Model

In our design, integrases compute the output of the logic gates. Integrases allow to flip one fragment of DNA. The model we developped is described here.

Chemical Species

Modeling DNA-binding sites

Each dimer of integrases can specifically bind to a DNA binding site. As the flipping is irreversible, these DNA binding sites can be three possible states:

• SI_{IntegraseName}: inactive DNA binding site. No dimer is bound to this site, which has never been flipped.

• SA_{IntegraseName}: active DNA binding site. A dimer is to this site.

• SF_{IntegraseName}: flipped DNA binding site. This DNA binding site has been used by a flipping.

The three different states of DBxb1-DNA binding sites.

Reactions

For Bxb1

$$ \begin{align} Bxb1 + Bxb1 &\leftrightarrow DBxb1 \\ DBxb1 + SI_{Bxb1} & \leftrightarrow SA_{Bxb1}\\ Bxb1 &\rightarrow \\ DBxb1 &\rightarrow \end{align}$$

For ΦC31

\begin{align} \phi C31 + \phi C31 &\leftrightarrow D\phi C 31 \\ D\phi C 31 + SI_{\phi C31} & \leftrightarrow SA_{\phi C31}\\ \phi C31 &\rightarrow \\ D\phi C31 &\rightarrow \end{align}

Parameters

Replacing every occurence of Bxb1 by ΦC31 gives the set of parameters for ΦC31. The same status can be applied to those parameters.

Even if degradation rates were not determined specifically for the serine integrases and their dimerized form, degradation rates of proteins in E. coli are available. To characterize integrases behavior, we focus on finding the parameters for dimerization and DNA-binding.

Differential Equations

Applying mass action kinetic laws, we obtain the following set of differential equations for Bxb1.

$$\frac{d[Bxb1]}{dt}=-2 k_{DBxb1}[Bxb1]^2+ 2 k_{-DBxb1}[DBxb1]-d_{Bxb1}[Bxb1]$$

$$\frac{d[DBxb1]}{dt}=-k_{SABxb1}[DBxb1][SI_{Bxb1}]+k_{-SABxb1}[SA_{Bxb1}]+k_{DBxb1}[Bxb1]^2-k_{-DBxb1}[DBxb1]-d_{DBxb1}[DBxb1]$$

$$\frac{d[SA_{Bxb1}]}{dt}=k_{SABxb1}[DBxb1][SI_{Bxb1}]-k_{-SABxb1}[SA_{Bxb1}]$$

Replacing every occurence of Bxb1 by ΦC31 gives the set of differential equations for ΦC31.

Characterization: K_SABxb1

Data

The parameter fitting is based on Bonnet's paper. Their experimental setup is different from ours. However, they experimentally retrieve a transfer function between aTc and Bxb1 switching rate. Here is the figure of interest in our case.

Transfer function from aTc to Bxb1. The experimental data corresponds to the points. They fitted this data with their own model. Supplementary figure S4 of Bonnet's paper Amplifying Genetic Logic Gates

To use their experimental data, we have to model their induction mechanism using aTc. We use a simplify version of it proposed by the 2013 iGEM team UCSF. They modeled the induction with aTc as a leaky Hill function. In the following table are the set of parameters introduced to model induction.

We obtain the following set of differential equations:

$$\begin{align*} \frac{d[Bxb1]}{dt} &= k_{mRNA_{Bxb1}}*(A_L + B_L * \frac{[aTc]^n}{[aTc]^n+K_L^n})- 2 k_{DBxb1}*[Bxb1]^2 + 2k_{-DBxb1}*[DBxb1] - d_{Bxb1}*[Bxb1] \\ \frac{d[DBxb1]}{dt} &= k_{DBxb1}*[Bxb1]^2 - k_{-DBxb1}*[DBxb1] - k_{SABxb1}*[DBxb1]*[SI_{Bxb1}] + k_{-SABxb1}*[SA_{Bxb1}] - d_{DBxb1}*[DBxb1] \\ \frac{d[SA_{Bxb1}]}{dt} &= k_{SABxb1}*[DBxb1]*[SI_{Bxb1}] - k_{-SABxb1}*[SA_{Bxb1}] \end{align*}$$

Assumptions

Assumption A

The back-reaction from DBxb1 binding to site inactive is considered to be negligible, compared to the flipping rate. That is to say that once a site is active, it can only be flipped. Thus, an active site would only be a transitional state in our whole cell model. As the flipping is not modeled in our integrase subsystem, active sites are not transformed into flipped sites at the end of the information pipeline. Thus, we consider that we can express the switching rate given active site concentration.

Assumption B

As switching needs two active sites to be effective (for more information on flipping, check the XOR gate page), the switching rate is approximated to: $${(\frac{SA_{Bxb1}}{S_{TOT}})}^2$$ This approximation is understated by statistical considerations.

Assumption C

We assume quasi-steady state for SA_Bxb1 and for DBxb1, as they are both involved in binding reactions.

Assumption D

The degradation rate of Bxb1, d_Bxb1, is related to the degradation rate of DBxb1, d_DBxb1, by a factor 2. d_Bxb1 = 2 * d_DBxb1

Assumption E

The activation by aTc is assumed to be dominant over degradation of Bxb1 and dimerization of Bxb1. It is supposed to be valid on the range of aTc concentration considered.$$\frac{k_{mRNA_{Bxb1}}*(A_L + B_L * \frac{[aTc]^n}{[aTc]^n+K_L^n})}{d_{Bxb1}K_{DBxb1}} >> 1$$ with $$K_{DBxb1} = \frac{k_{-DBxb1} + d_{DBxb1}}{k_{DBxb1}}$$

Parameter fitting

Range of validity of the assumptions

Characterization: K_DBxb1

Data

The parameter fitting is based on Bonnet's paper. Their experimental setup is different from ours. However, they experimentally retrieve a transfer function between aTc and Bxb1 switching rate. Here is the figure of interest in our case.

Transfer function from aTc to Bxb1. The experimental data corresponds to the points. They fitted this data with their own model. Supplementary figure S4 of Bonnet's paper Amplifying Genetic Logic Gates

We do the same modeling steps, as for the previous characterization.Thus, we obtain the following set of differential equations:

$$\begin{align*} \frac{d[Bxb1]}{dt} &= a_{}*(A_L + B_L * \frac{[aTc]^n}{[aTc]^n+K_L^n})- 2 k_{DBxb1}*[Bxb1]^2 + 2k_{-DBxb1}*[DBxb1] - d_{Bxb1}*[Bxb1] \\ \frac{d[DBxb1]}{dt} &= k_{DBxb1}*[Bxb1]^2 - k_{-DBxb1}*[DBxb1] - k_{SABxb1}*[DBxb1]*[SI_{Bxb1}] + k_{-SABxb1}*[SA_{Bxb1}] - d_{DBxb1}*[DBxb1] \\ \frac{d[SA_{Bxb1}]}{dt} &= k_{SABxb1}*[DBxb1]*[SI_{Bxb1}] - k_{-SABxb1}*[SA_{Bxb1}] \end{align*}$$

Assumptions

Assumption A

The back-reaction from DBxb1 binding to site inactive is considered to be negligible, compared to the flipping rate. That is to say that once a site is active, it can only be flipped. Thus, an active site would only be a transitional state in our whole cell model. As the flipping is not modeled in our integrase subsystem, active sites are not transformed into flipped sites at the end of the information pipeline. Thus, we consider that we can express the switching rate given active site concentration.

Assumption B

As switching needs two active sites to be effective (for more information on flipping, check the XOR gate page), the switching rate is approximated to: $${(\frac{SA_{Bxb1}}{S_{TOT}})}^2$$ This approximation is understated by statistical considerations.

Assumption C

We assume quasi-steady state for SA_Bxb1 and for DBxb1, as they are both involved in binding reactions.

Assumption F

We neglect the degradation rate of DBxb1, d_DBxb1, with respect to the dimerization reaction.

Parameter fitting

Range of validity of the assumptions