5
design strategies extensively rely on iterative cycles of designing,
building, and testing synthetic protein switches (Fig. 1) with the
emphasis on empirical testing that is costly and time-consuming.
The following chapter thus provides a summary of the key experimental techniques and theoretical considerations that apply to the
construction of synthetic protein switches.
2 Designing Synthetic Protein Switches
A key goal in synthetic biology is to engineer biological functions
a priori [15, 16]. This is to accelerate the design-build-test cycle
and reduce the need for costly empirical optimization. In addition,
a capacity to engineer biological functions a priori reflects on our
fundamental understanding of the underlying biological processes
and phenomena. In the context of proteins, significant progress
Fig. 1 Summary of the key experimental steps in the design-build-test cycle of
synthetic protein switches. The design of synthetic protein switches is based on
structural intuition that is increasingly complemented by computer-assisted
design processes based on the molecular modeling of protein structures and statistical sequence analysis that aim to render the design stage more rational and
automated (see Subheading 3). Once designed, synthetic protein switches can be
built using a variety of DNA assembly procedures that include DNA homology and
non-homology-dependent recombination methods as well as ligation-dependent
strategies (see Subheading 4). Individual designs are then tested empirically for
their correct function. Depending on the likelihood that designs are correct, tailored screening systems of varying throughput are required (see Subheading 5)
Engineering Synthetic Protein Switches
design strategies extensively rely on iterative cycles of designing,
building, and testing synthetic protein switches (Fig. 1) with the
emphasis on empirical testing that is costly and time-consuming.
The following chapter thus provides a summary of the key experimental techniques and theoretical considerations that apply to the
construction of synthetic protein switches.
2 Designing Synthetic Protein Switches
A key goal in synthetic biology is to engineer biological functions
a priori [15, 16]. This is to accelerate the design-build-test cycle
and reduce the need for costly empirical optimization. In addition,
a capacity to engineer biological functions a priori reflects on our
fundamental understanding of the underlying biological processes
and phenomena. In the context of proteins, significant progress
Fig. 1 Summary of the key experimental steps in the design-build-test cycle of
synthetic protein switches. The design of synthetic protein switches is based on
structural intuition that is increasingly complemented by computer-assisted
design processes based on the molecular modeling of protein structures and statistical sequence analysis that aim to render the design stage more rational and
automated (see Subheading 3). Once designed, synthetic protein switches can be
built using a variety of DNA assembly procedures that include DNA homology and
non-homology-dependent recombination methods as well as ligation-dependent
strategies (see Subheading 4). Individual designs are then tested empirically for
their correct function. Depending on the likelihood that designs are correct, tailored screening systems of varying throughput are required (see Subheading 5)
Engineering Synthetic Protein Switches