Characterization of NADP-dependent L-arginine dehydrogenase as a novel amino acid dehydrogenase and its application to an L-arginine assay

L-Arginine dehydrogenase (L-ArgDH, EC 1.4.1.25) is an amino acid dehydrogenase which catalyzes the reversible oxidative deamination of L-arginine to the oxo analog in the presence of NADP. Although the enzyme activity is detected in the cell extract of Pseudomonas aruginosa , the purification and characterization of the enzyme have not been achieved to date. We here found the gene homolog of L-ArgDH in genome data of Pseudomonas veronii and succeeded in expression of P. veronii JCM11942 gene in E. coli. The gene product exhibited strong NADP-dependent L-ArgDH activity. The crude enzyme was unstable under neutral pH conditions, but was markedly stabilized by the addition of 10% glycerol. The enzyme was purified to homogeneity through a single Ni-chelate affinity ch romatography step and consisted of a homodimeric protein with a molecular mass of about 65 kDa. The enzyme selectively catalyzed l-arginine oxidation in the presence of NADP with maximal activity at pH 9.5. The apparent K m values for l-arginine and NADP were 2.5 and 0.21 mM, respectively. The nucleotide sequence coding the enzyme gene ( was determined and the amino acid sequence was deduced from the nucleotide sequence. As an application of the enzyme, simple colorimetric microassay for L-arginine using the enzyme was achieved.

Biochemical Characterization of Two Rhamnogalacturonan Lyases From Bacteroides ovatus ATCC 8483 With Preference for RG-I Substrates

Rhamnogalacturonan lyase (RGL) cleaves backbone α-1,4 glycosidic bonds between L-rhamnose and D-galacturonic acid residues in type I rhamnogalacturonan (RG-I) by β-elimination to generate RG oligosaccharides with various degrees of polymerization. Here, we cloned, expressed, purified and biochemically characterized two RGLs (Bo3128 and Bo4416) in the PL11 family from Bacteroides ovatus ATCC 8483. Bo3128 and Bo4416 displayed maximal activity at pH 9.5 and pH 6.5, respectively. Whereas the activity of Bo3128 could be increased 1.5 fold in the presence of 5 mM Ca2+, Bo4416 required divalent metal ions to show any enzymatic activity. Both of RGLs showed a substrate preference for RG-I compared to other pectin domains. Bo4416 and Bo3128 primarily yielded unsaturated RG oligosaccharides, with Bo3128 also producing them with short side chains, with yields of 32.4 and 62.4%, respectively. Characterization of both RGLs contribute to the preparation of rhamnogalacturonan oligosaccharides, as well as for the analysis of the fine structure of RG-I pectins.

Moving Mountains: Reshaping the Activity Volcano of Electrocatalysis with Fluxional Subnano Clusters

The activity volcano derived from Sabatier analysis provides intuitive guide for catalyst design, but it also imposes fundamental limitations on the maximal activity and the pool of high-performance elements. Here we show that the activity volcano for oxygen reduction reaction (ORR) can be shifted and reshaped in the subnano regime. The fluxional behavior of subnano clusters, in both isolated and graphite-supported forms, not only breaks the linear scaling relationships but also causes an overall strengthening in adsorbate binding. The metals with optimal adsorbate binding in the bulk form (Pt/Pd) thus suffer over-binding issues, while the metals that under-bind in the bulk form (Ag/Au) gain optimal reaction energetics. In addition, the potential-dependence of isomer energies differ, causing non-linear reaction free energy-potential relations and enabling population-tuning of specific isomers, thereby surpassing the apex of the activity volcano. The shift of the volcano that puts under-binding elements closer to the top is likely general in fluxional cluster catalysis, and can be used for cluster catalyst design.

Biochemical and Structural Characterization of a Novel Bacterial Tannase From Lachnospiraceae bacterium in Ruminant Gastrointestinal Tract

Tannases are a family of esterases that catalyze the hydrolysis of ester and depside bonds present in hydrolyzable tannins to release gallic acid. Here, a novel tannase from Lachnospiraceae bacterium (TanALb) was characterized. The recombinant TanALb exhibited maximal activity at pH 7.0 and 50°C, and it maintained more than 70% relative activity from 30°C to 55°C. The activity of TanALb was enhanced by Mg2+ and Ca2+, and was dramatically reduced by Cu2+ and Mn2+. TanALb is capable of degrading esters of phenolic acids with long-chain alcohols, such as lauryl gallate as well as tannic acid. The Km value and catalytic efficiency (kcat /Km) of TanALb toward five substrates showed that tannic acid (TA) was the favorite substrate. Homology modeling and structural analysis indicated that TanALb contains an insertion loop (residues 341–450). Based on the moleculer docking and molecular dynamics (MD) simulation, this loop was observed as a flap-like lid to interact with bulk substrates such as tannic acid. TanALb is a novel bacterial tannase, and the characteristics of this enzyme make it potentially interesting for industrial use.

Purification and characterization of actinidin from Actinidia deliciosa and its utilization in inactivation of α-amylase

Background Actinidin is an anionic thiol-proteinase predominant and unique to Chinese gooseberry or kiwifruit, whose strong digestibility enables proteins or enzymes vulnerable to digestion. The arrangement of active cysteine–thiol residues (Cys22-Cys65, Cys56-Cys98, and Cys156-Cys206) stabilizes the catalytic unit, thus allowing an effective Inhibition of α-amylase protein on exposure to the highest concentrations of actinidin under optimum conditions. When starch-rich foods are consumed with kiwifruit, starch digestion may be slowed by the inactivation of α-amylase (digestive enzyme), specifically reducing the blood sugar levels by hindering starch digestion that is helpful in diabetes mellitus. Thus, the study aimed at actinidin purification, optimization for maximal activity, and its demonstration as a potential to degrade α-amylase. Results Protease showed a molecular mass of 27 kDa on SDS-PAGE analysis. One factor at a time method was applied for process optimization, increasing the actinidin yield up to 176.03 U/mg. The enzyme was stable at a wide pH range; however, it was most active and stable at pH 7.5. The enzyme possessed half‐life at 35 °C of 5.5 h, at 40 °C of 4.5 h, at 45 °C of 2.5 h, and at 50 °C of 1 h. Lineweaver–Burk plot showed Michaelis–Menten constant (Km: 3.14 mg/ml) and maximal velocity (Vmax: 1.428 mmol/ml/min) using casein. The actinidin activity was enhanced with Ca2+ while it was inhibited by Cd2+ and Hg2+ ions. The α-amylase protein was successfully inactivated upon incubation with actinidin for 30 min; around ~ 85% of the α-amylase activity diminished. IC50 for inhibition of α-amylase was 2.54 mg/ml for crude actinidin and 1.86 mg/ml for purified actinidin. Conclusions Purified Actinidin showed a 1.28-fold increase in proteolytic activity. The proteinase showed an active pH range of 3.5–8.5 under varied buffer conditions and thermostability up to 50 °C. The results revealed a significant potential utility of actinidin to retard amylase as it effectively degraded the amylolytic enzyme under in vitro conditions and could be beneficial for lowering glycemic response to ingested starch. However, further in vitro as well as in vivo studies need to be conducted under gastrointestinal conditions to establish the hypothesis.

Modified Rhodopsins From Aureobasidium pullulans Excel With Very High Proton-Transport Rates

Aureobasidium pullulans is a black fungus that can adapt to various stressful conditions like hypersaline, acidic, and alkaline environments. The genome of A. pullulans exhibits three genes coding for putative opsins ApOps1, ApOps2, and ApOps3. We heterologously expressed these genes in mammalian cells and Xenopus oocytes. Localization in the plasma membrane was greatly improved by introducing additional membrane trafficking signals at the N-terminus and the C-terminus. In patch-clamp and two-electrode-voltage clamp experiments, all three proteins showed proton pump activity with maximal activity in green light. Among them, ApOps2 exhibited the most pronounced proton pump activity with current amplitudes occasionally extending 10 pA/pF at 0 mV. Proton pump activity was further supported in the presence of extracellular weak organic acids. Furthermore, we used site-directed mutagenesis to reshape protein functions and thereby implemented light-gated proton channels. We discuss the difference to other well-known proton pumps and the potential of these rhodopsins for optogenetic applications.

826 Establishing the preclinical/translational PK/PD relationship for BT7480, a nectin-4/CD137 Bicycle tumor-targeted immune cell agonist™ (Bicycle TICA™)

BackgroundA new class of modular synthetic drugs, termed Bicycle tumor-targeted immune cell agonists (Bicycle TICAs), based on constrained bicyclic peptides has been developed as agonists of immune costimulatory receptors in cancer therapeutics.1 One example is BT7480 which binds simultaneously to Nectin-4 on tumor cells and CD137 on primed immune cells with activation (agonism) of CD137 being dependent on co-ligation of Nectin-4.MethodsIn vitro CD137 reporter activity and cytokine secretion data were generated using Bicycle TICAs including BT7480. These Bicycle TICAs could display a concentration-dependent activation (e.g. CD137 activation increases IFN-gamma production) reaching a maximal activity, which then decreases as the drug concentration increases.2 We developed a mathematical model to analyse this behaviour.We also modelled plasma and tumor pharmacokinetics of BT7480 in CT26-Nectin-4 tumor-bearing mice. A two-compartment model described the drug plasma profile after intravenous dosing and the tumor profile was described by a one effect compartment model. A tumor growth inhibition model for BT7480 was used to describe the preclinical data by placing the model within a mixed effect framework to estimate the population model parameters, i.e., tumor size at time 0 and tumor size growth rate, and to predict the parameter values for each mouse. We assessed how the tumor growth rate values correlate with the immune system markers collected.ResultsWe assessed the predictions of the in vitro model against the experimental observations and found that the position of the turning point could be predicted from the dissociation constants (Kd's). The combined BT7480 pharmacokinetic model shows that the elimination rate from plasma is faster than that from the tumor. We hypothesized that this results from BT7480 binding to Nectin-4 in the tumor. Also, we found that the level of tumor infiltrating CD8+ T-cells fully captures the treatment effect of BT7480 on tumor growth. Therefore, we established a likely causal link: from pharmacokinetic/dose to CD8+ T-cell infiltration changes and ultimately to tumor growth inhibition.ConclusionsA PK/PD modelling framework was developed that predicts preclinical biomarker level and tumor growth inhibition in response to changes in the BT7480 dose and dosing schedule. In addition, plasma and tumor drug concentration levels can be associated with the target concentration estimated using in vitro data.2 Namely, the product of the square-root of the two target Kds is likely to be the free drug concentration at which maximal activity of the trimer [T-Cell—BT7480—Tumor-Cell] is achieved.ReferencesUpadhyaya P. Anticancer immunity induced by a synthetic tumor-targeted CD137 agonist. Journal for ImmunoTherapy of Cancer 2021;9:e001762.Perelson AS. Receptor clustering on a cell surface. III. theory of receptor cross-linking by multivalent ligands: description by ligand states. Mathematical Biosciences 1981;53:1–39.

New Insights to Regulation of Fructose-1,6-bisphosphatase during Anoxia in Red-Eared Slider, Trachemys scripta elegans

The red-eared slider (Trachemys scripta elegans) undergoes numerous changes to its physiological and metabolic processes to survive without oxygen. During anoxic conditions, its metabolic rate drops drastically to minimize energy requirements. The alterations in the central metabolic pathways are often accomplished by the regulation of key enzymes. The regulation of one such enzyme, fructose-1,6-bisphosphatase (FBPase; EC 3.1.3.11), was characterized in the present study during anoxia in liver. FBPase is a crucial enzyme of gluconeogenesis. The FBPase was purified from liver tissue in both control and anoxic conditions and subsequently assayed to determine the kinetic parameters of the enzyme. The study revealed the relative degree of post-translational modifications in the FBPase from control and anoxic turtles. Further, this study demonstrated a significant decrease in the maximal activity in anoxic FBPase and decreased sensitivity to its substrate fructose-1,6-bisphosphate (FBP) when compared to the control. Immunoblotting demonstrated increased threonine phosphorylation (~1.4-fold) in the anoxic FBPase. Taken together, these results suggest that the phosphorylation of liver FBPase is an important step in suppressing FBPase activity, ultimately leading to the inhibition of gluconeogenesis in the liver of the red-eared slider during anaerobic conditions.

Expression, biochemical and structural characterization of high-specific-activity β-amylase from Bacillus aryabhattai GEL-09 for application in starch hydrolysis

Background β-amylase (EC 3.2.1.2) is an exo-enzyme that shows high specificity for cleaving the α-1,4-glucosidic linkage of starch from the non-reducing end, thereby liberating maltose. In this study, we heterologously expressed and characterized a novel β-amylase from Bacillus aryabhattai. Results The amino acid-sequence alignment showed that the enzyme shared the highest sequence identity with β-amylase from Bacillus flexus (80.73%) followed by Bacillus cereus (71.38%). Structural comparison revealed the existence of an additional starch-binding domain (SBD) at the C-terminus of B. aryabhattai β-amylase, which is notably different from plant β-amylases. The recombinant enzyme purified 4.7-fold to homogeneity, with a molecular weight of ~ 57.6 kDa and maximal activity at pH 6.5 and 50 °C. Notably, the enzyme exhibited the highest specific activity (3798.9 U/mg) among reported mesothermal microbial β-amylases and the highest specificity for soluble starch, followed by corn starch. Kinetic analysis showed that the Km and kcat values were 9.9 mg/mL and 116961.1 s− 1, respectively. The optimal reaction conditions to produce maltose from starch resulted in a maximal yield of 87.0%. Moreover, molecular docking suggested that B. aryabhattai β-amylase could efficiently recognize and hydrolyze maltotetraose substrate. Conclusions These results suggested that B. aryabhattai β-amylase could be a potential candidate for use in the industrial production of maltose from starch.

Identification of FadT as a Novel Quorum Quenching Enzyme for the Degradation of Diffusible Signal Factor in Cupriavidus pinatubonensis Strain HN-2

Quorum sensing (QS) is a microbial cell–cell communication mechanism and plays an important role in bacterial infections. QS-mediated bacterial infections can be blocked through quorum quenching (QQ), which hampers signal accumulation, recognition, and communication. The pathogenicity of numerous bacteria, including Xanthomonas campestris pv. campestris (Xcc), is regulated by diffusible signal factor (DSF), a well-known fatty acid signaling molecule of QS. Cupriavidus pinatubonensis HN-2 could substantially attenuate the infection of XCC through QQ by degrading DSF. The QQ mechanism in strain HN-2, on the other hand, is yet to be known. To understand the molecular mechanism of QQ in strain HN-2, we used whole-genome sequencing and comparative genomics studies. We discovered that the fadT gene encodes acyl-CoA dehydrogenase as a novel QQ enzyme. The results of site-directed mutagenesis demonstrated the requirement of fadT gene for DSF degradation in strain HN-2. Purified FadT exhibited high enzymatic activity and outstanding stability over a broad pH and temperature range with maximal activity at pH 7.0 and 35 °C. No cofactors were required for FadT enzyme activity. The enzyme showed a strong ability to degrade DSF. Furthermore, the expression of fadT in Xcc results in a significant reduction in the pathogenicity in host plants, such as Chinese cabbage, radish, and pakchoi. Taken together, our results identified a novel DSF-degrading enzyme, FadT, in C. pinatubonensis HN-2, which suggests its potential use in the biological control of DSF-mediated pathogens.