Reaction dynamics analysis of an E. coli protein translation system by computational modeling
September 24-28, 2017
A single enzymatic reaction can often be described by Michaelis-Menten kinetics, but once reactions are connected to one other, it becomes difficult to understand and capture a complete description of the reaction dynamics due to its high dimensionality. To elucidate the dynamic features of a biologically relevant large-scale reaction network, we constructed a computational model of minimal protein synthesis consisting of 241 components and 968 reactions that synthesize the Met-Gly-Gly (MGG) peptide based on an Escherichia coli-based reconstituted in vitro translation (IVT) system . We performed a simulation using parameters collected primarily from the literature and found that the rate of MGG peptide synthesis becomes nearly constant in minutes, thus achieving a steady-state similar to experimental observations. In addition, concentration changes to 70% of the components, including intermediates, reached a plateau in a few minutes. However, the concentration change of each component exhibits several temporal plateaus, or a quasi-stationary state (QSS), before reaching the final plateau. To understand the complex dynamics, we focused on whether the components reached a QSS, mapped the arrangement of components in a QSS in the entire reaction network structure and investigated time-dependent changes. We found that components in a QSS form clusters that grow over time but not in a linear fashion and that this process involves the collapse and regrowth of clusters before the formation of a final large single cluster. These observations might commonly occur in other large-scale biological reaction networks. This developed analysis might be useful for understanding large-scale enzymatic reactions, thereby extracting the characteristics of the reaction network, including phase transitions. As the reconstituted IVT has been used for various applications inducing directed evolution of membrane proteins [2,3], the developed computational model might be useful in further enhancement of the yield of synthesized proteins using the reconstituted IVT.
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Tomoaki Matsuura, Naoki Tanimura, Kazufumi Hosoda, Tetsuya Yomo, and Yoshihiro Shimizu, "Reaction dynamics analysis of an E. coli protein translation system by computational modeling" in "Enzyme Engineering XXIV", Pierre Monsan, Toulouse White Biotechnology, France Magali Remaud-Simeon, LISBP-INSA, University of Toulouse, France Eds, ECI Symposium Series, (2017). https://dc.engconfintl.org/enzyme_xxiv/164