Team:SMS Shenzhen/Model
Modeling Overview
In the modeling part, in order to create an effective gum degrading system, we utilize simulations and algorithms to model our degradation enzyme system from cellular metabolism to protein structure. The figure below shows how our different modeling aspects interact and provides a clear perspective of our modeling project.
Firstly, to improve Laccase CotA's enzyme activity, we proceeded with rational design. We performed homology protein modeling, molecular docking, and amino acid mutation to discover the possible residue mutations that could increase Laccase CotA's substrate affinity. Once we selected the possible mutations, we actualized them in wetlab to test the improvement in enzyme activity.
Secondly, in order to compare the enzyme activity of the original Laccase CotA with that of mutated Laccase CotA's, we conducted an enzyme-catalysed reaction model based on Michaelis-Menten Equation.
Thirdly, we utilized the ordinary differential equation in every part of protein expression to display the relationship between time and the amount of protein expression. Through the relationship graph, we could find the optimal bacterial culture time, which could be fed into wetlab to get the best yield of our protein.
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