Optimizing recombinant antibodies for intracellular function using hitchhiker-mediated survival selection

The 'hitchhiker' mechanism of the bacterial twin-arginine translocation pathway has previously been adapted as a genetic selection for detecting pairwise protein interactions in the cytoplasm of living Escherichia coli cells. Here, we extended this method, called FLI-TRAP, for rapid isolation of intracellular antibodies (intrabodies) in the single-chain Fv format that possess superior traits simply by demanding bacterial growth on high concentrations of antibiotic. Following just a single round of survival-based enrichment using FLI-TRAP, variants of an intrabody against the dimerization domain of the yeast Gcn4p transcription factor were isolated having significantly greater intracellular stability that translated to yield enhancements of >10-fold. Likewise, an intrabody specific for the non-amyloid component region of α-synuclein was isolated that has ~8-fold improved antigen-binding affinity. Collectively, our results illustrate the potential of the FLI-TRAP method for intracellular stabilization and affinity maturation of intrabodies, all without the need for purification or immobilization of the antigen.

High-resolution crystal structure of spectrin SH3 domain fused with a proline-rich peptide

A new chimeric protein, named WT-CIIA, was designed by connecting the proline-rich decapeptide PPPVPPYSAG to the C-terminus of the alpha-spectrin SH3 domain through a natural twelve-residue linker to obtain a single-chain model that would imitate intramolecular SH3-ligand interaction. The crystal structure of this fusion protein was determined at 1.7 Å resolution. The asymmetric unit of the crystal contained two SH3 globules contacting with one PPPVPPY fragment located between them. The domains are related by the two-fold non-crystallographic axis and the ligand lies in two opposite orientations with respect to the conservative binding sites of SH3 domains.

Identifying and optimizing intracellular protein-protein interactions using bacterial genetic selection

Protein-protein interactions are crucial for the vast majority of biological processes. To fully understand these processes therefore requires methods for identifying protein interactions within the complex cellular environment. To isolate interacting proteins, we have developed a simple and reliable genetic selection by exploiting the inbuilt "hitchhiker" mechanism of the Escherichia coli twin-arginine translocation (Tat) pathway. This method is based on the unique ability of the Tat system to efficiently co-localize noncovalent complexes of two folded polypeptides to the periplasmic space of E. coli. The genetic selection is comprised of two engineered fusion proteins: an N-terminal Tat signal peptide fused to the protein of interest, and the known or putative partner protein fused to mature TEM-1 β-lactamase. The efficiency with which co-localized β-lactamase chimeras are exported in the periplasm, and thus confer ampicillin resistance to cells, is directly linked to the relative binding affinity of the protein-ligand system. Thus, ampicillin resistance can be used as a convenient readout for identifying and optimizing protein interactions in E. coli. Furthermore, because Tat substrates must be correctly folded for export, our method favors the identification of soluble, non-aggregating, protease-resistant protein pairs. Overall, we anticipate that this new selection tool will be useful for discovering and engineering protein drugs, protein complexes for structural biology, factors that inhibit PPIs, and components for synthetic biology.