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Reactive Sites (reactive + site)
Selected AbstractsRe-evaluation of intramolecular long-range electron transfer between tyrosine and tryptophan in lysozymesFEBS JOURNAL, Issue 17 2003Evidence for the participation of other residues One-electron oxidation of six different c-type lysozymes from hen egg white, turkey egg white, human milk, horse milk, camel stomach and tortoise was studied by gamma- and pulse-radiolysis. In the first step, one tryptophan side chain is oxidized to indolyl free radical, which is produced quantitatively. As shown already, the indolyl radical subsequently oxidizes a tyrosine side chain to the phenoxy radical in an intramolecular reaction. However this reaction is not total and its stoichiometry depends on the protein. Rate constants also vary between proteins, from 120·s,1 to 1000·s,1 at pH 7.0 and room temperature [extremes are hen and turkey egg white (120·s,1) and human milk (1000·s,1)]. In hen and turkey egg white lysozymes we show that another reactive site is the Asn103,Gly104 peptidic bond, which gets broken radiolytically. Tryptic digestion followed by HPLC separation and identification of the peptides was performed for nonirradiated and irradiated hen lysozyme. Fluorescence spectra of the peptides indicate that Trp108 and/or 111 remain oxidized and that Tyr20 and 53 give bityrosine. Tyr23 appears not to be involved in the process. Thus new features of long-range intramolecular electron transfer in proteins appear: it is only partial and other groups are involved which are silent in pulse radiolysis. [source] Factors controlling the carbon isotope fractionation of tetra- and trichloroethene during reductive dechlorination by Sulfurospirillum ssp. and Desulfitobacterium sp. strain PCE-SFEMS MICROBIOLOGY ECOLOGY, Issue 1 2007Danuta Cichocka Abstract Carbon stable isotope fractionation of tetrachloroethene (PCE) and trichloroethene (TCE) was investigated during reductive dechlorination. Growing cells of Sulfurospirillum multivorans, Sulfurospirillum halorespirans, or Desulfitobacterium sp. strain PCE-S, the respective crude extracts and the abiotic reaction with cyanocobalamin (vitamin B12) were used. Fractionation of TCE (,C=1.0132,1.0187) by S. multivorans was more than one order of magnitude higher than values previously observed for tetrachloroethene (PCE) (,C=1.00042,1.0017). Similar differences in fractionation were observed during reductive dehalogenation by the close relative S. halorespirans with ,C=1.0046,1.032 and ,C=1.0187,1.0229 for PCE and TCE respectively. TCE carbon isotope fractionation (,C=1.0150) by the purified PCE-reductive dehalogenase from S. multivorans was more than one order of magnitude higher than fractionation of PCE (,C=1.0017). Carbon isotope fractionation of TCE by Desulfitobacterium sp. strain PCE-S (,C=1.0109,1.0122) as well as during the abiotic reaction with cyanocobalamin (,C=1.0154) was in a similar range to previously reported values for fractionation by mixed microbial cultures. In contrast with previous results with PCE, no effects due to rate limitations, uptake or transport of the substrate to the reactive site could be observed during TCE dechlorination. Our results show that prior to a mechanistic interpretation of stable isotope fractionation factors it has to be carefully verified how other factors such as uptake or transport affect the isotope fractionation during degradation experiments with microbial cultures. [source] Theoretical study of the substituent effect on the intramolecular hydrogen bonds in di(4-hydroxycoumarin) derivativesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2006Tzvetan Mihaylov Abstract Geometry optimization of ortho -, meta -, and para -pyridyl-substituted di(4-hydroxycoumarin) [di(4-HC)] was performed with the density functional theory (DFT) [B3LYP/6-31G(d)] method. Two asymmetrical intramolecular OH,O hydrogen bonds (HBs) stabilized the structures. The calculated single HB energies varied from ,62.56 to ,47.53 kJ mol,1 and pointed to a relative strong hydrogen bond in the systems studied. The 2- and 6-pyridyl substituents produced the largest geometrical changes in di(4-hydroxycoumarin) fragment. The highest total HB energy was found for 2-pyridyl-substituted and the lowest one for 6-pyridyl-substituted di(4-hydroxycoumarin). The HB energy variations were confirmed with rotational barrier method calculations. Both steric and electrostatic factors were found to be responsible for the HB asymmetry in the compounds studied. According to the molecular electrostatic potential (MEP) calculations the most preferred reactive site for electrophilic attack of pyridyl-substituted di(4-hydroxycoumarin)s are the pyridine nitrogen and the carbonyl oxygens, followed by the hydroxyl oxygens. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Self-assembled films of hydrophobin protein HFBIII from Trichoderma reeseiJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2007Kaisa Kisko Hydrophobins are a group of small amphiphilic proteins which are known to self-assemble on interfaces. They contain eight conserved cysteine residues, which make four disulfide bridges. A new hydrophobin protein, HFBIII, from the fungus Trichoderma reesei contains one extra cysteine residue, giving the protein a naturally reactive site. The self-assembly of hydrophobin protein HFBIII was studied using grazing-incidence X-ray diffraction and reflectivity. HFBIII self-assembles into a hexagonally ordered monolayer at an air/water interface and also forms crystalline coatings on a silicon substrate. The lattice constants for the hexagonal coatings are a = b = 56.5,Å, , = 120°. The self-assembled structure in the HFBIII film is very similar to those formed by two other T. reesei hydrophobins, HFBI and HFBII. [source] Relationship between temporary inhibition and structure of disulfide-linkage analogs of marinostatin, a natural ester-linked protein protease inhibitorCHEMICAL BIOLOGY & DRUG DESIGN, Issue 2 2005M. Taniguchi Abstract:, A 12-residue marinostatin [MST(1,12): 1FATMRYPSDSDE12] which contains two ester linkages of Thr3,Asp9 and Ser8,Asp11 strongly inhibits subtilisin. In order to study the relationship between the inhibitory activity, structure, and stability of MST, MST analogs were prepared by changing ester linkages to a disulfide linkages. The analogs without the disulfide linkage between 3 and 9 positions lost their inhibitory activity. The Ki value of 1SS(C3,C9) (1FACMRYPSCSDE12), which has a single disulfide linkage of Cys3,Cys9 was comparable with those of MST(1,12) and MST-2SS (1FACMRYPCCSCE12), a doubly linked analog of Cys3,Cys9 and Cys8,Cys11. However, 1SS(C3,C9) and MST-2SS showed temporary inhibition, but not MST(1,12): These analogs were inactivated after incubation with subtilisin for 30 min, and were specifically hydrolyzed at the reactive site. 1H NMR study showed that 1SS(C3,C9) has two conformations, which contain a cis - (70%) or trans - (30%) Pro residue, while MST-2SS as well as MST(1,12) takes a single conformation containing only a cis -Pro residue. Hydrogen,deuterium exchange rate of the Arg5 (P1,) NH proton of the MST analogs was about 100 times faster than that of MST(1,12). These results indicate that the linkage between the positions 8 and 11 plays a role for fixing the cis -conformation of the Pro7 residue, and that the linkage between 3 and 9 is indispensable for the inhibition, but not enough for stable protease-inhibitor complex. [source] Mineral surfaces and soil organic matterEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 2 2003K. Kaiser Summary The organic carbon content of soil is positively related to the specific surface area (SSA), but large amounts of organic matter in soil result in reduced SSA as determined by applying the Brunauer,Emmett,Teller (BET) equation to the adsorption of N2. To elucidate some of the controlling mechanisms of this relation, we determined the SSA and the enthalpy of N2 adsorption of separates with a density > 1.6 g cm,3 from 196 mineral horizons of forest soils before and after removal of organic matter with NaOCl. Likewise, we investigated these characteristics before and after sorption of increasing amounts of organic matter to four mineral soil samples, oxides (amorphous Al(OH)3, gibbsite, ferrihydrite, goethite, haematite), and phyllosilicates (kaolinite, illite). Sorption of organic matter reduced the SSA, depending on the amount sorbed and the type of mineral. The reduction in SSA decreased at larger organic matter loadings. The SSA of the mineral soils was positively related to the content of Fe oxyhydroxides and negatively related to the content of organic C. The strong reduction in SSA at small loadings was due primarily to the decrease in the micropores to which N2 was accessible. This suggests preferential sorption of organic matter at reactive sites in or at the mouths of micropores during the initial sorption and attachment to less reactive sites at increasing loadings. The exponential decrease of the heat of gas adsorption with the surface loading points also to a filling or clogging of micropores at early stages of organic matter accumulation. Desorption induced a small recovery of the total SSA but not of the micropore surface area. Destruction of organic matter increased the SSA of all soil samples. The SSA of the uncovered mineral matrix related strongly to the amounts of Fe oxyhydroxides and the clay. Normalized to C removed, the increase in SSA was small in topsoils and illuvial horizons of Podzols rich in C and large for the subsoils containing little C. This suggests that micropores preferentially associate with organic matter, especially at small loadings. The coverage of the surface of the soil mineral matrix as calculated from the SSA before and after destruction of organic matter was correlated only with depth, and the relation appeared to be linear. We conclude that mineralogy is the primary control of the relation between surface area and sorption of organic matter within same soil compartments (i.e. horizons). But at the scale of complete profiles, the surface accumulation and stabilization of organic matter is additionally determined by its input. [source] Solvent effect on the reactivity of CIS -platinum (II) complexes: A density functional approachINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 8 2008Pubalee Sarmah Abstract The structure and chemical reactivity of some selected cis -platinum(II) complexes, including clinically used drug molecules, cisplatin, carboplatin, and oxaliplatin are investigated using density functional theory (DFT) calculations. Calculated geometries of the complexes are in agreement with their available X-ray data. The global and local reactivity descriptors, such as hardness, chemical potential, electrophilicity index, Fukui function, and local philicity are calculated to investigate the usefulness of these descriptors for understanding the reactive nature and reactive sites of the complexes. Inclusion of solvent effect shows that both global and local descriptors change the trend of reactivity with respect to their trend in the gas phase. The stability of the complexes increases with the inclusion of water molecules. Simple regression analysis is applied to build up a quantitative structure-activity relationship (QSAR) model based on DFT derived electrophilicity index for the Pt(II) complexes against A2780 human ovarian adenocarcinoma cell line to establish the importance of the descriptor in predicting cytotoxicity. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Understanding selenocysteine through conformational analysis, proton affinities, acidities and bond dissociation energiesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2008Damanjit Kaur Abstract Density functional methods have been employed to characterize the gas phase conformations of selenocysteine. The 33 stable conformers of selenocysteine have been located on the potential energy surface using density functional B3LYP/6-31+G* method. The conformers are analyzed in terms of intramolecular hydrogen bonding interactions. The proton affinity, gas phase acidities, and bond dissociation energies have also been evaluated for different reactive sites of selenocysteine for the five lowest energy conformers at B3LYP/6-311++G*//B3LYP/6-31+G* level. Evaluation of these intrinsic properties reflects the antioxidant activity of selenium in selenocysteine. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Quantum chemical studies on molecular structural conformations and hydrated forms of salicylamide and O-hydroxybenzoyl cyanideINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2005K. Anandan Abstract Ab initio and density functional theory (DFT) methods have been employed to study the molecular structural conformations and hydrated forms of both salicylamide (SAM) and O-hydroxybenzoyl cyanide (OHBC). Molecular geometries and energetics have been obtained in the gaseous phase by employing the Møller,Plesset type 2 MP2/6-311G(2d,2p) and B3LYP/6-311G(2d,2p) levels of theory. The presence of an electron-releasing group (SAM) leads to an increase in the energy of the molecular system, while the presence of an electron-withdrawing group (OHBC) drastically decreases the energy. Chemical reactivity parameters (, and ,) have been calculated using the energy values of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) obtained at the Hartree,Fock (HF)/6-311G(2d,2p) level of theory for all the conformers and the principle of maximum hardness (MHP) has been tested. The condensed Fukui functions have been calculated using the atomic charges obtained through the natural bond orbital (NBO) analysis scheme for all the optimized structures at the B3LYP/6-311G(2d,2p) level of theory, and the most reactive sites of the molecules have been identified. Nuclear magnetic resonance (NMR) studies have been carried out at the B3LYP/6-311G(2d,2p) level of theory for all the conformers in the gaseous phase on the basis of the method of Cheeseman and coworkers. The calculated chemical shift values have been used to discuss the delocalization activity of the electron clouds. The dimeric structures of the most stable conformers of both SAM and OHBC in the gaseous phase have been optimized at the B3LYP/6-311G(2d,2p) level of theory, and the interaction energies have been calculated. The most stable conformers of both compounds bear an intramolecular hydrogen bond, which gives rise to the formation of a pseudo-aromatic ring. These conformers have been allowed to interact with the water molecule. Special emphasis has been given to analysis of the intermolecular hydrogen bonds of the hydrated conformers. Self-consistent reaction field (SCRF) theory has been employed to optimize all the conformers in the aqueous phase (, = 78.39) at the B3LYP/6-311G(2d,2p) level of theory, and the solvent effect has been studied. Vibrational frequency analysis has been performed for all the optimized structures at MP2/6-311G(2d,2p) level of theory, and the stationary points corresponding to local minima without imaginary frequencies have been obtained for all the molecular structures. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [source] Effect of solvent quality on kinetics of tethered layer formationJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 21 2004Heqing Huang Abstract We conducted a study of the effect of solvent quality on the kinetics of formation of a layer of polymer chains tethered to a solid substrate. In these experiments, tethering was accomplished by means of chemical bond formation between reactive sites on the surface and the end-functional groups of the polymer chains in solution. All experimental variables were held constant except for the ,-parameter between the polymer and solvent. Variation in the ,-parameter was achieved by use of a series of nonpolar, organic solvents. The distinct three-regime kinetics, typical of tethering reactions run in a good solvent and in the absence of segmental adsorption, was observed over the range of values for the ,-parameter. As expected, an increase in the ,-parameter (a decrease in solvent quality) did result in increased tethering density, but, contrary to expectation, no increase in tethering rate was observed. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5530,5537, 2004 [source] Specificity and reactive loop length requirements for crmA inhibition of serine proteasesPROTEIN SCIENCE, Issue 2 2005Lisa D. Tesch Abstract The viral serpin, crmA, is distinguished by its small size and ability to inhibit both serine and cysteine proteases utilizing a reactive loop shorter than most other serpins. Here, we characterize the mechanism of crmA inhibition of serine proteases and probe the reactive loop length requirements for inhibition with two crmA reactive loop variants. P1 Arg crmA inhibited the trypsin-like proteases, thrombin, and factor Xa, with moderate efficiencies (,102,104 M,1sec,1), near equimolar inhibition stoichiometries, and formation of SDS-stable complexes which were resistant to dissociation (kdiss ,10,7 sec,1), consistent with a serpin-type inhibition mechanism. Trypsin was not inhibited, but efficiently cleaved the variant crmA as a substrate (kcat/KM of ,106 M,1 sec,1). N-terminal sequencing confirmed that the P1 Arg,P1,Cys bond was the site of cleavage. Altering the placement of the Arg in a double mutant P1 Gly-P1,Arg crmA resulted in minimal ability to inhibit any of the trypsin family proteases. This variant was cleaved by the proteases ,10-fold less efficiently than P1 Arg crmA. Surprisingly, pancreatic elastase was rapidly inhibited by wild-type and P1 Arg crmAs (105,106 M,1sec,1), although with elevated inhibition stoichiometries and higher rates of complex dissociation. N-terminal sequencing showed that elastase attacked the P1,Cys,P2,Ala bond, indicating that crmA can inhibit proteases using a reactive loop length similar to that used by other serpins, but with variations in this inhibition arising from different effective P2 residues. These results indicate that crmA inhibits serine proteases by the established serpin conformational trapping mechanism, but is unusual in inhibiting through either of two adjacent reactive sites. [source] Photocrosslinking of a novel ,,, -unsaturated copolyamide: mass spectrometric study on model compounds with benzophenone as photoinitiatorRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 23 2009Marion N'Negue Mintsa The aim of this work was to understand the reactions involved in the photocrosslinking processes of a ,,, -unsaturated copolyamide foreseen as a new UV-curable powder coating. The crosslinking reaction was photoinitiated with benzophenone. In this paper, the photochemical reaction between benzophenone and several model compounds was investigated. The model compounds contained functional groups which could be present in copolyamide. The products resulting from UV curing were identified using a combination of high-resolution mass spectrometry and MSn experiments. The characterization of the products allowed localization of the hydrogen abstraction by the type II photoinitiator during UV curing and, consequently, the determination of the reactive sites of the unsaturated polyamide chain which were involved in the photochemical reaction. Copyright © 2009 John Wiley & Sons, Ltd. [source] | |||||||||||||