3
Viktor Stein (ed.), Synthetic Protein Switches: Methods and Protocols, Methods in Molecular Biology, vol. 1596,
DOI 10.1007/978-1-4939-6940-1_1, © Springer Science+Business Media LLC 2017
Chapter 1
Synthetic Protein Switches: Theoretical
and Experimental Considerations
Viktor Stein
Abstract
Synthetic protein switches with tailored response functions are finding increasing applications as tools in
basic research and biotechnology. With a number of successful design strategies emerging, the construction
of synthetic protein switches still frequently necessitates an integrated approach that combines detailed biochemical and biophysical characterization in combination with high-throughput screening to construct tailored synthetic protein switches. This is increasingly complemented by computational strategies that aim to
reduce the need for costly empirical optimization and thus facilitate the protein design process. Successful
computational design approaches range from analyzing phylogenetic data to infer useful structural, biophysical, and biochemical information to modeling the structure and function of proteins ab initio. The
following chapter provides an overview over the theoretical considerations and experimental approaches that
have been successful applied in the construction of synthetic protein switches.
Key words Protein switches, Protein engineering, Synthetic biology, Protein signaling, Genetic
circuits
1 Introduction
Synthetic protein switches with tailored response functions are
finding increasing applications as tools in basic research helping
dissect the molecular mechanisms that underlie the function of a
cell, or in biotechnology as diagnostic reagents reporting in an
autonomous fashion on distinct molecular biomarkers that are specific for a disease process [1, 2]. Common to all synthetic protein
switches is a receptor that recognizes a distinct molecular queue
(such as ligand binding or a posttranslational modification) and an
actuator that is functionally coupled to the receptor and thus able
to translate the primary molecular recognition event into a change
in biophysical, chemical, or enzymatic signal depending on the
preferred readout.
At the molecular level, a number of architectures have been
successfully devised to construct synthetic protein switches with
tailored response functions: These range from integrated designs
Viktor Stein (ed.), Synthetic Protein Switches: Methods and Protocols, Methods in Molecular Biology, vol. 1596,
DOI 10.1007/978-1-4939-6940-1_1, © Springer Science+Business Media LLC 2017
Chapter 1
Synthetic Protein Switches: Theoretical
and Experimental Considerations
Viktor Stein
Abstract
Synthetic protein switches with tailored response functions are finding increasing applications as tools in
basic research and biotechnology. With a number of successful design strategies emerging, the construction
of synthetic protein switches still frequently necessitates an integrated approach that combines detailed biochemical and biophysical characterization in combination with high-throughput screening to construct tailored synthetic protein switches. This is increasingly complemented by computational strategies that aim to
reduce the need for costly empirical optimization and thus facilitate the protein design process. Successful
computational design approaches range from analyzing phylogenetic data to infer useful structural, biophysical, and biochemical information to modeling the structure and function of proteins ab initio. The
following chapter provides an overview over the theoretical considerations and experimental approaches that
have been successful applied in the construction of synthetic protein switches.
Key words Protein switches, Protein engineering, Synthetic biology, Protein signaling, Genetic
circuits
1 Introduction
Synthetic protein switches with tailored response functions are
finding increasing applications as tools in basic research helping
dissect the molecular mechanisms that underlie the function of a
cell, or in biotechnology as diagnostic reagents reporting in an
autonomous fashion on distinct molecular biomarkers that are specific for a disease process [1, 2]. Common to all synthetic protein
switches is a receptor that recognizes a distinct molecular queue
(such as ligand binding or a posttranslational modification) and an
actuator that is functionally coupled to the receptor and thus able
to translate the primary molecular recognition event into a change
in biophysical, chemical, or enzymatic signal depending on the
preferred readout.
At the molecular level, a number of architectures have been
successfully devised to construct synthetic protein switches with
tailored response functions: These range from integrated designs