Front Bioeng Biotechnol. 2016 Feb 15;4:13. doi: 10.3389/fbioe.2016.00013. eCollection 2016.

Model-Based Design of Biochemical Microreactors.

Frontiers in bioengineering and biotechnology

Tobias Elbinger, Markus Gahn, Maria Neuss-Radu, Falk M Hante, Lars M Voll, Günter Leugering, Peter Knabner

PMID: 26913283 PMCID: PMC4753381 DOI: 10.3389/fbioe.2016.00013

Abstract

Mathematical modeling of biochemical pathways is an important resource in Synthetic Biology, as the predictive power of simulating synthetic pathways represents an important step in the design of synthetic metabolons. In this paper, we are concerned with the mathematical modeling, simulation, and optimization of metabolic processes in biochemical microreactors able to carry out enzymatic reactions and to exchange metabolites with their surrounding medium. The results of the reported modeling approach are incorporated in the design of the first microreactor prototypes that are under construction. These microreactors consist of compartments separated by membranes carrying specific transporters for the input of substrates and export of products. Inside the compartments of the reactor multienzyme complexes assembled on nano-beads by peptide adapters are used to carry out metabolic reactions. The spatially resolved mathematical model describing the ongoing processes consists of a system of diffusion equations together with boundary and initial conditions. The boundary conditions model the exchange of metabolites with the neighboring compartments and the reactions at the surface of the nano-beads carrying the multienzyme complexes. Efficient and accurate approaches for numerical simulation of the mathematical model and for optimal design of the microreactor are developed. As a proof-of-concept scenario, a synthetic pathway for the conversion of sucrose to glucose-6-phosphate (G6P) was chosen. In this context, the mathematical model is employed to compute the spatio-temporal distributions of the metabolite concentrations, as well as application relevant quantities like the outflow rate of G6P. These computations are performed for different scenarios, where the number of beads as well as their loading capacity are varied. The computed metabolite distributions show spatial patterns, which differ for different experimental arrangements. Furthermore, the total output of G6P increases for scenarios where microcompartimentation of enzymes occurs. These results show that spatially resolved models are needed in the description of the conversion processes. Finally, the enzyme stoichiometry on the nano-beads is determined, which maximizes the production of glucose-6-phosphate.

Keywords: PDE-constrained optimization; biochemical microreactor; model-based design; multienzymes complexes; numerical simulation; spatio-temporal mathematical model

References

1. Chem Soc Rev. 2013 Jan 21;42(2):512-29 - PubMed
2. Biochim Biophys Acta. 2009 Feb;1794(2):315-23 - PubMed
3. Biochemistry. 2011 Nov 1;50(43):9283-95 - PubMed
4. J Am Soc Mass Spectrom. 2003 Mar;14(3):173-81 - PubMed
5. J R Soc Interface. 2009 Aug 6;6 Suppl 4:S535-46 - PubMed
6. Appl Environ Microbiol. 2011 Sep;77(17):6148-57 - PubMed
7. Bioessays. 2009 Dec;31(12):1299-308 - PubMed
8. Nat Rev Mol Cell Biol. 2009 Jun;10(6):410-22 - PubMed
9. J Biol Chem. 2005 Apr 8;280(14):14105-13 - PubMed
10. Annu Rev Biophys. 2010;39:515-37 - PubMed
11. Anal Chem. 2004 Sep 15;76(18):5498-502 - PubMed
12. Trends Cell Biol. 2012 Dec;22(12):662-70 - PubMed
13. Molecules. 2011 Jul 19;16(7):6041-59 - PubMed

Publication Types

• Journal Article