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1.
Biosens Bioelectron ; 263: 116620, 2024 Nov 01.
Article in English | MEDLINE | ID: mdl-39094288

ABSTRACT

The possibility to print electronics by means of office tools has remarkedly increased the possibility to design affordable and robust point-of-care/need devices. However, conductive inks suffer from low electrochemical and rheological performances limiting their applicability in biosensors. Herein, a fast CO2 laser approach to activate printed carbon inks towards direct enzymatic bioelectrocatalysis (3rd generation) is proposed and exploited to build biosensors for D-fructose analysis in biological fluids. The CO2 laser treatment was compared with two lab-grade printed transducers fabricated with solvent (SB) and water (WB) based carbon inks. The use of the laser revealed significant morpho-chemical variations on the printed inks and was investigated towards enzymatic direct catalysis, using Fructose dehydrogenase (FDH) integrated into entirely lab-produced biosensors. The laser-driven activation of the inks unveils the inks' direct electron transfer (DET) ability between FDH and the electrode surface. Sub-micromolar limits of detection (SB-ink LOD = 0.47 µM; WB-ink LOD = 0.24 µM) and good linear ranges (SB-ink: 5-100 µM; WB-ink: 1-50 µM) were obtained, together with high selectivity due to use of the enzyme and the low applied overpotential (0.15 V vs. pseudo-Ag/AgCl). The laser-activated biosensors were successfully used for D-fructose determination in complex synthetic and real biological fluids (recoveries: 93-112%; RSD ≤8.0%, n = 3); in addition, the biosensor ability for continuous measurement (1.5h) was also demonstrated simulating physiological D-fructose fluctuations in cerebrospinal fluid.


Subject(s)
Biosensing Techniques , Fructose , Graphite , Ink , Fructose/analysis , Fructose/chemistry , Graphite/chemistry , Humans , Carbohydrate Dehydrogenases/chemistry , Electrochemical Techniques/methods , Electron Transport , Limit of Detection , Lasers, Gas , Enzymes, Immobilized/chemistry , Electrodes
2.
J Biol Chem ; 300(8): 107501, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38944119

ABSTRACT

L-Fucose (6-deoxy-L-galactose), a monosaccharide abundant in glycolipids and glycoproteins produced by mammalian cells, has been extensively studied for its role in intracellular biosynthesis and recycling of GDP-L-fucose for fucosylation. However, in certain mammalian species, L-fucose is efficiently broken down to pyruvate and lactate in a poorly understood metabolic pathway. In the 1970s, L-fucose dehydrogenase, an enzyme responsible for the initial step of this pathway, was partially purified from pig and rabbit livers and characterized biochemically. However, its molecular identity remained elusive until recently. This study reports the purification, identification, and biochemical characterization of the mammalian L-fucose dehydrogenase. The enzyme was purified from rabbit liver approximately 340-fold. Mass spectrometry analysis of the purified protein preparation identified mammalian hydroxysteroid 17-ß dehydrogenase 14 (HSD17B14) as the sole candidate enzyme. Rabbit and human HSD17B14 were expressed in HEK293T and Escherichia coli, respectively, purified, and demonstrated to catalyze the oxidation of L-fucose to L-fucono-1,5-lactone, as confirmed by mass spectrometry and NMR analysis. Substrate specificity studies revealed that L-fucose is the preferred substrate for both enzymes. The human enzyme exhibited a catalytic efficiency for L-fucose that was 359-fold higher than its efficiency for estradiol. Additionally, recombinant rat HSD17B14 exhibited negligible activity towards L-fucose, consistent with the absence of L-fucose metabolism in this species. The identification of the gene-encoding mammalian L-fucose dehydrogenase provides novel insights into the substrate specificity of enzymes belonging to the 17-ß-hydroxysteroid dehydrogenase family. This discovery also paves the way for unraveling the physiological functions of the L-fucose degradation pathway, which remains enigmatic.


Subject(s)
17-Hydroxysteroid Dehydrogenases , Fucose , Rabbits , Animals , Humans , Fucose/metabolism , 17-Hydroxysteroid Dehydrogenases/metabolism , 17-Hydroxysteroid Dehydrogenases/genetics , Liver/enzymology , Liver/metabolism , Substrate Specificity , Kinetics , Carbohydrate Dehydrogenases/metabolism , Carbohydrate Dehydrogenases/genetics , Carbohydrate Dehydrogenases/chemistry , Recombinant Proteins/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics
3.
J Agric Food Chem ; 72(19): 10995-11001, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38701424

ABSTRACT

The titer of the microbial fermentation products can be increased by enzyme engineering. l-Sorbosone dehydrogenase (SNDH) is a key enzyme in the production of 2-keto-l-gulonic acid (2-KLG), which is the precursor of vitamin C. Enhancing the activity of SNDH may have a positive impact on 2-KLG production. In this study, a computer-aided semirational design of SNDH was conducted. Based on the analysis of SNDH's substrate pocket and multiple sequence alignment, three modification strategies were established: (1) expanding the entrance of SNDH's substrate pocket, (2) engineering the residues within the substrate pocket, and (3) enhancing the electron transfer of SNDH. Finally, mutants S453A, L460V, and E471D were obtained, whose specific activity was increased by 20, 100, and 10%, respectively. In addition, the ability of Gluconobacter oxidans WSH-004 to synthesize 2-KLG was improved by eliminating H2O2. This study provides mutant enzymes and metabolic engineering strategies for the microbial-fermentation-based production of 2-KLG.


Subject(s)
Bacterial Proteins , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Gluconobacter/enzymology , Gluconobacter/genetics , Gluconobacter/metabolism , Sugar Acids/metabolism , Sugar Acids/chemistry , Fermentation , Protein Engineering , Metabolic Engineering , Carbohydrate Dehydrogenases/metabolism , Carbohydrate Dehydrogenases/genetics , Carbohydrate Dehydrogenases/chemistry , Kinetics
4.
ACS Appl Mater Interfaces ; 16(17): 22443-22454, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38629300

ABSTRACT

Herein, a strategy to stamp laser-produced reduced graphene oxide (rGO) onto flexible polymers using only office-grade tools, namely, roll-to-roll thermal stamping, is proposed, proving for the first time its effectiveness for direct bioelectrocatalysis. This straightforward, scalable, and low-cost approach allows us to overcome the limits of the integration of laser-induced rGO-films in bioanalytical devices. Laser-produced rGO has been thermally stamped (TS) onto different polymeric substrates (PET, PVC, and EVA) using a simple roll-laminator; the obtained TS-rGO films have been compared with the native rGO (untransferred) via morphochemical and electrochemical characterization. Particularly, the direct electron transfer (DET) reaction between fructose dehydrogenase (FDH) and TS-rGO transducers has been investigated, with respect to the influence of the amount of enzyme on the catalytic process. Remarkable differences have been observed among TS-rGO transducers; PET proved to be the elective substrate to support the transfer of the laser-induced rGO, allowing the preservation of the morphochemical features of the native material and returning a reduced capacitive current. Noteworthily, TS-rGOs ensure superior electrocatalysis using a very low amount of FDH units (15 mU). Eventually, TS-rGO-based third-generation complete enzymatic biosensors were fabricated via low-cost benchtop technologies. TS-rGOPET exhibited bioanalytical performances superior to the native rGO, allowing a sensitive (0.0289 µA cm-2 µM-1) and reproducible (RSD = 3%, n = 3) d-fructose determination at the nanomolar level (LOD = 0.2 µM). TS-rGO exploitability as a point-of-need device was proved via the monitoring of d-fructose during banana (Musa acuminata) postharvest ripening, returning accurate (recoveries 110-90%; relative error -13/+1%) and reproducible (RSD ≤ 7%; n = 3) data.


Subject(s)
Graphite , Lasers , Graphite/chemistry , Electron Transport , Electrochemical Techniques , Carbohydrate Dehydrogenases/chemistry , Carbohydrate Dehydrogenases/metabolism , Biosensing Techniques , Oxidation-Reduction
5.
Chembiochem ; 24(22): e202300431, 2023 11 16.
Article in English | MEDLINE | ID: mdl-37768852

ABSTRACT

The function of cellobiose dehydrogenase (CDH) in biosensors, biofuel cells, and as a physiological redox partner of lytic polysaccharide monooxygenase (LPMO) is based on its role as an electron donor. Before donating electrons to LPMO or electrodes, an interdomain electron transfer from the catalytic FAD-containing dehydrogenase domain to the electron shuttling cytochrome domain of CDH is required. This study investigates the role of two crucial amino acids located at the dehydrogenase domain on domain interaction and interdomain electron transfer by structure-based engineering. The electron transfer kinetics of wild-type Myriococcum thermophilum CDH and its variants M309A, R698S, and M309A/R698S were analyzed by stopped-flow spectrophotometry and structural effects were studied by small-angle X-ray scattering. The data show that R698 is essential to pull the cytochrome domain close to the dehydrogenase domain and orient the heme propionate group towards the FAD, while M309 is an integral part of the electron transfer pathway - its mutation reducing the interdomain electron transfer 10-fold. Structural models and molecular dynamics simulations pinpoint the action of these two residues on the domain interaction and interdomain electron transfer.


Subject(s)
Carbohydrate Dehydrogenases , Electrons , Amino Acids/metabolism , Fungal Proteins/chemistry , Electron Transport , Carbohydrate Dehydrogenases/chemistry , Mixed Function Oxygenases/metabolism , Polysaccharides/metabolism , Cytochromes/metabolism
6.
Protein Sci ; 32(8): e4702, 2023 08.
Article in English | MEDLINE | ID: mdl-37312580

ABSTRACT

Cellobiose dehydrogenase (CDH) is a bioelectrocatalyst that enables direct electron transfer (DET) in biosensors and biofuel cells. The application of this bidomain hemoflavoenzyme for physiological glucose measurements is limited by its acidic pH optimum and slow interdomain electron transfer (IET) at pH 7.5. The reason for this rate-limiting electron transfer step is electrostatic repulsion at the interface between the catalytic dehydrogenase domain and the electron mediating cytochrome domain (CYT). We applied rational interface engineering to accelerate the IET for the pH prevailing in blood or interstitial fluid. Phylogenetic and structural analyses guided the design of 17 variants in which acidic amino acids were mutated at the CYT domain. Five mutations (G71K, D160K, Q174K, D177K, M180K) increased the pH optimum and IET rate. Structure-based analysis of the variants suggested two mechanisms explaining the improvements: electrostatic steering and stabilization of the closed state by hydrogen bonding. Combining the mutations into six combinatorial variants with up to five mutations shifted the pH optimum from 4.5 to 7.0 and increased the IET at pH 7.5 over 12-fold from 0.1 to 1.24 s-1 . While the mutants sustained a high enzymatic activity and even surpassed the IET of the wild-type enzyme, the accumulated positive charges on the CYT domain decreased DET, highlighting the importance of CYT for IET and DET. This study shows that interface engineering is an effective strategy to shift the pH optimum and improve the IET of CDH, but future work needs to maintain the DET of the CYT domain for bioelectronic applications.


Subject(s)
Carbohydrate Dehydrogenases , Electrons , Phylogeny , Carbohydrate Dehydrogenases/genetics , Carbohydrate Dehydrogenases/chemistry , Cytochromes/metabolism , Electron Transport/physiology
7.
FEBS J ; 290(19): 4726-4743, 2023 10.
Article in English | MEDLINE | ID: mdl-37287434

ABSTRACT

The interdomain electron transfer (IET) between the catalytic flavodehydrogenase domain and the electron-transferring cytochrome domain of cellobiose dehydrogenase (CDH) plays an essential role in biocatalysis, biosensors and biofuel cells, as well as in its natural function as an auxiliary enzyme of lytic polysaccharide monooxygenase. We investigated the mobility of the cytochrome and dehydrogenase domains of CDH, which is hypothesised to limit IET in solution by small angle X-ray scattering (SAXS). CDH from Myriococcum thermophilum (syn. Crassicarpon hotsonii, syn. Thermothelomyces myriococcoides) was probed by SAXS to study the CDH mobility at different pH and in the presence of divalent cations. By comparison of the experimental SAXS data, using pair-distance distribution functions and Kratky plots, we show an increase in CDH mobility at higher pH, indicating alterations of domain mobility. To further visualise CDH movement in solution, we performed SAXS-based multistate modelling. Glycan structures present on CDH partially masked the resulting SAXS shapes, we diminished these effects by deglycosylation and studied the effect of glycoforms by modelling. The modelling shows that with increasing pH, the cytochrome domain adopts a more flexible state with significant separation from the dehydrogenase domain. On the contrary, the presence of calcium ions decreases the mobility of the cytochrome domain. Experimental SAXS data, multistate modelling and previously reported kinetic data show how pH and divalent ions impact the closed state necessary for the IET governed by the movement of the CDH cytochrome domain.


Subject(s)
Carbohydrate Dehydrogenases , Cytochromes , Scattering, Small Angle , X-Rays , X-Ray Diffraction , Carbohydrate Dehydrogenases/chemistry , Polysaccharides , Ions , Cellobiose
8.
Langmuir ; 39(16): 5880-5890, 2023 04 25.
Article in English | MEDLINE | ID: mdl-37053024

ABSTRACT

Cellobiose dehydrogenase (CDH) is capable of direct electron transfer (DET) on electrodes and is a promising redox enzyme for bioelectrochemical applications. Its unique two-domain structure makes the function of CDH adsorbed on the surface of the electrode deeply affected by the external environment, such as ion species, strength, pH, and surface charge density. To date, however, the exact mechanism of how the external environment tailors the structure and dynamics of CDH adsorbed on the electrode surface still remains poorly understood. Here, multiscale simulations were performed to look for insight into the effect of Na+ and Ca2+ ions on the activation of CDH on oppositely charged self-assembled monolayer (NH2-SAM and COOH-SAM) surfaces with different surface charge densities (SCDs). Both Na+ and Ca2+ can promote CDH conformation switch from the open state to the closed state, while the promotion effect of Ca2+ is stronger than that of Na+ at the same conditions. However, the high ionic strength (IS) of Ca2+ renders the cytochrome (CYT) domain of CDH away from the NH2-SAM with low SCD. In contrast, whatever the IS, the NH2-SAM surface with high SCD can not only enhance the CYT-surface interaction but also achieve a closed-state conformation due to a similar role of Ca2+. Overall, this study gains molecular-level insights into the role of ion species and surface charge in modulating the structure and conformation of CDH on the SAM surface, thereby tailoring its activity.


Subject(s)
Carbohydrate Dehydrogenases , Adsorption , Electron Transport , Oxidation-Reduction , Carbohydrate Dehydrogenases/chemistry , Carbohydrate Dehydrogenases/metabolism , Electrodes
9.
Colloids Surf B Biointerfaces ; 220: 112941, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36270138

ABSTRACT

Multi-functional small molecules attached to an electrode surface can bind non-covalently to the redox enzyme fructose dehydrogenase (FDH) to ensure efficient electrochemical electron transfer (ET) and electrocatalysis of the enzyme in both mediated (MET) and direct (DET) ET modes. The present work investigates the potential of exploiting secondary, electrostatic and hydrophobic interactions between substituents on a small molecular bridge and the local FDH surfaces. Such interactions ensure alignment of the enzyme in an orientation favourable for both MET and DET. We have used a group of novel synthesized anthraquinones as the small molecule bridge, functionalised with electrostatically neutral, anionic, or cationic substituents. Particularly, we investigated the immobilisation of FDH on a nanoporous gold (NPG) electrode decorated with the novel synthesised anthraquinones using electrochemical methods. The best DET-capable fraction out of four anthraquinone derivatives tested is achieved for an anthraquinone functionalised with an anionic sulphonate group. Our study demonstrates, how the combination of chemical design and bioelectrochemistry can be brought to control alignment of enzymes in productive orientations on electrodes, a paradigm for thiol modified surfaces in biosensors and bioelectronics.


Subject(s)
Biosensing Techniques , Carbohydrate Dehydrogenases , Anthraquinones , Carbohydrate Dehydrogenases/chemistry , Carbohydrate Dehydrogenases/metabolism , Electrodes , Electron Transport , Electrons , Enzymes, Immobilized/chemistry , Fructose/chemistry , Fructose/metabolism
10.
J Biol Chem ; 297(4): 101210, 2021 10.
Article in English | MEDLINE | ID: mdl-34547290

ABSTRACT

Marine algae catalyze half of all global photosynthetic production of carbohydrates. Owing to their fast growth rates, Ulva spp. rapidly produce substantial amounts of carbohydrate-rich biomass and represent an emerging renewable energy and carbon resource. Their major cell wall polysaccharide is the anionic carbohydrate ulvan. Here, we describe a new enzymatic degradation pathway of the marine bacterium Formosa agariphila for ulvan oligosaccharides involving unsaturated uronic acid at the nonreducing end linked to rhamnose-3-sulfate and glucuronic or iduronic acid (Δ-Rha3S-GlcA/IdoA-Rha3S). Notably, we discovered a new dehydratase (P29_PDnc) acting on the nonreducing end of ulvan oligosaccharides, i.e., GlcA/IdoA-Rha3S, forming the aforementioned unsaturated uronic acid residue. This residue represents the substrate for GH105 glycoside hydrolases, which complements the enzymatic degradation pathway including one ulvan lyase, one multimodular sulfatase, three glycoside hydrolases, and the dehydratase P29_PDnc, the latter being described for the first time. Our research thus shows that the oligosaccharide dehydratase is involved in the degradation of carboxylated polysaccharides into monosaccharides.


Subject(s)
Aquatic Organisms/enzymology , Bacterial Proteins/chemistry , Carbohydrate Dehydrogenases/chemistry , Flavobacteriaceae/enzymology , Polysaccharides/chemistry , Bacterial Proteins/metabolism , Carbohydrate Dehydrogenases/metabolism , Polysaccharides/metabolism , Uronic Acids/chemistry
11.
FEBS Lett ; 595(5): 637-646, 2021 03.
Article in English | MEDLINE | ID: mdl-33482017

ABSTRACT

Several microorganisms can utilize l-rhamnose as a carbon and energy source through the nonphosphorylative metabolic pathway, in which l-rhamnose 1-dehydrogenase (RhaDH) catalyzes the NAD(P)+ -dependent oxidization of l-rhamnose to l-rhamnono-1,4-lactone. We herein investigated the crystal structures of RhaDH from Azotobacter vinelandii in ligand-free, NAD+ -bound, NADP+ -bound, and l-rhamnose- and NAD+ -bound forms at 1.9, 2.1, 2.4, and 1.6 Å resolution, respectively. The significant interactions with the 2'-phosphate group of NADP+ , but not the 2'-hydroxyl group of NAD+ , were consistent with a preference for NADP+ over NAD+ . The C5-OH and C6-methyl groups of l-rhamnose were recognized by specific residues of RhaDH through hydrogen bonds and hydrophobic contact, respectively, which contribute to the different substrate specificities from other aldose 1-dehydrogenases in the short-chain dehydrogenase/reductase superfamily.


Subject(s)
Azotobacter vinelandii/enzymology , Bacterial Proteins/chemistry , Carbohydrate Dehydrogenases/chemistry , Coenzymes/chemistry , NADP/chemistry , Rhamnose/chemistry , Amino Acid Sequence , Azotobacter vinelandii/genetics , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Carbohydrate Dehydrogenases/genetics , Carbohydrate Dehydrogenases/metabolism , Carbohydrate Metabolism , Catalytic Domain , Cloning, Molecular , Coenzymes/metabolism , Crystallography, X-Ray , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Kinetics , Models, Molecular , NADP/metabolism , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protein Multimerization , Protein Subunits/chemistry , Protein Subunits/genetics , Protein Subunits/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Rhamnose/metabolism , Sequence Alignment , Sequence Homology, Amino Acid , Substrate Specificity
12.
Prep Biochem Biotechnol ; 51(5): 488-496, 2021.
Article in English | MEDLINE | ID: mdl-33063604

ABSTRACT

Termitomyces sp. OE 147 is one of the active cellulose degraders in the ecosphere and produces large amount of cellobiose dehydrogenase (CDH) and ß-glucosidases when cultivated on cellulose. In order to investigate its effect on cellulose, a highly purified preparation of CDH was obtained from the culture supernatant of the fungus cultivated on cellulose. A combination of ultrafiltration, ion-exchange and gel-filtration chromatography was used to purify CDH by ∼172-fold to a high specific activity of ∼324 U/mg protein on lactose which was used for routine measurement of enzyme activity. The enzyme displayed a pH optimum of 5.0 and stability between pH 5.0 and 8.0 with maximum catalytic efficiency (kcat/Km) of 397 mM-1 s-1 on cellobiose. Incubation of microcrystalline cellulose with the purified CDH led to production of reducing sugars which was accelerated by the addition of FeCl3 during the early stages of incubation. A mass spectrometric analysis revealed fragmentation products of cellulose which were concluded to be cellodextrins, sugars, and corresponding aldonic acids suggesting that CDH can release reducing sugars in the absence of externally added lytic polysaccharide monooxygenases. Polymerized products of glucose were also detected at low intensity.


Subject(s)
Carbohydrate Dehydrogenases , Cellulose/chemistry , Fungal Proteins , Termitomyces/enzymology , Carbohydrate Dehydrogenases/chemistry , Carbohydrate Dehydrogenases/isolation & purification , Enzyme Stability , Fungal Proteins/chemistry , Fungal Proteins/isolation & purification , Substrate Specificity , Termitomyces/growth & development
13.
Chembiochem ; 21(24): 3511-3514, 2020 12 11.
Article in English | MEDLINE | ID: mdl-32939899

ABSTRACT

The ß-hydroxyacid dehydrogenase from Thermocrinus albus (Ta-ßHAD), which catalyzes the NADP+ -dependent oxidation of ß-hydroxyacids, was engineered to accept imines as substrates. The catalytic activity of the proton-donor variant K189D was further increased by the introduction of two nonpolar flanking residues (N192 L, N193 L). Engineering the putative alternative proton donor (D258S) and the gate-keeping residue (F250 A) led to a switched substrate specificity as compared to the single and triple variants. The two most active Ta-ßHAD variants were applied to biocatalytic asymmetric reductions of imines at elevated temperatures and enabled enhanced product formation at a reaction temperature of 50 °C.


Subject(s)
Carbohydrate Dehydrogenases/metabolism , Imines/metabolism , Protein Engineering , Temperature , Bacteria/enzymology , Carbohydrate Dehydrogenases/chemistry , Enzyme Stability , Imines/chemistry , Models, Molecular , Molecular Structure , Oxidation-Reduction
14.
Enzymes ; 47: 457-489, 2020.
Article in English | MEDLINE | ID: mdl-32951832

ABSTRACT

Cellobiose dehydrogenase (CDH) is an extracellular hemoflavoenzyme secreted by fungi to assist lignocellulolytic enzymes in biomass degradation. Its catalytic flavodehydrogenase (DH) domain is a member of the glucose-methanol-choline oxidoreductase family similar to glucose oxidase. The catalytic domain is linked to an N-terminal electron transferring cytochrome (CYT) domain which interacts with lytic polysaccharide monooxygenase (LPMO) in oxidative cellulose and hemicellulose depolymerization. Based on CDH sequence analysis, four phylogenetic classes were defined. CDHs in these classes exhibit different structural and catalytic properties in regard to cellulose binding, substrate specificity, and the pH optima of their catalytic reaction or the interdomain electron transfer between the DH and CYT domain. The structure, reaction mechanism and kinetics of CDHs from Class-I and Class-II have been characterized in detail and recombinant expression allows the application in many areas, such as biosensors, biofuel cells biomass hydrolysis, biosynthetic processes, and the antimicrobial functionalization of surfaces.


Subject(s)
Carbohydrate Dehydrogenases/chemistry , Fungal Proteins/chemistry , Carbohydrate Dehydrogenases/classification , Cellulose/metabolism , Electron Transport , Fungal Proteins/classification , Phylogeny
15.
Biochem Biophys Res Commun ; 530(1): 203-208, 2020 09 10.
Article in English | MEDLINE | ID: mdl-32828286

ABSTRACT

L-Arabinose 1-dehydrogenase (AraDH) is responsible for the first step of the non-phosphorylative L-arabinose pathway from bacteria, and catalyzes the NAD(P)+-dependent oxidation of L-arabinose to L-arabinonolactone. This enzyme belongs to the so-called Gfo/Idh/MocA protein superfamily, but has a very poor phylogenetic relationship with other functional members. We previously reported the crystal structures of AraDH without a ligand and in complex with NADP+. To clarify the underlying catalytic mechanisms in more detail, we herein elucidated the crystal structure in complex with L-arabinose and NADP+. In addition to the previously reported five amino acid residues (Lys91, Glu147, His153, Asp169, and Asn173), His119, Trp152, and Trp231 interacted with L-arabinose, which were not found in substrate recognition by other Gfo/Idh/MocA members. Structure-based site-directed mutagenic analyses suggested that Asn173 plays an important role in catalysis, whereas Trp152, Trp231, and His119 contribute to substrate binding. The preference of NADP+ over NAD+ was significantly subjected by a pair of Ser37 and Arg38, whose manners were similar to other Gfo/Idh/MocA members.


Subject(s)
Arabinose/metabolism , Azospirillum brasilense/metabolism , Bacterial Proteins/metabolism , Carbohydrate Dehydrogenases/metabolism , NADP/metabolism , Amino Acid Sequence , Arabinose/chemistry , Azospirillum brasilense/chemistry , Bacterial Proteins/chemistry , Carbohydrate Dehydrogenases/chemistry , Crystallography, X-Ray , Models, Molecular , NADP/chemistry , Protein Conformation
16.
Anal Chem ; 92(3): 2620-2627, 2020 02 04.
Article in English | MEDLINE | ID: mdl-31916434

ABSTRACT

Changes in the tertiary conformation of adsorbed biomolecules can induce detectable shifts (Δθr) in the surface plasmon resonance (SPR) angle. Here it is shown how to calculate the corresponding shifts in the adsorbate's center of mass (Δzavg) along the sensing surface normal from the measured Δθr. The novel developed model was used for determining the mean distance between the cytochrome (CYT) and flavodehydrogenase (DH) domains of the enzyme cellobiose dehydrogenase (CDH) isolated from the fungi Neurospora crassa, Corynascus thermophilus, and Myriococcum thermophilum as a function of pH, [Ca2+], and substrate concentration. SPR confirmed the results from earlier electrochemical and SAXS studies stating that the closed conformation, where the two domains are in close vicinity, is stabilized by a lower pH and an increased [Ca2+]. Interestingly, an increasing substrate concentration in the absence of any electron acceptors stabilizes the open conformation as the electrostatic repulsion due to the reaped electrons pushes the DH and CYT domains apart. The accuracy of distance determination was limited mostly by the random fluctuations between replicate measurements, and it was possible to detect movements <1 nm of the domains with respect to each other. The results agreed with calculations using already established models treating conformational changes as contraction or expansion of the thickness of the adsorbate layer (tprotein). Although the models yielded equivalent results, in this case, the Δzavg-based method also works in situations, where the adsorbate's mass is not evenly distributed within the layer.


Subject(s)
Carbohydrate Dehydrogenases/chemistry , Cytochromes/chemistry , Carbohydrate Dehydrogenases/metabolism , Cytochromes/metabolism , Electrochemical Techniques , Enzymes, Immobilized/chemistry , Enzymes, Immobilized/metabolism , Models, Molecular , Neurospora crassa/enzymology , Sordariales/enzymology , Surface Plasmon Resonance
17.
Mater Sci Eng C Mater Biol Appl ; 108: 110499, 2020 Mar.
Article in English | MEDLINE | ID: mdl-31923978

ABSTRACT

Polymicrobial biofilm related infections have been a major threat in health care. In this study, the co-immobilization of cellobiose dehydrogenase (CDH) and deoxyribonuclease I (DNase) on positively charged chitosan nanoparticles (CSNPs) resulted in a bi-functional nanoparticle (CSNP-DNase-CDH) targeting both biofilm matrix and microorganisms. The in-vitro antibiofilm activities of CSNPs against monomicrobial and polymicrobial biofilms of Candida albicans and Staphylococcus aureus were evaluated. The results showed that CSNPs were able to penetrate across the matrix of biofilms and interfere with embedded microbial cells. CSNP-DNase-CDH exhibited a higher activity than CSNPs loaded with only DNase or CDH for inhibiting monomicrobial and polymicrobial biofilm formation as well as for disrupting pre-formed biofilms. Furthermore, CSNP-DNase-CDH could disrupt the biofilm formation through degradation of eDNA, reduce biofilm thickness, and kill microbial cells on silicone. The bi-functional CSNP is applicable for the protection of medical devices from polymicrobial biofilms or the treatment of device associated infections.


Subject(s)
Biofilms , Carbohydrate Dehydrogenases/chemistry , Chitosan/chemistry , Deoxyribonuclease I/chemistry , Keratinocytes/microbiology , Anti-Bacterial Agents/pharmacology , Antifungal Agents/pharmacology , Candida albicans/drug effects , Cell Line , Cell Survival/drug effects , Enzymes, Immobilized/chemistry , Extracellular Polymeric Substance Matrix , Humans , Keratinocytes/cytology , Microbial Sensitivity Tests , Microbial Viability/drug effects , Microscopy, Electron, Scanning , Nanoparticles/chemistry , Silicones/chemistry , Staphylococcus aureus/drug effects , Trichoderma/drug effects
18.
Biochim Biophys Acta Proteins Proteom ; 1868(2): 140335, 2020 02.
Article in English | MEDLINE | ID: mdl-31785381

ABSTRACT

Pyranose oxidase (POx) catalyzes the oxidation of d-glucose to 2-ketoglucose with concurrent reduction of oxygen to H2O2. POx from Trametes ochracea (ToPOx) is known to react with alternative electron acceptors including 1,4-benzoquinone (1,4-BQ), 2,6-dichlorophenol indophenol (DCPIP), and the ferrocenium ion. In this study, enzyme variants with improved electron acceptor turnover and reduced oxygen turnover were characterized as potential anode biocatalysts. Pre-steady-state kinetics of the oxidative half-reaction of ToPOx variants T166R, Q448H, L545C, and L547R with these alternative electron acceptors were evaluated using stopped-flow spectrophotometry. Higher kinetic constants were observed as compared to the wild-type ToPOx for some of the variants. Subsequently, the variants were immobilized on glassy carbon electrodes. Cyclic voltammetry measurements were performed to measure the electrochemical responses of these variants with glucose as substrate in the presence of 1,4-BQ, DCPIP, or ferrocene methanol as redox mediators. High catalytic efficiencies (Imaxapp/KMapp) compared to the wild-type POx proved the potential of these variants for future bioelectrocatalytic applications, in biosensors or biofuel cells. Among the variants, L545C showed the most desirable properties as determined kinetically and electrochemically.


Subject(s)
Carbohydrate Dehydrogenases/metabolism , Electrochemical Techniques/methods , 2,6-Dichloroindophenol/chemistry , Benzoquinones/chemistry , Biocatalysis , Carbohydrate Dehydrogenases/chemistry , Carbohydrate Dehydrogenases/genetics , Catalytic Domain , Electrodes , Ferrous Compounds/chemistry , Glucose/chemistry , Glucose/metabolism , Kinetics , Metallocenes/chemistry , Mutagenesis, Site-Directed , Oxidation-Reduction , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Trametes/enzymology
19.
Bioelectrochemistry ; 132: 107399, 2020 Apr.
Article in English | MEDLINE | ID: mdl-31835110

ABSTRACT

Pyranose dehydrogenase is a flavin-dependent carbohydrate oxidoreductase classified among Auxiliary Activities Family 3, along with structurally and catalytically related enzymes like pyranose oxidase and cellobiose dehydrogenase, and probably fulfils biological functions in lignocellulose breakdown. It is limited to a rather small group of litter-decomposing basidiomycetes adapted to humic-rich habitats, and shows an equally rare combination of structural and biochemical properties. It displays broader substrate specificity and regioselectivity compared to similar enzymes, catalyzing monooxidations at C1, C2, C3 or dioxidations at C2, 3 or C3, 4, depending on the pyranose sugar form (mono-/di-/oligo-saccharide or glycoside) and the enzyme source. It is unable to utilize oxygen as electron acceptor, using substituted benzoquinones and (organo)metallic ions instead, which suggests a role in redox cycling of (hydro)quinones and complexed metal ions. Pyranose dehydrogenase is a promising candidate for enzymatic sensors of various sugars, for the anodic reaction in enzymatic biofuel cells powered by carbohydrate mixtures, and as a versatile biocatalyst for the production of di- and tri-carbonyl sugar derivatives as chiral intermediates for the synthesis of rare sugars, novel drugs and fine chemicals.


Subject(s)
Biocatalysis , Carbohydrate Dehydrogenases/metabolism , Electrochemical Techniques/methods , Agaricus/enzymology , Bioelectric Energy Sources , Carbohydrate Dehydrogenases/chemistry , Electrons , Glycosylation , Oxidation-Reduction , Substrate Specificity
20.
Mol Divers ; 24(3): 593-601, 2020 Aug.
Article in English | MEDLINE | ID: mdl-31154590

ABSTRACT

Cellobiose dehydrogenase (CDH, EC 1.1.99.18) from white rot fungi Phanerochaete chrysosporium can be used for constructing biosensors and biofuel cells, for bleaching cotton in textile industry, and recently, the enzyme has found an important application in biomedicine as an antimicrobial and antibiofilm agent. Stability and activity of the wild-type (wt) CDH and mutants at methionine residues in the presence of hydrogen peroxide were investigated. Saturation mutagenesis libraries were made at the only methionine in heme domain M65 and two methionines M685 and M738 in the flavin domain that were closest to the active site. After screening the libraries, three mutants with increased activity and stability in the presence of peroxide were found, M65F with 70% of residual activity after 6 h of incubation in 0.3 M hydrogen peroxide, M738S with 80% of residual activity and M685Y with over 90% of residual activity compared to wild-type CDH that retained 40% of original activity. Combined mutants showed no activity. The most stable mutant M685Y with 5.8 times increased half-life in the presence of peroxide showed also 2.5 times increased kcat for lactose compared to wtCDH and could be good candidate for applications in biofuel cells and biocatalysis for lactobionic acid production.


Subject(s)
Carbohydrate Dehydrogenases/genetics , Carbohydrate Dehydrogenases/metabolism , Peroxides/pharmacology , Protein Engineering , Carbohydrate Dehydrogenases/chemistry , Enzyme Stability/drug effects , Kinetics , Models, Molecular , Mutation , Oxidation-Reduction , Phanerochaete/enzymology , Protein Conformation
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