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Author (up) Farrugia, J.M.; Taverner, T.; O'Hair, R.A.J. file  url
doi  openurl
  Title Side-chain involvement in the fragmentation reactions of the protonated methyl esters of histidine and its peptides Type Journal Article
  Year 2001 Publication International Journal of Mass Spectrometry Abbreviated Journal International Journal of Mass Spectrometry  
  Volume 209 Issue 2-3 Pages 99-112  
  Keywords Histidine; Protonated peptide fragmentation; Multistage mass spectrometry; Ab initio calculations  
  Abstract The gas phase fragmentation reactions of [M+H]+ ions of the methyl esters of histidine and histidine containing di- and tripeptides were examined by electrospray ionization (ESI) multistage mass spectrometry (MSn) experiments using a quadrupole ion trap mass spectrometer. The MS/MS spectra tend to be dominated by bn sequence ions, whose structures were probed via MS3 experiments and ab initio calculations at the MP2(FC)/6-31G∗//HF6-31G∗ level of theory (for bn ions where n = 1 and 2). The ab initio calculations suggest a structure for the b1 ion that is stabilized by the formation of a bicyclic ring via involvement of the side-chain imidazole ring. In contrast, MS3 experiments reveal that the b2 ion derived from the sequences HG-Y and GH-Y yield identical spectra to the MS/MS spectrum of the protonated diketopiperazine of (GH). These experimental results are consistent with ab initio calculations that reveal the side-chain protonated diketopiperazine of (GH) to be thermodynamically favored over all other b2 isomeric structures. Thus, the histidine side chain appears to exert both a direct and an indirect (through base catalysis) role in the formation of bn sequence ions from protonated peptides.  
  Call Number Serial 568  
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Author (up) Jaswal, S.S. file  url
  Title Biological insights from hydrogen exchange mass spectrometry Type Journal Article
  Year 2013 Publication Biochimica et Biophysica Acta Abbreviated Journal Biochim Biophys Acta  
  Volume 1834 Issue 6 Pages 1188-1201  
  Keywords Deuterium/chemistry; Deuterium Exchange Measurement/methods; Hydrogen/*chemistry; Kinetics; Mass Spectrometry/*methods; Protein Conformation; Protein Folding; Thermodynamics  
  Abstract Over the past two decades, hydrogen exchange mass spectrometry (HXMS) has achieved the status of a widespread and routine approach in the structural biology toolbox. The ability of hydrogen exchange to detect a range of protein dynamics coupled with the accessibility of mass spectrometry to mixtures and large complexes at low concentrations result in an unmatched tool for investigating proteins challenging to many other structural techniques. Recent advances in methodology and data analysis are helping HXMS deliver on its potential to uncover the connection between conformation, dynamics and the biological function of proteins and complexes. This review provides a brief overview of the HXMS method and focuses on four recent reports to highlight applications that monitor structure and dynamics of proteins and complexes, track protein folding, and map the thermodynamics and kinetics of protein unfolding at equilibrium. These case studies illustrate typical data, analysis and results for each application and demonstrate a range of biological systems for which the interpretation of HXMS in terms of structure and conformational parameters provides unique insights into function. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.  
  Call Number Serial 975  
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Author (up) Kolpin, D.W.; Blazer, V.S.; Gray, J.L.; Focazio, M.J.; Young, J.A.; Alvarez, D.A.; Iwanowicz, L.R.; Foreman, W.T.; Furlong, E.T.; Speiran, G.K.; Zaugg, S.D.; Hubbard, L.E.; Meyer, M.T.; Sandstrom, M.W.; Barber, L.B. file  url
doi  openurl
  Title Chemical contaminants in water and sediment near fish nesting sites in the Potomac River basin: determining potential exposures to smallmouth bass (Micropterus dolomieu) Type Journal Article
  Year 2013 Publication The Science of the Total Environment Abbreviated Journal Sci Total Environ  
  Volume 443 Issue Pages 700-716  
  Keywords Animals; Bass/*metabolism/physiology; Gas Chromatography-Mass Spectrometry; Geologic Sediments/*chemistry; Quality Control; Rivers; Water Pollutants, Chemical/*analysis  
  Abstract The Potomac River basin is an area where a high prevalence of abnormalities such as testicular oocytes (TO), skin lesions, and mortality has been observed in smallmouth bass (SMB, Micropterus dolomieu). Previous research documented a variety of chemicals in regional streams, implicating chemical exposure as one plausible explanation for these biological effects. Six stream sites in the Potomac basin (and one out-of-basin reference site) were sampled to provide an assessment of chemicals in these streams. Potential early life-stage exposure to chemicals detected was assessed by collecting samples in and around SMB nesting areas. Target chemicals included those known to be associated with important agricultural and municipal wastewater sources in the Potomac basin. The prevalence and severity of TO in SMB were also measured to determine potential relations between chemistry and biological effects. A total of 39 chemicals were detected at least once in the discrete-water samples, with atrazine, caffeine, deethylatrazine, simazine, and iso-chlorotetracycline being most frequently detected. Of the most frequently detected chemicals, only caffeine was detected in water from the reference site. No biogenic hormones/sterols were detected in the discrete-water samples. In contrast, 100 chemicals (including six biogenic hormones/sterols) were found in a least one passive-water sample, with 25 being detected at all such samples. In addition, 46 chemicals (including seven biogenic hormones/sterols) were found in the bed-sediment samples, with caffeine, cholesterol, indole, para-cresol, and sitosterol detected in all such samples. The number of herbicides detected in discrete-water samples per site had a significant positive relation to TO(rank) (a nonparametric indicator of TO), with significant positive relations between TO(rank) and atrazine concentrations in discrete-water samples and to total hormone/sterol concentration in bed-sediment samples. Such significant correlations do not necessarily imply causation, as these chemical compositions and concentrations likely do not adequately reflect total SMB exposure history, particularly during critical life stages.  
  Call Number Serial 924  
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Author (up) Sawalha, M.F.; Sengupta, M.K.; Ohira, S.-I.; Idowu, A.D.; Gill, T.E.; Rojo, L.; Barnes, M.; Dasgupta, P.K. file  url
  Title Measurement of soil/dust arsenic by gas phase chemiluminescence Type Journal Article
  Year 2008 Publication Talanta Abbreviated Journal Talanta  
  Volume 77 Issue 1 Pages 372-379  
  Keywords Arsenic/*analysis; Dust/*analysis; Gases/*chemistry; Luminescent Measurements/*instrumentation/*methods; Mass Spectrometry; Soil/*analysis  
  Abstract A gas phase chemiluminescence (GPCL)-based method for trace measurement of arsenic has been recently described for the measurement of arsenic in water. The principle is based on the reduction of inorganic As to AsH(3) at a controlled pH (the choice of pH governs whether only As(III) or all inorganic As is converted) and the reaction of AsH(3) with O(3) to produce chemiluminescence (Idowu et al., Anal. Chem. 78 (2006) 7088-7097). The same general principle has also been used in postcolumn reaction detection of As, where As species are separated chromatographically, then converted into inorganic As by passing through a UV photochemical reactor followed by AsH(3) generation and CL reaction with ozone (Idowu and Dasgupta, Anal. Chem. 79 (2007) 9197-9204). In the present paper we describe the measurement of As in different soil and dust samples by serial extraction with water, citric acid, sulfuric acid and nitric acid. We also compare parallel measurements for total As by induction coupled plasma mass spectrometry (ICP-MS). As(V) was the only species found in our samples. Because of chloride interference of isobaric ArCl(+) ICP-MS analyses could only be carried out by standard addition; these results were highly correlated with direct GPCL and LC-GPCL results (r(2)=0.9935 and 1.0000, respectively). The limit of detection (LOD) in the extracts was 0.36 microg/L by direct GPCL compared to 0.1 microg/L by ICP-MS. In sulfuric acid-based extracts, the LC-GPCL method provided LODs inferior to those previously observed for water-based standards and were 2.6, 1.3, 6.7, and 6.4 microg/L for As(III), As(V), dimethylarsinic acid (DMA) and monomethylarsonic acid (MMA), respectively.  
  Call Number Serial 1018  
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Author (up) Schenone, M.; Dancik, V.; Wagner, B.K.; Clemons, P.A. file  url
  Title Target identification and mechanism of action in chemical biology and drug discovery Type Journal Article
  Year 2013 Publication Nature Chemical Biology Abbreviated Journal Nat Chem Biol  
  Volume 9 Issue 4 Pages 232-240  
  Keywords Animals; Biomarkers, Pharmacological/chemistry/*metabolism; *Drug Discovery; *Drug Evaluation, Preclinical; *High-Throughput Screening Assays; Humans; Isotope Labeling; Mass Spectrometry; Molecular Targeted Therapy; Phenotype; RNA Interference; Reverse Genetics; Saccharomyces cerevisiae/drug effects/genetics/metabolism; Small Molecule Libraries/chemistry/*metabolism/pharmacology; Validation Studies as Topic  
  Abstract Target-identification and mechanism-of-action studies have important roles in small-molecule probe and drug discovery. Biological and technological advances have resulted in the increasing use of cell-based assays to discover new biologically active small molecules. Such studies allow small-molecule action to be tested in a more disease-relevant setting at the outset, but they require follow-up studies to determine the precise protein target or targets responsible for the observed phenotype. Target identification can be approached by direct biochemical methods, genetic interactions or computational inference. In many cases, however, combinations of approaches may be required to fully characterize on-target and off-target effects and to understand mechanisms of small-molecule action.  
  Call Number Serial 1592  
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Author (up) Thaker, B.T.; Barvalia, R.S. file  url
doi  openurl
  Title Microwave assisted synthesis and characterization of unsymmetrical tetradentate Schiff base complexes of VO(IV) and MoO(V) Type Journal Article
  Year 2011 Publication Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy Abbreviated Journal Spectrochim Acta A Mol Biomol Spectrosc  
  Volume 84 Issue 1 Pages 51-61  
  Keywords Electron Spin Resonance Spectroscopy; Electrons; Ligands; Magnetic Phenomena; Magnetic Resonance Spectroscopy; Mass Spectrometry; *Microwaves; Molybdenum/*chemistry; Oxides/*chemistry; Physical Phenomena; Powders; Schiff Bases/*chemical synthesis/*chemistry; Spectrophotometry, Ultraviolet; Spectroscopy, Fourier Transform Infrared; Stereoisomerism; Temperature; Thermogravimetry; Vanadates/*chemistry  
  Abstract Microwave synthesis, is green chemical method, simple, sensitive, reducing solvent amount and reaction time. The attempt was made to synthesize the unsymmetrical tetradentate N(2)O(2) ligands and their VO(IV) and MoO(V) unsymmetrical tetradentate Schiff base complexes by classical and microwave techniques using domestic microwave oven. The resulting unsymmetrical Schiff base ligands L(1)-L(3) characterized by different spectral methods. Their complexes with oxocations of VO(IV) and MoO(V) have been synthesized and characterized by elemental analyses, conductometric measurements, infrared and electronic absorption, (1)H NMR spectra, mass spectrometry, ESR spectra, magnetic susceptibility measurement and thermal study. The study suggests that the oxo metal ion is bonded to the ligand through the oxygen and imino nitrogen and the geometry around metal ion is distorted octahedral.  
  Call Number Serial 426  
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Author (up) Tsutsui, Y.; Wintrode, P.L. file  url
  Title Hydrogen/deuterium exchange-mass spectrometry: a powerful tool for probing protein structure, dynamics and interactions Type Journal Article
  Year 2007 Publication Current Medicinal Chemistry Abbreviated Journal Curr Med Chem  
  Volume 14 Issue 22 Pages 2344-2358  
  Keywords Deuterium; Deuterium Exchange Measurement/*methods; Hydrogen; Mass Spectrometry/*methods; Molecular Structure; Protein Binding; Protein Conformation; Proteins/*chemistry/*metabolism  
  Abstract Knowledge of the structure and dynamics of proteins and protein assemblies is critical both for understanding the molecular basis of physiological and patho-physiological processes and for guiding drug design. While X-ray crystallography and nuclear magnetic resonance spectroscopy are both excellent techniques for this purpose, both suffer from limitations, including the requirement for high quality crystals and large amounts of material. Recently, hydrogen/deuterium exchange measured using mass spectrometry (HXMS) has emerged as a powerful new tool for the study of protein structure, dynamics and interactions in solution. HXMS exploits the fact that backbone amide hydrogens can exchange with deuterium when a protein is incubated in D(2)O, and that the rate of the exchange process is highly dependent on the local structural environment. Several features of HXMS make it an especially attractive approach, including small sample requirements and the ability to study extremely large protein assemblies that are not amenable to other techniques. Here, we provide an overview of HXMS and describe several recent applications to problems of medical interest. After reviewing the molecular basis of the H/D exchange process, the different steps of the HXMS experiment--labeling, rapid proteolysis, fragment separation and mass measurement--are described, followed by a discussion of data analysis methods. Finally, we describe recent results on the application of HXMS to 1) mapping drug/inhibitor binding sites and detecting drug induced conformational changes, 2) studying viral capsid structure and assembly, and 3) characterizing the structure of pathological protein conformations, specifically amyloid fibrils.  
  Call Number Serial 974  
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Author (up) Zhang, Q.; Riechers, D.E. file  url
doi  openurl
  Title Proteomic characterization of herbicide safener-induced proteins in the coleoptile of Triticum tauschii seedlings Type Journal Article
  Year 2004 Publication Proteomics Abbreviated Journal Proteomics  
  Volume 4 Issue 7 Pages 2058-2071  
  Keywords Chromatography, Liquid; Cotyledon/chemistry/metabolism; Databases as Topic; Electrophoresis, Gel, Two-Dimensional; Electrophoresis, Polyacrylamide Gel; Glutathione Transferase/metabolism; Herbicides/chemistry/*metabolism; Hydrogen-Ion Concentration; Image Processing, Computer-Assisted; Immunoblotting; Mass Spectrometry; Poaceae/metabolism; Proteins/chemistry; Proteome; Proteomics/*methods; Seedling/metabolism; Seeds/*metabolism; Silver Staining; Tritium/*metabolism  
  Abstract Proteomic methods such as two-dimensional gel electrophoresis and liquid chromatography tandem mass spectrometry, as well as immunoblotting, were used to identify herbicide safener-induced proteins in the coleoptile of Triticum tauschii, a diploid wheat containing the D genome also found in the cultivated, hexaploid wheat Triticum aestivum. The herbicide safener fluxofenim dramatically increased protein abundance in the molecular weight (M(r)) range of 24 to 30 kDa, as well as a few higher M(r) proteins, in the coleoptile of T. tauschii seedlings. In total, twenty proteins were identified in this study. Eleven proteins were highly safener induced and only weakly expressed in the control; seven proteins were new safener induced proteins that were not detected in the control. Two other proteins were constitutively expressed in both the control and safener-treated coleoptiles. Among the eighteen inducible proteins, fifteen were glutathione S-transferase (GST) subunits that fall into three subclasses: eight proteins were from the tau subclass, six proteins were from the phi subclass, and one protein was from the lambda class. Another three safener inducible proteins showed homology to the aldo/keto reductase family and with proteins that have roles in glycolysis and the Krebs cycle. Two constitutively expressed proteins were identified, one having highest homology to the dehydroascorbate reductase subclass of GSTs and one with an ascorbate peroxidase. Immunoblot analyses, using two different antisera raised against the same GST protein but differing in their specificity, were used to further characterize the GST proteins expressed in response to safener treatment. Results from immunoblotting, combined with mass spectral analysis, showed that post-translational modification of GST proteins in control and safener-treated coleoptiles may occur.  
  Call Number Serial 397  
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