Team:GIFU TOKAI/Model
Modeling
Mathematical expectation of our project
Abstract
In this project, translation rate is a factor that must be considered. Especially, Initiation speed is expected to be differed between circRNA and linear RNA. Utilizing the parameters defined in some paper, we decided to show how large the translation speed is. In this modeling, translation process is decided into three step, initiation step, elongation step and release step. We, at first, defined the rate of expression of sfGFP. Using the time rate, we calculated the initiation speed of expression of the protein in case of linear RNA and circular RNA.
Methods/Assumption
Considering the reaction of translation, there are 3 steps. At first, we defined the rate of each step to perform calculation of protein expression.
Average translation initiation rate is one time per 5 minutes per 1 mRNA molecule according to the report of Bremer and Dennis. In this report, they mentioned the rate in E.coli cell, but it could be partially applied into our model since myTXTL is originally derived from E.coli.
Fig.1 Initiation of translation
In elongation step, the average speed of elongation is defined as 16.5 AA/sec from the parameters of the previous report. Thus, the average spped of elongation is thought to be 49.5 bp/sec. In this case, we used sfGFP gene and the time to finish the elongation step of sfGFP is 14.55 sec.
Fig.2 Elongation of peptides
As our assumption, just after translation is done, all of the ribosomes would release immediately.
Fig.3 Releasing of mRNA from ribosome
Using Lineweaver-Burk plot, our case can be modeled.
Results
From the result of assessment of sfGFP quantification, V is .
DIscussion
In this project, translation rate is a factor that must be considered. Especially, Initiation speed is expected to be differed between circRNA and linear RNA. Utilizing the parameters defined in some paper, we decided to show how large the translation speed is. In this modeling, translation process is decided into three step, initiation step, elongation step and release step. We, at first, defined the rate of expression of sfGFP. Using the time rate, we calculated the initiation speed of expression of the protein in case of linear RNA and circular RNA.