scholarly journals Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues

2021 ◽  
Author(s):  
Ethan J Walker ◽  
John Q Bettinger ◽  
Kevin A Welle ◽  
Jennifer R Hryhorenko ◽  
Adrian M Molina Vargas ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Solvent Accessibility ◽  
Optimal Growth ◽  
Methionine Oxidation ◽  
Native State ◽  
E Coli ◽  
Oxidation Rates ◽  
Wide Range ◽  
Methionine Residues ◽  
Neighboring Residue

The oxidation of protein-bound methionines to form methionine sulfoxides has a broad range of biological ramifications, making it important to delineate factors that influence methionine oxidation rates within a protein. This is especially important for biopharmaceuticals, where oxidation can lead to deactivation and degradation. Previously, neighboring residue effects and solvent accessibility (SA) have been shown to impact the susceptibility of methionine residues to oxidation. In this study, we provide proteome-wide evidence that oxidation rates of buried methionine residues are also strongly influenced by the thermodynamic folding stability of proteins. We surveyed the E. coli proteome using several proteomic methodologies and globally measured oxidation rates of methionines in the presence and absence of tertiary structure, as well as folding stabilities of methionine containing domains. The data indicate that buried methionines have a wide range of protection factors against oxidation which correlate strongly with folding stabilities. Concordantly, we show that in comparison to E. coli, the proteome of the thermophile T. thermophilus is significantly more stable and thus more resistant to methionine oxidation. These results indicate that oxidation rates of buried methionines from the native state of proteins can be used as a metric of folding stability. To demonstrate the utility of this correlation, we used native methionine oxidation rates to survey the folding stabilities of E. coli and T. thermophilus proteomes at various temperatures and suggest a model that relates the temperature dependence of the folding stabilities of these two species to their optimal growth temperatures.

scholarly journals Chemical and Metabolic Controls on Dihydroxyacetone Metabolism Lead to Suboptimal Growth ofEscherichia coli

2019 ◽  
Vol 85 (15) ◽  
Author(s):  
Camille Peiro ◽  
Pierre Millard ◽  
Alessandro de Simone ◽  
Edern Cahoreau ◽  
Lindsay Peyriga ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Value Added ◽  
Optimal Growth ◽  
System Level ◽  
Nuclear Magnetic Resonance Analysis ◽  
Aerobic Conditions ◽  
Content Type ◽  
E Coli ◽  
Wide Range ◽  
Pharmaceutical Industries

ABSTRACTIn this work, we shed light on the metabolism of dihydroxyacetone (DHA), a versatile, ubiquitous, and important intermediate for various chemicals in industry, by analyzing its metabolism at the system level inEscherichia coli. Using constraint-based modeling, we show that the growth ofE. colion DHA is suboptimal and identify the potential causes. Nuclear magnetic resonance analysis shows that DHA is degraded nonenzymatically into substrates known to be unfavorable to high growth rates. Transcriptomic analysis reveals that DHA promotes genes involved in biofilm formation, which may reduce the bacterial growth rate. Functional analysis of the genes involved in DHA metabolism proves that under the aerobic conditions used in this study, DHA is mainly assimilated via the dihydroxyacetone kinase pathway. In addition, these results show that the alternative routes of DHA assimilation (i.e., the glycerol and fructose-6-phosphate aldolase pathways) are not fully activated under our conditions because of anaerobically mediated hierarchical control. These pathways are therefore certainly unable to sustain fluxes as high as the ones predictedin silicofor optimal aerobic growth on DHA. Overexpressing some of the genes in these pathways releases these constraints and restores the predicted optimal growth on DHA.IMPORTANCEDHA is an attractive triose molecule with a wide range of applications, notably in cosmetics and the food and pharmaceutical industries. DHA is found in many species, from microorganisms to humans, and can be used byEscherichia colias a growth substrate. However, knowledge about the mechanisms and regulation of this process is currently lacking, motivating our investigation of DHA metabolism inE. coli. We show that under aerobic conditions,E. coligrowth on DHA is far from optimal and is hindered by chemical, hierarchical, and possibly allosteric constraints. We show that optimal growth on DHA can be restored by releasing the hierarchical constraint. These results improve our understanding of DHA metabolism and are likely to help unlock biotechnological applications involving DHA as an intermediate, such as the bioconversion of glycerol or C1substrates into value-added chemicals.

Small Molecule Permeation Across Membrane Channels: Chemical Modification to Quantify Transport Across OmpF

2018 ◽  
Author(s):  
Jiajun Wang ◽  
Jayesh Arun Bafna ◽  
Satya Prathyusha Bhamidimarri ◽  
Mathias Winterhalter
Keyword(s):  
Dwell Time ◽  
Covalent Binding ◽  
Channel Structure ◽  
Ion Current ◽  
E Coli ◽  
Current Fluctuation ◽  
Wide Range ◽  
Outer Membrane Channel ◽  
Biological Channels ◽  
Constriction Region

Biological channels facilitate the exchange of small molecules across membranes, but surprisingly there is a lack of general tools for the identification and quantification of transport (i.e., translocation and binding). Analyzing the ion current fluctuation of a typical channel with its constriction region in the middle does not allow a direct conclusion on successful transport. For this, we created an additional barrier acting as a molecular counter at the exit of the channel. To identify permeation, we mainly read the molecule residence time in the channel lumen as the indicator whether the molecule reached the exit of the channel. As an example, here we use the well-studied porin, OmpF, an outer membrane channel from <i>E. coli</i>. Inspection of the channel structure suggests that aspartic acid at position 181 is located below the constriction region (CR) and we subsequently mutated this residue to cysteine, where else cysteine free and functionalized it by covalent binding with 2-sulfonatoethyl methanethiosulfonate (MTSES) or the larger glutathione (GLT) blockers. Using the dwell time as the signal for transport, we found that both mono-arginine and tri-arginine permeation process is prolonged by 20% and 50% respectively through OmpF<sub>E181C</sub>MTSES, while the larger sized blocker modification OmpF<sub>E181C</sub>GLT drastically decreased the permeation of mono-arginine by 9-fold and even blocked the pathway of the tri-arginine. In case of the hepta-arginine as substrate, both chemical modifications led to an identical ‘blocked’ pattern observed by the dwell time of ion current fluctuation of the OmpF<sub>wt</sub>. As an instance for antibiotic permeation, we analyzed norfloxacin, a fluoroquinolone antimicrobial agent. The modulation of the interaction dwell time suggests possible successful permeation of norfloxacin across OmpF<sub>wt</sub>. This approach may discriminate blockages from translocation events for a wide range of substrates. A potential application could be screening for scaffolds to improve the permeability of antibiotics.

An Improved Membrane Filtration Method for Enumeration of Faecal Coliforms and E. Coli by a Fluorogenic β-Glucuronidase Assay

1993 ◽  
Vol 27 (3-4) ◽  
pp. 267-270 ◽  
Author(s):  
M. T. Augoustinos ◽  
N. A. Grabow ◽  
B. Genthe ◽  
R. Kfir
Keyword(s):  
Escherichia Coli ◽  
Water Samples ◽  
Membrane Filtration ◽  
Faecal Coliforms ◽  
Environmental Waters ◽  
Filtration Method ◽  
E Coli ◽  
Wide Range ◽  
Pure Cultures ◽  
Glucuronidase Assay

A fluorogenic β-glucuronidase assay comprising membrane filtration followed by selective enumeration on m-FC agar at 44.5°C and further confirmation using tlie 4-metliylumbelliferyl-β-D-glucuronide (MUG) containing medium was evaluated for the detection of Escherichia coli in water. A total of 200 typical blue and non-typical blue colonies were isolated from sea and fresh water samples using initial selective enumeration on m-FC agar. Pure cultures of the selected colonies were further tested using the MUG assay and identified using the API 20E method. Of the colonies tested which were shown to be positive using the MUG assay 99.4% were Escherichia coli. The results of this study indicate the combination of the m-FC method followed by the MUG assay to be highly efficient for the selection and confirmation of E. coli from a wide range of environmental waters.

Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry

2019 ◽  
Vol 26 (1) ◽  
pp. 35-43 ◽  
Author(s):  
Natalie K. Garcia ◽  
Galahad Deperalta ◽  
Aaron T. Wecksler
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Protein Interactions ◽  
Quaternary Structure ◽  
Solvent Accessibility ◽  
Higher Order ◽  
Structure Characterization ◽  
Order Structure ◽  
Protein Footprinting ◽  
Wide Range

Background: Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. Conclusion: Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.

The Influence of Ultra-Low Concentrations of Potassium Anphen on the Bioenergetic Characteristics of Mitochondria

2020 ◽  
Vol 16 (4) ◽  
pp. 537-542
Author(s):  
Zhigacheva Irina ◽  
Volodkin Aleksandr ◽  
Rasulov Maksud
Keyword(s):  
Functional State ◽  
Membrane Lipids ◽  
Biological Effects ◽  
Dose Dependence ◽  
Stress Factors ◽  
Mitochondrial Membranes ◽  
Oxidation Rates ◽  
Pea Seedlings ◽  
Low Concentrations ◽  
Wide Range

Background: One of the main sources of ROS in stress conditions is the mitochondria. Excessive generation of ROS leads to oxidation of thiol groups of proteins, peroxidation of membrane lipids and swelling of the mitochondria. In this regard, there is a need to search for preparationsadaptogens that increase the body's resistance to stress factors. Perhaps, antioxidants can serve as such adaptogens. This work aims at studying the effect of antioxidant; the potassium anphen in a wide range of concentrations on the functional state of 6 day etiolated pea seedlings mitochondria (Pisum sativum L). Methods: The functional state of mitochondria was studied per rates of mitochondria respiration, by the level of lipid peroxidation and study of fatty acid composition of mitochondrial membranes by chromatography technique. Results: Potassium anphen in concentrations of 10-5 - 10-8 M and 10-13-10-16 prevented the activation of LPO in the mitochondrial membranes of pea seedlings, increased the oxidation rates of NAD-dependent substrates and succinate in the respiratory chain of mitochondria that probably pointed to the anti-stress properties of the drug. Indeed, the treatment of pea seeds with the preparation in concentrations of 10-13 M prevented the inhibition of growth of seedlings in conditions of water deficiency. Conclusion: It is assumed that the dose dependence of the biological effects of potassium anphen and the manifestation of these effects in ultra-low concentrations are due to its ability in water solutions to form a hydrate containing molecular ensembles (structures).

scholarly journals Soluble Expression and Efficient Purification of Recombinant Class I Hydrophobin DewA

2021 ◽  
Vol 22 (15) ◽  
pp. 7843
Author(s):  
Sang-Oh Ahn ◽  
Ho-Dong Lim ◽  
Sung-Hwan You ◽  
Dae-Eun Cheong ◽  
Geun-Joong Kim
Keyword(s):  
Tertiary Structure ◽  
Signal Sequence ◽  
Soluble Expression ◽  
Class I ◽  
Soluble Form ◽  
Two Phase ◽  
E Coli ◽  
Small Proteins ◽  
Industrial Use ◽  
Shed Light

Hydrophobins are small proteins (<20 kDa) with an amphipathic tertiary structure that are secreted by various filamentous fungi. Their amphipathic properties provide surfactant-like activity, leading to the formation of robust amphipathic layers at hydrophilic–hydrophobic interfaces, which make them useful for a wide variety of industrial fields spanning protein immobilization to surface functionalization. However, the industrial use of recombinant hydrophobins has been hampered due to low yield from inclusion bodies owing to the complicated process, including an auxiliary refolding step. Herein, we report the soluble expression of a recombinant class I hydrophobin DewA originating from Aspergillus nidulans, and its efficient purification from recombinant Escherichia coli. Soluble expression of the recombinant hydrophobin DewA was achieved by a tagging strategy using a systematically designed expression tag (ramp tag) that was fused to the N-terminus of DewA lacking the innate signal sequence. Highly expressed recombinant hydrophobin DewA in a soluble form was efficiently purified by a modified aqueous two-phase separation technique using isopropyl alcohol. Our approach for expression and purification of the recombinant hydrophobin DewA in E. coli shed light on the industrial production of hydrophobins from prokaryotic hosts.

scholarly journals Urinary Excretion and Bactericidal Activities of a Single Oral Dose of 400 Milligrams of Fleroxacin versus a Single Oral Dose of 800 Milligrams of Pefloxacin in Healthy Volunteers

1998 ◽  
Vol 42 (7) ◽  
pp. 1659-1665 ◽  
Author(s):  
Kurt G. Naber ◽  
Ursula Theuretzbacher ◽  
Martina Kinzig ◽  
Orlin Savov ◽  
Fritz Sörgel
Keyword(s):  
Oral Dose ◽  
Healthy Volunteers ◽  
Single Oral Dose ◽  
E Coli ◽  
Wide Range ◽  
The Mean ◽  
Bactericidal Activities ◽  
Tract Infections ◽  
Time Kill ◽  
Randomized Crossover Study

ABSTRACT Twelve healthy volunteers participated in this randomized crossover study to compare the concentrations and recovery levels of fleroxacin and pefloxacin in urine and to assess their bactericidal activities against 12 strains of urinary pathogens with different susceptibilities over a wide range of MICs. The volunteers received a single oral dose of 400 mg of fleroxacin or 800 mg of pefloxacin. The mean cumulative renal excretion of unchanged fleroxacin,N-demethyl-fleroxacin, and N-oxide-fleroxacin accounted for 67, 7, and 6% of the total dose, respectively. The total urinary recovery of pefloxacin and the active metabolite norfloxacin was 34%. In the time-kill and the urinary bactericidal titer (UBT) studies, only the subjects’ urine not supplemented with broth was used. With most tested organisms and both quinolones it took more than 8 h to achieve a reduction in CFU of 99.9% (3 log units). Overall, there was a good correlation between UBTs and MICs for the strains. Against Escherichia coli ATCC 25922 the median UBTs were similar for both antibiotics and at least 1:8 for 96 h; against the E. coli strain for which the MIC was 0.5 μg/ml the UBT was at least 1:4 for 48 h. The UBTs of both drugs against Klebsiella pneumoniae were at least 1:16 for 72 h. The UBTs for Staphylococcus aureus (the MIC for which was 16 μg/ml) of both antibiotics were low, and in some of the samples, no bactericidal titers were observed. UBTs for Proteus mirabilis of pefloxacin are significantly higher than those of fleroxacin. For Pseudomonas aeruginosa the median UBTs were present for the 24-to-48-h interval. The same is true forEnterococcus faecalis. Against Staphylococcus saprophyticus, UBTs were present for at least 48 h with both quinolones. Overall, a single oral dose of 400 mg of fleroxacin exhibits UBTs comparable to those of 800 mg of pefloxacin. Therefore, it may be expected that half of the dose of fleroxacin gives comparable results in the treatment of urinary tract infections; this should be substantiated in comparative clinical trials.

scholarly journals Vibrio cholerae Triggers SOS and Mutagenesis in Response to a Wide Range of Antibiotics: a Route towards Multiresistance

2011 ◽  
Vol 55 (5) ◽  
pp. 2438-2441 ◽  
Author(s):  
Zeynep Baharoglu ◽  
Didier Mazel
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Vibrio Cholerae ◽  
Fluorescent Protein ◽  
Resistance Development ◽  
Content Type ◽  
E Coli ◽  
Wide Range ◽  
Green Fluorescent ◽  
Regulated Promoters

ABSTRACTAntibiotic resistance development has been linked to the bacterial SOS stress response. InEscherichia coli, fluoroquinolones are known to induce SOS, whereas other antibiotics, such as aminoglycosides, tetracycline, and chloramphenicol, do not. Here we address whether various antibiotics induce SOS inVibrio cholerae. Reporter green fluorescent protein (GFP) fusions were used to measure the response of SOS-regulated promoters to subinhibitory concentrations of antibiotics. We show that unlike the situation withE. coli, all these antibiotics induce SOS inV. cholerae.

Optimization of Growth Conditions of Citrus Anthracnose Agent Colletotrichum gloeosporioides Isolates in Tunisia

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Ben Hadj-Daoud H ◽  
◽  
Ben Salem I ◽  
Boughalleb-M’Hamdi N ◽  
◽  
...  
Keyword(s):  
Morphological Traits ◽  
Laboratory Experiments ◽  
Plant Pathogens ◽  
Colletotrichum Gloeosporioides ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Fruit Drop ◽  
Nutritional Conditions ◽  
Solid Media ◽  
Wide Range

Background: Colletotrichum gloeosporioides is important plant pathogens on a wide range of plant hosts such as citrus causing pre- or post-harvest infections as anthracnose, post-bloom fruit drop, tearstain and stem-end rot on fruit, or wither-tip of twigs. Method: The optimization of growth conditions of this pathogen was performed (solid media, temperature, pH and water potential under laboratory experiments). Results: Our results revealed that the maximum radial growth of C. gloeosporioides was recorded on SDA medium. All isolates were able to grow on PDA at temperatures of 15 and 30°C (over 0.7cm/day). Optimal growth radial was recorded at pH 5, 6, 7 and 8. Similar responses were obtained with both salt types, but, in general, C. gloeosporioides was more tolerant to KCl than NaCl. Conclusion: Studies of cultural, morphological traits of the pathogen are prominent to understand the response of the pathogen in different environmental and nutritional conditions.

Kinetic Study of the Thermo-Oxidative Degradation of Squalane (C30H62) Modelling the Base Oil of Engine Lubricants

2009 ◽  
Author(s):  
Moussa Diaby ◽  
Michel Sablier ◽  
Anthony Le Negrate ◽  
Mehdi El Fassi
Keyword(s):  
Oxidative Degradation ◽  
Engine Oil ◽  
Ongoing Research ◽  
Base Oil ◽  
Rate Law ◽  
Tert Butyl ◽  
Oxidation Rates ◽  
Base Oils ◽  
Wide Range ◽  
Thermo Oxidative Degradation

On the basis of ongoing research conducted on the clarification of processes responsible for lubricant degradation in the environment of piston grooves in EGR diesel engines, an experimental investigation was aimed to develop a kinetic model which can be used for the prediction of lubricant oxidative degradation correlated to endurance test conducted on engines. Knowing that base oils are a complex blend of paraffins and naphtenes with a wide range of sizes and structures, their chemistry analysis during the oxidation process can be highly convoluted. In the present work, investigations were carried out with the squalane (C30H62) chosen for its physical and chemical similarities with the lubricant base oils used during the investigations. Thermo-oxidative degradation of this hydrocarbon was conducted at atmospheric pressure in a tubular furnace, while varying temperature and duration of the tests in order to establish an oxidation reaction rate law. The same experimental procedures was applied to squalane doped with two different phenolic antioxidants usually present in engine oil composition: 2,6-di-tert-butyl-4-methylphenol (BHT), and octadecyl-3-(3,5-di-tert-butyl-4-hydroxyphenyl)propionate (OBHP). Thus, the effect of both antioxidants on the oxidation rate law was investigated. Data analysis of the oxidized samples (FTIR spectroscopy, gas chromatography/mass spectrometry GC/MS) allowed to rationalize the thermo-oxidative degradation of squalane. The resulting kinetic modelling provides a practical analytical tool to follow the thermal degradation processes, which can be used for prediction of base oil hydrocarbon ageing. If experiments confirmed the role of phenolic additives as an affective agent to lower oxidation rates, the main results lay in the observation of a threshold temperature where a reversed activity of these additives was observed.

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