Creation of a Ligand-Dependent Enzyme by Fusing Circularly Permuted Antibody Variable Region Domains

The Use of a β-lactamase-based Conductimetric Biosensor Assay to Detect Biomolecular Interactions

Biosensors are becoming increasingly important and implemented in various fields such as pathogen detection, molecular diagnosis, environmental monitoring, and food safety control. In this context, we used β-lactamases as efficient reporter enzymes in several protein-protein interaction studies. Furthermore, their ability to accept insertions of peptides or structured proteins/domains strongly encourages the use of these enzymes to generate chimeric proteins. In a recent study, we inserted a single-domain antibody fragment into the Bacillus licheniformis BlaP β-lactamase. These small domains, also called nanobodies, are defined as the antigen-binding domains of single chain antibodies from camelids. Like common double chain antibodies, they show high affinities and specificities for their targets. The resulting chimeric protein exhibited a high affinity against its target while retaining the β-lactamase activity. This suggests that the nanobody and β-lactamase moieties remain functional. In the present work, we report a detailed protocol that combines our hybrid β-lactamase system to the biosensor technology. The specific binding of the nanobody to its target can be detected thanks to a conductimetric measurement of the protons released by the catalytic activity of the enzyme.

Creation of Antigen-Dependent β-Lactamase Fusion Protein Tethered by Circularly Permuted Antibody Variable Domains

Antibody-based molecular switches that are able to recognize a range of exogenous antigens can be highly useful as a versatile biosensor. However, regulating the catalytic activity of enzymes by antibodies is still hard to achieve. Here, we describe a design method of unique antibody variable region Fv introduced with two circular permutations, called Clampbody. By tethering the Clampbody to a circularly permuted TEM-1 β-lactamase (BLA), we successfully constructed a genetically encoded molecular switch Cbody-cpBLA that shows antigen-dependent catalytic activity.

Synthetic Protein Switches: Theoretical and Experimental Considerations

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.