Biology Reference
In-Depth Information
AND Gate Models
SynBioSS has been shown to play an instrumental role in designing various synthetic
biological AND gates.
16
As described above, these AND gates consist of molecular parts
from the tetracycline and lactose operons, and switch on gene expression if and only if two
inducer molecules, namely aTc and IPTG, are present. See above for details regarding these
experimental systems (and reference
16
). As the molecular components of these synthetic
systems are well-characterized and found in the BioBricks database, SynBioSS can be used to
develop a complete model of the systems (see references
16,55,68
) and can then be used to
accurately predict their behavior under a wide range of conditions. Therefore, the
simulations can inform the experimental design of different and more complex AND gates
and systems containing AND gates. Let us now discuss how SynBioSS can aid in the design
and characterization of two synthetic biological switches that have been recently developed.
proTeOn and proTeOff Models
Using the SynBioSS DS, two new biological switches were recently designed, built, and
simulated. As discussed in the previous section, these switches, proTeOn and proTeOff,
robustly switch the expression of a target gene on and off in prokaryotic cells in an
aTc-dependent fashion. Their experimental design and characterization are described in
the previous section, and can be found in reference
15
. Briefly, proTeOn up-regulates gene
expression from basal to high levels in response to aTc. On the other hand, proTeOff
up-regulates gene expression only in the absence of aTc. Basal expression is achieved in
thepresenceofaTcwiththissystem.Eventhough similar gene expression regulation
devices have been designed previously for eukaryotic systems,
28
31
to the author
'
s
knowledge this is the first time that two similar prokaryotic switches have been
developed. Furthermore, these switches exhibit the exact opposite functionality from one
another relative to the presence and absence of aTc. This was accomplished for proTeOn
and proTeOff with only a single amino acid difference between the regulatory proteins
PROTEON and PROTEOFF.
132
Pairing the experimental efforts with computation, proTeOn and proTeOff were initially built
and tested in vivo, and then the strength of their governing biomolecular interactions were
quantified in silico
.
To do this, a detailed reaction network was developed, capturing the
biomolecular interplay between the components comprising proTeOn and proTeOff. The
model was simulated stochastically using the SynBioSS DS and validated against the
experimental data
.
The important feature of this model is its high level of detail as it captures
most of the biological processes (molecule transport, transcription activation and repression,
gene transcription and mRNA translation, and protein folding and degradation).
The model describing the behavior of proTeOn and proTeOff consists of 25 species and
32 reactions. The value of only five key kinetic parameters differentiates the proTeOn from
the proTeOff model. In other words, the same model can accurately capture the behavior of
both genetic switches by modifying the five unique kinetic parameters (for details see
15
).
The majority of the kinetic parameters used in the model were adopted from the literature.
However, as a number of the synthetic molecular parts used were novel, some parameters
did not exist previously. These parameters were first estimated as values close to similar
systems
parameters and then adjusted such that the computational results matched with the
experimental phenotype.
'
The procedure to simulate the behavior of these two synthetic biological switches is as follows:
1.
Open the main SynBioSS DS window.
2.
Click on
to open a new window (in case you have previously devel-
oped and saved the model, you can load it by clicking on
'
Create the Model
'
'
Load a Saved File
'
).
