Hemoglobin in five genetically diverse Frankia strains

2002 ◽  
Vol 48 (12) ◽  
pp. 1048-1055 ◽  
Author(s):  
Jason Beckwith ◽  
John D Tjepkema ◽  
Robert E Cashon ◽  
Christa R Schwintzer ◽  
Louis S Tisa
Keyword(s):  
Hemoglobin Concentration ◽  
Dissociation Rate ◽  
Size Exclusion ◽  
Facilitated Diffusion ◽  
Truncated Hemoglobin ◽  
Oxygen Dissociation ◽  
Wide Range ◽  
Exclusion Chromatography ◽  
N Treatment ◽  
Dissociation Rate Constants

Five strains of Frankia were selected to represent a wide range of genetic diversity and examined for presence of hemoglobin. All five strains produced hemoglobin when grown on media without (–N) or with (+N) combined nitrogen. This indicates that hemoglobin is common in Frankia and is not directly associated with nitrogen fixation. Frankia strain EAN1pec was examined in more detail. It showed greater hemoglobin concentration when grown at 2% O2 than at 20% O2 in the –N treatment but no effect of oxygen on hemoglobin concentration in the +N treatment. At both oxygen levels, it produced substantially more biomass in +N than in –N culture. It also produced significantly more biomass when the medium contained 0.2% CO2 than in the absence of CO2. The molecular mass of the hemo- globin as determined by size exclusion chromatography was 13.4 ± 0.2 kDa (mean ± SE, n = 3) and is consistent with that of a truncated hemoglobin. The hemoglobin had absorption spectra that were typical of a hemoglobin. The oxygen dissociation rate constants for the hemoglobin were 131.2 ± 5.8 s–1 for –N culture and 166 ± 8.2 s–1 for +N culture. These rapid rates are consistent with a function in facilitated diffusion of oxygen.Key words: Frankia, hemoglobin, truncated hemoglobin.

scholarly journals Effect of Posttranslational Modifications on the Structure and Activity of FTO Demethylase

2021 ◽  
Vol 22 (9) ◽  
pp. 4512
Author(s):  
Michał Marcinkowski ◽  
Tomaš Pilžys ◽  
Damian Garbicz ◽  
Jan Piwowarski ◽  
Damian Mielecki ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Size Exclusion Chromatography ◽  
Posttranslational Modifications ◽  
Size Exclusion ◽  
Saxs Data ◽  
Wide Range ◽  
Exclusion Chromatography ◽  
Demethylase Activity ◽  
Structure And Activity

The FTO protein is involved in a wide range of physiological processes, including adipogenesis and osteogenesis. This two-domain protein belongs to the AlkB family of 2-oxoglutarate (2-OG)- and Fe(II)-dependent dioxygenases, displaying N6-methyladenosine (N6-meA) demethylase activity. The aim of the study was to characterize the relationships between the structure and activity of FTO. The effect of cofactors (Fe2+/Mn2+ and 2-OG), Ca2+ that do not bind at the catalytic site, and protein concentration on FTO properties expressed in either E. coli (ECFTO) or baculovirus (BESFTO) system were determined using biophysical methods (DSF, MST, SAXS) and biochemical techniques (size-exclusion chromatography, enzymatic assay). We found that BESFTO carries three phosphoserines (S184, S256, S260), while there were no such modifications in ECFTO. The S256D mutation mimicking the S256 phosphorylation moderately decreased FTO catalytic activity. In the presence of Ca2+, a slight stabilization of the FTO structure was observed, accompanied by a decrease in catalytic activity. Size exclusion chromatography and MST data confirmed the ability of FTO from both expression systems to form homodimers. The MST-determined dissociation constant of the FTO homodimer was consistent with their in vivo formation in human cells. Finally, a low-resolution structure of the FTO homodimer was built based on SAXS data.

scholarly journals Human Plasma and Recombinant Hemopexins: Heme Binding Revisited

2021 ◽  
Vol 22 (3) ◽  
pp. 1199
Author(s):  
Elena Karnaukhova ◽  
Catherine Owczarek ◽  
Peter Schmidt ◽  
Dominik J. Schaer ◽  
Paul W. Buehler
Keyword(s):  
Protein S ◽  
Soret Band ◽  
Cell System ◽  
Size Exclusion ◽  
Heme Binding ◽  
Systematic Analysis ◽  
Molar Ratios ◽  
Recombinant Production ◽  
Wide Range ◽  
Exclusion Chromatography

Plasma hemopexin (HPX) is the key antioxidant protein of the endogenous clearance pathway that limits the deleterious effects of heme released from hemoglobin and myoglobin (the term “heme” is used in this article to denote both the ferrous and ferric forms). During intra-vascular hemolysis, heme partitioning to protein and lipid increases as the plasma concentration of HPX declines. Therefore, the development of HPX as a replacement therapy during high heme stress could be a relevant intervention for hemolytic disorders. A logical approach to enhance HPX yield involves recombinant production strategies from human cell lines. The present study focuses on a biophysical assessment of heme binding to recombinant human HPX (rhHPX) produced in the Expi293FTM (HEK293) cell system. In this report, we examine rhHPX in comparison with plasma HPX using a systematic analysis of protein structural and functional characteristics related to heme binding. Analysis of rhHPX by UV/Vis absorption spectroscopy, circular dichroism (CD), size-exclusion chromatography (SEC)-HPLC, and catalase-like activity demonstrated a similarity to HPX fractionated from plasma. In particular, the titration of HPX apo-protein(s) with heme was performed for the first time using a wide range of heme concentrations to model HPX–heme interactions to approximate physiological conditions (from extremely low to more than two-fold heme molar excess over the protein). The CD titration data showed an induced bisignate CD Soret band pattern typical for plasma and rhHPX versions at low heme-to-protein molar ratios and demonstrated that further titration is dependent on the amount of protein-bound heme to the extent that the arising opposite CD couplet results in a complete inversion of the observed CD pattern. The data generated in this study suggest more than one binding site in both plasma and rhHPX. Furthermore, our study provides a useful analytical platform for the detailed characterization of HPX–heme interactions and potentially novel HPX fusion constructs.

Differentiation of wastewater effluent organic matter (EfOM) from natural organic matter (NOM) using multiple analytical techniques

2008 ◽  
Vol 57 (7) ◽  
pp. 1009-1015 ◽  
Author(s):  
Seong-Nam Nam ◽  
Gary Amy
Keyword(s):  
Organic Matter ◽  
Natural Organic Matter ◽  
Dissolved Organic Nitrogen ◽  
Organic Nitrogen ◽  
Analytical Techniques ◽  
Size Exclusion ◽  
Effluent Organic Matter ◽  
Fluorescence Excitation ◽  
Wide Range ◽  
Exclusion Chromatography

Using three analytical techniques of size exclusion chromatography (SEC), fluorescence excitation-emission matrix (EEM), and dissolved organic nitrogen (DON) measurement, differentiating characteristics of effluent organic matter (EfOM) from natural organic matter (NOM) have been investigated. SEC reveals a wide range of molecular weight (MW) for EfOM and high amount of high MW polysaccharides, and low MW organic acids compared to NOM. Clear protein-like peaks using fluorescence EEM were a major feature of EfOM distinguishing it from NOM. Fluorescence index (FI), an indicator to distinguish autochthonous origin from allochthonous origin, differentiated EfOM from NOM by exhibiting higher values, indicating a microbial origin. In EfOM samples, DON present in higher amounts than NOM.

NEW ELASTOMERIC MATERIALS FROM BIOMASS: STEREOSELECTIVE POLYMERIZATION OF LINEAR TERPENES AND THEIR COPOLYMERIZATION WITH BUTADIENE BY USING A COBALT COMPLEX WITH PHOSPHANE LIGANDS

2020 ◽  
Vol 93 (4) ◽  
pp. 605-614
Author(s):  
David Hermann Lamparelli ◽  
Veronica Paradiso ◽  
Carmine Capacchione
Keyword(s):  
Room Temperature ◽  
Cobalt Complex ◽  
Size Exclusion ◽  
Resonance Spectroscopy ◽  
New Materials ◽  
Scanning Calorimetry ◽  
Wide Range ◽  
Elastomeric Materials ◽  
Exclusion Chromatography ◽  
Stereoregular Polymers

ABSTRACT The polymerization of bio-renewable terpenes such as β-ocimene (O), β-myrcene (M), and β-farnesene (F) promoted by CoCl2(PCyPh2)2 (1) in combination with modified methylalumoxane at room temperature is reported. Stereoregular polymers of O, M, and F were obtained. 1 also promoted, showing good stereoselectivity, the copolymerization of O and M with butadiene (B) in a wide range of compositions by suitably varying the alimentation feed: up to 67 and 75 mol% of O and M incorporated for poly(ocimene-butadiene) and poly(myrcene-butadiene) copolymers, respectively. These new materials with elastomeric properties (glass transition temperatures observed in the range of −5.7 to −72.5 °C) were fully characterized by differential scanning calorimetry, size exclusion chromatography, and nuclear magnetic resonance spectroscopy (1H, 13C, and two-dimensional experiments).

Measuring dissolved organic matter in estuarine and marine waters: size-exclusion chromatography with various detection methods

2018 ◽  
Vol 15 (7) ◽  
pp. 436 ◽  
Author(s):  
Gabriel Dulaquais ◽  
Johann Breitenstein ◽  
Matthieu Waeles ◽  
Rémi Marsac ◽  
Ricardo Riso
Keyword(s):  
Molecular Weight ◽  
Organic Matter ◽  
Organic Carbon ◽  
Dissolved Organic Matter ◽  
Humic Substances ◽  
Size Exclusion Chromatography ◽  
Size Exclusion ◽  
Marine Waters ◽  
Wide Range ◽  
Exclusion Chromatography

Environmental contextDissolved organic matter (DOM), a key parameter in aquatic biogeochemistry, is difficult to characterise owing to its variable composition and structure. We report a chromatographic method with carbon, nitrogen and absorbance detection able to record the size distribution of DOM and changes in its composition. The method could be used to identify additional sources to river or coastal waters as well as monitoring the DOM size/reactivity continuum in open oceans. AbstractWe studied the performance and limitations of size-exclusion chromatography with organic carbon, ultraviolet and organic nitrogen detectors (SEC-OCD-UVD-OND) for characterising dissolved organic matter (DOM) in estuarine and marine waters. We identified a strong salt effect on dissolved organic carbon (DOC) determination; however, calibration gave good results at salinity levels close to those of the sample analysed (ΔS ± 2 psu (practical salinity units)), with limited matrix effects, enabling an accurate measurement of DOC, as demonstrated by an intercalibration exercise. The repeatability, reproducibility and limit of detection (3 ppb for both carbon and nitrogen) for the three detectors demonstrated the robustness of the method for a wide range of natural waters, including carbon-rich freshwaters and deep seawaters with low carbon content (6000 ppb-C to 300 ppb-C). Deeper analysis of the SEC demonstrated that proteins and polysaccharides are partly fractionated within the column, and that terrestrial humic substances, isolated on a XAD-8 resin, can also be eluted in both fractions associated with biopolymers and low-molecular-weight neutrals. Application of the method to the study of DOM along a macrotidal estuary that was influenced by agricultural activities revealed significant changes in its composition despite a conservative DOC distribution. Distinct origins and qualities of high-molecular-weight (>500 kDa) organic compounds were identified for riverine and marine end-members. A new diagram to track changes in DOM lability is proposed to complete the humic-substances diagram.

scholarly journals Structural and functional characterization of TesB fromYersinia pestisreveals a unique octameric arrangement of hotdog domains

2015 ◽  
Vol 71 (4) ◽  
pp. 986-995 ◽  
Author(s):  
C. M. D. Swarbrick ◽  
M. A. Perugini ◽  
N. Cowieson ◽  
J. K. Forwood
Keyword(s):  
Analytical Ultracentrifugation ◽  
Quaternary Structure ◽  
Functional Characterization ◽  
Fatty Acyl ◽  
Size Exclusion ◽  
X Ray Scattering ◽  
Wide Range ◽  
Exclusion Chromatography ◽  
Enzyme Families

Acyl-CoA thioesterases catalyse the hydrolysis of the thioester bonds present within a wide range of acyl-CoA substrates, releasing free CoASH and the corresponding fatty-acyl conjugate. The TesB-type thioesterases are members of the TE4 thioesterase family, one of 25 thioesterase enzyme families characterized to date, and contain two fused hotdog domains in both prokaryote and eukaryote homologues. Only two structures have been elucidated within this enzyme family, and much of the current understanding of the TesB thioesterases has been based on theEscherichia colistructure.Yersinia pestis, a highly virulent bacterium, encodes only one TesB-type thioesterase in its genome; here, the structural and functional characterization of this enzyme are reported, revealing unique elements both within the protomer and quaternary arrangements of the hotdog domains which have not been reported previously in any thioesterase family. The quaternary structure, confirmed using a range of structural and biophysical techniques including crystallography, small-angle X-ray scattering, analytical ultracentrifugation and size-exclusion chromatography, exhibits a unique octameric arrangement of hotdog domains. Interestingly, the same biological unit appears to be present in both TesB structures solved to date, and is likely to be a conserved and distinguishing feature of TesB-type thioesterases. Analysis of theY. pestisTesB thioesterase activity revealed a strong preference for octanoyl-CoA and this is supported by structural analysis of the active site. Overall, the results provide novel insights into the structure of TesB thioesterases which are likely to be conserved and distinguishing features of the TE4 thioesterase family.

scholarly journals New insights on the interaction mechanism of rhTNFα with its antagonists Adalimumab and Etanercept

2020 ◽  
Vol 477 (17) ◽  
pp. 3299-3311
Author(s):  
María Angélica Contreras ◽  
Luis Macaya ◽  
Pedro Neira ◽  
Frank Camacho ◽  
Alaín González ◽  
...  
Keyword(s):  
High Performance ◽  
Interaction Mechanism ◽  
Protein Detection ◽  
Size Exclusion ◽  
Reducing Conditions ◽  
Kd Values ◽  
Wide Range ◽  
Exclusion Chromatography ◽  
New Association ◽  
Linear Epitopes

TNFα is a pro-inflammatory cytokine that is a therapeutic target for inflammatory autoimmune disorders. Thus, TNFα antagonists are successfully used for the treatment of these disorders. Here, new association patterns of rhTNFα and its antagonists Adalimumab and Etanercept are disclosed. Active rhTNFα was purified by IMAC from the soluble fraction of transformed Escherichia coli. Protein detection was assessed by SDS–PAGE and Western blot. The KD values for rhTNFα interactions with their antagonists were obtained by non-competitive ELISA and by microscale thermophoresis (MST). Molecular sizes of the complexes were evaluated by size-exclusion chromatography-high performance liquid chromatography (SEC-HPLC). Surprisingly, both antagonists recognized the monomeric form of rhTNFα under reducing and non-reducing conditions, indicating unexpected bindings of the antagonists to linear epitopes and to rhTNFα monomers. For the first time, the interactions of rhTNFα with Adalimumab and Etanercept were assessed by MST, which allows evaluating molecular interactions in solution with a wide range of concentrations. Biphasic binding curves with low and high KD values (<10−9 M and >10−8 M) were observed during thermophoresis experiments, suggesting the generation of complexes with different stoichiometry, which were confirmed by SEC-HPLC. Our results demonstrated the binding of TNFα-antagonists with rhTNFα monomers and linear epitopes. Also, complexes of high molecular mass were observed. This pioneer investigation constitutes valuable data for future approaches into the study of the interaction mechanism of TNFα and its antagonists.

Oxygen affinity and amino acid sequence of myoglobins from endothermic and ectothermic fish

2001 ◽  
Vol 280 (4) ◽  
pp. R1123-R1133 ◽  
Author(s):  
David J. Marcinek ◽  
Joseph Bonaventura ◽  
Jonathan B. Wittenberg ◽  
Barbara A. Block
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Rate Constants ◽  
Oxygen Affinity ◽  
Dissociation Rate ◽  
Low Oxygen ◽  
Dissociation Kinetics ◽  
Oxygen Dissociation ◽  
Dissociation Rate Constants

Myoglobin (Mb) buffers intracellular O2 and facilitates diffusion of O2 through the cell. These functions of Mb will be most effective when intracellular Po 2 is near the partial pressure of oxygen at which Mb is half saturated (P50) of the molecule. We test the hypothesis that Mb oxygen affinity has evolved such that it is conserved when adjusted for body temperature among closely related animals. We measure oxygen P50s tonometrically and oxygen dissociation rate constants with stopped flow and generate amino acid sequence from cDNA of Mbs from fish with different body temperatures. P50s for the endothermic bluefin tuna, skipjack tuna, and blue marlin at 20°C were 0.62 ± 0.02, 0.59 ± 0.01, 0.58 ± 0.04 mmHg, respectively, and were significantly lower than those for ectothermic bonito (1.03 ± 0.07 mmHg) and mackerel (1.39 ± 0.03 mmHg). Because the oxygen affinity of Mb decreases with increasing temperature, the above differences in oxygen affinity between endothermic and ectothermic fish are reduced when adjusted for the in vivo muscle temperature of the animal. Oxygen dissociation rate constants at 20°C for the endothermic species ranged from 34.1 to 49.3 s−1, whereas those for mackerel and bonito were 102 and 62 s−1, respectively. Correlated with the low oxygen affinity and fast dissociation kinetics of mackerel Mb is a substitution of alanine for proline that would likely result in a more flexible mackerel protein.

scholarly journals Size-Based Characterization of Freshwater Dissolved Organic Matter finds Similarities within a Water Body Type across Different Canadian Ecozones

2020 ◽  
Author(s):  
Pieter J. K. Aukes ◽  
Sherry L. Schiff ◽  
Jason J. Venkiteswaran ◽  
Richard J. Elgood ◽  
John Spoelstra
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Size Exclusion Chromatography ◽  
Water Body ◽  
Size Exclusion ◽  
List Type ◽  
Body Type ◽  
Wide Range ◽  
Exclusion Chromatography ◽  
Dom Composition

ABSTRACTDissolved Organic Matter (DOM) represents a mixture of organic molecules that vary due to different source materials and degree of processing. Characterizing how DOM composition evolves along the aquatic continuum can be difficult. Using a size-exclusion chromatography technique (LC-OCD), we assessed the variability in DOM composition from both surface and groundwaters across a number of Canadian ecozones (mean annual temperature spanning −10 to +6 C). A wide range in DOM concentration was found from 0.2 to 120 mg C/L. Proportions of different size-based groupings across ecozones were variable, yet similarities between specific water-body types, regardless of location, suggest commonality in the processes dictating DOM composition. A PCA identified 70% of the variation in LC-OCD derived DOM compositions could be explained by the water-body type. We find that DOM composition within a specific water-body type is similar regardless of the differences in climate or surrounding vegetation where the sample originated from.HighlightsSize-exclusion chromatography (using LC-OCD) is a fast and effective tool to quantify differences in DOM composition across different environmentsProportions of biopolymers and low molecular weight fractions can distinguish between surface and groundwater DOMSimilar water-body types have comparable DOM size compositions across ecozones that range in annual air temperatures from –10 to 6ºC

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