Team:Pittsburgh/Model

What are we Modeling?

We focused on modeling the chemotactic response of E. coli and the effects photoswitchable Dronpa has on bacterial motility. When wild type E. coli are exposed to a chemical repellant, the main chemotaxis protein CheY will become phosphorylated by the autophosphorylated CheA. Next, the now phosphorylated CheY, (CheY~P) will be able to bind with high affinity to FliM, one of the proteins in the flagellar motor. This interaction between CheY~P and FliM is one of the main determinants behind the swimming versus tumbling behavior in bacteria.

We wanted to investigate this system because it is possible to compare the modeling results with experimental data obtained through microscopy videos. In addition, since the chemotaxis system has many aspects such as the reaction rates of kinase activity that we may not have considered, the model can give us more insight on potential research areas. Because our model is clearly based on certain rules that govern the interaction between the different chemotaxis proteins, we are able to use Rule Based Modeling.

What is Rule-Based Modeling and Our Model Design?

Rule-based modeling focuses on representing molecules as structured objects that interact with each other with set rules that can transform states of these objects (Faeder et al., 2009). For example, CheY would be a structured object that can interact with CheA and be transformed from an unphosphorylated to phosphorylated state.

In our model, the molecules we represented include the main chemotaxis protein CheY, CheA which undergoes autophosphorylation, the flagellar motor FliM, CheZ which dephosphorylates CheY~P, and phosphate to ensure we simulate a repellent bath like environment in our model. The rate constants and initial concentrations for the different components of our model were based off of the supplementary resources of the Sourjik paper (Sourjik and C.). The reaction rules were based off literature of the E. coli chemotaxis system with some modifications and assumptions we adapted to simplify and clarify the model. We have two forms of CheY, the native wild type and a mutant version. The wild type acts such that under a repellent condition, it will get phosphorylated by CheA, transform to the phosphorylated state and have high affinity to FliM. On the other hand, mutant CheY has been designed such that it always acts as if it is phosphorylated. Therefore, regardless whether or not there is repellent in the environment, mutant CheY always acts as if it is in the phosphorylated state. This is represented in our code by deactivating the CheZ dephosphorylation event for mutant CheY*. To simulate Dronpa’s photoswitchable dimerizing activity, we assumed rates lambda1 and lambda2 for dimerizing activity to allow us to see a change in behavior from a swimming trend to a tumbling trend. This allows us to observe trends in motility in all of our chemotaxis protein and Dronpa systems in comparison to one another.

We used the BioNetGen language (BNGL) developed by Dr. Jim Faeder which is based off of rule-based model to not only model the chemotactic response but also use the results and data obtained to be the basis for our interactive game.

System Overview

Contact Map

wt(wt~U~P~D)

wt is CheY and we have defined 3 states for it: it can be unphosphorylated (U), phosphorylated (P), or it can be dimerized (D) when 400nM light dimerizes Dronpa.

cheA(cheA~U~P)

cheA is CheA the protein responsible for autophosphoryation and we have defined 2 states for it: it can be unphosphorylated (U) or phosphorylated (P) Since we have have designed our model to be over saturated with phosphate, cheA should almost always be in the state of phosphorylated CheA to phosphorylate CheY

cheZ(cheZ)

cheZ is CheZ which is the protein responsible for dephosphorylation. In our model we have also utilized this ability to help define our mutant CheY. CheZ also has no other state it can transform into.

flag(S~U~F~FF~FFF)

flag is Flag which is the flagellar motor protein. We have defined 4 states for it: unbound (U), 1 FliM site bound by CheY-P (F), 2 FliM sites bound by CheY-P (FF), and 3 FliM sites bound by CheY-P (FFF).

p(p)

p is Phosphate groups with no other it can transform into.