Transfer Step (transfer + step)

Distribution by Scientific Domains

Kinds of Transfer Step

  • electron transfer step
  • proton transfer step


  • Selected Abstracts


    Tyr235 of human cytosolic phosphoenolpyruvate carboxykinase influences catalysis through an anion,quadrupole interaction with phosphoenolpyruvate carboxylate

    FEBS JOURNAL, Issue 23 2008
    Lakshmi Dharmarajan
    Tyr235 of GTP-dependent phosphoenolpyruvate (PEP) carboxykinase is a fully invariant residue. The aromatic ring of this residue establishes an energetically favorable weak anion,quadrupole interaction with PEP carboxylate. The role of Tyr235 in catalysis was investigated via kinetic analysis of site-directed mutagenesis-derived variants. The Y235F change lowered the apparent Km for PEP by about six-fold, raised the apparent Km for Mn2+ by about 70-fold, and decreased oxaloacetate (OAA)-forming activity by about 10-fold. These effects were due to an enhanced anion,quadrupole interaction between the aromatic side chain at position 235, which now lacked a hydroxyl group, and PEP carboxylate, which probably increased the distance between PEP and Mn2+ and consequently affected the phosphoryl transfer step and overall catalysis. For the Y235A and Y235S changes, an elimination of the favorable edge-on interaction increased the apparent Km for PEP by four- and six-fold, respectively, and the apparent Km for Mn2+ by eight- and six-fold, respectively. The pyruvate kinase-like activity, representing the PEP dephosphorylation step of the OAA-forming reaction, was affected by the substitutions in a similar way to the complete reaction. These observations indicate that the aromatic ring of Tyr235 helps to position PEP in the active site and the hydroxyl group allows an optimal PEP,Mn2+ distance for efficient phosphoryl transfer and overall catalysis. The Y235A and Y235S changes drastically reduced the PEP-forming and OAA decarboxylase activities, probably due to the elimination of the stabilizing interaction between Tyr235 and the respective products, PEP and pyruvate. [source]


    The function of D1-H332 in Photosystem II electron transport studied by thermoluminescence and chlorophyll fluorescence in site-directed mutants of Synechocystis 6803

    FEBS JOURNAL, Issue 17 2004
    Yagut Allahverdiyeva
    The His332 residue of the D1 protein has been identified as the likely ligand of the catalytic Mn ions in the water oxidizing complex (Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J. & Iwata, S. (2004) Science 303, 1831,1838). However, its function has not been fully clarified. Here we used thermoluminescence and flash-induced chlorophyll fluorescence measurements to characterize the effect of the D1-H333E, D1-H332D and D1-H332S mutations on the electron transport of Photosystem II in intact cells of the cyanobacterium Synechocystis 6803. Although the mutants are not photoautotrophic they all show flash-induced thermoluminescence and chlorophyll fluorescence, which originate from the S2QA, and S2QB, recombinations demonstrating that charge stabilization takes place in the water oxidizing complex. However, the conversion of S2 to higher S states is inhibited and the energetic stability of the S2QA, charge pair is increased by 75, 50 and 7 mV in the D1-H332D, D1-H332E and D1-H332S mutants, respectively. This is most probably caused by a decrease of Em(S2/S1). Concomitantly, the rate of electron donation from Mn to Tyr-Z, during the S1 to S2 transition is slowed down, relative to the wild type, 350- and 60-fold in the D1-H332E and D1-H332D mutants, respectively, but remains essentially unaffected in D1-H332S. A further effect of the D1-H332E and D1-H332D mutations is the retardation of the QA to QB electron transfer step as an indirect consequence of the donor side modification. Our data show that although the His residue in the D1-332 position can be substituted by other metal binding residues for binding photo-oxidisable Mn it is required for controlling the functional redox energetics of the Mn cluster. [source]


    Kinetics and mechanism of oxidation of aurate(I) by peroxydisulphate in aqueous hydrochloric acid

    INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 10 2002
    R. M. Babshet
    The reaction between Au(I), generated by reaction of thallium(I) with Au(III), and peroxydisulphate was studied in 5 mol dm,3 hydrochloric acid. The reaction proceeds with the formation of an ion-pair between peroxydisulphate and chloride ion as the Michealis,Menten plot was linear with intercept. The ion-pair thus formed oxidizes AuCl2, in a slow two-electron transfer step without any formation of free radicals. The ion-pair formation constant and the rate constant for the slow step were determined as 113 ± 20 dm,3 mol,1 and 5.0 ± 1.0 × 10,2 dm3 mol,1 s,1, respectively. The reaction was retarded by hydrogen ion, and formation of unreactive protonated form of the reductant, HAuCl2, causes the rate inhibition. From the hydrogen ion dependence of the reaction rate, the protonation constant was calculated to be as 0.6 ± 0.1 dm3 mol,1. The activation parameters were determined and the values support the proposed mechanism. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 589,594, 2002 [source]


    Factor analysis of spectroelectrochemical reduction of FAD reveals the pKa of the reduced state and the reduction pathway

    JOURNAL OF CHEMOMETRICS, Issue 12 2007
    Edmund R. Malinowski
    Abstract The free flavin adenine dinucleotide (FAD) cofactor is known to exhibit a pH-dependent midpoint potential involving a simultaneous two-electron transfer step (n,=,2). Uv-vis spectroelectrochemical reductions of FAD at constant pH, ranging from 5 to 9, were recorded and analyzed by factor analysis. Principal factor analysis was used to determine the number of species present at each pH. The results indicate that only two composite forms of FAD are present: the oxidized and the reduced forms. Window factor analysis was used to extract the concentration profiles of the controlling species. The oxidized form was found to be a single pH-independent species, whereas the reduced form consists of two species. The pH-dependent spectroscopic changes of reduced FAD were best modeled by a single proton transfer step involving two different ionization states with an apparent pKa,=,6.3. This value compares favorably with those obtained from NMR and from midpoint potential measurements. At pH 6, the reduction of FAD was found to be first order, whereas at pH 9 the reduction is zero order; these observations are explained in terms of the reaction pathway involving xanthine oxidase, its substrate, and the pH. Copyright © 2007 John Wiley & Sons, Ltd. [source]


    An extended dead-end elimination algorithm to determine gap-free lists of low energy states

    JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2007
    Edda Kloppmann
    Abstract Proteins are flexible systems and commonly populate several functionally important states. To understand protein function, these states and their energies have to be identified. We introduce an algorithm that allows the determination of a gap-free list of the low energy states. This algorithm is based on the dead-end elimination (DEE) theorem and is termed X-DEE (extended DEE). X-DEE is applicable to discrete systems whose state energy can be formulated as pairwise interaction between sites and their intrinsic energies. In this article, the computational performance of X-DEE is analyzed and discussed. X-DEE is implemented to determine the lowest energy protonation states of proteins, a problem to which DEE has not been applied so far. We use X-DEE to calculate a list of low energy protonation states for two bacteriorhodopsin structures that represent the first proton transfer step of the bacteriorhodopsin photocycle. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source]


    Site-specific deposition of Ag nanoparticles on ZnO nanorod arrays via galvanic reduction and their SERS applications

    JOURNAL OF RAMAN SPECTROSCOPY, Issue 9 2010
    Wei Song
    Abstract A controllable heterostructure consisting of ZnO nanorod arrays with attached Ag nanoparticles at only one end has been synthesized via a facile and convenient galvanic reduction method. Scanning electron microscopic images of these nanostructures showed good selectivity of Ag deposition on the tip of ZnO nanorod arrays. The formation of these regular AgZnO heterogeneous nanorod arrays can be explained by a localization of the electrons at the ends of the ZnO nanorods after the electron transfer step. By tuning the reaction time and the concentration of silver nitrate, the density of Ag nanoparticles on the tip of ZnO nanorods can be well controlled. Owing to the introduction of Ag nanoparticles with different densities, the resulting AgZnO heterogeneous nanorod arrays have been proved to be a versatile substrate for surface-enhanced Raman scattering not only for common organic molecules but also for label-free protein detection. Copyright © 2009 John Wiley & Sons, Ltd. [source]


    Controlled free-radical polymerization of vinyl chloride

    JOURNAL OF VINYL & ADDITIVE TECHNOLOGY, Issue 3 2005
    Dietrich Braun
    Owing to the importance of poly(vinyl chloride) (PVC) as the second-largest plastic in volume after the polyolefins and above styrene polymers, the control of the free-radical polymerization of vinyl chloride (VC) is of high industrial and academic interest. But still the term "controlled" polymerization is not yet clearly defined. Often it is used for quasi-living polymerizations with equilibrium reactions in the initiation and/or termination step or for the control of the molecular weight distribution (MWD), but it can also be applied to several structural aspects such as stereochemistry, branching, or special technical properties. In the present article, the control of chain growth and chain transfer is discussed. It has been well known for many years that the propagation step in the VC polymerization is terminated to a large degree by the rather frequent and temperature-dependent chain transfer of the growing macromolecules to the monomer. Therefore, the degree of polymerization is strongly governed by the polymerization temperature. However, this transfer step does not result in a controlled or a narrow MWD. By means of free-radical nitroxide-mediated polymerization of VC in suspension, PVC with a narrower MWD can be obtained also at higher polymerization temperatures. The resulting PVC with nitroxide end groups can act as a macro-initiator for various monomers, resulting in two-block copolymers, which are, e.g., interesting compatibilizers in blends with PVC. J. VINYL ADDIT. TECHNOL., 11:86,90, 2005. © 2005 Society of Plastics Engineers [source]


    Data reliability and structure in the Swedish National Cataract Register

    ACTA OPHTHALMOLOGICA, Issue 5 2001
    Ingemar Håkansson
    ABSTRACT. Purpose: A Swedish National Cataract Register was instituted in 1992, monitoring nearly all cataract operations in Sweden, and since its inception comprising about 95% of all operations. Data from a total of approximately 290 000 operations have been collected during 1992,1998. Data quality is an important factor, and we have therefore assessed the various types and frequencies of data entry errors in the material. Methods: The medical records for all operations in five selected participating clinics were retrieved for a set month. Each data transfer step from the record to the final data base was monitored for a total of 574 operations. A total of 10 variables were recorded for each operation. Results: Significant sources of error were absent in most variables. However, possibly important errors appeared in three: "date entering waiting list", "preoperative best corrected visual acuity in the operated eye", or "visual acuity in the fellow eye". There were also noteworthy variations between the five clinics, different for different parameters. Errors were predominantly prone to appear at the very first step of registration. In most cases this was due to deviations from the data collection instructions. Conclusions: The reliability is good for most values entered into the register, but it is important to ensure that data definitions are exact and adhered to. Repeated information to the involved persons on how to fill in the forms appears to be a requisite for maintaining good input quality. [source]


    New Pentadentate Carboxylate-Derivatized Sulfur Ligands Affording Water Soluble Iron Complexes with [Fe(NS4)] Cores that Bind Small Molecules (CO, NO, PMe3) as Co-Ligands

    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 3 2004
    Dieter Sellmann
    Abstract In the search for polydentate sulfur ligands that are able to form water-soluble iron complexes which can bind nitrogenase relevant molecules, the new pentadentate ligands pyCO2MeS4,H2 [2,6-bis[2-mercapto-3-(methoxycarbonyl)phenylthio]dimethylpyridine] (1) and pyCO2HS4,H2 [2,6-bis(2-mercapto-3-carboxyphenylthio)dimethylpyridine] (2) having NS4 donor atom sets and terminal thiolate donors have been synthesized. The starting material was CO2MeS2,H2 (2,3-dimercapto benzoic acid methyl ester) which was alkylated with 2,6-bis[(tosyloxy)methyl]pyridine. The problem of specifically achieving regioselective mono-alkylation of this 1,2-benzene-dithiol derivative was solved by carrying out the alkylation of CO2MeS2,H2 at ,78 °C in the presence of stoichiometric amounts of a base. Saponification of 1 afforded the carboxylic acid derivative. Coordination of pyCO2MeS42, to FeII in the presence of co-ligands (L = CO, PMe3) yielded the complexes [Fe(L)(pyCO2MeS4)] where L = CO (5) or PMe3 (4). Upon treatment with NOBF4, complex 5 afforded [Fe(NO)(pyCO2MeS4)]BF4 (7) which could be subsequently converted to the isolable 19 valence electron species [Fe(NO)(pyCO2MeS4)] (8) upon reduction with N2H4. In the absence of potential co-ligands, coordination of pyCO2MeS42, to FeII afforded the dinuclear complex [Fe(pyCO2MeS4)]2 (6) whilst coordination to NiII gave [Ni(pyCO2MeS4)]x (3). Solubility of these complexes in water could be achieved by replacing the CO2Me groups with CO2H substituents. The ligand pyCO2HS42, afforded the iron complexes [Fe(L)(pyCO2HS4)] [L = CO (10) and PMe3 (12)] and [Fe(NO)(pyCO2HS4)]BF4 (11). Both 10 and 12 could be reversibly deprotonated to give the corresponding water-soluble salts (NMe4)2[Fe(L)(pyCO2S4)] with L = CO {(NMe4)2 [9]} and PMe3 {(NMe4)2 [13]}. The complexes were characterized by elemental analysis, spectroscopic methods and X-ray structural determinations. The molecular structure of [Fe(PMe3)(pyCO2HS4)] (12) was found to exhibit inter- and intramolecular O,H···O and O,H···S hydrogen bonds which serve as models for proton transfer steps from external sources to the active sites of metal sulfur enzymes. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source]


    Energy Collection, Transport, and Trapping by a Supramolecular Organization of Dyes in Hexagonal Zeolite Nanocrystals,

    ADVANCED FUNCTIONAL MATERIALS, Issue 2 2006
    C. Minkowski
    Abstract The incorporation of guest molecules into the cavities of molecular sieves leads to a large variety of highly interesting materials. Zeolite,L,an aluminosilicate with one-dimensional channels of open diameter 7.1,Å,is a very versatile material for building highly organized host,guest systems. We present materials where organic dye molecules have been incorporated into the channels of zeolite,L by means of diffusion, to build artificial photonic antenna systems. The channel entrance can be plugged by adding closure molecules that then connect the guest molecules inside with materials or molecules outside of the zeolite channels, since they can act as extensions of the interior of the zeolite crystal. The photophysical processes taking place in such dye-loaded zeolite,L antennae can be studied either on single-micrometer- or submicrometer-sized crystals or on crystals dispersed in a solvent or coated as thin layers on a support. The energy-transfer process occurring is of the Förster-type, and its transfer rate can be tuned by separating the donor dyes and the acceptor dyes locally by varying amounts of spacer molecules. The distribution of the dye molecules and empty sites within a zeolite crystal has been modeled by means of a Monte Carlo simulation. The Förster energy migration and transfer steps are described as a random walk. [source]


    Modeling aspects of mechanisms for reactions catalyzed by metalloenzymes

    JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2001
    P. E. M. Siegbahn
    Different models to treat metal-catalyzed enzyme reactions are investigated. The test case chosen is the recently suggested full catalytic cycle of manganese catalase including eight different steps. This cycle contains OO and OH activations, as well as electron transfer steps and redox active reactions, and is therefore believed to be representative of many similar systems. Questions concerning modeling of ligands and the accuracy of the computational model are studied. Imidazole modeling of histidines are compared to ammonia modeling, and formate modeling compared to acetate modeling of glutamates. The basis set size required for the geometry optimization and for the final energy evaluation is also investigated. The adequacy of the model is judged in relation to the inherent accuracy achievable with the hybrid DFT method B3LYP. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1634,1645, 2001 [source]


    IMPACT OF IRON LIMITATION ON THE PHOTOSYNTHETIC APPARATUS OF THE DIATOM CHAETOCEROS MUELLERI (BACILLARIOPHYCEAE)

    JOURNAL OF PHYCOLOGY, Issue 6 2001
    Margaret Davey
    Iron starvation induced marked increases in flavodoxin abundance and decreases in light-saturated and light-limited photosynthesis rates in the diatom Chaetoceros muelleri. Consistent with the substitution of flavodoxin for ferredoxin as an early response to iron starvation, increases of flavodoxin abundance were observed before declines of cell division rate or chl a specific photosynthesis rates. Changes in the abundance of flavodoxin after the addition of iron to iron-starved cells indicated that flavodoxin was not actively degraded under iron-replete conditions. Greater declines in light-saturated oxygen evolution rates than dark oxygen consumption rates indicated that the mitochondrial electron transfer chain was not affected as greatly by iron starvation as the photosynthetic electron transfer chain. The carbon:nitrogen ratio was unaffected by iron starvation, suggesting that photosynthetic electron transfer was a primary target of iron starvation and that reductions in nitrate assimilation were due to energy limitation (the C:N ratio would be expected to rise under nitrogen-limited but energy-replete conditions). Parallel changes were observed in the maximum light-saturated photosynthesis rate and the light-limited initial slope of the photosynthesis-light curve during iron starvation and recovery. The lowest photosynthesis rates were observed in iron-starved cells and the highest values in iron-replete cells. The light saturation parameter, Ik, was not affected by iron starvation, nor was the chl-to-C ratio markedly reduced. These observations were consistent with iron starvation having a similar or greater effect on photochemical charge separation in PSII than on downstream electron transfer steps. Declines of the ratio of variable to maximum fluorescence in iron-starved cells were consistent with PSII being a primary target of iron starvation. The functional cross-section of PSII was affected only marginally (<20%) by iron starvation, with the largest values observed in iron-starved cells. The rate constant for electron transfer calculated from fast repetition rate fluorescence was found to covary with the light-saturated photosynthesis rate; it was lowest in the most severely starved cells. [source]


    The basis of asymmetry in IS2 transposition

    MOLECULAR MICROBIOLOGY, Issue 4 2001
    Leslie A. Lewis
    In the first step of IS2 transposition, the formation of an IS2 minicircle, the roles of the two IS ends differ. Terminal cleavage initiates exclusively at the right inverted repeat (IRR) , the donor end , whereas IRL is always the target. At the resulting minicircle junction, the two abutted ends are separated by a spacer of 1 or 2 basepairs. In this study, we have identified the determinants of donor and target function. The inability of IRL to act as a donor results largely from two sequence differences between IRL and IRR , an extra basepair between the conserved transposase binding sequences and the end of the element, and a change of the terminal dinucleotide from CA-3, to TA-3,. These two changes also impose a characteristic size on the minicircle junction spacer. The only sequences required for the efficient target function of IRL appear to be contained within the segment from position 11,42. Although IRR can function as a target, its shorter length and additional contacts with transposase (positions 1,7) result in minicircles with longer, and inappropriate, spacers. We propose a model for the synaptic complex in which the terminus of IRL makes different contacts with the transposase for the initial and final strand transfer steps. The sequence differences between IRR and IRL, and the behavioural characteristics of IRL that result from them, have probably been selected because they optimize expression of transposase from the minicircle junction promoter, Pjunc. [source]


    A Role for Internal Water Molecules in Proton Affinity Changes in the Schiff Base and Asp85 for One-way Proton Transfer in Bacteriorhodopsin,

    PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008
    Joel E. Morgan
    Light-induced proton pumping in bacteriorhodospin is carried out through five proton transfer steps. We propose that the proton transfer to Asp85 from the Schiff base in the L-to-M transition is accompanied by the relocation of a water cluster on the cytoplasmic side of the Schiff base from a site close to the Schiff base in L to the Phe219-Thr46 region in M. The water cluster present in L, formed at 170 K, is more rigid than that at room temperature. This may be responsible for blocking the conversion of L to M at 170 K. In the photocycle at room temperature, this water cluster returns to the site close to the Schiff base in N, with a rigid structure similar to that of L at 170 K. The increase in the proton affinity of Asp85, which is a prerequisite for the one-way proton transfer in the M-to-N transition, is suggested to be facilitated by a structural change which disrupts interactions between Asp212 and the Schiff base, and between Asp212 and Arg82. We propose that this liberation of Asp212 is accompanied by a rearrangement of the structure of water molecules between Asp85 and Asp212, stabilizing the protonated Asp85 in M. [source]


    Collision-induced dissociation of protonated tetrapeptides containing , -alanine, , -aminobutyric acid, , -aminocaproic acid or 4-aminomethylbenzoic acid residues,

    RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 22 2006
    Erach R. Talaty
    The influence of the presence and position of a single , -alanine, , -aminobutyric acid, , -aminocaproic acid or 4-aminomethylbenzoic acid residue on the tendency to form b - and y -type product ions was determined using a group of protonated tetrapeptides with general sequence XAAG, AXAG and AAXG (where X refers to the position of amino acid substitution). The hypothesis tested was that the ,alternative' amino acids would influence product ion signal intensities by inhibiting or suppressing either the nucleophilic attack or key proton transfer steps by forcing the adoption of large cyclic intermediates or blocking cyclization altogether. We found that specific b ions are diminished or eliminated completely when ,A, ,Abu, Cap or 4AMBz residues are positioned such that they should interfere with the intramolecular nucleophilic attack step. In addition, differences in the relative proton affinities of the alternative amino acids influence the competition between complementary bn and yn ions. For both the AXAG and the XAAG series of peptides, collision-induced dissociation (CID) generated prominent b ions despite potential inhibition or suppression of intramolecular proton migration by the ,A, ,Abu, Cap or 4AMBz residues. The prominent appearance of b ions from the AXAG and XAAG peptide is noteworthy, and suggests either that proton migration occurs through larger, ,whole' peptide cyclic intermediates or that fragmentation proceeds through a population of [M+H]+ isomers that are initially protonated at amide O atoms. Copyright © 2006 John Wiley & Sons, Ltd. [source]


    Redox Activity and Structural Transition of Heptyl Viologen Adlayers on Cu(100),

    CHEMPHYSCHEM, Issue 7 2010
    Min Jiang Dr.
    Abstract The redox behaviour and potential-dependent adsorption structure of heptyl viologen (1,1,-diheptyl-4,4,-bipyridinium dichloride, DHV2+) on a Cu(100) electrode was investigated in a chloride-containing electrolyte solution by cyclic voltammetry (CV) and in situ electrochemical scanning tunneling microscopy (EC,STM). The dicationic DHV molecules generate a few pairs of current waves in CV measurements which are ascribed to two typical one-electron transfer steps. STM images obtained in a KCl-containing electrolyte solution disclose a well-ordered c(2×2) chloride adlayer on a Cu(100) electrode surface. After injecting DHV2+ molecules into the KCl electrolyte solution, a highly ordered 2D "dot-array" structure in STM images emerges on the c(2×2)-Cl modified Cu(100) electrode surface. DHV2+ molecules spontaneously arrange themselves with their molecular planes facing the electrode surface and their long molecular axis parallel to the step edge. Such adsorption structure can be described by mirror domains and rotational domains which stably exist between 200 mV and ,100 mV. One-electron reduction of the dications DHV2+ around ,150 mV causes a phase transition from a ,dot-array' assembly to a stripe pattern formed by DHV.+ radical monocations in STM images which has a bilayer structure. With a further decrease of the applied electrode potential, the structure of the DHV.+ adlayer undergoes a change from a loose stripe phase to a more compact stripe phase, a subsequent decay of the compact structure, and finally the formation of a new dimer phase. A further electron transfer reaction at ,400 mV causes the formation of an amorphous phase on the chloride free electrode surface. In a reverse anodic sweep, the reproduction of the ordered DHV.+ stacking phase occurs again on top of the chloride lattice. [source]