Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2020 Feb 27;11:1098. doi: 10.1038/s41467-020-14830-y

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Fig. 3 — The complete pathway analysis (one-pot cascade) with all enzymes present at t = 0 min. Metabolite concentrations were determined using NMR and the experiments were simulated with a detailed mathematical model (see Supplementary Note 1 for the model description). The results for the reference state incubation (without NAD⁺ recycling) and the effect of NAD⁺ recycling using LDH and pyruvate is shown for the reference state in a and b, respectively. In c, the XLA was not added to the incubation, to test whether the non-enzymatic conversion of d-xylonolactone to d-xylonate limits the overall pathway flux, and in d the relative enzyme concentrations were changed (with the same total enzyme concentrations) based on model simulations for the optimal conversion, i.e., highest conversion efficiency to α-ketoglutarate. The number of independent experiments equals n = 2 (Fig. 3a, b and c) using two independent isolates for all panels. In the experiment of d, enzyme preparations from two independent enzyme expressions and purifications were used either as fresh enzymes (duplicate) or as stored enzymes with reduced activity (at adapted concentrations, see Supplementary Note 1 and Supplementary Table 9) (n = 3). Error bars represent the SEM for the independent experiments and the shaded bands indicate the simulation confidence showing the solution space for the model simulations with a 10% error margin for the parameters. For abbreviations, see Fig. 1; LAC, lactate. Source data are provided as a Source Data file. It also can be accessed via the following DOI and SED-ML: Fig. 3a: 10.15490/FAIRDOMHUB.1.ASSAY.987.2 or https://jjj.bio.vu.nl/models/experiments/shen2020_fig3a/simulate; Fig. 3b: 10.15490/FAIRDOMHUB.1.ASSAY.989.2 or https://jjj.bio.vu.nl/models/experiments/shen2020_fig3b/simulate; Fig. 3c: 10.15490/FAIRDOMHUB.1.ASSAY.988.2 or https://jjj.bio.vu.nl/models/experiments/shen2020_fig3c/simulate; Fig. 3d: 10.15490/FAIRDOMHUB.1.ASSAY.991.2 or https://jjj.bio.vu.nl/models/experiments/shen2020_fig3d/simulate.