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1.
Methods Mol Biol ; 2153: 447-458, 2021.
Article in English | MEDLINE | ID: mdl-32840798

ABSTRACT

Homologous recombination (HR) has been extensively studied in response to DNA double-strand breaks (DSBs). In contrast, much less is known about how HR deals with DNA lesions other than DSBs (e.g., at single-stranded DNA) and replication forks, despite the fact that these DNA structures are associated with most spontaneous recombination events. A major handicap for studying the role of HR at non-DSB DNA lesions and replication forks is the difficulty of discriminating whether a recombination protein is associated with the non-DSB lesion per se or rather with a DSB generated during their processing. Here, we describe a method to follow the in vivo binding of recombination proteins to non-DSB DNA lesions and replication forks. This approach is based on the cleavage and subsequent electrophoretic analysis of the target DNA by the recombination protein fused to the micrococcal nuclease.


Subject(s)
DNA Breaks , Deoxyribonucleases/metabolism , Rad52 DNA Repair and Recombination Protein/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Bacterial Proteins/metabolism , Chromatin/genetics , Chromatin/metabolism , DNA Replication , Electrophoresis, Gel, Two-Dimensional , Homologous Recombination , Micrococcus/enzymology , Saccharomyces cerevisiae/genetics
2.
Biomed Res Int ; 2020: 5085369, 2020.
Article in English | MEDLINE | ID: mdl-33150175

ABSTRACT

As potential inhibitors target to biological enzymes, antibiotics may have certain impacts on the biochemical treatment process. With micrococcus catalase (CAT) served as the target molecule, the impact and inhibition mechanism for typical tetracyclines (TCs) were evaluated. Toxicity experiments showed that TCs had significant inhibition on CAT in the sequence of tetracycline>chlortetracycline>oxytetracycline>doxycycline. To clarify the inhibition mechanism between TCs and CAT which was explored with the assistance of fluorescence spectroscopy and MOE molecule simulation. According to fluorescence analysis, TCs quenched the fluorescence signal of CAT by the mode of static quenching. Combined with toxicity data, it could be presumed that TCs combined with the catalytic active center and thus inhibited CAT. Above presumption was further verified by the molecular simulation data. When TCs combined with the catalytic center of CAT, the compounds have increased combination areas and prominent energy change (compared with the compounds formed by TCs and noncatalytic center recommend by MOE software). IBM SPSS statistics showed that TC toxicity positively correlated with the hydrogen bonds such as O13→Glu252, O1←Arg195, and O6→Asp249, but negatively correlated with the hydrogen bonds such as O10→Pro363, O10→Lys455, and O12 â†’ Asn127. TC toxicity also positively correlated with the ion bonds ofN4-Glu252, but negatively correlated with the ion bonds of N4-Asp379. Hydrogen bonds and ion bonds for above key sites were closely related to the inhibition effect of TCs on CAT.


Subject(s)
Bacterial Proteins/antagonists & inhibitors , Catalase/antagonists & inhibitors , Chlortetracycline/chemistry , Doxycycline/chemistry , Enzyme Inhibitors/chemistry , Oxytetracycline/chemistry , Tetracycline/chemistry , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Catalase/chemistry , Catalase/genetics , Catalase/metabolism , Catalytic Domain , Chlortetracycline/metabolism , Doxycycline/metabolism , Enzyme Inhibitors/metabolism , Hydrogen Bonding , Micrococcus/chemistry , Micrococcus/enzymology , Molecular Docking Simulation , Oxytetracycline/metabolism , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Spectrometry, Fluorescence , Tetracycline/metabolism
3.
Biomater Sci ; 7(6): 2511-2519, 2019 May 28.
Article in English | MEDLINE | ID: mdl-30968104

ABSTRACT

Herein, we demonstrate the use of lysozyme (Lys) as a model to fabricate a protein carrier system based on gold nanoparticles (AuNPs) via the Layer-by-Layer (LbL) technology. Poly(ethyleneimine) (PEI) and poly(sodium 4-styrenesulfonate) (PSS) were used as cationic and anionic polymers respectively to grow oppositely charged layers. Mild aqueous conditions were utilized to avoid protein denaturation and activity instead of organic solvents that have been used in other encapsulation systems. Two different strategies were used: (A) lysozyme acting as a reducing and stabilizing agent in the formation of AuNPs at a temperature of 45 ± 2 °C followed by only two subsequent polymeric layers deposited by LbL, and (B) citrate acting as a reducing agent prior to stabilization of the AuNPs by mercaptoundecanoic acid. Dynamic light scattering, UV-vis spectroscopy, IR spectroscopy and transmission electron microscopy were used to characterize the nanoconjugates. Furthermore, the enzymatic activity of the resulting protein/nanoparticle conjugates was evaluated using the bacteria Micrococcus lysodeikticus as a substrate.


Subject(s)
Biocompatible Materials/chemistry , Gold/chemistry , Metal Nanoparticles/chemistry , Muramidase/chemistry , Biocompatible Materials/chemical synthesis , Chemistry Techniques, Synthetic , Citric Acid/chemistry , Micrococcus/enzymology , Models, Molecular , Molecular Conformation , Muramidase/metabolism , Polyethyleneimine/chemistry , Polystyrenes/chemistry , Temperature
4.
Bioorg Chem ; 82: 17-25, 2019 02.
Article in English | MEDLINE | ID: mdl-30267970

ABSTRACT

To understand the effect of counter ions (Na+) on the secondary conformation and functionality of the lysozyme, we have studied the interaction of lysozyme with counterion associated iron oxide nanoparticles (IONPs). The investigation was carried out at pH 7.4 and 9.0, with three different types of NPs, namely, bare IONPs, low molecular weight chitosan modified IONPs (LMWC-IONPs) and the counterion (Na+) associated sodium tripolyphosphate IONPs (STP-LMWC-IONPs) and confirmed by using various spectroscopy techniques. The difference in UV-vis absorbance (ΔA) between native and STP-LMWC-IONPs interacted hen egg white lysozyme (HEWL) was greater than that between native and NPs interacted HEWL at pH 9.0 compared with pH 7.4. Furthermore, STP-LMWC-IONPs exhibited quenching effect on lysozyme fluorescence spectrum at pH 9.0 due to binding of Na+ counterions to the protein, confirming denaturation of the latter. After HEWL interaction with STP-LMWC-IONPs (pH 9.0), CD spectra revealed a conformational change in the secondary structure of HEWL. Also, counterion induced lysozyme inactivation, due to interaction with nanoparticles at pH 9.0, was confirmed by enzymatic activity assay involving lysis of Micrococcus lysodeikticus. In conclusion, pH 9.0 was observed to be a more favorable condition, compared to pH 7.4, for the strongest electrostatic interaction between lysozyme and NPs. We postulate that the counterions in nanoparticle surface-coating can ameliorate protein misfolding or unfolding and also prevent their aggregation and, therefore, can be considered as a powerful and potential therapeutic strategy to treat incurable neurodegenerative disorders.


Subject(s)
Ferric Compounds/metabolism , Metal Nanoparticles/chemistry , Muramidase/metabolism , Animals , Catalytic Domain , Chickens , Chitosan/chemistry , Chitosan/metabolism , Cross-Linking Reagents/chemistry , Cross-Linking Reagents/metabolism , Ferric Compounds/chemistry , Hydrogen-Ion Concentration , Micrococcus/enzymology , Molecular Weight , Muramidase/chemistry , Polyphosphates/chemistry , Polyphosphates/metabolism , Protein Binding , Protein Structure, Secondary/drug effects , Sodium/chemistry , Static Electricity
5.
Chembiochem ; 20(1): 51-56, 2019 01 02.
Article in English | MEDLINE | ID: mdl-30184296

ABSTRACT

To expand the arsenal of industrially applicable oxidative enzymes, fusions of alcohol dehydrogenases with an NADPH-oxidase were designed. Three different alcohol dehydrogenases (LbADH, TbADH, ADHA) were expressed with a thermostable NADPH-oxidase fusion partner (PAMO C65D) and purified. The resulting bifunctional biocatalysts retained the catalytic properties of the individual enzymes, and acted essentially like alcohol oxidases: transforming alcohols to ketones by using dioxygen as mild oxidant, while merely requiring a catalytic amount of NADP+ . In small-scale reactions, the purified fusion enzymes show good performances, with 69-99 % conversion, 99 % ee with a racemic substrate, and high cofactor and enzyme total turnover numbers. As the fusion enzymes essentially act as oxidases, we found that commonly used high-throughput oxidase-activity screening methods can be used. Therefore, if needed, the fusion enzymes could be easily engineered to tune their properties.


Subject(s)
Alcohol Dehydrogenase/chemistry , Alcohol Oxidoreductases/chemistry , Multifunctional Enzymes/chemistry , NADPH Oxidases/chemistry , Recombinant Fusion Proteins/chemistry , Alcohol Dehydrogenase/genetics , Animals , Armoracia/enzymology , Benzyl Alcohols/chemistry , Biocatalysis , Cattle , Cyclohexanols/chemistry , Escherichia coli/genetics , Levilactobacillus brevis/enzymology , Micrococcus/enzymology , Multifunctional Enzymes/genetics , NADPH Oxidases/genetics , Oxidation-Reduction , Protein Engineering , Recombinant Fusion Proteins/genetics , Thermoanaerobacter/enzymology
6.
Biochemistry ; 56(26): 3347-3357, 2017 07 05.
Article in English | MEDLINE | ID: mdl-28603981

ABSTRACT

OleT is a cytochrome P450 enzyme that catalyzes the removal of carbon dioxide from variable chain length fatty acids to form 1-alkenes. In this work, we examine the binding and metabolic profile of OleT with shorter chain length (n ≤ 12) fatty acids that can form liquid transportation fuels. Transient kinetics and product analyses confirm that OleT capably activates hydrogen peroxide with shorter substrates to form the high-valent intermediate Compound I and largely performs C-C bond scission. However, the enzyme also produces fatty alcohol side products using the high-valent iron oxo chemistry commonly associated with insertion of oxygen into hydrocarbons. When presented with a short chain fatty acid that can initiate the formation of Compound I, OleT oxidizes the diagnostic probe molecules norcarane and methylcyclopropane in a manner that is reminiscent of reactions of many CYP hydroxylases with radical clock substrates. These data are consistent with a decarboxylation mechanism in which Compound I abstracts a substrate hydrogen atom in the initial step. Positioning of the incipient substrate radical is a crucial element in controlling the efficiency of activated OH rebound.


Subject(s)
Bacterial Proteins/metabolism , Caproates/metabolism , Caprylates/metabolism , Cytochrome P-450 Enzyme System/metabolism , Decanoic Acids/metabolism , Lauric Acids/metabolism , Micrococcus/enzymology , Models, Molecular , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Biocatalysis , Biofuels/analysis , Caprylates/chemistry , Carboxy-Lyases/chemistry , Carboxy-Lyases/genetics , Carboxy-Lyases/metabolism , Catalytic Domain , Cyclopropanes/chemistry , Cyclopropanes/metabolism , Cytochrome P-450 Enzyme System/chemistry , Cytochrome P-450 Enzyme System/genetics , Decanoic Acids/chemistry , Decarboxylation , Guaiacol/metabolism , Hydrogen Peroxide/chemistry , Hydrogen Peroxide/metabolism , Lauric Acids/chemistry , Molecular Conformation , Oxidation-Reduction , Substrate Specificity , Terpenes/chemistry , Terpenes/metabolism
7.
Appl Microbiol Biotechnol ; 101(5): 2033-2041, 2017 Mar.
Article in English | MEDLINE | ID: mdl-27858137

ABSTRACT

Psychrophilic enzymes display efficient activity at moderate or low temperatures (4-25 °C) and are therefore of great interest in biotechnological industries. We previously examined the crystal structure of BglU, a psychrophilic ß-glucosidase from the bacterium Micrococcus antarcticus, at 2.2 Å resolution. In structural comparison and sequence alignment with mesophilic (BglB) and thermophilic (GlyTn) counterpart enzymes, BglU showed much lower contents of Pro residue and of charged amino acids (particularly positively charged) on the accessible surface area. In the present study, we investigated the roles of specific amino acid residues in the cold adaptedness of BglU. Mutagenesis assays showed that the mutations G261R and Q448P increased optimal temperature (from 25 to 40-45 °C) at the expense of low-temperature activity, but had no notable effects on maximal activity or heat lability. Mutations A368P, T383P, and A389E significantly increased optimal temperature (from 25 to 35-40 °C) and maximal activity (~1.5-fold relative to BglU). Thermostability of A368P and A389E increased slightly at 30 °C. Mutations K163P, N228P, and H301A greatly reduced enzymatic activity-almost completely in the case of H301A. Low contents of Pro, Arg, and Glu are important factors contributing to BglU's psychrophilic properties. Our findings will be useful in structure-based engineering of psychrophilic enzymes and in production of mutants suitable for a variety of industrial processes (e.g., food production, sewage treatment) at cold or moderate temperatures.


Subject(s)
Adaptation, Physiological/genetics , Bacterial Proteins/genetics , Micrococcus/enzymology , Micrococcus/metabolism , beta-Glucosidase/genetics , beta-Glucosidase/metabolism , Amino Acid Sequence , Amino Acids/genetics , Bacterial Proteins/metabolism , Cold Temperature , Enzyme Stability , Micrococcus/genetics , Mutagenesis, Site-Directed , Protein Conformation , Sequence Alignment
8.
Appl Environ Microbiol ; 82(7): 2021-2030, 2016 Jan 22.
Article in English | MEDLINE | ID: mdl-26801571

ABSTRACT

Psychrophilic enzymes play crucial roles in cold adaptation of microbes and provide useful models for studies of protein evolution, folding, and dynamic properties. We examined the crystal structure (2.2-Å resolution) of the psychrophilic ß-glucosidase BglU, a member of the glycosyl hydrolase 1 (GH1) enzyme family found in the cold-adapted bacterium Micrococcus antarcticus. Structural comparison and sequence alignment between BglU and its mesophilic and thermophilic counterpart enzymes (BglB and GlyTn, respectively) revealed two notable features distinct to BglU: (i) a unique long-loop L3 (35 versus 7 amino acids in others) involved in substrate binding and (ii) a unique amino acid, His299 (Tyr in others), involved in the stabilization of an ordered water molecule chain. Shortening of loop L3 to 25 amino acids reduced low-temperature catalytic activity, substrate-binding ability, the optimal temperature, and the melting temperature (Tm). Mutation of His299 to Tyr increased the optimal temperature, the Tm, and the catalytic activity. Conversely, mutation of Tyr301 to His in BglB caused a reduction in catalytic activity, thermostability, and the optimal temperature (45 to 35°C). Loop L3 shortening and H299Y substitution jointly restored enzyme activity to the level of BglU, but at moderate temperatures. Our findings indicate that loop L3 controls the level of catalytic activity at low temperatures, residue His299 is responsible for thermolability (particularly heat lability of the active center), and long-loop L3 and His299 are jointly responsible for the psychrophilic properties. The described structural basis for the cold adaptedness of BglU will be helpful for structure-based engineering of new cold-adapted enzymes and for the production of mutants useful in a variety of industrial processes at different temperatures.


Subject(s)
Bacterial Proteins/chemistry , Micrococcus/enzymology , beta-Glucosidase/chemistry , Amino Acid Sequence , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Binding Sites , Crystallization , Enzyme Stability , Hot Temperature , Kinetics , Micrococcus/chemistry , Micrococcus/genetics , Models, Molecular , Molecular Sequence Data , Sequence Alignment , Temperature , beta-Glucosidase/genetics , beta-Glucosidase/metabolism
9.
J Agric Food Chem ; 63(16): 4170-8, 2015 Apr 29.
Article in English | MEDLINE | ID: mdl-25817823

ABSTRACT

This work describes the identification and characterization of an amine oxidase from Kocuria varians LTH 1540 (syn. Micrococcus varians) primarily acting on putrescine. Data from MALDI-TOF MS/MS and the identification of Δ(1)-pyrroline as degradation product from putrescine indicate that the enzyme is a flavin-dependent putrescine oxidase (PuO). Properties of partially purified enzyme have been determined. The enzyme oxidizes diamines, putrescine and cadaverine, and, to a lesser extent, polyamines, such as spermidine, but not monoamines. The kinetic constants (Km and Vmax) for the two major substrates were 94 ± 10 µM and 2.3 ± 0.1 µmol/min·mg for putrescine and 75 ± 5 µM and 0.15 ± 0.02 µmol/min·mg for cadaverine. Optimal temperature and pH were 45 °C and 8.5, respectively. Enzyme was stable until 50 °C. K. varians PuO is sensitive to human flavin-dependent amine oxidase inhibitors and carboxyl-modifying compounds. The new enzyme has been isolated from a bacterial starter used in the manufacture of fermented meat. One of the problems of fermented foods or beverages is the presence of toxic biogenic amines produced by bacteria. The importance of this works lies in the description of a new enzyme able to degrade two of the most abundant biogenic amines (putrescine and cadaverine), the use of which could be envisaged to diminish biogenic amines content in foods in the future.


Subject(s)
Bacterial Proteins/metabolism , Micrococcus/enzymology , Oxidoreductases Acting on CH-NH Group Donors/metabolism , Putrescine/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Biodegradation, Environmental , Enzyme Stability , Hydrogen-Ion Concentration , Kinetics , Micrococcus/chemistry , Micrococcus/genetics , Oxidoreductases Acting on CH-NH Group Donors/chemistry , Oxidoreductases Acting on CH-NH Group Donors/genetics
10.
RNA ; 20(4): 447-61, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24570482

ABSTRACT

RNA aptamers are being developed as inhibitors of macromolecular and cellular function, diagnostic tools, and potential therapeutics. Our understanding of the physical nature of this emerging class of nucleic acid-protein complexes is limited; few atomic resolution structures have been reported for aptamers bound to their protein target. Guided by chemical mapping, we systematically minimized an RNA aptamer (Lys1) selected against hen egg white lysozyme. The resultant 59-nucleotide compact aptamer (Lys1.2minE) retains nanomolar binding affinity and the ability to inhibit lysozyme's catalytic activity. Our 2.0-Å crystal structure of the aptamer-protein complex reveals a helical stem stabilizing two loops to form a protein binding platform that binds lysozyme distal to the catalytic cleft. This structure along with complementary solution analyses illuminate a novel protein-nucleic acid interface; (1) only 410 Å(2) of solvent accessible surface are buried by aptamer binding; (2) an unusually small fraction (∼18%) of the RNA-protein interaction is electrostatic, consistent with the limited protein phosphate backbone contacts observed in the structure; (3) a single Na(+) stabilizes the loops that constitute the protein-binding platform, and consistent with this observation, Lys1.2minE-lysozyme complex formation takes up rather than displaces cations at low ionic strength; (4) Lys1.2minE inhibits catalysis of large cell wall substrates but not catalysis of small model substrates; and (5) the helical stem of Lys1.2minE can be shortened to four base pairs (Lys1.2minF) without compromising binding affinity, yielding a 45-nucleotide aptamer whose structure may be an adaptable protein binding platform.


Subject(s)
Aptamers, Nucleotide/pharmacology , Muramidase/antagonists & inhibitors , Muramidase/metabolism , Sodium/metabolism , Animals , Aptamers, Nucleotide/chemistry , Base Pairing , Base Sequence , Catalysis , Chickens , Magnetic Resonance Spectroscopy , Micrococcus/enzymology , Models, Molecular , Molecular Sequence Data , Muramidase/genetics , Nucleic Acid Conformation , Osmolar Concentration , Protein Binding , Protein Conformation , Sodium/chemistry , Static Electricity , Substrate Specificity , Ultracentrifugation , X-Ray Diffraction
11.
Appl Microbiol Biotechnol ; 98(3): 1223-35, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24270893

ABSTRACT

The yellow-pigmented soil bacterium Corynebacterium glutamicum ATCC13032 is accumulating the cyclic C50 carotenoid decaprenoxanthin and its glucosides. Carotenoid pathway engineering was previously shown to allow for efficient lycopene production. Here, engineering of C. glutamicum for production of endogenous decaprenoxanthin as well as of the heterologous C50 carotenoids C.p.450 and sarcinaxanthin is described. Plasmid-borne overexpression of genes for lycopene cyclization and hydroxylation from C. glutamicum, Dietzia sp., and Micrococcus luteus, in a lycopene-producing platform strain constructed here, resulted in accumulation of these three C50 carotenoids to concentrations of about 3-4 mg/g CDW. Chromosomal deletion of a putative carotenoid glycosyltransferase gene cg0730/crtX in these strains entailed production of non-glucosylated derivatives of decaprenoxanthin, C.p.450, and sarcinaxanthin, respectively. Upon introduction of glucosyltransferase genes from M. luteus, C. glutamicum, and Pantoea ananatis, these hydroxylated C50 carotenoids were glucosylated. We here also demonstrate production of the C40 carotenoids ß-carotene and zeaxanthin in recombinant C. glutamicum strains and co-expression of the P. ananatis crtX gene was used to obtain glucosylated zeaxanthin. Together, our results show that C. glutamicum is a potentially valuable host for production of a wide range of glucosylated C40 and C50 carotenoids.


Subject(s)
Corynebacterium glutamicum/genetics , Corynebacterium glutamicum/metabolism , Metabolic Engineering/methods , Xanthophylls/metabolism , Actinomycetales/enzymology , Actinomycetales/genetics , Corynebacterium glutamicum/enzymology , Glycosylation , Micrococcus/enzymology , Micrococcus/genetics , Pantoea/enzymology , Pantoea/genetics
12.
Pharm Dev Technol ; 18(3): 752-9, 2013.
Article in English | MEDLINE | ID: mdl-23137392

ABSTRACT

Formulation development of protein therapeutics using polymeric nanoparticles has found very little success in recent years. Major formulation challenges include rapid denaturation, susceptibility to lose bioactivity in presence of organic solvents and poor encapsulation in polymeric matrix. In the present study, we have prepared hydrophobic ion pairing (HIP) complex of lysozyme, a model protein, using dextran sulfate (DS) as a complexing polymer. We have optimized the process of formation and dissociation of HIP complex between lysozyme and DS. The effect of HIP complexation on enzymatic activity of lysozyme was also studied. Nanoparticles were prepared and characterized using spontaneous emulsion solvent diffusion method. Furthermore, we have also investigated release of lysozyme from nanoparticles along with its enzymatic activity. Results of this study indicate that nanoparticles can sustain the release of lysozyme without compromising its enzymatic activity. HIP complexation using a polymer may also be employed to formulate sustained release dosage forms of other macromolecules with enhanced encapsulation efficiency.


Subject(s)
Chemistry, Pharmaceutical/methods , Drug Carriers/chemical synthesis , Drug Design , Hydrophobic and Hydrophilic Interactions , Muramidase/chemical synthesis , Nanoparticles/chemistry , Drug Carriers/administration & dosage , Drug Evaluation, Preclinical/methods , Drug Stability , Macromolecular Substances/administration & dosage , Macromolecular Substances/chemical synthesis , Micrococcus/drug effects , Micrococcus/enzymology , Muramidase/administration & dosage , Nanoparticles/administration & dosage , Static Electricity , Thermodynamics
13.
Enzyme Microb Technol ; 51(5): 258-62, 2012 Oct 10.
Article in English | MEDLINE | ID: mdl-22975122

ABSTRACT

The novel putrescine oxidase based amperometric biosensor selectively measures putrescine, which can be considered as an indicator of microbial spoilage. Putrescine oxidase (PUOX, EC 1.4.3.10) was isolated from Kocuria rosea (Micrococcus rubens) by an improved and simplified purification process. Cells were grown on brain heart infusion medium supplemented with putrescine. Cell-free extract was prepared in Tris buffer (pH 8.0) by Bead-beater. A newly elaborated step based on three-phase partitioning (TPP) was applied in the purification protocol of PUOX. The purified enzyme was immobilized on the surface of a spectroscopic graphite electrode in redox hydrogel with horseradish peroxidase, Os mediator and poly(ethylene glycol) (400) diglycidyl ether (PEGDGE) as crosslinking agent. This modified working electrode was used in wall-jet type amperometric cell together with the Ag/AgCl (0.1M KCl) reference electrode and a platinum wire as auxiliary electrode in flow injection analysis system (FIA). Hydrogel composition, pH and potential dependence were studied. Optimal working conditions were 0.45 mLmin(-1) flow rate of phosphate buffer (66 mM, pH 8.0) and +50 mV polarizing potential vs. Ag/AgCl. The linear measuring range of the method was 0.01-0.25 mM putrescine, while the detection limit was 5 µM. Beer samples were investigated by the putrescine biosensor and the results were compared by those of HPLC reference method.


Subject(s)
Beer/analysis , Biosensing Techniques/methods , Biotechnology/methods , Micrococcus/enzymology , Oxidoreductases Acting on CH-NH Group Donors/isolation & purification , Putrescine/metabolism , Carbon , Culture Media , Electrodes , Micrococcus/classification , Micrococcus/growth & development , Oxidoreductases Acting on CH-NH Group Donors/metabolism , Putrescine/analysis , Quality Control
14.
Int J Biol Macromol ; 50(1): 95-102, 2012 Jan 01.
Article in English | MEDLINE | ID: mdl-22020156

ABSTRACT

The tandem starch-binding domains (KvSBD) located at carboxy-terminal region of halophilic α-amylase from moderate halophile, Kocuria varians, were expressed in E. coli with amino-terminal hexa-His-tag and purified to homogeneity. The recombinant KvSBD showed binding activity to raw starch granules at low to high salt concentrations. The binding activity of KvSBD to starch was fully reversible after heat-treatment at 85°C. Circular dichroism and thermal scanning experiments indicated that KvSBD showed fully reversible refolding upon cooling after complete melting at 70°C in the presence of 0.2-2.0M NaCl. The refolding rate was enhanced with higher salt concentration.


Subject(s)
Micrococcus/enzymology , alpha-Amylases/chemistry , Bacillus/metabolism , Circular Dichroism , Hot Temperature , Kinetics , Protein Conformation , Protein Denaturation , Protein Folding , Protein Structure, Tertiary , Recombinant Fusion Proteins/chemistry , Salts/chemistry , Sodium Chloride/chemistry , Solubility , Starch/chemistry , Static Electricity , Surface Properties , Temperature
15.
Carbohydr Res ; 347(1): 16-22, 2012 Jan 10.
Article in English | MEDLINE | ID: mdl-22137737

ABSTRACT

The enzymatic synthesis of an α-chitin-like substance via a non-biosynthetic pathway has been achieved by transglycosylation in an aqueous system of the corresponding substrate, tri-N-acetylchitotriose [(GlcNAc)(3)] for lysozyme. A significant amount of water-insoluble product precipitated out from the reaction system. MALDI-TOFMS analysis showed that the resulting precipitate had a degree of polymerization (DP) of up to 15 from (GlcNAc)(3). Solid-state (13)C NMR analysis revealed that the resulting water-insoluble product is a chitin-like substance consisting of N-acetylglucosamine (GlcNAc) residues joined exclusively in a ß-(1→4)-linked chain with stringent regio-/stereoselection. X-ray diffraction (XRD) measurement as well as (13)C NMR analysis showed that the crystal structure of synthetic product corresponds to α-chitin with a high degree of crystallinity. We propose that the multiple oligomers form an α-chitin-like substance as a result of self-assembly via oligomer-oligomer interaction when they precipitate.


Subject(s)
Chemistry Techniques, Synthetic/methods , Chitin/chemistry , Chitin/chemical synthesis , Green Chemistry Technology/methods , Muramidase/metabolism , Carbohydrate Sequence , Glycosylation , Micrococcus/enzymology , Molecular Sequence Data , Stereoisomerism , Substrate Specificity
16.
Enzyme Microb Technol ; 49(1): 94-9, 2011 Jun 10.
Article in English | MEDLINE | ID: mdl-22112277

ABSTRACT

The gene bglU encoding a cold-adapted ß-glucosidase (BglU) was cloned from Micrococcus antarcticus. Sequence analysis revealed that the bglU contained an open reading frame of 1419 bp and encoded a protein of 472 amino acid residues. Based on its putative catalytic domains, BglU was classified as a member of the glycosyl hydrolase family 1 (GH1). BglU possessed lower arginine content and Arg/(Arg+Lys) ratio than mesophilic GH1 ß-glucosidases. Recombinant BglU was purified with Ni2+ affinity chromatography and subjected to enzymatic characterization. SDS-PAGE and native staining showed that it was a monomeric protein with an apparent molecular mass of 48 kDa. BglU was particularly thermolabile since its half-life time was only 30 min at 30°C and it exhibited maximal activity at 25°C and pH 6.5. Recombinant BglU could hydrolyze a wide range of aryl-ß-glucosides and ß-linked oligosaccharides with highest activity towards cellobiose and then p-nitrophenyl-ß-d-glucopyranoside (pNPG). Under the optimal conditions with pNPG as substrate, the K(m) and k(cat) were 7 mmol/L and 7.85 × 103/s, respectively. This is the first report of cloning and characterization of a cold-adapted ß-glucosidase belonging to GH1 from a psychrotolerant bacterium.


Subject(s)
Genes, Bacterial , Micrococcus/enzymology , Micrococcus/genetics , beta-Glucosidase/genetics , beta-Glucosidase/metabolism , Adaptation, Physiological , Amino Acid Sequence , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Base Sequence , Cloning, Molecular , Cold Temperature , DNA, Bacterial/genetics , Kinetics , Molecular Sequence Data , Molecular Weight , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Homology, Amino Acid , Substrate Specificity , beta-Glucosidase/chemistry
17.
Enzyme Microb Technol ; 48(4-5): 416-26, 2011 Apr 07.
Article in English | MEDLINE | ID: mdl-22112959

ABSTRACT

The present study deals with immobilization of purified CA and whole cell of Pseudomonas fragi, Micrococcus lylae, and Micrococcus luteus 2 on different biopolymer matrices. Highest enzyme immobilization was achieved with P. fragi CA (89%) on chitosan-KOH beads, while maximum cell immobilization was achieved with M. lylae (75%) on chitosan-NH(4)OH beads. A maximum increase of 1.08-1.18 fold stability between 35 and 55°C was observed for M. lylae immobilized CA. The storage stability was improved by 2.02 folds after immobilization. FTIR spectra confirmed the adsorption of CA on chitosan-KOH beads following hydrophilic interactions. Calcium carbonate precipitation was achieved using chitosan-KOH immobilized P. fragi CA. More than 2 fold increase in sequestration potential was observed for immobilized system as compared to free enzyme. XRD spectra revealed calcite as the dominant phase in biomimetically produced calcium carbonate.


Subject(s)
Biomimetic Materials/metabolism , Carbon Dioxide/metabolism , Carbonic Anhydrases/metabolism , Cells, Immobilized/enzymology , Enzymes, Immobilized/metabolism , Pseudomonas fragi/enzymology , Alginates/chemistry , Biotechnology/methods , Calcium Carbonate/metabolism , Carbonic Anhydrases/chemistry , Carbonic Anhydrases/isolation & purification , Chitosan/chemistry , Enzymes, Immobilized/chemistry , Glucuronic Acid/chemistry , Hexuronic Acids/chemistry , Micrococcus/enzymology , Micrococcus luteus/enzymology
18.
Biochemistry ; 50(27): 6102-12, 2011 Jul 12.
Article in English | MEDLINE | ID: mdl-21661747

ABSTRACT

Nonenzymatic modification of proteins in hyperglycemia is a major mechanism causing diabetic complications. These modifications can have pathogenic consequences when they target active site residues, thus affecting protein function. In the present study, we examined the role of glucose autoxidation in functional protein damage using lysozyme and RGD-α3NC1 domain of collagen IV as model proteins in vitro. We demonstrated that glucose autoxidation induced inhibition of lysozyme activity as well as NC1 domain binding to α(V)ß(3) integrin receptor via modification of critical arginine residues by reactive carbonyl species (RCS) glyoxal (GO) and methylglyoxal while nonoxidative glucose adduction to the protein did not affect protein function. The role of RCS in protein damage was confirmed using pyridoxamine which blocked glucose autoxidation and RCS production, thus protecting protein function, even in the presence of high concentrations of glucose. Glucose autoxidation may cause protein damage in vivo since increased levels of GO-derived modifications of arginine residues were detected within the assembly interface of collagen IV NC1 domains isolated from renal ECM of diabetic rats. Since arginine residues are frequently present within protein active sites, glucose autoxidation may be a common mechanism contributing to ECM protein functional damage in hyperglycemia and oxidative environment. Our data also point out the pitfalls in functional studies, particularly in cell culture experiments, that involve glucose treatment but do not take into account toxic effects of RCS derived from glucose autoxidation.


Subject(s)
Arginine/metabolism , Glucose/physiology , Proteins/antagonists & inhibitors , Proteins/physiology , Amino Acid Motifs , Animals , Collagen Type IV/antagonists & inhibitors , Collagen Type IV/chemistry , Collagen Type IV/metabolism , Diabetes Mellitus, Experimental/enzymology , Diabetes Mellitus, Experimental/metabolism , Glyoxal/adverse effects , Hyperglycemia/enzymology , Hyperglycemia/metabolism , Male , Micrococcus/enzymology , Muramidase/antagonists & inhibitors , Muramidase/metabolism , Protein Carbonylation , Protein Structure, Tertiary , Proteins/metabolism , Pyruvaldehyde/adverse effects , Random Allocation , Rats , Rats, Sprague-Dawley
19.
Environ Technol ; 32(13-14): 1487-95, 2011 Oct.
Article in English | MEDLINE | ID: mdl-22329139

ABSTRACT

The haloalkaliphilic bacterium Micrococcus sp. VKMM 037, isolated from an effluent of the caustic soda industry, was found to produce a protease. Maximal proteolytic activity was observed in cell culture grown at 40 degrees C using 2% (w/v) glycerol, 2% (w/v) beef extract and 2% (w/v) peptone as nutrients in medium also containing 0.85 M NaCl with a pH of 10.0. An efficient purification procedure combining ammonium sulphate precipitation and Q-Sepharose ion-exchange chromatography was developed. The purified 41 kDa protease was stable in a temperature range between 20 degrees C and 60 degrees C. The protease remained active over a wide range of pH values (4.0-12.0) and NaCl concentrations (0-3.42 M) with an optimum at pH 10.0 and 0.85 M NaCl, respectively. Furthermore, the enzyme remained stable or was only marginally inhibited in the presence of various organic solvents, surfactants and reducing agents. The purified protease of Micrococcus sp. VKMM 037 efficiently removed blood stains within 40 minutes of treatment. Given the biochemical characteristics determined, this novel protease could be exploited as an additive in the detergent industry and also for the synthesis of biomolecules and the degradation of protein.


Subject(s)
Micrococcus/classification , Micrococcus/enzymology , Peptide Hydrolases/chemistry , Peptide Hydrolases/isolation & purification , Water Microbiology , Enzyme Activation , Enzyme Stability , Species Specificity
20.
Int J Pharm ; 392(1-2): 111-7, 2010 Jun 15.
Article in English | MEDLINE | ID: mdl-20307635

ABSTRACT

PEGylation is a strategy that has been used to improve the biochemical properties of proteins and their physical and thermal stabilities. In this study, hen egg-white lysozyme (EC 3.2.1.17; LZ) was modified with methoxypolyethylene glycol-p-nitrophenyl carbonate (mPEG-pNP, MW 5000). This PEGylation of LZ produced conjugates that retained full enzyme activity with glycol chitosan, independent of degree of enzyme modification; its biological activity with the substrate Micrococcus lysodeikticus was altered according to its degree of modification. The conjugate obtained with a low degree of mPEG-pNP/NH(2) modification was studied by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF), demonstrating a spectral peak at m/z 19,988 Da with 77% of its original enzymatic activity. Spectroscopic studies of Fourier transform infrared (FTIR) and circular dichroism (CD) did not show any relevant differences in protein structure between the native and conjugate LZ. Studies of the effects of pH and temperature on PEGylated LZ indicated that the conjugate was active over a broad pH range, stable at 50 degrees C, and demonstrated resistance to proteolytic degradation.


Subject(s)
Carbonates/chemistry , Chemistry, Pharmaceutical/methods , Chitosan/chemistry , Drug Carriers/chemistry , Muramidase/chemistry , Nitrobenzenes/chemistry , Polyethylene Glycols/chemistry , Biochemical Phenomena , Biophysical Phenomena , Circular Dichroism , Drug Stability , Electrophoresis, Polyacrylamide Gel , Hydrogen-Ion Concentration , Micrococcus/enzymology , Protein Stability , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Spectroscopy, Fourier Transform Infrared , Temperature
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