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Hydrogen Exchange (hydrogen + exchange)
Selected AbstractsSpecific Processes and Scrambling in the Dehydrogenation of Ethane and the Degenerate Hydrogen Exchange in the Gas-Phase Ion Chemistry of the Ni(C,H3,O)+/C2H6 CoupleHELVETICA CHIMICA ACTA, Issue 5 2007Maria Schlangen Abstract A mechanistically unprecedented situation characterizes the gas-phase ion chemistry of Ni(C,H3,O)+ when reacted under thermal, single-collision conditions with ethane. A dehydrogenation channel leading to Ni(C3,H7,O)+ is to 90% preceded by a complete loss of positional identity of all nine H-atoms of the encounter complex (,scrambling'), whereas ca. 10% of the reaction exhibit a selective CH bond activation of the alkane. In addition, a degenerate H exchange between ethane and the (C,H3,O) unit occurs as a side reaction, the mechanistic details of which remain unknown for the time being. [source] Binding of the volatile general anesthetics halothane and isoflurane to a mammalian ,-barrel proteinFEBS JOURNAL, Issue 2 2005Jonas S. Johansson A molecular understanding of volatile anesthetic mechanisms of action will require structural descriptions of anesthetic,protein complexes. Porcine odorant binding protein is a 157 residue member of the lipocalin family that features a large ,-barrel internal cavity (515 ± 30 Å3) lined predominantly by aromatic and aliphatic residues. Halothane binding to the ,-barrel cavity was determined using fluorescence quenching of Trp16, and a competitive binding assay with 1-aminoanthracene. In addition, the binding of halothane and isoflurane were characterized thermodynamically using isothermal titration calorimetry. Hydrogen exchange was used to evaluate the effects of bound halothane and isoflurane on global protein dynamics. Halothane bound to the cavity in the ,-barrel of porcine odorant binding protein with dissociation constants of 0.46 ± 0.10 mm and 0.43 ± 0.12 mm determined using fluorescence quenching and competitive binding with 1-aminoanthracene, respectively. Isothermal titration calorimetry revealed that halothane and isoflurane bound with Kd values of 80 ± 10 µm and 100 ± 10 µm, respectively. Halothane and isoflurane binding resulted in an overall stabilization of the folded conformation of the protein by ,0.9 ± 0.1 kcal·mol,1. In addition to indicating specific binding to the native protein conformation, such stabilization may represent a fundamental mechanism whereby anesthetics reversibly alter protein function. Because porcine odorant binding protein has been successfully analyzed by X-ray diffraction to 2.25 Å resolution [1], this represents an attractive system for atomic-level structural studies in the presence of bound anesthetic. Such studies will provide much needed insight into how volatile anesthetics interact with biological macromolecules. [source] Removal of the N-terminal hexapeptide from human ,2-microglobulin facilitates protein aggregation and fibril formationPROTEIN SCIENCE, Issue 5 2000G. Esposito Abstract The solution structure and stability of N-terminally truncated ,2-microglobulin (,N6,2-m), the major modification in ex vivo fibrils, have been investigated by a variety of biophysical techniques. The results show that ,N6,2-m has a free energy of stabilization that is reduced by 2.5 kcal/mol compared to the intact protein. Hydrogen exchange of a mixture of the truncated and full-length proteins at ,M concentrations at pH 6.5 monitored by electrospray mass spectrometry reveals that ,N6,2-m is significantly less protected than its wild-type counterpart. Analysis of ,N6,2-m by NMR shows that this loss of protection occurs in , strands I, III, and part of II. At mM concentration gel filtration analysis shows that ,N6,2-m forms a series of oligomers, including trimers and tetramers, and NMR analysis indicates that strand V is involved in intermolecular interactions that stabilize this association. The truncated species of ,2-microglobulin was found to have a higher tendency to self-associate than the intact molecule, and unlike wild-type protein, is able to form amyloid fibrils at physiological pH. Limited proteolysis experiments and analysis by mass spectrometry support the conformational modifications identified by NMR and suggest that ,N6,2-m could be a key intermediate of a proteolytic pathway of ,2-microglobulin. Overall, the data suggest that removal of the six residues from the N-terminus of ,2-microglobulin has a major effect on the stability of the overall fold. Part of the tertiary structure is preserved substantially by the disulfide bridge between Cys25 and Cys80, but the pairing between ,-strands far removed from this constrain is greatly perturbed. [source] Treatment methods for the determination of ,2H and ,18O of hair keratin by continuous-flow isotope-ratio mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 17 2005Gabriel J. Bowen The structural proteins that comprise ,90% of animal hair have the potential to record environmentally and physiologically determined variation in ,2H and ,18O values of body water. Broad, systematic, geospatial variation in stable hydrogen and oxygen isotopes of environmental water and the capacity for rapid, precise measurement via methods such as high-temperature conversion elemental analyzer/isotope ratio mass spectrometry (TC/EA-IRMS) make these isotope systems particularly well suited for applications requiring the geolocation of hair samples. In order for such applications to be successful, however, methods must exist for the accurate determination of hair ,2H and ,18O values reflecting the primary products of biosynthesis. Here, we present the results of experiments designed to examine two potential inaccuracies affecting ,2H and ,18O measurements of hair: the contribution of non-biologic hydrogen and oxygen to samples in the form of sorbed molecular water, and the exchange of hydroxyl-bound hydrogen between hair keratin and ambient water vapor. We show that rapid sorption of molecular water from the atmosphere can have a substantial effect on measured ,2H and ,18O values of hair (comprising ,7.7% of the measured isotopic signal for H and up to ,10.6% for O), but that this contribution can be effectively removed through vacuum-drying of samples for 6 days. Hydrogen exchange between hair keratin and ambient vapor is also rapid (reaching equilibrium within 3,4 days), with 9,16% of the total hydrogen available for exchange at room temperature. Based on the results of these experiments, we outline a recommended sample treatment procedure for routine measurement of ,2H and ,18O in mammal hair. Copyright © 2005 John Wiley & Sons, Ltd. [source] Addition, elimination, exchange, and epimerization in nitro sulfonesJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 3 2007Charles A. Kingsbury Abstract Three reactions were studied in the diastereomers of 1-(benzenesulfonyl)-2-nitro-1-phenylpropane (1A and 1B) and briefly in related compounds: elimination of the benzenesulfonyl group, epimerization of one diastereomer to the other, and deuterium/hydrogen exchange at the methine group next to nitro in starting material. The two diastereomers showed quite different reactivity. The high melting diasteromer showed rapid elimination and some exchange. The low melting diastereomer (at approximately a half-life) showed extensive epimerization, and elimination to the alkene, but little exchange. There is little effect of aromatic substituents on reaction course. The situation is complicated by re-addition of benzenesulfinate to the alkene. The addition reaction was similar to elimination in agreement with the Principle of Microscopic Reversibility expectations. An electron transfer mechanism for addition is calculated to be comparatively favorable. Copyright © 2007 John Wiley & Sons, Ltd. [source] The Reductive Elimination of Methane from ansa -Hydrido(methyl)metallocenes of Molybdenum and Tungsten: Application of Hammond's Postulate to Two-State ReactionsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 15 2005José-Luis Carreón-Macedo Abstract The energetic profile of the methane reductive elimination from a selected number of hydrido(methyl)molybdenocene and -tungstenocene derivatives has been calculated by DFT methods. The calculations were carried out for the CH2(C5H4)2M (a -M), SiH2(C5H4)2M (a -H2Si,M), and SiMe2(C5Me4)2M (a -Me2Si,M*) ansa -metallocene systems for M = Mo, W. They include the full optimization of minima [the hydrido(methyl) starting complexes, M(H)(CH3), the intermediate methane complexes, M(CH4), and the metallocene products in the singlet and triplet configurations, (3M and 1M)], transition states (for the methyl hydride reductive elimination, M,TSins, and for the hydrogen exchange, M,TSexch), and the minimum energy crossing point (M,MECP) leading from the singlet methane complexes to the corresponding triplet metallocenes. The results are compared with those previously obtained for the simpler (C5H5)2M (Cp2M) systems (J. C. Green, J. N. Harvey, and R. Poli, J. Chem. Soc., Dalton Trans.2002, 1861). The calculated energy profiles, notably the relative energies of M,TSins and M,MECP, are in agreement with available experimental observations for the a -Me2Si,M* systems. The comparison of the energies and geometries of the rate-determining M,TSins and M,MECP structures with those of the thermodynamically relevant minima for the various systems show the applicability of Hammond's postulate to two-state reactions. However, one notable exception serves to show that the principle is only quantitatively reliable when all the potential energy surfaces for the set of analogous reactions have similar shapes. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] On the use of DXMS to produce more crystallizable proteins: Structures of the T. maritima proteins TM0160 and TM1171PROTEIN SCIENCE, Issue 12 2004Glen Spraggon DXMS, deuterium exchange mass spectroscopy Abstract The structure of two Thermotoga maritima proteins, a conserved hypothetical protein (TM0160) and a transcriptional regulator (TM1171), have now been determined at 1.9 Å and 2.3 Å resolution, respectively, as part of a large-scale structural genomics project. Our first efforts to crystallize full-length versions of these targets were unsuccessful. However, analysis of the recombinant purified proteins using the technique of enhanced amide hydrogen/deuterium exchange mass spectroscopy (DXMS) revealed substantial regions of rapid amide deuterium hydrogen exchange, consistent with flexible regions of the structures. Based on these exchange data, truncations were designed to selectively remove the disordered C-terminal regions, and the resulting daughter proteins showed greatly enhanced crystallizability. Comparative DXMS analysis of full-length protein versus truncated forms demonstrated complete and exact preservation of the exchange rate profiles in the retained sequence, indicative of conservation of the native folded structure. This study presents the first structures produced with the aid of the DXMS method for salvaging intractable crystallization targets. The structure of TM0160 represents a new fold and highlights the use of this approach where any prior structural knowledge is absent. The structure of TM1171 represents an example where the lack of a substrate/cofactor may impair crystallization. The details of both structures are presented and discussed. [source] Two-state vs. multistate protein unfolding studied by optical melting and hydrogen exchangePROTEIN SCIENCE, Issue 10 2000Leland Mayne Abstract A direct conflict between the stabilization free energy parameters of cytochrome c determined by optical methods and by hydrogen exchange (HX) is quantitatively explained when the partially folded intermediates seen by HX are taken into account. The results support the previous HX measurements of intermediate populations, show how intermediates can elude the standard melting analysis, and illustrate how they confuse the analysis when they are significantly populated within the melting transition region. [source] Assessment of the repeatability and reproducibility of hydrogen/deuterium exchange mass spectrometry measurements,RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 23 2008William Burkitt A system to perform automated hydrogen/deuterium exchange mass spectrometry measurements was constructed using an XYZ robotic autosampler that was capable of performing solvent manipulations and a 4.7 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The system included features such as the first demonstration of a ,dual column' high-performance liquid chromatography (HPLC) setup, and a novel digestion strategy. The performance of the system, in terms of the repeatability and reproducibility of the measurement of protein hydrogen/deuterium exchange, was assessed over a 2-month period. The sensitivity of the measurement of hydrogen exchange towards several parameters was assessed, which allowed their impact on the reproducibility to be discussed. The parameters assessed were the temperature of the HPLC columns and switching valves, the temperature of the quench solutions, the pH of the mobile phase, the pH of the quenched solution, the acid used in the mobile phase and the analytical column used. Copyright © 2008 John Wiley & Sons, Ltd. [source] Negative ion electrospray ionization mass spectrometry of nucleoside phosphoramidate monoesters: elucidation of novel rearrangement mechanisms by multistage mass spectrometry incorporating in-source deuterium labellingRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 19 2008Peng-Xiang Xu Several O-2,,3,-isopropylideneuridine-O-5,-phosphoramidate monoesters were synthesized and analyzed by negative ion electrospray ionization tandem mass spectrometry (ESI-MSn). Two kinds of novel rearrangement reactions were observed due to the difference in the amino acid in the nucleoside phosphoramidate monoesters, and possible mechanisms were proposed. One involves a five-membered cyclic transition state. The other is formation of a stable five-membered ring intermediate by Michael addition. Results were confirmed by tandem mass spectrometry and isotopically labeled hydrogen atoms. Furthermore, the internal hydrogen exchange between active hydrogen and methyl acrylate in the heated capillary of the mass spectrometer was found. The characteristic fragmentation behavior in ESI-MS may be used to monitor this kind of compounds in the biological metabolism. Copyright © 2008 John Wiley & Sons, Ltd. [source] Effects of electrospray capillary temperature on amide hydrogen exchangeRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 9 2008Stephen J. Coales Amide hydrogen/deuterium (H/D) exchange coupled with proteolysis, high-perfeomance liquid chromatographic (HPLC) separation and mass spectrometry (MS) has become a powerful tool to study protein dynamics in solution. Prior to the execution of H/D exchange experiments, various experimental parameters have to be set, including proteolysis, HPLC, and MS conditions. Here we investigate the effects of electrospray capillary temperature on deuterium retention in backbone amides of various pepsin-generated cytochrome c peptides. Lower capillary temperature generally helps retain more deuterium than higher capillary temperature. When the capillary temperature was 150°C, on average 26% more deuterium was retained than when the capillary temperature was set at 250°C. The effects of capillary temperature varied depending on the ions monitored. There was little difference in deuterium retention among different charge state species of the same peptide at 150°C. However, a lower charge state ion loses more deuterium atoms going from 150°C to 250°C than the corresponding higher charge state species. These results indicate that the capillary temperature should be optimized not only to maximize the signal-to-noise of each ion followed in H/D exchange experiments, but also to minimize the deuterium loss of the ions. Also the loss of deuterium in several ions, especially lower charge state ones, should be monitored in the optimization, as the temperature effects vary among ions and are more significant for lower charge state ions. Copyright © 2008 John Wiley & Sons, Ltd. [source] Use of different proteases working in acidic conditions to improve sequence coverage and resolution in hydrogen/deuterium exchange of large proteinsRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 21 2003Laetitia Cravello The combination of hydrogen exchange and mass spectrometry has been widely used in structural biology, providing views on protein structure and protein dynamics. One of the constraints is to use proteases working at low pH and low temperature to limit back-exchange during proteolysis. Although pepsin works in these conditions and is currently used in such experiments, sequence coverage is not always complete especially for large proteins, and the spatial resolution of the exchange rate is limited by the size of the resulting peptides. In this study we tried two other proteases, protease type XIII from Aspergillus saitoi and protease type XVIII from Rhizhopus species. The penicillin-binding protein X (PBP-2X*), a 77-kDa protein, was selected as a model. Like pepsin, neither of these proteases is really specific, but we found very good reproducibility in the digestion pattern. Compared with using pepsin alone, combining the results of the three independent proteolyses increased the coverage for the peptide mapping, thus avoiding missing some potentially interesting regions of the protein. Furthermore, we obtained a better spatial resolution for deuterium incorporation data, specifying accurately the deuterated regions. Copyright © 2003 John Wiley & Sons, Ltd. [source] Regions of Tau Implicated in the Paired Helical Fragment Core as Defined by NMRCHEMBIOCHEM, Issue 10 2005Alain Sillen Dr. Abstract We have studied the mature Alzheimer-like fibers of tau by fluorescence and NMR spectroscopy. Assembly of the protein into paired helical filaments after incubation with heparin at 37,°C was verified by electron microscopy and size-exclusion chromatography. NMR spectroscopy on these mature fibers revealed different regions of residual mobility for tau: the N-terminal domain was found to maintain solution-like dynamics and was followed by a large domain of decreasing mobility; finally the core region was distinguished by a solid-like character. Heteronuclear-NOE data indicate that the decreasing mobility is due to both a slowing down of the rapid nanosecond movements and the introduction of slower movements that lead to exchange broadening. Fluorescence spectroscopy confirmed the presence of this rigid core, and some degree of protection from hydrogen exchange for those residues was observed. Hence, our data give a more precise picture of the dynamics of tau when it is integrated into mature filaments and should provide further understanding of the molecular processes that govern aggregation. [source] Significant Influence of Zn on Activation of the C-H Bonds of Small Alkanes by Brønsted Acid Sites of Zeolite,CHEMPHYSCHEM, Issue 17 2008Alexander G. Stepanov Prof. Abstract Herein, we analyze earlier obtained and new data about peculiarities of the H/D hydrogen exchange of small C1,n -C4 alkanes on Zn-modified high-silica zeolites ZSM-5 and BEA in comparison with the exchange for corresponding purely acidic forms of these zeolites. This allows us to identify an evident promoting effect of Zn on the activation of CH bonds of alkanes by zeolite Brønsted sites. The effect of Zn is demonstrated by observing the regioselectivity of the H/D exchange for propane and n- butane as well as by the increase in the rate and a decrease in the apparent activation energy of the exchange for all C1,n -C4 alkanes upon modification of zeolites with Zn. The influence of Zn on alkane activation has been rationalized by dissociative adsorption of alkanes on Zn oxide species inside zeolite pores, which precedes the interaction of alkane with Brønsted acid sites. [source] Intracellular pH, intrauterine growth and the insulin resistance syndromeCLINICAL PHYSIOLOGY AND FUNCTIONAL IMAGING, Issue 6 2001Jonathan H. Pinkney Defects of both sodium,hydrogen exchange (NHE) and sodium,lithium countertransport (SLC) have been described in subjects at increased risk of coronary heart disease (CHD). Sodium transport is linked to the regulation of cell volume, intracellular pH and cell growth, which may explain aspects of this association. However, impaired growth in early life is also linked to adult CHD, and ,programmed' alterations of cell behaviour are postulated to be responsible for this. In this study, therefore, we examined whether NHE or SLC in adults are predicted by anthropometric measures at birth, as well as being associated with insulin resistance syndrome (IRS) variables in adulthood. Red cell SLC was measured in 26 adults, and NHE in dermal fibroblasts from another 15 subjects characterized anthropometrically at birth. SLC activity correlated with LDL cholesterol, triglycerides and urate (r=0·42 , 0·49; 0·05 > P>0·01), but not birth anthropometry. NHE Vmax correlated with plasma insulin (r=0·80; P<0·001), but birth weight was unrelated to Vmax, Km or Hill coefficient for H+i. However, pHi correlated with birth weight (r=0·74; P=0·002), insulin sensitivity (r=0·52; P<0·05), fasting glucose (r=,0·52; P<0·05) 2 h insulin (r=0·51; P<0·05) 2 h glucose (r=,0·54; P<0·05). In conclusion, red cell SLC is related to IRS variables, but not with birth weight measures. In contrast, low intracellular pHi is related to both low birth weight and adult insulin resistance, suggesting it might be a ,programmed' cell phenotype, although this is not apparently explained by altered NHE kinetics. [source] | ||||||||||