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. 2020 Oct 16;11:5260. doi: 10.1038/s41467-020-18948-x

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© 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/.

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Fig. 1 — A reduced pathway for elongation with amino acids cysteine (aminoacyl-tRNA Cys) and glutamine (aa-tRNA Gln1, Gln2) is represented in Systems Biology Graphical Notation. Initiation: free (unbound) ribosome gets converted to active ribosome, modulated by mRNA. Termination: active ribosome converts back to free ribosome at a rate fixed by the desired protein production rate. Active ribosome state transition: active ribosome instantaneously binds to codons (61 codons in full model, 4 here) at the fractions set by the specified proteome composition. Ternary complex formation: charged tRNAs (40 aa-tRNAs in full model, 3 here), replenished from a pool, combine with EF-Tu*GTP to form ternary complexes (40 TCs in the full model). Kinetic parameters of these reversible processes depend on the aa-tRNA. Elongation: labeled ribosome binds with the cognate TC to elongate the protein with the respective amino acid. The ribosome returns to its active state and EF-Tu*GDP is released. Other products of this reaction, such as deacylated tRNA, are not modeled. Nucleotide exchange (see right panel): EF-Tu*GDP is reactivated to EF-Tu*GTP in a sequence of steps modeled by reversible mass action kinetics. GTP and GDP pools are modeled with fixed concentrations. The nucleotide exchange is supported by EF-Ts, and the main flux is carried through the complexes formed by EF-Tu with EF-Ts.