Preparation and structural characterization of a novel dicopper(ii) complex with a terminal hydroxide: a structural model of an active site in phosphohydrolasesElectronic supplementary information (ESI) available: the effective magnetic moments and the molar magnetic susceptibilities of 1, the positive ion electrospray ionization mass spectrum of [CuII2(TNPDO)(OH)(F)]+ and the structure of HTNPDO. See http://www.rsc.org/suppdata/dt/b3/b303787h/

2003 ◽  
pp. 2115 ◽  
Author(s):  
Hidekazu Arii ◽  
Yasuhiro Funahashi ◽  
Koichiro Jitsukawa ◽  
Hideki Masuda
Keyword(s):  
Active Site ◽  
Structural Model ◽  
Magnetic Moments ◽  
Supplementary Information ◽  
Ionization Mass ◽  
Magnetic Susceptibilities ◽  
Ionization Mass Spectrum ◽  
Electrospray Ionization Mass Spectrum ◽  
Positive Ion

Structure, anion, and solvent effects on cation response in ESI-MS

2019 ◽  
Author(s):  
Isaac Omari ◽  
Parmissa Randhawa ◽  
Jaiya Randhawa ◽  
Jenny Yu ◽  
J Scott McIndoe
Keyword(s):  
Predictive Power ◽  
Solution Concentration ◽  
High Reactivity ◽  
Chemical Processes ◽  
Ionization Mass ◽  
Solution Composition ◽  
Ionization Mass Spectrum ◽  
Electrospray Ionization Mass Spectrum ◽  
Cation Response ◽  
Insight Into

<p>The abundance of an ion in an electrospray ionization mass spectrum is dependent on many factors beyond just solution concentration. Even in cases where the ions are permanently charged and do not rely on protonation or other chemical processes to acquire the necessary charge, factors such as cation structure, molecular weight, solvent, and the identity of the anion can perturb results. Screening of a variety of combinations of cation, anion and solvent provided insight into some of the more important factors. Rigid cations and high conductivity anions tended to provide the highest responses, while acetonitrile was the most accurate solvent for reflecting solution composition. Functional groups that had affinity for the solvent tended to depress response. These observations will provide predictive power when accounting for ions that for reasons of high reactivity can not be isolated.</p><br>

Oxidative Desulfurization of Dibenzothiophene Catalyzed by Polyoxometalate-Based Ionic Liquid

2014 ◽  
Vol 1033-1034 ◽  
pp. 65-69
Author(s):  
Min Wang ◽  
Qin Wu ◽  
Han Sheng Li ◽  
Yun Zhao ◽  
Qing Ze Jiao
Keyword(s):  
Ionic Liquid ◽  
Sulfonic Acid ◽  
Sulfur Removal ◽  
Oxidative Desulfurization ◽  
Ionization Mass ◽  
Thermogravimetric Analyzer ◽  
Catalytic Oxidative Desulfurization ◽  
Ionization Mass Spectrum ◽  
Electrospray Ionization Mass Spectrum ◽  
Desulfurization Process

A polyoxometalate-based ionic liquid, 1-(4-sulfonic acid) methylimidazolium phosphotungstate ([MIMBS]3PW12O40), was synthesized and characterized by Fourier transform infrared spectrum, nuclear magnetic resonance, electrospray ionization mass spectrum and thermogravimetric analyzer. [MIMBS]3PW12O40exhibited high activity for the extractive catalytic oxidative desulfurization process, together with H2O2and CH3CN/H2O. The sulfur removal of DBT could reach 99.9% under wild conditions, and the catalyst could be used three times with only a slight decline in activity.

Structure, anion, and solvent effects on cation response in ESI-MS

2019 ◽  
Author(s):  
Isaac Omari ◽  
Parmissa Randhawa ◽  
Jaiya Randhawa ◽  
Jenny Yu ◽  
J Scott McIndoe
Keyword(s):  
Predictive Power ◽  
Solution Concentration ◽  
High Reactivity ◽  
Chemical Processes ◽  
Ionization Mass ◽  
Solution Composition ◽  
Ionization Mass Spectrum ◽  
Electrospray Ionization Mass Spectrum ◽  
Cation Response ◽  
Insight Into

<p>The abundance of an ion in an electrospray ionization mass spectrum is dependent on many factors beyond just solution concentration. Even in cases where the ions are permanently charged and do not rely on protonation or other chemical processes to acquire the necessary charge, factors such as cation structure, molecular weight, solvent, and the identity of the anion can perturb results. Screening of a variety of combinations of cation, anion and solvent provided insight into some of the more important factors. Rigid cations and high conductivity anions tended to provide the highest responses, while acetonitrile was the most accurate solvent for reflecting solution composition. Functional groups that had affinity for the solvent tended to depress response. These observations will provide predictive power when accounting for ions that for reasons of high reactivity can not be isolated.</p><br>

scholarly journals Biochemical characterization of the chondroitinase ABC I active site

2005 ◽  
Vol 390 (2) ◽  
pp. 395-405 ◽  
Author(s):  
Vikas Prabhakar ◽  
Rahul Raman ◽  
Ishan Capila ◽  
Carlos J. Bosques ◽  
Kevin Pojasek ◽  
...  
Keyword(s):  
Active Site ◽  
Structural Model ◽  
Catalytic Mechanism ◽  
Biochemical Characterization ◽  
Chondroitin Sulphate ◽  
Critical Role ◽  
Site Directed Mutagenesis ◽  
Chondroitinase Abc ◽  
Enzyme Substrate

cABC I (chondroitinase ABC I) from Proteus vulgaris is a GalAG (galactosaminoglycan) depolymerizing lyase that cleaves its substrates at the glycosidic bond via β-elimination. cABC I cleaves a particularly broad range of GalAG substrates, including CS (chondroitin sulphate), DS (dermatan sulphate) and hyaluronic acid. We recently cloned and recombinantly expressed cABC I in Escherichia coli, and completed a preliminary biochemical characterization of the enzyme. In the present study, we have coupled site-directed mutagenesis of the recombinant cABC I with a structural model of the enzyme–substrate complex in order to investigate in detail the roles of active site amino acids in the catalytic action of the enzyme. The putative catalytic residues His-501, Tyr-508, Arg-560 and Glu-653 were probed systematically via mutagenesis. Assessment of these mutants in kinetic and end-point assays provided direct evidence on the catalytic roles of these active-site residues. The crystal structure of the native enzyme provided a framework for molecular docking of representative CS and DS substrates. This enabled us to construct recombinant enzyme–substrate structural complexes. These studies together provided structural insights into the effects of the mutations on the catalytic mechanism of cABC I and the differences in its processing of CS and DS substrates. All His-501 mutants were essentially inactive and thereby implicating this amino acid to play the critical role of proton abstraction during catalysis. The kinetic data for Glu-653 mutants indicated that it is involved in a hydrogen bonding network in the active site. The proximity of Tyr-508 to the glycosidic oxygen of the substrate at the site of cleavage suggested its potential role in protonating the leaving group. Arg-560 was proximal to the uronic acid C-5 proton, suggesting its possible role in the stabilization of the carbanion intermediate formed during catalysis.

scholarly journals Synthesis and characterization of 2-pyridineformamide 3-pyrrolidinylthiosemicarbazone

2013 ◽  
Vol 29 ◽  
pp. 28-33
Author(s):  
B. Shakya ◽  
P. N. Yadav
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrum ◽  
Nmr Spectroscopy ◽  
13C Nmr Spectroscopy ◽  
Synthesis And Characterization ◽  
Ionization Mass ◽  
Transamination Reaction ◽  
Ionization Mass Spectrum ◽  
Esi Mass Spectrometry

Pyrrolidine-1-carbothiohydrazide was prepared by the transamination reaction of 4-methyl-4-phenyl-3-thiosemicarbazide with pyrrolidine in MeCN. 2-pyridineformamide 3-pyrrolidinyl-thiosemicarbazone (HAmPyrr) was synthesized by the reduction of cyanopyridine in the presence of pyrrolidine-1-carbothiohydrazide in MeOH with Na metal. The synthesized compound was characterized by elemental analysis, IR, 1H-NMR, 13C-NMR spectroscopy and ESI mass spectrometry. The prominent (M+1) peak (m/z) of HAmPyrr in the electron spray ionization mass spectrum was found at 250.09 which correspond to the molecular ion plus H. DOI: http://dx.doi.org/10.3126/jncs.v29i0.9234Journal of Nepal Chemical SocietyVol. 29, 2012Page: 28-33Uploaded date : 12/3/2013

scholarly journals Characterization of Glycerol Trinitrate Reductase (NerA) and the Catalytic Role of Active-Site Residues

2004 ◽  
Vol 186 (6) ◽  
pp. 1802-1810 ◽  
Author(s):  
Samantha J. Marshall ◽  
Doreen Krause ◽  
Dayle K. Blencowe ◽  
Graham F. White
Keyword(s):  
Active Site ◽  
Structural Model ◽  
Flavin Mononucleotide ◽  
Active Site Residues ◽  
Old Yellow Enzyme ◽  
Ping Pong ◽  
Glycerol Trinitrate ◽  
Catalytic Role

ABSTRACT Glycerol trinitrate reductase (NerA) from Agrobacterium radiobacter, a member of the old yellow enzyme (OYE) family of oxidoreductases, was expressed in and purified from Escherichia coli. Denaturation of pure enzyme liberated flavin mononucleotide (FMN), and spectra of NerA during reduction and reoxidation confirmed its catalytic involvement. Binding of FMN to apoenzyme to form the holoenzyme occurred with a dissociation constant of ca. 10−7 M and with restoration of activity. The NerA-dependent reduction of glycerol trinitrate (GTN; nitroglycerin) by NADH followed ping-pong kinetics. A structural model of NerA based on the known coordinates of OYE showed that His-178, Asn-181, and Tyr-183 were close to FMN in the active site. The NerA mutation H178A produced mutant protein with bound FMN but no activity toward GTN. The N181A mutation produced protein that did not bind FMN and was isolated in partly degraded form. The mutation Y183F produced active protein with the same k cat as that of wild-type enzyme but with altered Km values for GTN and NADH, indicating a role for this residue in substrate binding. Correlation of the ratio of Km GTN to Km NAD(P)H, with sequence differences for NerA and several other members of the OYE family of oxidoreductases that reduce GTN, indicated that Asn-181 and a second Asn-238 that lies close to Tyr-183 in the NerA model structure may influence substrate specificity.

Characterization of an Abnormal Antithrombin (Milano 2) with Defective Thrombin Binding

1986 ◽  
Vol 56 (03) ◽  
pp. 349-352 ◽  
Author(s):  
A Tripodi ◽  
A Krachmalnicoff ◽  
P M Mannucci
Keyword(s):  
Venous Thromboembolism ◽  
Active Site ◽  
Inhibitory Activity ◽  
Antithrombin Iii ◽  
Factor Xa ◽  
Molecular Defect ◽  
Affinity Adsorption ◽  
Italian Family ◽  
Crossed Immunoelectrophoresis

SummaryFour members of an Italian family (two with histories of venous thromboembolism) had a qualitative defect of antithrombin III reflected by normal antigen concentrations and halfnormal antithrombin activity with or without heparin. Anti-factor Xa activities were consistently borderline low (about 70% of normal). For the propositus’ plasma and serum the patterns of antithrombin III in crossed-immunoelectrophoresis with or without heparin were indistinguishable from those of normal plasma or serum. A normal affinity of antithrombin III for heparin was documented by heparin-sepharose chromatography. Affinity adsorption of the propositus’ plasma to human α-thrombin immobilized on sepharose beads revealed defective binding of the anti thrombin III to thrombin-sepharose. Hence the molecular defect of this variant appears to be at the active site responsible for binding and neutralizing thrombin, thus accounting for the low thrombin inhibitory activity.

Strongly Coupled Redox-Linked Conformational Switching at the Active Site of the Non-Heme Iron-Dependent Dioxygenase, TauD

2019 ◽  
Author(s):  
Christopher John ◽  
Greg M. Swain ◽  
Robert P. Hausinger ◽  
Denis A. Proshlyakov
Keyword(s):  
Active Site ◽  
Structural Model ◽  
Heme Iron ◽  
Chemical Transformations ◽  
Experimental Conditions ◽  
Strongly Coupled ◽  
Non Heme Iron ◽  
Reversible Redox ◽  
Wide Range ◽  
Complex Structural

2-Oxoglutarate (2OG)-dependent dioxygenases catalyze C-H activation while performing a wide range of chemical transformations. In contrast to their heme analogues, non-heme iron centers afford greater structural flexibility with important implications for their diverse catalytic mechanisms. We characterize an <i>in situ</i> structural model of the putative transient ferric intermediate of 2OG:taurine dioxygenase (TauD) by using a combination of spectroelectrochemical and semi-empirical computational methods, demonstrating that the Fe (III/II) transition involves a substantial, fully reversible, redox-linked conformational change at the active site. This rearrangement alters the apparent redox potential of the active site between -127 mV for reduction of the ferric state and 171 mV for oxidation of the ferrous state of the 2OG-Fe-TauD complex. Structural perturbations exhibit limited sensitivity to mediator concentrations and potential pulse duration. Similar changes were observed in the Fe-TauD and taurine-2OG-Fe-TauD complexes, thus attributing the reorganization to the protein moiety rather than the cosubstrates. Redox difference infrared spectra indicate a reorganization of the protein backbone in addition to the involvement of carboxylate and histidine ligands. Quantitative modeling of the transient redox response using two alternative reaction schemes across a variety of experimental conditions strongly supports the proposal for intrinsic protein reorganization as the origin of the experimental observations.

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