Probing the recognition of post-translational modifications by combining sortase-mediated ligation and phage-assisted selection

Employing unnatural promiscuity of sortase to construct peptide macrocycle libraries for ligand discovery

With the increasing attention paid to macrocyclic scaffolds in peptide drug development, genetically encoded peptide macrocycle libraries have become invaluable sources for the discovery of high-affinity peptide ligands targeting disease-associated proteins. The traditional phage display technique of constructing disulfide-tethered macrocycles by cysteine oxidation has the inherent drawback of reduction instability of the disulfide bond. Chemical macrocyclization solves the problem of disulfide bond instability, but the involved highly electrophilic reagents are usually toxic to phages and may bring undesirable side reactions. Here, we report a unique Sortase-mediated Peptide Ligation and One-pot Cyclization strategy (SPLOC) to generate peptide macrocycle libraries, avoiding the undesired reactions of electrophiles with phages. The key to this platform is to mine the unnatural promiscuity of sortase on the X residue of the pentapeptide recognition sequence (LPXTG). Low reactive electrophiles are incorporated into the X-residue side chain, enabling intramolecular cyclization with the cysteine residue of the phage-displayed peptide library. Utilizing the genetically encoded peptide macrocycle library constructed by the SPLOC platform, we found a high-affinity bicyclic peptide binding TEAD4 with a nanomolar KD value (63.9 nM). Importantly, the binding affinity of the bicyclic peptide ligand is 102-fold lower than that of the acyclic analogue. To our knowledge, this is the first time to mine the unnatural promiscuity of ligases to generate peptide macrocycles, providing a new avenue for the construction of genetically encoded cyclic peptide libraries.

Expanding the Chemical Diversity of Genetically Encoded Libraries

The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.

Enzymatic Installation of Functional Molecules on Amyloid-Based Polymers

We produced a functional polymer whose framework comprised transthyretin (TTR) amyloid fibrils. In order to immobilize functional molecules onto the amyloid fibrils, transpeptidase sortase A (srtA), which catalyzes the covalent binding of LPXTG with polyglycine, was employed. After the preparation of the amyloid fibril of LPETGG-tagged TTR, immobilization of Gly5-fused GFP on the amyloid fibrils by srtA-mediated transpeptidation was carried out. SrtA recognized the amyloid fibrils consisting of an LPETGG-tagged TTR variant (L55P) as a good substrate, resulting in successful preparation of a GFP-immobilized amyloid. Intriguingly, the replacement of GFP with Gly5-fused luciferase was confirmed when the GFP-immobilized amyloids were mixed with Gly5-luciferase in the presence of srtA. Thus, it was found that functional molecules covalently immobilized on amyloid could be detached and substituted with other tagged molecules by using srtA.

Sortase-mediated chemical protein synthesis reveals the bidentate binding of bisphosphorylated p62 with K63 diubiquitin

Phosphorylation of S403 or S407 of the autophagic receptor protein p62 has recently been discovered to enhance the binding of p62 with ubiquitinated protein substrates to upregulate selective autophagy. To elucidate the molecular mechanism of how phosphorylation regulates the recruitment of ubiquitinated proteins, we report the first chemical synthesis of homogeneously phosphorylated p62, which enables the setting up of accurate in vitro systems for biochemical studies. Our synthesis employs the technology of sortase A-mediated protein hydrazide ligation, which successfully affords three types of phosphorylated p62 at the multi-milligram scale. Quantitative biochemical measurements show that the binding affinity of S403/S407-bisphosphorylated p62 to K63 diubiquitin is significantly higher than that of mono-phosphorylated p62. This finding suggests that phosphorylated S403 and S407 sites should bind to different epitopes on the ubiquitin chain. Furthermore, glutamate mutation is found to give a significantly impaired binding affinity, implying the necessity of using chemically synthesized phosphorylated p62 for the biochemical study of selective autophagy.

Identification of sortase substrates by specificity profiling

Sortases catalyze the attachment of surface proteins to the peptidoglycan layer of gram-positive bacteria and further represent powerful tools of protein chemistry. During catalysis sortases cleave a donor substrate containing the LPxTG (x=any amino acid) sorting motif under formation of an enzyme-bound thioester and ligate this intermediate to an acceptor protein containing an N-terminal glycine residue. In addition to the well-established sortase A of Staphylococcus aureus several homologs of this enzyme have been identified in the genomes of gram-positive bacteria. We have profiled the specificity of seven sortases of Staphylococci and Streptococci origin and observed that sortases of the latter class displayed a more relaxed specificity for donor and acceptor substrates than their Staphylococci counterparts. Streptococci sortases prefer an LPKLG donor substrate sequence compared to the canonical sorting motif LPKTG. These findings might facilitate the use of Streptococci sortases as tools of protein chemistry.

Engineering sortase A by screening a second-generation library using phage display

Sortase-mediated ligation is one of the most commonly used chemo-enzymatic techniques for the site-specific modification of proteins. We have established a new library of sortase mutants for directed evolution of sortase substrate selectivity. Phage display screens of this second-generation library yielded sortase mutants that ligate substrate proteins containing an APxTG or FPxTG recognition sequence instead of the canonical LPxTG sorting motif. These findings indicate that the second-generation sortase library is well suited for sortase engineering in order to increase the versatility of sortase-mediated ligation. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Semisynthesis and initial characterization of sortase A mutants containing selenocysteine and homocysteine

The bacterial transpeptidase sortase A is a well-established tool in protein chemistry and catalyzes the chemoselective ligation of peptides and proteins. During catalysis sortase A cleaves the conserved Leu-Pro-X-Thr-Gly sorting motif at the Thr residue under concomitant thioester formation at active site Cys184. We have used expressed protein ligation (EPL) to generate sortase mutants with Cys184 replaced by selenocysteine (Sec) and homocysteine (Hcy). Sec-sortase showed a moderate 2-3-fold reduction in catalytic activity in contrast to Hcy-sortase which is a poor catalyst with less than 1% of wild-type activity. The sensitivity of the active site nucleophiles towards an alkylation reagent correlated with the pKa values of the mutated residues. Furthermore, the pH-profile of Sec-sortase was shifted to more acidic conditions when compared to the wild-type enzyme. These observations provide information on sortase catalysis and the semisynthetic enzymes might represent useful tools for further biochemical investigations and engineering approaches of sortases A.

Sortase-mediated ligations for the site-specific modification of proteins

Sortase-mediated ligation (SML) is one of the most commonly used techniques for the site-specific modification of proteins. Here, a brief overview on advantages and limitations of this technology in comparison with other chemoselective protein modification techniques is provided and successful approaches that extend the application range of SML are discussed.

Flow-based enzymatic ligation by sortase A

Sortase-mediated ligation (sortagging) is a versatile, powerful strategy for protein modification. Because the sortase reaction reaches equilibrium, a large excess of polyglycine nucleophile is often employed to drive the reaction forward and suppress sortase-mediated side reactions. A flow-based sortagging platform employing immobilized sortase A within a microreactor was developed that permits efficient sortagging at low nucleophile concentrations. The platform was tested with several reaction partners and used to generate a protein bioconjugate inaccessible by solution-phase batch sortagging.

Chemo-enzymatic three-fragment assembly of semisynthetic proteins

Here, we report the development of a method for three-fragment assemblies of semisynthetic proteins by combining sortase-mediated ligation with site-specific bioconjugation catalyzed by the 4'-phosphopantetheine transferase Sfp. This method enables the introduction of synthetic peptides into central regions of proteins without the need to purify intermediates. The assembled proteins are linked at the N-terminal junction with a 4'-phosphopantetheine moiety and with a peptide bond at the C-terminal ligation site. We have demonstrated the applicability of this method by assembling a semisynthetic model protein derived from fluorescence resonance energy transfer-based reporters from three fragments in a one-pot reaction.