Biochemical characterization of Caulobacter crescentus xylose dehydrogenase

Lee, Charles C.; Jordan, Douglas B.; Stoller, J. Rose; Kibblewhite, Rena E.; Wagschal, Kurt

doi:10.1016/j.ijbiomac.2018.06.124

Cited by 7 publications

(6 citation statements)

References 25 publications

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“…With our initial rate experiments, we confirmed the results for the XDH, XLA and XAD previously determined 33,[38][39][40][41] . We observed some variations in kinetic constants, which are most likely due to differences in the assays that were used (e.g., with respect to buffer system, temperature and metal ions) and differences in enzyme-storage conditions 42 .…”

Section: Discussionsupporting

confidence: 88%

“…Due to a lack of quantitative models, rational pathway design is not widely applied and time-consuming combinatorial approaches are used instead. For the Weimberg pathway of C. crescentus, only the XDH, the XAD and the KDXD had been partially kinetically characterized [38][39][40][41][42] , and although XLAs were characterized, e.g., from Azospirillum brasilense, Haloferax volcanii and partially from C. crescentus 9,10,33,49 , kinetic constants for C. crescentus were not available. As a prerequisite for rational pathway design and detailed kinetic modelling, we herein established purification procedures and kinetic enzyme assays, and in addition developed protocols for effective synthesis and determination of pathway intermediates.…”

Section: Discussionmentioning

confidence: 99%

“…For the Weimberg pathway in C. crescentus, enzyme kinetic data are available for three of the five enzymes: XDH, XAD and KDXD, and for XAD also the crystal structure was solved [38][39][40][41][42] . However, product inhibition or inhibition by Weimberg intermediates has not been addressed so far and, to our knowledge, no kinetic model for the pathway has been reported.…”

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confidence: 99%

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A combined experimental and modelling approach for the Weimberg pathway optimisation

et al. 2020

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The oxidative Weimberg pathway for the five-step pentose degradation to α-ketoglutarate is a key route for sustainable bioconversion of lignocellulosic biomass to added-value products and biofuels. The oxidative pathway from Caulobacter crescentus has been employed in in-vivo metabolic engineering with intact cells and in in-vitro enzyme cascades. The performance of such engineering approaches is often hampered by systems complexity, caused by non-linear kinetics and allosteric regulatory mechanisms. Here we report an iterative approach to construct and validate a quantitative model for the Weimberg pathway. Two sensitive points in pathway performance have been identified as follows: (1) product inhibition of the dehydrogenases (particularly in the absence of an efficient NAD + recycling mechanism) and (2) balancing the activities of the dehydratases. The resulting model is utilized to design enzyme cascades for optimized conversion and to analyse pathway performance in C. cresensus cellfree extracts.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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A combined experimental and modelling approach for the Weimberg pathway optimisation

et al. 2020

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“…after NAD + has bound, suggesting an ordered bi−bi mechanism. 59 To further investigate the NAD + dependency of the phenol lead class, we performed cross-titrations of test compounds and NAD + at varying concentrations in the human HSD17B13 enzyme assay, while keeping estradiol constant at the highest, practically feasible concentration. In these experiments, we observed a significant NAD + -dependent decrease of the IC 50 values for the phenols (Figure 10A) and compound 45 (BI-3231) (Figure 10B), illustrating an uncompetitive mode of inhibition.…”

Section: ■ Introductionmentioning

confidence: 99%

Discovery of a Novel Potent and Selective HSD17B13 Inhibitor, BI-3231, a Well-Characterized Chemical Probe Available for Open Science

et al. 2023

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Genome-wide association studies in patients revealed HSD17B13 as a potential new target for the treatment of nonalcoholic steatohepatitis (NASH) and other liver diseases. However, the physiological function and the disease-relevant substrate of HSD17B13 remain unknown. In addition, no suitable chemical probe for HSD17B13 has been published yet. Herein, we report the identification of the novel potent and selective HSD17B13 inhibitor BI-3231. Through high-throughput screening (HTS), using estradiol as substrate, compound 1 was identified and selected for subsequent optimization resulting in compound 45 (BI-3231). In addition to the characterization of compound 45 for its functional, physicochemical, and drug metabolism and pharmacokinetic (DMPK) properties, NAD + dependency was investigated. To support Open Science, the chemical HSD17B13 probe BI-3231 will be available to the scientific community for free via the opnMe platform, and thus can help to elucidate the pharmacology of HSD17B13.

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“…Theoretical investigations using quantum chemistry methodologies can provide reliable atomic and molecular information regarding the chemical mechanisms of molecular systems with biological, pharmaceutical, and industrial applications. − To the best of our knowledge, no computational investigation can be found in the literature regarding the essential oils and their iron chelating process. This kind of study can be very useful because the analysis of the experimental characterization and spectroscopic data can be, in many cases, a rather complex task so that these studies can help to better understand the experimental findings. − …”

Section: Introductionmentioning

confidence: 99%

Antioxidant and Cytotoxic Activity of Essential Oils and Their Principal Components: Spectrophotometric, Voltammetric, and Theoretical Investigation of the Chelating Effect of Eugenol and Carvacrol

Ferreira

Militani

Almeida

et al. 2023

ACS Food Sci. Technol.

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The antioxidant and chelating properties of essential oils of Syzygium aromaticum L. and Origanum vulgare L. and their principal eugenol and carvacrol constituents were evaluated by the thiobarbituric acid reactive substance (TBARS) assay and in the presence of iron(II) ions by cyclic voltammetry. In the TBARS assay, carvacrol and eugenol were more efficient than the butylated hydroxytoluene (BHT) standard. The anodic current of iron(II) decreased by 99.7% in the presence of S. aromaticum oil, 99.8% for eugenol, 89.3% for O. vulgare, and 99.4% for carvacrol. The UV spectra contained a band at 390 nm for the interaction between Fe(II) and ligands. Thermodynamically stable complexes are formed in the ratios of 1:3 Fe(II)/eugenol and 1:2 Fe(II)/ carvacrol. The essential oils and their principal constituents eugenol and carvacrol can be used in food preservation because they have a low cytotoxicity and act as antioxidants through chelation of metal ions.

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Biochemical characterization of Caulobacter crescentus xylose dehydrogenase

Cited by 7 publications

References 25 publications

A combined experimental and modelling approach for the Weimberg pathway optimisation

A combined experimental and modelling approach for the Weimberg pathway optimisation

Discovery of a Novel Potent and Selective HSD17B13 Inhibitor, BI-3231, a Well-Characterized Chemical Probe Available for Open Science

Antioxidant and Cytotoxic Activity of Essential Oils and Their Principal Components: Spectrophotometric, Voltammetric, and Theoretical Investigation of the Chelating Effect of Eugenol and Carvacrol

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