. Red cell antigens: Structure and function

    PubMed Central

    Pourazar, Abbasali

    2007-01-01

    Landsteiner and his colleagues demonstrated that human beings could be classified into four groups depending on the presence of one (A) or another (B) or both (AB) or none (O) of the antigens on their red cells. The number of the blood group antigens up to 1984 was 410. In the next 20 years, there were 16 systems with 144 antigens and quite a collection of antigens waiting to be assigned to systems, pending the discovery of new information about their relationship to the established systems. The importance of most blood group antigens had been recognized by immunological complications of blood transfusion or pregnancies; their molecular structure and function however remained undefined for many decades. Recent advances in molecular genetics and cellular biochemistry resulted in an abundance of new information in this field of research. In this review, we try to give some examples of advances made in the field of ‘structure and function of the red cell surface molecules.’ PMID:21938229

  9. Eosinophil crystalloid granules: structure, function, and beyond

    PubMed Central

    Muniz, Valdirene S.; Weller, Peter F.; Neves, Josiane S.

    2012-01-01

    Eosinophils are granulocytes associated with host defense against parasitic helminths with allergic conditions and more recently, with immunoregulatory responses. Eosinophils are distinguished from leukocytes by their dominant population of cytoplasmic crystalloid (also termed secretory, specific, or secondary) granules that contain robust stores of diverse, preformed cationic proteins. Here, we provide an update on our knowledge about the unique and complex structure of human eosinophil crystalloid granules. We discuss their significance as rich sites of a variety of receptors and review our own recent research findings and those of others that highlight discoveries concerning the function of intracellular receptors and their potential implications in cell signaling. Special focus is provided on how eosinophils might use these intracellular receptors as mechanisms to secrete, selectively and rapidly, cytokines or chemokines and enable cell-free extracellular eosinophil granules to function as independent secretory structures. Potential roles of cell-free eosinophil granules as immune players in the absence of intact eosinophils will also be discussed. PMID:22672875

  10. Structure, function, and plasticity of GABA transporters

    PubMed Central

    Scimemi, Annalisa

    2014-01-01

    GABA transporters belong to a large family of neurotransmitter:sodium symporters. They are widely expressed throughout the brain, with different levels of expression in different brain regions. GABA transporters are present in neurons and in astrocytes and their activity is crucial to regulate the extracellular concentration of GABA under basal conditions and during ongoing synaptic events. Numerous efforts have been devoted to determine the structural and functional properties of GABA transporters. There is also evidence that the expression of GABA transporters on the cell membrane and their lateral mobility can be modulated by different intracellular signaling cascades. The strength of individual synaptic contacts and the activity of entire neuronal networks may be finely tuned by altering the density, distribution and diffusion rate of GABA transporters within the cell membrane. These findings are intriguing because they suggest the existence of complex regulatory systems that control the plasticity of GABAergic transmission in the brain. Here we review the current knowledge on the structural and functional properties of GABA transporters and highlight the molecular mechanisms that alter the expression and mobility of GABA transporters at central synapses. PMID:24987330

  11. The lipocalin protein family: structure and function.

    PubMed Central

    Flower, D R

    1996-01-01

    The lipocalin protein family is a large group of small extracellular proteins. The family demonstrates great diversity at the sequence level; however, most lipocalins share three characteristic conserved sequence motifs, the kernel lipocalins, while a group of more divergent family members, the outlier lipocalins, share only one. Belying this sequence dissimilarity, lipocalin crystal structures are highly conserved and comprise a single eight-stranded continuously hydrogen-bonded antiparallel beta-barrel, which encloses an internal ligand-binding site. Together with two other families of ligand-binding proteins, the fatty-acid-binding proteins (FABPs) and the avidins, the lipocalins form part of an overall structural superfamily: the calycins. Members of the lipocalin family are characterized by several common molecular-recognition properties: the ability to bind a range of small hydrophobic molecules, binding to specific cell-surface receptors and the formation of complexes with soluble macromolecules. The varied biological functions of the lipocalins are mediated by one or more of these properties. In the past, the lipocalins have been classified as transport proteins; however, it is now clear that the lipocalins exhibit great functional diversity, with roles in retinol transport, invertebrate cryptic coloration, olfaction and pheromone transport, and prostaglandin synthesis. The lipocalins have also been implicated in the regulation of cell homoeostasis and the modulation of the immune response, and, as carrier proteins, to act in the general clearance of endogenous and exogenous compounds. PMID:8761444

  12. Structure, expression and functions of MTA genes.

    PubMed

    Kumar, Rakesh; Wang, Rui-An

    2016-05-15

    Metastatic associated proteins (MTA) are integrators of upstream regulatory signals with the ability to act as master coregulators for modifying gene transcriptional activity. The MTA family includes three genes and multiple alternatively spliced variants. The MTA proteins neither have their own enzymatic activity nor have been shown to directly interact with DNA. However, MTA proteins interact with a variety of chromatin remodeling factors and complexes with enzymatic activities for modulating the plasticity of nucleosomes, leading to the repression or derepression of target genes or other extra-nuclear and nucleosome remodeling and histone deacetylase (NuRD)-complex independent activities. The functions of MTA family members are driven by the steady state levels and subcellular localization of MTA proteins, the dynamic nature of modifying signals and enzymes, the structural features and post-translational modification of protein domains, interactions with binding proteins, and the nature of the engaged and resulting features of nucleosomes in the proximity of target genes. In general, MTA1 and MTA2 are the most upregulated genes in human cancer and correlate well with aggressive phenotypes, therapeutic resistance, poor prognosis and ultimately, unfavorable survival of cancer patients. Here we will discuss the structure, expression and functions of the MTA family of genes in the context of cancer cells. PMID:26869315

  13. The influence of a transmembrane pH gradient on protonation probabilities of bacteriorhodopsin: the structural basis of the back-pressure effect.

    PubMed

    Calimet, Nicolas; Ullmann, G Matthias

    2004-06-01

    Bacteriorhodopsin pumps protons across a membrane using the energy of light. The proton pumping is inhibited when the transmembrane proton gradient that the protein generates becomes larger than four pH units. This phenomenon is known as the back-pressure effect. Here, we investigate the structural basis of this effect by predicting the influence of a transmembrane pH gradient on the titration behavior of bacteriorhodopsin. For this purpose we introduce a method that accounts for a pH gradient in protonation probability calculations. The method considers that in a transmembrane protein, which is exposed to two different aqueous phases, each titratable residue is accessible for protons from one side of the membrane depending on its hydrogen-bond pattern. This method is applied to several ground-state structures of bacteriorhodopsin, which residues already present complicated titration behaviors in the absence of a proton gradient. Our calculations show that a pH gradient across the membrane influences in a non-trivial manner the protonation probabilities of six titratable residues which are known to participate in the proton transfer: D85, D96, D115, E194, E204, and the Schiff base. The residues connected to one side of the membrane are influenced by the pH on the other side because of their long-range electrostatic interactions within the protein. In particular, D115 senses the pH at the cytoplasmic side of the membrane and transmits this information to D85 and the Schiff base. We propose that the strong electrostatic interactions found between D85, D115, and the Schiff base as well as the interplay of their respective protonation states under the influence of a transmembrane pH gradient are responsible for the back-pressure effect on bacteriorhodopsin.

  14. Structure and Function of KH Domains

    SciTech Connect

    Valverde, R.; Regan, E

    2008-01-01

    The hnRNP K homology (KH) domain was first identified in the protein human heterogeneous nuclear ribonucleoprotein K (hnRNP K) 14 years ago. Since then, KH domains have been identified as nucleic acid recognition motifs in proteins that perform a wide range of cellular functions. KH domains bind RNA or ssDNA, and are found in proteins associated with transcriptional and translational regulation, along with other cellular processes. Several diseases, e.g. fragile X mental retardation syndrome and paraneoplastic disease, are associated with the loss of function of a particular KH domain. Here we discuss the progress made towards understanding both general and specific features of the molecular recognition of nucleic acids by KH domains. The typical binding surface of KH domains is a cleft that is versatile but that can typically accommodate only four unpaired bases. Van der Waals forces and hydrophobic interactions and, to a lesser extent, electrostatic interactions, contribute to the nucleic acid binding affinity. 'Augmented' KH domains or multiple copies of KH domains within a protein are two strategies that are used to achieve greater affinity and specificity of nucleic acid binding. Isolated KH domains have been seen to crystallize as monomers, dimers and tetramers, but no published data support the formation of noncovalent higher-order oligomers by KH domains in solution. Much attention has been given in the literature to a conserved hydrophobic residue (typically Ile or Leu) that is present in most KH domains. The interest derives from the observation that an individual with this Ile mutated to Asn, in the KH2 domain of fragile X mental retardation protein, exhibits a particularly severe form of the syndrome. The structural effects of this mutation in the fragile X mental retardation protein KH2 domain have recently been reported. We discuss the use of analogous point mutations at this position in other KH domains to dissect both structure and function.

  15. Structure and physiological function of calpains.

    PubMed Central

    Sorimachi, H; Ishiura, S; Suzuki, K

    1997-01-01

    For a long time now, two ubiquitously expressed mammalian calpain isoenzymes have been used to explore the structure and function of calpain. Although these two calpains, mu- and m-calpains, still attract intensive interest because of their unique characteristics, various distinct homologues to the protease domain of mu- and m-calpains have been identified in a variety of organisms. Some of these 'novel' calpain homologues are involved in important biological functions. For example, p94 (also called calpain 3), a mammalian calpain homologue predominantly expressed in skeletal muscle, is genetically proved to be responsible for limb-girdle muscular dystrophy type 2A. Tra-3, a calpain homologue in nematodes, is involved in the sex determination cascade during early development. PalB, a key gene product involved in the alkaline adaptation of Aspergillus nidulans, is the first example of a calpain homologue present in fungi. These findings indicate various important functional roles for intracellular proteases belonging to the calpain superfamily. PMID:9396712

  16. Sialylation regulates brain structure and function

    PubMed Central

    Yoo, Seung-Wan; Motari, Mary G.; Susuki, Keiichiro; Prendergast, Jillian; Mountney, Andrea; Hurtado, Andres; Schnaar, Ronald L.

    2015-01-01

    Every cell expresses a molecularly diverse surface glycan coat (glycocalyx) comprising its interface with its cellular environment. In vertebrates, the terminal sugars of the glycocalyx are often sialic acids, 9-carbon backbone anionic sugars implicated in intermolecular and intercellular interactions. The vertebrate brain is particularly enriched in sialic acid-containing glycolipids termed gangliosides. Human congenital disorders of ganglioside biosynthesis result in paraplegia, epilepsy, and intellectual disability. To better understand sialoglycan functions in the nervous system, we studied brain anatomy, histology, biochemistry, and behavior in mice with engineered mutations in St3gal2 and St3gal3, sialyltransferase genes responsible for terminal sialylation of gangliosides and some glycoproteins. St3gal2/3 double-null mice displayed dysmyelination marked by a 40% reduction in major myelin proteins, 30% fewer myelinated axons, a 33% decrease in myelin thickness, and molecular disruptions at nodes of Ranvier. In part, these changes may be due to dysregulation of ganglioside-mediated oligodendroglial precursor cell proliferation. Neuronal markers were also reduced up to 40%, and hippocampal neurons had smaller dendritic arbors. Young adult St3gal2/3 double-null mice displayed impaired motor coordination, disturbed gait, and profound cognitive disability. Comparisons among sialyltransferase mutant mice provide insights into the functional roles of brain gangliosides and sialoglycoproteins consistent with related human congenital disorders.—Yoo, S.-W., Motari, M. G., Susuki, K., Prendergast, J., Mountney, A., Hurtado, A., Schnaar, R. L. Sialylation regulates brain structure and function. PMID:25846372

  17. Melanocortin 1 Receptor: Structure, Function, and Regulation

    PubMed Central

    Wolf Horrell, Erin M.; Boulanger, Mary C.; D’Orazio, John A.

    2016-01-01

    The melanocortin 1 receptor (MC1R) is a melanocytic Gs protein coupled receptor that regulates skin pigmentation, UV responses, and melanoma risk. It is a highly polymorphic gene, and loss of function correlates with a fair, UV-sensitive, and melanoma-prone phenotype due to defective epidermal melanization and sub-optimal DNA repair. MC1R signaling, achieved through adenylyl cyclase activation and generation of the second messenger cAMP, is hormonally controlled by the positive agonist melanocortin, the negative agonist agouti signaling protein, and the neutral antagonist β-defensin 3. Activation of cAMP signaling up-regulates melanin production and deposition in the epidermis which functions to limit UV penetration into the skin and enhances nucleotide excision repair (NER), the genomic stability pathway responsible for clearing UV photolesions from DNA to avoid mutagenesis. Herein we review MC1R structure and function and summarize our laboratory’s findings on the molecular mechanisms by which MC1R signaling impacts NER. PMID:27303435

  18. Phototriggered functionalization of hierarchically structured polymer brushes.

    PubMed

    de los Santos Pereira, Andres; Kostina, Nina Yu; Bruns, Michael; Rodriguez-Emmenegger, Cesar; Barner-Kowollik, Christopher

    2015-06-01

    The precise design of bioactive surfaces, essential for the advancement of many biomedical applications, depends on achieving control of the surface architecture as well as on the ability to attach bioreceptors to antifouling surfaces. Herein, we report a facile avenue toward hierarchically structured antifouling polymer brushes of oligo(ethylene glycol) methacrylates via surface-initiated atom transfer radical polymerization (SI-ATRP) presenting photoactive tetrazole moieties, which permitted their functionalization via nitrile imine-mediated tetrazole-ene cyclocloaddition (NITEC). A maleimide-functional ATRP initiator was photoclicked to the side chains of a brush enabling a subsequent polymerization of carboxybetaine acrylamide to generate a micropatterned graft-on-graft polymer architecture as evidenced by X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Furthermore, the spatially resolved biofunctionalization of the tetrazole-presenting brushes was accessed by the photoligation of biotin-maleimide and subsequent binding of streptavidin. The functionalized brushes bearing streptavidin were able to resist the fouling from blood plasma (90% reduction with respect to bare gold). Moreover, they were employed to demonstrate a model biosensor by immobilization of a biotinylated antibody and subsequent capture of an antigen as monitored in real time by surface plasmon resonance. PMID:25961109

  19. Structure, dynamics, and function of biomolecules

    SciTech Connect

    Frauenfelder, H.; Berendzen, J.R.; Garcia, A.; Gupta, G.; Olah, G.A.; Terwilliger, T.C.; Trewhella, J.; Wood, C.C.; Woodruff, W.H.

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors enhanced Los Alamos' core competency in Bioscience and Biotechnology by building on present strengths in experimental techniques, theory, high-performance computing, modeling, and simulation applied to biomolecular structure, dynamics, and function. Specifically, the authors strengthened their capabilities in neutron/x-ray scattering, x-ray crystallography, NMR, laser, and optical spectroscopies. Initially they focused on supporting the Los alamos Neutron Science Center (LANSCE) in the design and implementation of new neutron scattering instrumentation, they developed new methods for analysis of scattering data, and they developed new projects to study the structures of biomolecular complexes. The authors have also worked to strengthen interactions between theory and experiment, and between the biological and physical sciences. They sponsored regular meetings of members from all interested LANL technical divisions, and supported two lecture series: ''Biology for Physicists'' and ''Issues in Modern Biology''. They also supported the formation of interdisciplinary/inter-divisional teams to develop projects in science-based bioremediation and an integrated structural biology resource. Finally, they successfully worked with a multidisciplinary team to put forward the Laboratory's Genome and Beyond tactical goal.

  20. Structures and Energetics of Protonated Clusters of Methylamine with Phenylalanine Analogs, Characterized by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations.

    PubMed

    Kleisath, Elizabeth; Marta, Rick A; Martens, Sabrina; Martens, Jon; McMahon, Terry

    2015-06-25

    Gas-phase clusters of protonated methylamine and phenylalanine (Phe) derivatives have been studied using infrared multiple photon dissociation (IRMPD) spectroscopy in combination with electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. Experiments were performed on several Phe derivatives including 4-chloro-l-phenylalanine (4Chloro-Phe), 4-nitro-l-phenylalanine (4Nitro-Phe), 3-cyano-l-phenylalanine (3Cyano-Phe), and 3-trifluoromethyl-l-phenylalanine (3CF3-Phe). Through comparisons between experimental IRMPD spectra and stimulated spectra obtained by electronic structure calculations, charge-solvated structures were found to be prevalent in both 4Chloro-Phe and 4Nitro-Phe, whereas 3Cyano-Phe favored zwitterionic structures and 3-CF3-Phe likely have both zwitterionic and charge-solvated structures present.

  1. Proton NMR studies of the electronic structure of ZrH/sub x/

    NASA Technical Reports Server (NTRS)

    Attalla, A.; Bowman, R. C., Jr.; Craft, B. D.; Venturini, E. L.; Rhim, W. K.

    1982-01-01

    The proton spin lattice relaxation times and Knight shifts were measured in f.c.c. (delta-phase) and f.c.t. (epsilon-phase) ZrH/sub x/ for 1.5 or = to x or = to 2.0. Both parameters indicate that N(E/sub F/) is very dependent upon hydrogen content with a maximum occurring at ZrH1 83. This behavior is ascribed to modifications in N(E/sub F/) through a fcc/fct distortion in ZrH/sub x/ associated with a Jahn-Teller effect.

  2. Studies on sodium metasilicate plus hydrazine sulphate gel as a possible proton conductor: I. Structural and ion transport studies

    NASA Astrophysics Data System (ADS)

    Rai, D. K.; Chandra, S.

    1997-07-01

    The new proton-conducting gel system 0022-3727/30/14/016/img1 is reported. The gel system is prepared by an aqueous-based sol - gel process. Structural studies have been carried out using IR, XRD and DTA/TGA techniques. The gel systems possess new structural phases and are thermally stable relative to the starting materials. The ion-transport studies in the gel have been carried out using various techniques like polarization, coulometry, TIC and complex impedance spectroscopy. The gel compositions have been found to be predominantly ionically conducting 0022-3727/30/14/016/img2 at room temperature as well as at high temperatures. The main transporting species are identified to be protonic (0022-3727/30/14/016/img3 and 0022-3727/30/14/016/img4) with respective transference numbers 0022-3727/30/14/016/img5 and 0022-3727/30/14/016/img6 are also identified to be mobile in the gel network. The mobilities of these ions have been evaluated at various temperatures. The electrical conductivity of these gels is very high (0022-3727/30/14/016/img7) and is found to vary with composition, temperature and relative humidity.

  3. Nitric oxide synthases: structure, function and inhibition.

    PubMed Central

    Alderton, W K; Cooper, C E; Knowles, R G

    2001-01-01

    This review concentrates on advances in nitric oxide synthase (NOS) structure, function and inhibition made in the last seven years, during which time substantial advances have been made in our understanding of this enzyme family. There is now information on the enzyme structure at all levels from primary (amino acid sequence) to quaternary (dimerization, association with other proteins) structure. The crystal structures of the oxygenase domains of inducible NOS (iNOS) and vascular endothelial NOS (eNOS) allow us to interpret other information in the context of this important part of the enzyme, with its binding sites for iron protoporphyrin IX (haem), biopterin, L-arginine, and the many inhibitors which interact with them. The exact nature of the NOS reaction, its mechanism and its products continue to be sources of controversy. The role of the biopterin cofactor is now becoming clearer, with emerging data implicating one-electron redox cycling as well as the multiple allosteric effects on enzyme activity. Regulation of the NOSs has been described at all levels from gene transcription to covalent modification and allosteric regulation of the enzyme itself. A wide range of NOS inhibitors have been discussed, interacting with the enzyme in diverse ways in terms of site and mechanism of inhibition, time-dependence and selectivity for individual isoforms, although there are many pitfalls and misunderstandings of these aspects. Highly selective inhibitors of iNOS versus eNOS and neuronal NOS have been identified and some of these have potential in the treatment of a range of inflammatory and other conditions in which iNOS has been implicated. PMID:11463332

  4. Evolution of the Photon Structure Function.

    NASA Astrophysics Data System (ADS)

    da Luz Vieira, J. H.

    1987-09-01

    Available from UMI in association with The British Library. Requires signed TDF. From the earliest QCD calculations of the transverse structure function, F_sp{2}{ gamma}(x,Q^2), it was hoped that experimental measurements would provide a test of Lambda_{rm QCD }. However, there were difficulties with singularities which could be removed mathematically at the expense of introducing initial conditions defined at a minimum cut -off Q_sp{0}{2}. Two different approaches to evaluating the parton densities for F_sp{2}{gamma }(x,Q^2) are considered with the intention of evolving the structure function to Q^2 from Q_sp{0 }{2} at which the parton densities are defined from experimental data. One technique is suitable for generalization to incorporate the initial parton densities, and a model was developed to evolve F_sp {2}{gamma}(x,Q ^2). The resulting predictions for F _sp{2}{gamma}(x,Q ^2) were compared to existing results from other authors and to the available experimental data. Various theories concerning the hadronic parametrizations of the photon structure function at low Q^2 are considered and employed to parametrize the low Q^2 TPC data to obtain the initial parton densities at Q_sp{0}{2 } = 0.7 GeV^2. It is assumed that perturbative QCD can describe the evolution of F_sp{2}{gamma} (x,Q^2) for Q^2 > Q_sp{0}{2 }, but the results show that using hadronic initial conditions produces predictions which do not correspond to the data, therefore this assumption is wrong. The experimental data at Q^2 = 5.3 GeV^2 can be described by perturbative QCD and are therefore translated into the initial parton densities at Q_sp{0 }{2} = 5.3 GeV^2. One is correct in assuming that the evolution of F _sp{2}{gamma}(x,Q ^2) can be predicted in perturbative QCD for Q^2 > Q_sp {0}{2}, but little is understood about the photon at 1 < Q^2 < 5 GeV^2. The resulting predictions at higher Q^2 correspond well with the data however due to the experimental error bars Lambda_{QCD} cannot be measured.

  5. Electronic spectra and hyperpolarizabilities of structurally similar donor-acceptor dyes. A density functional theory analysis

    NASA Astrophysics Data System (ADS)

    Sarkar, Amrita; Das, Mousumi; Bagchi, Sanjib

    2015-12-01

    Studies with density functional theory (DFT) have been done to reinforce our previous experimental findings involving the solvatochromism and the effect of protonation and for three structurally similar donor-acceptor dyes exhibiting intramolecular charge transfer transition. These dyes have similar donor (indole N/amino N) site and similar carbonyl O as the acceptor centre. The dye with an amino N donor site and indanone O as the acceptor centre has the lowest value of the energy gap between HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) and highest percentage of charge transfer from the N to the O centre. Time dependent density functional theory (TDDFT) has been used to calculate the excitation energy to the lowest singlet excited dipole-allowed states of the dyes. Effect of solvation on excitation energy has been studied by the use of polarisable continuum model (PCM). Computational results indicate that the excitation energy of these dyes is sensitive to solvent polarity and exhibits a red shift as polarity increases. The calculated excitation energies are in good agreement with the values of absorption maximum of these dyes in different solvents obtained in experiment. Studies on protonation of the dyes show that the carbonyl O to be the most favourable site of protonation for all the three dyes. Calculations of linear and first hyperpolarizabilities indicate these dyes to be suitable candidates for possible non-linear optical application.

  6. Changes in protein structure and dynamics as a function of hydration from 1H second moments

    NASA Astrophysics Data System (ADS)

    Diakova, Galina; Goddard, Yanina A.; Korb, Jean-Pierre; Bryant, Robert G.

    2007-12-01

    We report the proton second moment obtained directly from the Free Induction Decay (FID) of the NMR signal of variously hydrated bovine serum albumin (BSA) and hen egg white lysozyme (HEWL) and from the width of the NMR Z-spectrum of the cross-linked protein gels of different concentrations. The second moment of the proteins decreases in a continuous stepwise way as a function of increasing water content, which suggests that the structural and dynamical changes occur in small incremental steps. Although the second moment is dominated by the short range distances of nearest neighbors, the changes in the second moment show that the protein structure becomes more open with increasing hydration level. A difference between the apparent liquid content of the sample as found from decomposition of the FID and the analytically determined water content demonstrates that water absorbed in the early stages of hydration is motionally immobilized and magnetically indistinguishable from rigid protein protons while at high hydration levels some protein side-chain protons move rapidly contributing to liquid-like component of the NMR signal.

  7. Revealing proton shape fluctuations with incoherent diffraction at high energy

    NASA Astrophysics Data System (ADS)

    Mäntysaari, Heikki; Schenke, Björn

    2016-08-01

    The differential cross section of exclusive diffractive vector meson production in electron proton collisions carries important information on the geometric structure of the proton. More specifically, the coherent cross section as a function of the transferred transverse momentum is sensitive to the size of the proton, while the incoherent or proton dissociative cross section is sensitive to fluctuations of the gluon distribution in coordinate space. We show that at high energies the experimentally measured coherent and incoherent cross sections for the production of J /Ψ mesons are very well reproduced within the color glass condensate framework when strong geometric fluctuations of the gluon distribution in the proton are included. For ρ meson production, we also find reasonable agreement. We study in detail the dependence of our results on various model parameters, including the average proton shape, analyze the effect of saturation scale and color charge fluctuations and constrain the degree of geometric fluctuations.

  8. Water versus DNA: New insights into proton track-structure modeling in radiobiology and radiotherapy

    SciTech Connect

    Champion, Christophe; Galassi, Mariel E.; Weck, Philippe F.; Fojon, Omar A.; Hanssen, Jocelyn; Rivarola, Roberto D.

    2015-09-25

    Water is a common surrogate of DNA for modelling the charged particle-induced ionizing processes in living tissue exposed to radiations. The present study aims at scrutinizing the validity of this approximation and then revealing new insights into proton-induced energy transfers by a comparative analysis between water and realistic biological medium. In this context, a self-consistent quantum mechanical modelling of the ionization and electron capture processes is reported within the continuum distorted wave-eikonal initial state framework for both isolated water molecules and DNA components impacted by proton beams. Their respective probability of occurrence-expressed in terms of total cross sections-as well as their energetic signature (potential and kinetic) are assessed in order to clearly emphasize the differences existing between realistic building blocks of living matter and the controverted water-medium surrogate. Thus the consequences in radiobiology and radiotherapy will be discussed in particular in view of treatment planning refinement aiming at better radiotherapy strategies.

  9. Water versus DNA: New insights into proton track-structure modeling in radiobiology and radiotherapy

    DOE PAGES

    Champion, Christophe; Quinto, Michele A.; Monti, Juan M.; Galassi, Mariel E.; Weck, Philippe F.; Fojon, Omar A.; Hanssen, Jocelyn; Rivarola, Roberto D.

    2015-09-25

    Water is a common surrogate of DNA for modelling the charged particle-induced ionizing processes in living tissue exposed to radiations. The present study aims at scrutinizing the validity of this approximation and then revealing new insights into proton-induced energy transfers by a comparative analysis between water and realistic biological medium. In this context, a self-consistent quantum mechanical modelling of the ionization and electron capture processes is reported within the continuum distorted wave-eikonal initial state framework for both isolated water molecules and DNA components impacted by proton beams. Their respective probability of occurrence-expressed in terms of total cross sections-as well asmore » their energetic signature (potential and kinetic) are assessed in order to clearly emphasize the differences existing between realistic building blocks of living matter and the controverted water-medium surrogate. Thus the consequences in radiobiology and radiotherapy will be discussed in particular in view of treatment planning refinement aiming at better radiotherapy strategies.« less

  10. Ordered structures in proton conducting membranes from supramolecular liquid crystal polymers.

    PubMed

    Every, Hayley A; Mendes, Eduardo; Picken, Stephen J

    2006-11-30

    Highly sulfonated forms of poly(p-phenylene terephthalamide) (PPTA) have been prepared in three different molecular configurations; sulfonated diamine form (S-PPTA), sulfonated terephthalic acid form (S-invert-PPTA), and the bi-sulfonated form (S2-PPTA). All three polymers are water soluble to a certain degree and films were cast from solution for S-PPTA and S-invert-PPTA. S-PPTA films absorb less water than S-invert-PPTA (under controlled humidity conditions) and consequently, the conductivity for this polymer is also slightly lower. Although the conductivities are comparable to Nafion (of the order of 10(-2) to 10(-1) Scm(-1)), proton mobility is more restricted. X-ray diffraction showed that the rigid molecules are aligned in opposite directions for the two polymer films, being homeotropic in S-PPTA films and planar for S-invert-PPTA. SEM analysis demonstrated layering in the same direction as the alignment of the polymer chains. The variation in the polymer alignment is most likely the result of the differences in the solution properties and the film forming process. It is possible, however, that this alignment could be exploited to enhance proton transport and thus these films are of interest for fuel cell membranes. PMID:17125333

  11. Twist expansion of Drell-Yan structure functions in color dipole approach

    NASA Astrophysics Data System (ADS)

    Motyka, Leszek; Sadzikowski, Mariusz; Stebel, Tomasz

    2015-05-01

    The forward Drell-Yan process at the LHC probes the proton structure at a very small Bjorken- x and moderate hard scales. In this kinematical domain higher twist effects may be significant and introduce sizeable corrections to the standard leading twist description. We study the forward Drell-Yan process beyond the leading twist approximation within the color dipole model framework that incorporates multiple scattering effects. We derive the Mellin representation of the forward Drell-Yan impact factors for fully differential cross-sections. These results combined with the color dipole cross-section of the saturation model are used to perform the twist expansion of the Drell-Yan structure functions at arbitrary transverse momentum q T of the Drell-Yan pair and also of the structure functions integrated over q T . We also investigate the Lam-Tung relation, find that it is broken at twist 4 and provide explicit estimates for the breaking term.

  12. Structure and function of eukaryotic chromosomes

    SciTech Connect

    Hennig, W.

    1987-01-01

    Contents: Introduction; Polytene Chromosomel Giant Chromosomes in Ciliates; The sp-I Genes in the Balbiani Rings of Chironomus Salivary Glands; The White Locus of Drosophila Melanogaster; The Genetic and Molecular Organization of the Dense Cluster of Functionally Related Vital Genes in the DOPA Decarboxylase Region of the Drosophila melanogaster Genome; Heat Shock Puffs and Response to Environmental Stress; The Y Chromosomal Lampbrush Loops of Drosophila; Contributions of Electron Microscopic Spreading Preparations (''Miller Spreads'') to the Analysis of Chromosome Structure; Replication of DNA in Eukaryotic Chromosomes; Gene Amplification in Dipteran Chromosomes; The Significance of Plant Transposable Elements in Biologically Relevant Processes; Arrangement of Chromosomes in Interphase Cell Nuclei; Heterochromatin and the Phenomenon of Chromosome Banding; Multiple Nonhistone Protein-DNA Complexes in Chromatin Regulate the Cell- and Stage-Specific Activity of an Eukaryotic Gene; Genetics of Sex Determination in Eukaryotes; Application of Basic Chromosome Research in Biotechnology and Medicine. This book presents an overview of various aspects of chromosome research.

  13. Aegerolysins: Structure, function, and putative biological role

    PubMed Central

    Berne, Sabina; Lah, Ljerka; Sepčić, Kristina

    2009-01-01

    Aegerolysins, discovered in fungi, bacteria and plants, are highly similar proteins with interesting biological properties. Certain aegerolysins possess antitumoral, antiproliferative, and antibacterial activities. Further possible medicinal applications include their use in the prevention of atherosclerosis, or as vaccines. Additional biotechnological value of fungal aegerolysins lies in their involvement in development, which could improve cultivation of commercially important edible mushrooms. Besides, new insights on microheterogeneity of raft-like membrane domains could be gained by using aegerolysins as specific markers in cell and molecular biology. Although the exact function of aegerolysins in their producing organisms remains to be explained, they are biochemically well characterized all-β structured proteins sharing the following common features: low isoelectric points, similar molecular weights (15–17 kDa), and stability in a wide pH range. PMID:19309687

  14. Structure and Function of RSV Surface Glycoproteins

    PubMed Central

    McLellan, Jason S.; Ray, William C.; Peeples, Mark E.

    2014-01-01

    The two major glycoproteins on the surface of the RSV virion, the attachment glycoprotein (G) and the fusion (F) glycoprotein, control the initial phases of infection. G targets the ciliated cells of the airways, and F causes the virion membrane to fuse with a target cell membrane. The F protein is the major target for antiviral drug development, and both G and F glycoproteins are the antigens targeted by neutralizing antibodies induced by infection. In this chapter we review the structure and function of the RSV surface glycoproteins, including recent X-ray crystallographic data of the F glycoprotein in its pre- and postfusion conformations, and discuss how this information informs antigen selection and vaccine development. PMID:24362685

  15. Sheet metal hydroforming of functional composite structures

    NASA Astrophysics Data System (ADS)

    Ibis, M.; Griesheimer, S.; Salun, L.; Rausch, J.; Groche, P.

    2011-03-01

    This paper studies the formability of functional composite structures, consisting of a metal substrate, insulating plastic foils, flat copper conductors and printable conductive polymers. The aim is the production of smart components in a sheet metal hydroforming process. In addition to their mechanical properties, these components can also transfer energy and data. Conventional boundaries between mechanics and electronics will be relaxed expediently. The challenge of this study is the design of the forming process, so that all elements of the multi-layer composites will withstand the process conditions. In this context, an analytical method for estimating the formability of these smart components is presented. The main objectives are the definition of basic failure modes and the depiction of the process limits.

  16. Structural and functional diversity of desmosomes.

    PubMed

    Harmon, Robert M; Green, Kathleen J

    2013-12-01

    Desmosomes anchor intermediate filaments at sites of cell contact established by the interaction of cadherins extending from opposing cells. The incorporation of cadherins, catenin adaptors, and cytoskeletal elements resembles the closely related adherens junction. However, the recruitment of intermediate filaments distinguishes desmosomes and imparts a unique function. By linking the load-bearing intermediate filaments of neighboring cells, desmosomes create mechanically contiguous cell sheets and, in so doing, confer structural integrity to the tissues they populate. This trait and a well-established role in human disease have long captured the attention of cell biologists, as evidenced by a publication record dating back to the mid-1860s. Likewise, emerging data implicating the desmosome in signaling events pertinent to organismal development, carcinogenesis, and genetic disorders will secure a prominent role for desmosomes in future biological and biomedical investigations.

  17. Models of Protocellular Structure, Function and Evolution

    NASA Technical Reports Server (NTRS)

    New, Michael H.; Pohorille, Andrew; Szostak, Jack W.; Keefe, Tony; Lanyi, Janos K.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    In the absence of any record of protocells, the most direct way to test our understanding, of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction.

  18. Microbial light-activatable proton pumps as neuronal inhibitors to functionally dissect neuronal networks in C. elegans.

    PubMed

    Husson, Steven J; Liewald, Jana F; Schultheis, Christian; Stirman, Jeffrey N; Lu, Hang; Gottschalk, Alexander

    2012-01-01

    Essentially any behavior in simple and complex animals depends on neuronal network function. Currently, the best-defined system to study neuronal circuits is the nematode Caenorhabditis elegans, as the connectivity of its 302 neurons is exactly known. Individual neurons can be activated by photostimulation of Channelrhodopsin-2 (ChR2) using blue light, allowing to directly probe the importance of a particular neuron for the respective behavioral output of the network under study. In analogy, other excitable cells can be inhibited by expressing Halorhodopsin from Natronomonas pharaonis (NpHR) and subsequent illumination with yellow light. However, inhibiting C. elegans neurons using NpHR is difficult. Recently, proton pumps from various sources were established as valuable alternative hyperpolarizers. Here we show that archaerhodopsin-3 (Arch) from Halorubrum sodomense and a proton pump from the fungus Leptosphaeria maculans (Mac) can be utilized to effectively inhibit excitable cells in C. elegans. Arch is the most powerful hyperpolarizer when illuminated with yellow or green light while the action spectrum of Mac is more blue-shifted, as analyzed by light-evoked behaviors and electrophysiology. This allows these tools to be combined in various ways with ChR2 to analyze different subsets of neurons within a circuit. We exemplify this by means of the polymodal aversive sensory ASH neurons, and the downstream command interneurons to which ASH neurons signal to trigger a reversal followed by a directional turn. Photostimulating ASH and subsequently inhibiting command interneurons using two-color illumination of different body segments, allows investigating temporal aspects of signaling downstream of ASH. PMID:22815873

  19. Nuclear effects in the deuteron structure function

    NASA Astrophysics Data System (ADS)

    Epele, L. N.; Fanchiotti, H.; Canal, C. A. García; Sassot, R.

    1992-08-01

    An analysis of nuclear effects in the deuteron quark distributions is carried out in connection with the Gottfried sum rule (GSR), the Drell-Yan proton-neutron asymmetry and the Bjorken sum rule (BSR). It is shown that the small amount of nuclear effects necessary to saturate the GSR experimental data modifies the Drell-Yan asymmetry in an entirely different way as an asymmetric sea does. These effects are of little consequence in the convergence of the BSR to the expected value.

  20. Crystal structure of the CueO mutants at Glu506, the key amino acid located in the proton transfer pathway for dioxygen reduction

    SciTech Connect

    Komori, Hirofumi; Kajikawa, Takao; Kataoka, Kunishige; Higuchi, Yoshiki; Sakurai, Takeshi

    2013-09-06

    Highlights: •Proton transfer pathway in the four-electron reduction of dioxygen by CueO. •Compensatory hydrogen bond network comprised of only water molecules in the Glu to Ala mutant. •Shutdown of the hydrogen bond network by the Glu to Ile mutation. •X-ray crystal structures of the CueO mutants with the modified proton transport pathway. -- Abstract: Glu506 involved in the hydrogen bond network leading from solvent waters to the trinuclear copper center in a multicopper oxidase, CueO plays a crucial role to transport protons in the four-electron reduction of dioxygen to water. We performed X-ray crystal structure analyses of the Glu506Ala and Glu506Ile mutants, showing the formation of a compensatory proton transport pathway with only water molecules and a disruption of the hydrogen bond network due to the bulky side chain, respectively. We discuss the efficiency of proton transport through the hydrogen bond network based on the present results and our previous modification of the proton transport pathway by the Glu506 to Gln mutation, which have allowed us to trap and characterize the reaction intermediates.

  1. Structure, Function, and Evolution of Rice Centromeres

    SciTech Connect

    Jiang, Jiming

    2010-02-04

    The centromere is the most characteristic landmark of eukaryotic chromosomes. Centromeres function as the site for kinetochore assembly and spindle attachment, allowing for the faithful pairing and segregation of sister chromatids during cell division. Characterization of centromeric DNA is not only essential to understand the structure and organization of plant genomes, but it is also a critical step in the development of plant artificial chromosomes. The centromeres of most model eukaryotic species, consist predominantly of long arrays of satellite DNA. Determining the precise DNA boundary of a centromere has proven to be a difficult task in multicellular eukaryotes. We have successfully cloned and sequenced the centromere of rice chromosome 8 (Cen8), representing the first fully sequenced centromere from any multicellular eukaryotes. The functional core of Cen8 spans ~800 kb of DNA, which was determined by chromatin immunoprecipitation (ChIP) using an antibody against the rice centromere-specific H3 histone. We discovered 16 actively transcribed genes distributed throughout the Cen8 region. In addition to Cen8, we have characterized eight additional rice centromeres using the next generation sequencing technology. We discovered four subfamilies of the CRR retrotransposon that is highly enriched in rice centromeres. CRR elements are constitutively transcribed and different CRR subfamilies are differentially processed by RNAi. These results suggest that different CRR subfamilies may play different roles in the RNAi-mediated pathway for formation and maintenance of centromeric chromatin.

  2. The Structural and Functional Organization of Cognition

    PubMed Central

    Snow, Peter J.

    2016-01-01

    This article proposes that what have been historically and contemporarily defined as different domains of human cognition are served by one of four functionally- and structurally-distinct areas of the prefrontal cortex (PFC). Their contributions to human intelligence are as follows: (a) BA9, enables our emotional intelligence, engaging the psychosocial domain; (b) BA47, enables our practical intelligence, engaging the material domain; (c) BA46 (or BA46-9/46), enables our abstract intelligence, engaging the hypothetical domain; and (d) BA10, enables our temporal intelligence, engaging in planning within any of the other three domains. Given their unique contribution to human cognition, it is proposed that these areas be called the, social (BA9), material (BA47), abstract (BA46-9/46) and temporal (BA10) mind. The evidence that BA47 participates strongly in verbal and gestural communication suggests that language evolved primarily as a consequence of the extreme selective pressure for practicality; an observation supported by the functional connectivity between BA47 and orbital areas that negatively reinforce lying. It is further proposed that the abstract mind (BA46-9/46) is the primary seat of metacognition charged with creating adaptive behavioral strategies by generating higher-order concepts (hypotheses) from lower-order concepts originating from the other three domains of cognition. PMID:27799901

  3. Structure and functionality of bromine doped graphite.

    PubMed

    Hamdan, Rashid; Kemper, A F; Cao, Chao; Cheng, H P

    2013-04-28

    First-principles calculations are used to study the enhanced in-plane conductivity observed experimentally in Br-doped graphite, and to study the effect of external stress on the structure and functionality of such systems. The model used in the numerical calculations is that of stage two doped graphite. The band structure near the Fermi surface of the doped systems with different bromine concentrations is compared to that of pure graphite, and the charge transfer between carbon and bromine atoms is analyzed to understand the conductivity change along different high symmetry directions. Our calculations show that, for large interlayer separation between doped graphite layers, bromine is stable in the molecular form (Br2). However, with increased compression (decreased layer-layer separation) Br2 molecules tend to dissociate. While in both forms, bromine is an electron acceptor. The charge exchange between the graphite layers and Br atoms is higher than that with Br2 molecules. Electron transfer to the Br atoms increases the number of hole carriers in the graphite sheets, resulting in an increase of conductivity. PMID:23635160

  4. Bromodomains: Structure, function and pharmacology of inhibition.

    PubMed

    Ferri, Elena; Petosa, Carlo; McKenna, Charles E

    2016-04-15

    Bromodomains are epigenetic readers of histone acetylation involved in chromatin remodeling and transcriptional regulation. The human proteome comprises 46 bromodomain-containing proteins with a total of 61 bromodomains, which, despite highly conserved structural features, recognize a wide array of natural peptide ligands. Over the past five years, bromodomains have attracted great interest as promising new epigenetic targets for diverse human diseases, including inflammation, cancer, and cardiovascular disease. The demonstration in 2010 that two small molecule compounds, JQ1 and I-BET762, potently inhibit proteins of the bromodomain and extra-terminal (BET) family with translational potential for cancer and inflammatory disease sparked intense efforts in academia and pharmaceutical industry to develop novel bromodomain antagonists for therapeutic applications. Several BET inhibitors are already in clinical trials for hematological malignancies, solid tumors and cardiovascular disease. Currently, the field faces the challenge of single-target selectivity, especially within the BET family, and of overcoming problems related to the development of drug resistance. At the same time, new trends in bromodomain inhibitor research are emerging, including an increased interest in non-BET bromodomains and a focus on drug synergy with established antitumor agents to improve chemotherapeutic efficacy. This review presents an updated view of the structure and function of bromodomains, traces the development of bromodomain inhibitors and their potential therapeutic applications, and surveys the current challenges and future directions of this vibrant new field in drug discovery.

  5. Bromodomains: Structure, function and pharmacology of inhibition.

    PubMed

    Ferri, Elena; Petosa, Carlo; McKenna, Charles E

    2016-04-15

    Bromodomains are epigenetic readers of histone acetylation involved in chromatin remodeling and transcriptional regulation. The human proteome comprises 46 bromodomain-containing proteins with a total of 61 bromodomains, which, despite highly conserved structural features, recognize a wide array of natural peptide ligands. Over the past five years, bromodomains have attracted great interest as promising new epigenetic targets for diverse human diseases, including inflammation, cancer, and cardiovascular disease. The demonstration in 2010 that two small molecule compounds, JQ1 and I-BET762, potently inhibit proteins of the bromodomain and extra-terminal (BET) family with translational potential for cancer and inflammatory disease sparked intense efforts in academia and pharmaceutical industry to develop novel bromodomain antagonists for therapeutic applications. Several BET inhibitors are already in clinical trials for hematological malignancies, solid tumors and cardiovascular disease. Currently, the field faces the challenge of single-target selectivity, especially within the BET family, and of overcoming problems related to the development of drug resistance. At the same time, new trends in bromodomain inhibitor research are emerging, including an increased interest in non-BET bromodomains and a focus on drug synergy with established antitumor agents to improve chemotherapeutic efficacy. This review presents an updated view of the structure and function of bromodomains, traces the development of bromodomain inhibitors and their potential therapeutic applications, and surveys the current challenges and future directions of this vibrant new field in drug discovery. PMID:26707800

  6. Structure and functionality of bromine doped graphite

    SciTech Connect

    Hamdan, Rashid; Kemper, A. F.; Cao Chao; Cheng, H. P.

    2013-04-28

    First-principles calculations are used to study the enhanced in-plane conductivity observed experimentally in Br-doped graphite, and to study the effect of external stress on the structure and functionality of such systems. The model used in the numerical calculations is that of stage two doped graphite. The band structure near the Fermi surface of the doped systems with different bromine concentrations is compared to that of pure graphite, and the charge transfer between carbon and bromine atoms is analyzed to understand the conductivity change along different high symmetry directions. Our calculations show that, for large interlayer separation between doped graphite layers, bromine is stable in the molecular form (Br{sub 2}). However, with increased compression (decreased layer-layer separation) Br{sub 2} molecules tend to dissociate. While in both forms, bromine is an electron acceptor. The charge exchange between the graphite layers and Br atoms is higher than that with Br{sub 2} molecules. Electron transfer to the Br atoms increases the number of hole carriers in the graphite sheets, resulting in an increase of conductivity.

  7. Structure and functionality of bromine doped graphite.

    PubMed

    Hamdan, Rashid; Kemper, A F; Cao, Chao; Cheng, H P

    2013-04-28

    First-principles calculations are used to study the enhanced in-plane conductivity observed experimentally in Br-doped graphite, and to study the effect of external stress on the structure and functionality of such systems. The model used in the numerical calculations is that of stage two doped graphite. The band structure near the Fermi surface of the doped systems with different bromine concentrations is compared to that of pure graphite, and the charge transfer between carbon and bromine atoms is analyzed to understand the conductivity change along different high symmetry directions. Our calculations show that, for large interlayer separation between doped graphite layers, bromine is stable in the molecular form (Br2). However, with increased compression (decreased layer-layer separation) Br2 molecules tend to dissociate. While in both forms, bromine is an electron acceptor. The charge exchange between the graphite layers and Br atoms is higher than that with Br2 molecules. Electron transfer to the Br atoms increases the number of hole carriers in the graphite sheets, resulting in an increase of conductivity.

  8. Structure and function of carbonic anhydrases.

    PubMed

    Supuran, Claudiu T

    2016-07-15

    Carbonic anhydrases (CAs, EC 4.2.1.1) catalyse the interconversion between CO2 and bicarbonate as well as other hydrolytic reactions. Among the six genetic families known to date, the α-, β-, γ-, δ-, ζ- and η-CAs, detailed kinetic and X-ray crystallographic studies have allowed a deep understanding of the structure-function relationship in this superfamily of proteins. A metal hydroxide nucleophilic species of the enzyme, and a unique active site architecture, with half of it hydrophilic and the opposing part hydrophobic, allow these enzymes to act as some of the most effective catalysts known in Nature. The CA activation and inhibition mechanisms are also known in detail, with a large number of new inhibitor classes being described in the last years. Apart from the zinc binders, some classes of inhibitors anchor to the metal ion coordinated nucleophile, others occlude the entrance of the active site cavity and more recently, compounds binding outside the active site were described. CA inhibition has therapeutic applications for drugs acting as diuretics, antiepileptics, antiglaucoma, antiobesity and antitumour agents. Targeting such enzymes from pathogens may lead to novel anti-infectives. Successful structure-based drug design campaigns allowed the discovery of highly isoform selective CA inhibitors (CAIs), which may lead to a new generation of drugs targeting these widespread enzymes. The use of CAs in CO2 capture processes for mitigating the global temperature rise has also been investigated more recently. PMID:27407171

  9. Local duality in spin structure functions g1(p) and g1(d)

    SciTech Connect

    Yelena Prok

    2006-02-01

    Inclusive double spin asymmetries obtained by scattering polarized electrons off polarized protons and deuterons have been analyzed to address the issue of quark hadron duality in the polarized spin structure functions gp 1 and gd 1. A polarized electron beam, solid polarized NH3 and ND3 targets and the CEBAF Large Acceptance Spectrometer (CLAS) in Hall B were used to collect the data. The resulting gp 1 and gd 1 were averaged over the nucleon resonance energy region (M

  10. The proton structure in the region of high x{sub B}

    SciTech Connect

    Sanches, S. M. Jr.; Steffens, F. M.

    2013-03-25

    The hadron structure has been intensively studied over the last 20 years, but mostly in regions of medium and low Bjorken x. On the other hand, there are large experimental projects (Jlab 12 GeV and CERN COMPASS-II) that will produce a lot of data on lepton-nucleon deep inelastic scattering in kinematics regions not study yet, like the region where the parton carries a large momentum fraction of the parent nucleon. It is well known from literature that the high x{sub B} region is quite problematic, because, among other things, one needs to deal with the nucleon resonance region. To avoid this region, one should have an invariant mass for the system greater than 2 GeV. One can do this by lowering the values for x{sub B} (irrelevant for our current research), or by decreasing the value of Q{sup 2}. In the later case, there are not many experimental data and the projects mentioned will try to fill this gap. When one is in the low Q{sup 2} region, an extra problem appears: corrections in the form of M{sup 2}/Q{sup 2}, usually disregarded in the OPE expansion, have now to be taken care of. These corrections are referred to as Target Mass Corrections (TMC). Our work aims to find clean ways to separate these TMC from the experimental data and thus related them to the usual structure functions, measured in other experiments, with are free of effects coming from the finite value of the nucleon mass.

  11. Proton Pathways in Green Fluorescence Protein

    PubMed Central

    Agmon, Noam

    2005-01-01

    Proton pathways in green fluorescent protein (GFP) are more extended than previously reported. In the x-ray data of wild-type GFP, a two-step exit pathway exists from the active site to the protein surface, controlled by a threonine switch. A proton entry pathway begins at a glutamate-lysine cluster around Glu-5, and extends all the way to the buried Glu-222 near the active site. This structural evidence suggests that GFP may function as a portable light-driven proton-pump, with proton emitted in the excited state through the switchable exit pathway, and replenished from Glu-222 and the Glu-5 entry pathway in the ground state. PMID:15681647

  12. W-charge asymmetry at CDF, tests of structure functions

    SciTech Connect

    Budd, H.S.

    1994-09-01

    The charge asymmetry of W-bosons produced in p{bar p} collisions has been measured using 19,039 W {yields} e{nu} and W {yields} {mu}{nu} decays recorded by the CDF detector during the 1992-93 Tevatron collider run. The asymmetry is sensitive to the slope of the proton`s d/u quark distribution ratio down to x < 0.01 at Q{sup 2} {approx} M{sub W}{sup 2}, where nonperturbative QCD effects are minimal. Of recent parton distribution functions, those of Martin, Roberts and Stirling are favored over those of the CTEQ collaboration. This difference is seen even though both sets agree, at the level of the nuclear shadowing corrections, with the recent NMC measurements of F{sub 2}{sup {mu}n}/F{sub 2}{sup {mu}p}.

  13. New excitation functions for proton induced reactions on natural titanium, nickel and copper up to 70 MeV

    NASA Astrophysics Data System (ADS)

    Garrido, E.; Duchemin, C.; Guertin, A.; Haddad, F.; Michel, N.; Métivier, V.

    2016-09-01

    New excitation functions for proton induced nuclear reactions on natural titanium, nickel and copper were measured, using the stacked-foil technique and gamma spectrometry, up to 70 MeV. The experimental cross sections were measured using the Ti-nat(p,x) V-48, Ni-nat(p,x) Ni-57 and Cu-nat(p,x) Zn-62,Co-56 monitor reactions recommended by the International Atomic Energy Agency (IAEA), depending on the investigated energy range. Data have been extracted for the Ti-nat(p,x) Sc-43,44m,46,47,48, V-48, K-42,43, Ni-nat(p,x) Ni-56,57, Co-55,56,57,58, Mn-52,54, Cu-nat(p,x) Cu-61,64, Ni-57, Co-56,57,58,60, Zn-62,65, Mn-54 reactions. Our results are discussed and compared to the existing ones as well as with the TALYS code version 1.6 calculations using default models. Our experimental data are in overall good agreement with the literature. TALYS is able to reproduce, in most cases, the experimental trend. Our new experimental results allow to expand our knowledge on these excitation functions, to confirm the existing trends and to give additional values on a large energy range. This work is in line with the new Coordinated Research Project (CRP) launched by the IAEA to expand the database of monitor reactions.

  14. Predictions of diffractive cross sections in proton-proton collisions

    SciTech Connect

    Goulianos, Konstantin

    2013-04-15

    We review our pre-LHC predictions of the total, elastic, total-inelastic, and diffractive components of proton-proton cross sections at high energies, expressed in the form of unitarized expressions based on a special parton-model approach to diffraction employing inclusive proton parton distribution functions and QCD color factors and compare with recent LHC results.

  15. High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction

    PubMed Central

    Thomaston, Jessica L.; Alfonso-Prieto, Mercedes; Fraser, James S.; Klein, Michael L.; Fiorin, Giacomo; DeGrado, William F.

    2015-01-01

    The matrix 2 (M2) protein from influenza A virus is a proton channel that uses His37 as a selectivity filter. Here we report high-resolution (1.10 Å) cryogenic crystallographic structures of the transmembrane domain of M2 at low and high pH. These structures reveal that waters within the pore form hydrogen-bonded networks or “water wires” spanning 17 Å from the channel entrance to His37. Pore-lining carbonyl groups are well situated to stabilize hydronium via second-shell interactions involving bridging water molecules. In addition, room temperature crystallographic structures indicate that water becomes increasingly fluid with increasing temperature and decreasing pH, despite the higher electrostatic field. Complementary molecular dynamics simulations reveal a collective switch of hydrogen bond orientations that can contribute to the directionality of proton flux as His37 is dynamically protonated and deprotonated in the conduction cycle. PMID:26578770

  16. 1p3/2 proton-hole state in 132Sn and the shell structure along N = 82.

    PubMed

    Taprogge, J; Jungclaus, A; Grawe, H; Nishimura, S; Doornenbal, P; Lorusso, G; Simpson, G S; Söderström, P-A; Sumikama, T; Xu, Z Y; Baba, H; Browne, F; Fukuda, N; Gernhäuser, R; Gey, G; Inabe, N; Isobe, T; Jung, H S; Kameda, D; Kim, G D; Kim, Y-K; Kojouharov, I; Kubo, T; Kurz, N; Kwon, Y K; Li, Z; Sakurai, H; Schaffner, H; Steiger, K; Suzuki, H; Takeda, H; Vajta, Zs; Watanabe, H; Wu, J; Yagi, A; Yoshinaga, K; Benzoni, G; Bönig, S; Chae, K Y; Coraggio, L; Covello, A; Daugas, J-M; Drouet, F; Gadea, A; Gargano, A; Ilieva, S; Kondev, F G; Kröll, T; Lane, G J; Montaner-Pizá, A; Moschner, K; Mücher, D; Naqvi, F; Niikura, M; Nishibata, H; Odahara, A; Orlandi, R; Patel, Z; Podolyák, Zs; Wendt, A

    2014-04-01

    A low-lying state in 131In82, the one-proton hole nucleus with respect to double magic 132Sn, was observed by its γ decay to the Iπ=1/2- β-emitting isomer. We identify the new state at an excitation energy of Ex=1353  keV, which was populated both in the β decay of 131Cd83 and after β-delayed neutron emission from 132Cd84, as the previously unknown πp3/2 single-hole state with respect to the 132Sn core. Exploiting this crucial new experimental information, shell-model calculations were performed to study the structure of experimentally inaccessible N=82 isotones below 132Sn. The results evidence a surprising absence of proton subshell closures along the chain of N=82 isotones. The consequences of this finding for the evolution of the N=82 shell gap along the r-process path are discussed. PMID:24745408

  17. Fast modulations of pulsating proton aurora related to subpacket structures of Pc1 geomagnetic pulsations at subauroral latitudes

    DOE PAGES

    Ozaki, M.; Shiokawa, K.; Miyoshi, Y.; Kataoka, R.; Yagitani, S.; Inoue, T.; Ebihara, Y.; Jun, C. -W; Nomura, R.; Sakaguchi, K.; et al

    2016-08-14

    To understand the role of electromagnetic ion cyclotron (EMIC) waves in determining the temporal features of pulsating proton aurora (PPA) via wave-particle interactions at subauroral latitudes, high-time-resolution (1/8 s) images of proton-induced N2>+ emissions were recorded using a new electron multiplying charge-coupled device camera, along with related Pc1 pulsations on the ground. The observed Pc1 pulsations consisted of successive rising-tone elements with a spacing for each element of 100 s and subpacket structures, which manifest as amplitude modulations with a period of a few tens of seconds. In accordance with the temporal features of the Pc1 pulsations, the auroral intensitymore » showed a similar repetition period of 100 s and an unpredicted fast modulation of a few tens of seconds. Furthermore, these results indicate that PPA is generated by pitch angle scattering, nonlinearly interacting with Pc1/EMIC waves at the magnetic equator.« less

  18. Chromophore structure in bacteriorhodopsin's N intermediate: implications for the proton-pumping mechanism

    SciTech Connect

    Fodor, S.P.; Ames, J.B.; Gebhard, R.; van den Berg, E.M.; Stoeckenius, W.; Lugtenburg, J.; Mathies, R.A.

    1988-09-06

    By elevating the pH to 9.5 in 3 M KCl, the concentration of the N intermediate in the bacteriorhodopsin photocycle has been enhanced, and time-resolved resonance Raman spectra of this intermediate have been obtained. Kinetic Raman measurements show that N appears with a half-time of 4 +/- 2 ms, which agrees satisfactorily with our measured decay time of the M412 intermediate (2 +/- 1 ms). This argues that M412 decays directly to N in the light-adapted photocycle. The configuration of the chromophore about the C13 = C14 bond was examined by regenerating the protein with (12,14-2H)retinal. The coupled C12-2H + C14-2H rock at 946 cm-1 demonstrates that the chromophore in N is 13-cis. The shift of the 1642-cm-1 Schiff base stretching mode to 1618 cm-1 in D2O indicates that the Schiff base linkage to the protein is protonated. The insensitivity of the 1168-cm-1 C14-C15 stretching mode to N-deuteriation establishes a C = N anti (trans) Schiff base configuration. The high frequency of the C14-C15 stretching mode as well as the frequency of the 966-cm-1 C14-2H-C15-2H rocking mode shows that the chromophore is 14-s-trans. Thus, N contains a 13-cis, 14-s-trans, 15-anti protonated retinal Schiff base.(ABSTRACT TRUNCATED AT 250 WORDS)

  19. Neutron diffraction study of the monoclinic to tetragonal structural transition in LaNbO{sub 4} and its relation to proton mobility

    SciTech Connect

    Huse, M.; Skilbred, A.W.B.; Karlsson, M.; Eriksson, S.G.; Norby, T.; Haugsrud, R.; Knee, C.S.

    2012-03-15

    The fergusonite-scheelite structural transition of LaNbO{sub 4} was characterized by high-intensity variable temperature neutron powder diffraction in an effort to link structural changes to proton transport in the low temperature monoclinic and high temperature tetragonal polymorphs. The pronounced decrease in enthalpy of proton mobility with increasing temperature in monoclinic LaNbO{sub 4}, identified by Fjeld et al. , was found to coincide with the decrease in a key inter-tetrahedral oxygen separation. At temperatures above the transition, this oxygen to oxygen distance remains constant, behavior that is consistent with the invariant nature of the calculated enthalpy of mobility for the tetragonal phase. This oxygen separation is therefore proposed as the key structural parameter determining the success rate of proton transfer and ultimately the proton diffusion in LaNbO{sub 4}. Infrared measurements performed on acceptor-doped LaNbO{sub 4} show an absorption in the region 2500 to 3700 cm{sup -1} attributed to the O-H stretching motion influenced by hydrogen bonding. - Graphical Abstract: The structural phase transition from monoclinic fergusonite to tetragonal scheelite crystal structure clearly influences the proton conductivity of acceptor-doped LaNbO{sub 4} (see Figure). The present article attempts to explain why. Highlights: Black-Right-Pointing-Pointer Transition from monoclinic to tetragonal structure studied using neutron diffraction. Black-Right-Pointing-Pointer Change in proton mobility linked to contraction of a key oxygen separation. Black-Right-Pointing-Pointer Infra-red spectra reveal intermediate strength hydrogen bonding.

  20. Plant sex chromosomes: molecular structure and function.

    PubMed

    Jamilena, M; Mariotti, B; Manzano, S

    2008-01-01

    Recent molecular and genomic studies carried out in a number of model dioecious plant species, including Asparagus officinalis, Carica papaya, Silene latifolia, Rumex acetosa and Marchantia polymorpha, have shed light on the molecular structure of both homomorphic and heteromorphic sex chromosomes, and also on the gene functions they have maintained since their evolution from a pair of autosomes. The molecular structure of sex chromosomes in species from different plant families represents the evolutionary pathway followed by sex chromosomes during their evolution. The degree of Y chromosome degeneration that accompanies the suppression of recombination between the Xs and Ys differs among species. The primitive Ys of A. officinalis and C. papaya have only diverged from their homomorphic Xs in a short male-specific and non-recombining region (MSY), while the heteromorphic Ys of S. latifolia, R. acetosa and M. polymorpha have diverged from their respective Xs. As in the Y chromosomes of mammals and Drosophila, the accumulation of repetitive DNA, including both transposable elements and satellite DNA, has played an important role in the divergence and size enlargement of plant Ys, and consequently in reducing gene density. Nevertheless, the degeneration process in plants does not appear to have reached the Y-linked genes. Although a low gene density has been found in the sequenced Y chromosome of M. polymorpha, most of its genes are essential and are expressed in the vegetative and reproductive organs in both male and females. Similarly, most of the Y-linked genes that have been isolated and characterized up to now in S. latifolia are housekeeping genes that have X-linked homologues, and are therefore expressed in both males and females. Only one of them seems to be degenerate with respect to its homologous region in the X. Sequence analysis of larger regions in the homomorphic X and Y chromosomes of papaya and asparagus, and also in the heteromorphic sex chromosomes

  1. Protons and how they are transported by proton pumps.

    PubMed

    Buch-Pedersen, M J; Pedersen, B P; Veierskov, B; Nissen, P; Palmgren, M G

    2009-01-01

    The very high mobility of protons in aqueous solutions demands special features of membrane proton transporters to sustain efficient yet regulated proton transport across biological membranes. By the use of the chemical energy of ATP, plasma-membrane-embedded ATPases extrude protons from cells of plants and fungi to generate electrochemical proton gradients. The recently published crystal structure of a plasma membrane H(+)-ATPase contributes to our knowledge about the mechanism of these essential enzymes. Taking the biochemical and structural data together, we are now able to describe the basic molecular components that allow the plasma membrane proton H(+)-ATPase to carry out proton transport against large membrane potentials. When divergent proton pumps such as the plasma membrane H(+)-ATPase, bacteriorhodopsin, and F(O)F(1) ATP synthase are compared, unifying mechanistic premises for biological proton pumps emerge. Most notably, the minimal pumping apparatus of all pumps consists of a central proton acceptor/donor, a positively charged residue to control pK(a) changes of the proton acceptor/donor, and bound water molecules to facilitate rapid proton transport along proton wires.

  2. Theoretical investigation of protonated carbon dioxide

    NASA Technical Reports Server (NTRS)

    Green, S.; Schor, H.; Siegbahn, P.; Thaddeus, P.

    1976-01-01

    The equilibrium structure of CO2H(+) has been obtained from self-consistent field and configuration interaction wave functions. Only one stable form has been found, a linear O-C-O chain with the hydrogen bonded to oxygen and slightly off axis, in analogy with known isoelectronic species. A second structure protonated at carbon, which has been inferred from mass spectrometric studies, is found to be unstable with respect to spontaneous rearrangement. The proton affinity of CO2 is calculated to be 136 kcal/mole, in reasonable agreement with the most recent experimental value.

  3. A benchmark test suite for proton transfer energies and its use to test electronic structure model chemistries

    NASA Astrophysics Data System (ADS)

    Nachimuthu, Santhanamoorthi; Gao, Jiali; Truhlar, Donald G.

    2012-05-01

    We present benchmark calculations of nine selected points on potential energy surfaces describing proton transfer processes in three model systems, H5O2+, CH3OH…H+…OH2, and CH3COOH…OH2. The calculated relative energies of these geometries are compared to those calculated by various wave function and density functional methods, including the polarized molecular orbital (PMO) model recently developed in our research group and other semiempirical molecular orbital methods. We found that the SCC-DFTB and PMO methods (the latter available so far only for molecules consisting of only O and H and therefore only for the first of the three model systems) give results that are, on average, within 2 kcal/mol of the benchmark results. Other semiempirical molecular orbital methods have mean unsigned errors (MUEs) of 3-8 kcal/mol, local density functionals have MUEs in the range 0.7-3.7 kcal/mol, and hybrid density functionals have MUEs of only 0.3-1.0 kcal/mol, with the best density functional performance obtained by hybrid meta-GGAs, especially M06 and PW6B95.

  4. The extraction of the spin structure function, g2 (and g1) at low Bjorken x

    SciTech Connect

    Ndukum, Luwani Z.

    2015-08-01

    The Spin Asymmetries of the Nucleon Experiment (SANE) used the Continuous Electron Beam Accelerator Facility at Jefferson Laboratory in Newport News, VA to investigate the spin structure of the proton. The experiment measured inclusive double polarization electron asymmetries using a polarized electron beam, scattered off a solid polarized ammonia target with target polarization aligned longitudinal and near transverse to the electron beam, allowing the extraction of the spin asymmetries A1 and A2, and spin structure functions g1 and g2. Polarized electrons of energies of 4.7 and 5.9 GeV were used. The scattered electrons were detected by a novel, non-magnetic array of detectors observing a four-momentum transfer range of 2.5 to 6.5 GeV*V. This document addresses the extraction of the spin asymmetries and spin structure functions, with a focus on spin structure function, g2 (and g1) at low Bjorken x. The spin structure functions were measured as a function of x and W in four Q square bins. A full understanding of the low x region is necessary to get clean results for SANE and extend our understanding of the kinematic region at low x.

  5. 1,2,3-Triazole-Functionalized Polysulfone Synthesis through Microwave-Assisted Copper-Catalyzed Click Chemistry: A Highly Proton Conducting High Temperature Membrane.

    PubMed

    Sood, Rakhi; Donnadio, Anna; Giancola, Stefano; Kreisz, Aurélien; Jones, Deborah J; Cavaliere, Sara

    2016-07-01

    Microwave heating holds all the aces regarding development of effective and environmentally friendly methods to perform chemical transformations. Coupling the benefits of microwave-enhanced chemistry with highly reliable copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry paves the way for a rapid and efficient synthesis procedure to afford high performance thermoplastic materials. We describe herein fast and high yielding synthesis of 1,2,3-triazole-functionalized polysulfone through microwave-assisted CuAAC as well as explore their potential as phosphoric acid doped polymer electrolyte membranes (PEM) for high temperature PEM fuel cells. Polymers with various degrees of substitution of the side-chain functionality of 1,4-substituted 1,2,3-triazole with alkyl and aryl pendant structures are prepared by sequential chloromethylation, azidation, and microwave-assisted CuAAC using a range of alkynes (1-pentyne, 1-nonyne, and phenylacetylene). The completeness of reaction at each step and the purity of the clicked polymers were confirmed by (1)H-(13)C NMR, DOSY-NMR and FTIR-ATR spectroscopies. The thermal and thermochemical properties of the modified polymers were characterized by differential scanning calorimetry and thermogravimetric analysis coupled with mass spectroscopy (TG-MS), respectively. TG-MS analysis demonstrated that the commencement of the thermal degradation takes place with the decomposition of the triazole ring while its substituents have critical influence on the initiation temperature. Polysulfone functionalized with 4-phenyl-1,2,3-triazole demonstrates significantly higher Tg, Td, and elastic modulus than the ones bearing 4-propyl-1,2,3-triazole and 4-heptyl-1,2,3-triazole groups. After doping with phosphoric acid, the functionalized polymers with acid doping level of 5 show promising performance with high proton conductivity in anhydrous conditions (in the range of 27-35 mS/cm) and satisfactorily high elastic modulus (in the range

  6. 1,2,3-Triazole-Functionalized Polysulfone Synthesis through Microwave-Assisted Copper-Catalyzed Click Chemistry: A Highly Proton Conducting High Temperature Membrane.

    PubMed

    Sood, Rakhi; Donnadio, Anna; Giancola, Stefano; Kreisz, Aurélien; Jones, Deborah J; Cavaliere, Sara

    2016-07-01

    Microwave heating holds all the aces regarding development of effective and environmentally friendly methods to perform chemical transformations. Coupling the benefits of microwave-enhanced chemistry with highly reliable copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry paves the way for a rapid and efficient synthesis procedure to afford high performance thermoplastic materials. We describe herein fast and high yielding synthesis of 1,2,3-triazole-functionalized polysulfone through microwave-assisted CuAAC as well as explore their potential as phosphoric acid doped polymer electrolyte membranes (PEM) for high temperature PEM fuel cells. Polymers with various degrees of substitution of the side-chain functionality of 1,4-substituted 1,2,3-triazole with alkyl and aryl pendant structures are prepared by sequential chloromethylation, azidation, and microwave-assisted CuAAC using a range of alkynes (1-pentyne, 1-nonyne, and phenylacetylene). The completeness of reaction at each step and the purity of the clicked polymers were confirmed by (1)H-(13)C NMR, DOSY-NMR and FTIR-ATR spectroscopies. The thermal and thermochemical properties of the modified polymers were characterized by differential scanning calorimetry and thermogravimetric analysis coupled with mass spectroscopy (TG-MS), respectively. TG-MS analysis demonstrated that the commencement of the thermal degradation takes place with the decomposition of the triazole ring while its substituents have critical influence on the initiation temperature. Polysulfone functionalized with 4-phenyl-1,2,3-triazole demonstrates significantly higher Tg, Td, and elastic modulus than the ones bearing 4-propyl-1,2,3-triazole and 4-heptyl-1,2,3-triazole groups. After doping with phosphoric acid, the functionalized polymers with acid doping level of 5 show promising performance with high proton conductivity in anhydrous conditions (in the range of 27-35 mS/cm) and satisfactorily high elastic modulus (in the range

  7. Structure and properties of metal-exchanged zeolites studied using gradient-corrected and hybrid functionals. I. Structure and energetics

    NASA Astrophysics Data System (ADS)

    Göltl, Florian; Hafner, Jürgen

    2012-02-01

    The structural and energetic properties of purely siliceous, proton-, and Cu- and Co-exchanged chabazite have been studied using periodic density-functional (DFT) calculations with both conventional gradient-corrected exchange-correlation functionals and hybrid functionals mixing exact (i.e., Hartree-Fock) and DFT exchange. Spin-polarized and fixed-moment calculations have been performed to determine the equilibrium and excited spin-configurations of the metal-exchanged chabazites. For the purely siliceous chabazite, hybrid functionals predict a slightly more accurate cell volume and lattice geometry. For isolated Al/Si substitution sites, gradient-corrected functionals predict that the lattice distortion induced by the substitution preserves the local tetrahedral symmetry, whereas hybrid functionals lead to a distorted Al coordination with two short and two long Al-O bonds. Hybrid functionals yield a stronger cation-framework binding that conventional functionals in metal-exchanged zeolites, they favor shorter cation-oxygen bonds and eventually also a higher coordination of the cation. Both types of functionals predict the same spin in the ground-state. The structural optimization of the excited spin-states shows that the formation of a high-spin configuration leads to a strong lattice relaxation and a weaker cation-framework bonding. For both Cu- and Co-exchanged chabazite, the prediction of a preferred location of the cation in a six-membered ring of the zeolite agrees with experiment, but the energy differences between possible cation locations and the lattice distortion induced by the Al/Si substitution and the bonding of the cation depends quite significantly on the choice of the functional. All functionals predict similar energy differences for excited spin states. Spin-excitations are shown to be accompanied by significant changes in the cation coordination, which are more pronounced with hybrid functionals. The consequences of electronic spectra and

  8. Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

    SciTech Connect

    Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

    2007-09-02

    Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

  9. Proton scaling

    SciTech Connect

    Canavan, Gregory H

    2009-01-01

    This note presents analytic estimates of the performance of proton beams in remote surveillance for nuclear materials. The analysis partitions the analysis into the eight steps used by a companion note: (1) Air scattering, (2) Neutron production in the ship and cargo, (3) Target detection probability, (4) Signal produced by target, (5) Attenuation of signal by ship and cargo, (6) Attenuation of signal by air, (7) Geometric dilution, and (8) Detector Efficiency. The above analyses indicate that the dominant air scattering and loss mechanisms for particle remote sensing are calculable with reliable and accepted tools. They make it clear that the conversion of proton beams into neutron sources rapidly goes to completion in all but thinnest targets, which means that proton interrogation is for all purposes executed by neutrons. Diffusion models and limiting approximations to them are simple and credible - apart from uncertainty over the cross sections to be used in them - and uncertainty over the structure of the vessels investigated. Multiplication is essentially unknown, in part because it depends on the details of the target and its shielding, which are unlikely to be known in advance. Attenuation of neutron fluxes on the way out are more complicated due to geometry, the spectrum of fission neutrons, and the details of their slowing down during egress. The attenuation by air is large but less uncertain. Detectors and technology are better known. The overall convolution of these effects lead to large but arguably tolerable levels of attenuation of input beams and output signals. That is particularly the case for small, mobile sensors, which can more than compensate for size with proximity to operate reliably while remaining below flux limits. Overall, the estimates used here appear to be of adequate accuracy for decisions. That assessment is strengthened by their agreement with companion calculations.

  10. Changes in the structural and thermal properties of poly(vinylidene fluoride-chlorotrifluoroethylene) irradiated with 4 MeV protons

    NASA Astrophysics Data System (ADS)

    Singh, Arjun; Kishore, Prateek; Singh, Manjit; Srivastava, Alok

    2015-10-01

    The radiation effects on semicrystalline poly(vinylidene fluoride-chlorotrifluoroethylene) copolymer [poly(VDF-CTFE)] induced by proton beam irradiation were investigated. The poly(VDF-CTFE) films were exposed to 4 MeV protons at different fluence in the range of 2.7 × 1013 to 65.0 × 1013 protons/cm2. Changes in the chemical structural and thermal properties of pristine films as well as irradiated samples were studied using Fourier Transform Infrared (FTIR) and thermal analytical techniques, namely Thermogravimetric Analysis and Differential Scanning Calorimetry (DSC), respectively. FTIR spectroscopic data revealed two new bands at 1650 and 1747 cm-1 for irradiated samples whose intensities gradually increased with increasing ion fluence from 2.7 × 1013 to 27.0 × 1013 protons/cm2 due to the formation of carbon-carbon double bonds. The thermal stability was found to decrease after proton irradiation due to chain-scission. DSC data revealed that the proton irradiation was found to change in heat of fusion and crystallinity depending upon the applied dose.

  11. From object structure to object function

    NASA Astrophysics Data System (ADS)

    Zlateva, Stoyanka D.; Vaina, Lucia M.

    1991-03-01

    In this paper we provide a mathematical support for the nature of the shape representation methods useful for the computation of possible functions of an objects as derived from its shape structure. We discuss the concepts of parts and subparts of objects in the framework of axis based shape representation methods and boundary based methods. We propose a new method for obtaining descriptions of parts which based on a theorem from differential geometry (Pogorelov 1974) that any regular surface can be approximated in a finite environment with a given accuracy by a parabolloid of one of the following types - elliptic, hyperbolic and a parabolloid degenerating into a plane or a parabolic cylinder. Based on these considerations we suggest a heuristic for the approximation of convex object parts by a polyhedra, cylinder, ellipsoid or generalized cone with straight axis depending on the presence of plane, parabolic, elliptic subsets in their boundary, and nonconvex object parts by generalized cones with curved axis. This approach allows to obtain a primitive based shape description after the decomposition of the object shape through the more general boundary-based methods. We present examples of decomposing and describing shapes of common objects in terms of their parts, subparts and associated features.

  12. Structure and function of the Ca antigen.

    PubMed Central

    Bramwell, M. E.; Bhavanandan, V. P.; Wiseman, G.; Harris, H.

    1983-01-01

    The Ca antigen, which can be detected in a wide range of malignant human tumours by means of the Cal antibody, is a glycoprotein of the mucin type. At least 95% of the carbohydrate is 0-glycosidically linked to the polypeptide which contains high proportions of glycine, serine and glutamic acid. The carbohydrate has a very simple structure: it is composed almost entirely of tetra- tri- and disaccharides having the general formula (NeuNac)n leads to [Gal leads to GalNac] alpha leads to, where n = 0, 1 or 2. In many malignant cell lines, the antigen is produced constitutively in vitro; but in one that has been examined, its synthesis can be induced by high concentrations of lactate. Evidence is presented for the view that a primary function of this glycoprotein is to shield the cells that produce it from hydrogen ion concentrations outside of the physiological range. The presence of the Ca antigen in malignant tumours may thus be a reflection of metabolic conditions that are known to be characteristics of such tumours. Images Figure 1 Figure 2 PMID:6349673

  13. Anisotropic nanomaterials: structure, growth, assembly, and functions

    PubMed Central

    Sajanlal, Panikkanvalappil R.; Sreeprasad, Theruvakkattil S.; Samal, Akshaya K.; Pradeep, Thalappil

    2011-01-01

    Comprehensive knowledge over the shape of nanomaterials is a critical factor in designing devices with desired functions. Due to this reason, systematic efforts have been made to synthesize materials of diverse shape in the nanoscale regime. Anisotropic nanomaterials are a class of materials in which their properties are direction-dependent and more than one structural parameter is needed to describe them. Their unique and fine-tuned physical and chemical properties make them ideal candidates for devising new applications. In addition, the assembly of ordered one-dimensional (1D), two-dimensional (2D), and three-dimensional (3D) arrays of anisotropic nanoparticles brings novel properties into the resulting system, which would be entirely different from the properties of individual nanoparticles. This review presents an overview of current research in the area of anisotropic nanomaterials in general and noble metal nanoparticles in particular. We begin with an introduction to the advancements in this area followed by general aspects of the growth of anisotropic nanoparticles. Then we describe several important synthetic protocols for making anisotropic nanomaterials, followed by a summary of their assemblies, and conclude with major applications. PMID:22110867

  14. [Glutamate Metabotropic Receptors: Structure, Localisation, Functions].

    PubMed

    Perfilova, V N; Tyurenkov, I N

    2016-01-01

    The data on the structure, location and functions of the metabotropic glutamate receptor is shown. The family consists of 8 mGluRs subtypes and is divided into three groups: I group--mGluRs1/mGluRs5, II group--mGluRs2/mGluRs3, III group--mGluRs4/mGluRs6/mGluRs7/mGluRs8. They are associated with G-protein; signaling in the cells is carried out by IP3 or adenylate cyclase signaling pathways, in the result of which, mGluRs modify glial and neuronal excitability. Receptors are localized in the CNS and periphery in non-neuronal tissues: bone, heart, kidney, pancreas pod and platelets, the gastrointestinal tract, immune system. Their participation in the mechanisms of neurodegenerative diseases, mental and cognitive disorders, autoimmune processes, etc. is displayed. Agonists, antagonists, allosteric modulators of mGluRs are considered as potential medicines for treatment of mental diseases, including depression, fragile X syndrome, anxiety, obsessive-compulsive disorders, Parkinson's disease, etc. PMID:27530046

  15. Yeast peroxisomes: structure, functions and biotechnological opportunities.

    PubMed

    Sibirny, Andriy A

    2016-06-01

    Peroxisomes are ubiquitous organelles found in most eukaryotic cells. In yeasts, peroxisomes play important roles in cell metabolism, especially in different catabolic processes including fatty acid β-oxidation, the glyoxylic shunt and methanol metabolism, as well as some biosynthetic processes. In addition, peroxisomes are the compartment in which oxidases and catalase are localized. New peroxisomes mainly arise by fission of pre-existing ones, although they can also be formed from the endoplasmic reticulum (ER). Peroxisomes consist of matrix-soluble proteins and membrane proteins known as peroxins. A total of 34 PEX peroxin genes and proteins have been identified to date. and their functions have been elucidated. Protein import into peroxisomes depends on peroxins and requires specific signals in the structure of transported proteins: PTS1, PTS2 and mPTS. The mechanisms of metabolite penetration into peroxisomes are still poorly understood. Peroxisome number and the volume occupied by these organelles are tightly regulated. Methanol, fatty acids and methylamine act as efficient peroxisome proliferators, whereas glucose and ethanol induce peroxisome autophagic degradation (pexophagy). To date, 42 Atg proteins involved in pexophagy are known. Catabolism and alcoholic fermentation of the major pentose sugar, xylose, depend on peroxisomal enzymes. Overexpression of peroxisomal transketolase and transaldolase activates xylose fermentation. Peroxisomes could be useful as target organelles for overexpression of foreign toxic proteins. PMID:27189367

  16. Muscle structural assembly and functional consequences.

    PubMed

    Narici, Marco; Franchi, Martino; Maganaris, Constantinos

    2016-01-01

    The relationship between muscle structure and function has been a matter of investigation since the Renaissance period. Extensive use of anatomical dissections and the introduction of the scientific method enabled early scholars to lay the foundations of muscle physiology and biomechanics. Progression of knowledge in these disciplines led to the current understanding that muscle architecture, together with muscle fibre contractile properties, has a major influence on muscle mechanical properties. Recently, advances in laser diffraction, optical microendoscopy and ultrasonography have enabled in vivo investigations into the behaviour of human muscle fascicles and sarcomeres with varying joint angle and muscle contraction intensity. With these technologies it has become possible to identify the length region over which fascicles and sarcomeres develop maximum isometric force in vivo as well as the operating ranges of fascicles and sarcomeres during real-life activities such as walking. Also, greater insights into the remodelling of muscle architecture in response to overloading and unloading, and in ageing, have been obtained by the use of ultrasonography; these have led to the identification of clinical biomarkers of disuse atrophy and sarcopenia. Recent evidence also shows that the pattern of muscle hypertrophy in response to chronic loading is contraction-mode dependent (eccentric versus concentric), as similar gains in muscle mass, but through differing addition of sarcomeres in series and in parallel (as indirectly inferred from changes in fascicle length and pennation angle), have been found. These innovative observations prompted a new set of investigations into the molecular mechanisms regulating this contraction-specific muscle growth.

  17. Models of Protocellular Structure, Function and Evolution

    NASA Technical Reports Server (NTRS)

    New, Michael H.; Pohorille, Andrew; Szostak, Jack W.; Keefe, Tony; Lanyi, Janos K.

    2001-01-01

    In the absence of any record of protocells, the most direct way to test our understanding of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction. A mutagenic approach, in which the sequences of selected molecules are randomly altered, can yield further improvements in performance or alterations of specificities. Unfortunately, the catalytic potential of nucleic acids is rather limited. Proteins are more catalytically capable but cannot be directly amplified. In the new technique, this problem is circumvented by covalently linking each protein of the initial, diverse, pool to the RNA sequence that codes for it. Then, selection is performed on the proteins, but the nucleic acids are replicated. Additional information is contained in the original extended abstract.

  18. Proton therapy

    MedlinePlus

    ... direction of the tumor. A machine called a synchrotron or cyclotron creates and speeds up the protons. ... redness in the radiation area, and temporary hair loss. AFTER THE PROCEDURE Following proton therapy, you should ...

  19. Application of DFT and MP2 calculations on structural and water-assisted proton transfer in 3-amino-4-nitrofurazan

    NASA Astrophysics Data System (ADS)

    Beni, Alireza Salimi; Zarandi, Maryam

    2016-02-01

    Density functional theory (DFT) and MP2 calculations have been employed to study of 3-amino-4-nitrofurazan molecule using the standard 6-311++G( d, p) basis set. The chemical properties of the 3-amino-4-nitrofurazan have been extensively studied. The geometries of molecules in the gas phase were optimized and compared with the crystallography of this substance. The results suggest that A form is the most stable form in the gas phase and it is the predominant tautomer in solution according to the DFT and MP2 calculations, respectively. In addition, variation of dipole moments in the gas phase, the specific solvent effects with addition of one molecule of water near the electrophilic centers of tautomers, the transition state of proton transfer assisted by a water molecule, the NBO charges of atoms and the potential energy surface were investigated. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are presented.

  20. Structural changes in InP/Si solar cells following irradiation with protons to very high fluences

    NASA Astrophysics Data System (ADS)

    Messenger, S. R.; Jackson, E. M.; Burke, E. A.; Walters, R. J.; Xapsos, M. A.; Summers, G. P.

    1999-08-01

    Precisely how the short circuit current (JSC) is produced in a proton irradiated n+p InP/Si solar cell at very high fluence levels has been determined from combined measurements of the cell structure using electrochemical capacitance-voltage profiling and detailed analysis of the spectral quantum efficiency. Type conversion in the base region of the cell is shown to occur before an anomalous peak in the degradation curve for JSC is reached at high damage levels. The short circuit current, and hence the cell efficiency, ultimately collapse because the high absorption coefficient of InP eventually prevents the generation of electron-hole pairs close enough to the effective cell junction from being collected.