Evolving Accelerated Amidation by SpyTag/SpyCatcher to Analyze Membrane Dynamics

SpyTag is a peptide that forms a spontaneous amide bond with its protein partner SpyCatcher. This protein superglue is a broadly useful tool for molecular assembly, locking together biological building blocks efficiently and irreversibly in diverse architectures. We initially developed SpyTag and SpyCatcher by rational design, through splitting a domain from a Gram‐positive bacterial adhesin. In this work, we established a phage‐display platform to select for specific amidation, leading to an order of magnitude acceleration for interaction of the SpyTag002 variant with the SpyCatcher002 variant. We show that the 002 pair bonds rapidly under a wide range of conditions and at either protein terminus. SpyCatcher002 was fused to an intimin derived from enterohemorrhagic Escherichia coli . SpyTag002 reaction enabled specific and covalent decoration of intimin for live cell fluorescent imaging of the dynamics of the bacterial outer membrane as cells divide.     

Proximity‐Based Sortase‐Mediated Ligation

Protein bioconjugation has been a crucial tool for studying biological processes and developing therapeutics. Sortase A (SrtA), a bacterial transpeptidase, has become widely used for its ability to site‐specifically label proteins with diverse functional moieties, but a significant limitation is its poor reaction kinetics. In this work, we address this by developing proximity‐based sortase‐mediated ligation (PBSL), which improves the ligation efficiency to over 95 % by linking the target protein to SrtA using the SpyTag–SpyCatcher peptide–protein pair. By expressing the target protein with SpyTag C‐terminal to the SrtA recognition motif, it can be covalently captured by an immobilized SpyCatcher–SrtA fusion protein during purification. Following the ligation reaction, SpyTag is cleaved off, rendering PBSL traceless, and only the labeled protein is released, simplifying target protein purification and labeling to a single step.     

Engineering SpyCatcher Variants with Proteolytic Sites for Less‐Trace Ligation

The SpyTag/SpyCatcher reaction is a powerful tool for bioconjugation, but it leaves a complex of considerable size after ligation. To facilitate removal of the catalytic fragment, proteolytic recognition sites (such as DDDDK, AVLQ, and WELQ) were directly engineered into the first or second loop of SpyCatcher at locations after the reactive lysine to give a set of cleavable SpyCatcher variants. Among them, SpyCatcher^DDDDK exhibits excellent reactivity with SpyTag and could still be cleaved proteolytically by enterokinase after ligation. Notably, SpyCatcher^DDDDK is disordered in solution and forms an ordered complex upon reaction with SpyTag with a second order rate constant of 99.2 ± 0.1 M^–1·s^–1, which is comparable to, if not faster than, most click reactions. The results demonstrate the high sequence plasticity of SpyCatcher and suggest that covalent bond formation may confer robustness on the folded structure against extensive mutation. These variants add to the expanding toolbox of genetically‐encoded peptide‐protein chemistry with diverse features.     

SpyTag/SpyCatcher Cyclization Confers Resilience to Boiling on a Mesophilic Enzyme

SpyTag is a peptide that spontaneously forms an amide bond with its protein partner SpyCatcher. SpyTag was fused at the N terminus of β‐lactamase and SpyCatcher at the C terminus so that the partners could react to lock together the termini of the enzyme. The wild‐type enzyme aggregates above 37 °C, with irreversible loss of activity. Cyclized β‐lactamase was soluble even after heating at 100 °C; after cooling, the catalytic activity was restored. SpyTag/SpyCatcher cyclization led to a much larger increase in stability than that achieved through point mutation or alternative approaches to cyclization. Cyclized dihydrofolate reductase was similarly resilient. Analyzing unfolding through calorimetry indicated that cyclization did not increase the unfolding temperature but rather facilitated refolding after thermal stress. SpyTag/SpyCatcher sandwiching represents a simple and efficient route to enzyme cyclization, with potential to greatly enhance the robustness of biocatalysts.     

Cover Picture: Engineering SpyCatcher Variants with Proteolytic Sites for Less‐Trace Ligation (Chin. J. Chem. 2/2019)

The cover picture shows an approach toward less‐trace SpyTag‐SpyCatcher ligation. A proteolytic recognition sequence has been engineered into the second loop of SpyCatcher to produce SpyCatcher^DDDDK variant. The reaction between SpyTag and SpyCatcher^DDDDK is highly efficient both in vivo and in vitro, producing a stable covalent complex. The complex can be further cleaved at the second loop by enterokinase, resulting in only a small scar after ligation. This protocol adds to the expanding toolbox of genetically‐encoded peptide‐protein chemistry for protein topology engineering. More details are discussed in the article by Zhang et al. on page 113–118.

     

Cellular Synthesis of Protein Catenanes

Direct cellular production of topologically complex proteins is of great interest both in supramolecular chemistry and protein engineering. We describe the first cellular synthesis of protein catenanes through the use of the p53 dimerization domain to guide the intertwining of two protein chains and SpyTag–SpyCatcher chemistry for efficient cyclization. The catenane topology was unambiguously proven by SDS‐PAGE, SEC, and partial digestion experiments and was shown to confer enhanced stability toward trypsin digestion relative to monomeric control mutants. The assembly–reaction synergy enabled by protein folding and genetically encoded protein chemistry offers a convenient yet powerful approach for creating mechanically interlocked, complex protein topologies in vivo.     

Unleashing chemical power from protein sequence space toward genetically encoded “click” chemistry

We propose the concept of genetically encoded “click” chemistry (GECC) to describe the “perfect” peptide-protein reactive partners and use SpyTag/SpyCatcher chemistry as a prototype to illustrate their structural plasticity, robust interaction, and versatile applications.     

Active Template Synthesis of Protein Heterocatenanes

Covalent‐bond‐forming protein domains can be versatile tools for creating unconventional protein topologies. In this study, through rewiring the SpyTag–SpyCatcher complex to induce rationally designed chain entanglement, we developed a biologically enabled active template for the concise, modular, and programmable synthesis of protein heterocatenanes both in vitro and in vivo. It is a general and good‐yielding reaction for forming heterocatenanes with precisely controlled ring sizes and broad structural diversity. More importantly, such heterocatenation not only provides an efficient means of bioconjugation for integrating multiple native functions, but also enhances the stability of the component proteins against proteolytic digestion, thermal unfolding, and freeze/thaw‐induced mechanical denaturation, thus opening up a versatile path in the nascent field of protein‐topology engineering.     

Protein Catenation Enhances Both the Stability and Activity of Folded Structural Domains

Catenanes are intriguing molecular architectures with unique properties. Herein, we report the cellular synthesis of protein catenanes containing folded structural domains, aided by synergy between p53 dimerization and SpyTag/SpyCatcher chemistry. Concatenation of green fluorescent protein (GFP) was shown to increase chemical stability without disrupting the fluorescence properties, and concatenated dihydrofolate reductase (DHFR) exhibited a melting temperature around 4 °C higher and catalytic activity around 27 % higher than the wild‐type DHFR and the cyclic/linear controls. Catenation also confers considerable proteolytic resistance on DHFR. The results suggest that catenation could enhance both the stability and activity of folded proteins, thus making topology engineering an attractive approach for tailoring protein properties without varying their native sequences.     

Orthogonal Surface Tags for Whole‐Cell Biocatalysis

We herein describe the engineering of E. coli strains that display orthogonal tags for immobilization on their surface and overexpress a functional heterologous “protein content” in their cytosol at the same time. Using the outer membrane protein Lpp‐ompA, cell‐surface display of the streptavidin‐binding peptide, the SpyTag/SpyCatcher system, or a HaloTag variant allowed us to generate bacterial strains that can selectively bind to solid substrates, as demonstrated with magnetic microbeads. The simultaneous cytosolic expression of functional content was demonstrated for fluorescent proteins or stereoselective ketoreductase enzymes. The latter strains gave high selectivities for specific immobilization onto complementary surfaces and also in the whole‐cell stereospecific transformation of a prochiral C_S‐symmetric nitrodiketone.     

Interfacially Bridging Covalent Network Yields Hyperstable and Ultralong Virus‐Based Fibers for Engineering Functional Materials

We present a strategy of interfacially bridging covalent network within tobacco mosaic virus (TMV) virus‐like particles (VLPs). We arranged T103C cysteine to laterally conjugate adjacent subunits. In the axis direction, we set A74C mutation and systematically investigated candidate from E50C to P54C as the other thiol function site, for forming longitudinal disulfide bond chains. Significantly, the T103C‐TMV‐E50C‐A74C shows the highest robustness in assembly capability and structural stability with the largest length, for TMV VLP to date. The fibers with lengths from several to a dozen of micrometers even survive under pH 13. The robust nature of this TMV VLP allows for reducer‐free synthesis of excellent electrocatalysts for application in harshly alkaline hydrogen evolution.     

Study of intact virus‐like particles of human papillomavirus by capillary electrophoresis

Virus‐like particles of human papillomavirus (HPV‐VLP), resulting from the self‐assembly of the capsid proteins (L1 or L1 and L2), have been widely used to study HPV as they are similar to the native virion. Moreover, two prophylactic vaccines, Gardasil^® and Cervarix^®, are based on HPV‐VLP L1. Analytical techniques currently used to characterize HPV‐VLP, such as SDS‐PAGE, Western blot, ELISA, are time‐consuming and semiquantitative. In this study, CE was evaluated for the analysis of intact HPV16‐VLP. The usefulness of capillary inner wall coating as well as various BGEs, pH, and detergent additives were investigated. Reproducible HPV‐VLP analysis in CE was achieved using poly(ethylene oxide)‐coated capillary and a BGE containing high salt concentration and low SDS concentration. The developed method enables HPV‐VLP detection in less than 10 min (migration times RSD: 1.6%). The identity of HPV‐VLP peak was confirmed by comparison with a sample obtained from a wild‐type baculovirus and with VLP‐based vaccine, Gardasil^®, after adjuvant dissolution. Finally, we applied the developed methodology to VLP‐based vaccines, demonstrating that CE could be successfully used for vaccine quality control.     

Genetically Encoded Click Chemistry†

Genetically encoded click chemistry (GECC) refers to a category of peptide/protein reactions that can spontaneously form covalent linkages with high efficiency and selectivity under mild physiological conditions. The emergence of powerful SpyTag/SpyCatcher chemistry, a prototype of GECC, has opened the door to new fields such as in cellulo protein topology engineering and design of synthetic organelles. The continuing developments of GECC will surely provide great opportunities for future materials science and synthetic biology and open up a new avenue to information‐coded chemical reactions.     

Intracellular Assembly of Interacting Enzymes Yields Highly-Active Nanoparticles for Flow Biocatalysis

All-enzyme hydrogel (AEH) particles with a hydrodynamic diameter of up to 120 nm were produced intracellularly with an Escherichia coli-based in vivo system. The inCell-AEH nanoparticles were generated from polycistronic vectors enabling simultaneous expression of two interacting enzymes, the Lactobacillus brevis alcohol dehydrogenase (ADH) and the Bacillus subtilis glucose-1-dehydrogenase (GDH), fused with a SpyCatcher or SpyTag, respectively. Formation of inCell-AEH was analyzed by dynamic light scattering and atomic force microscopy. Using the stereoselective two-step reduction of a prochiral diketone substrate, we show that the inCell-AEH approach can be advantageously used in whole-cell flow biocatalysis, by which flow reactors could be operated for >4 days under constant substrate perfusion. More importantly, the inCell-AEH concept enables the recovery of efficient catalyst materials for stable flow bioreactors in a simple and economical one-step procedure from crude bacterial lysates. We believe that our method will contribute to further optimization of sustainable biocatalytic processes.     

Selective Uptake of Cylindrical Poly(2‐Oxazoline) Brush‐AntiDEC205 Antibody‐OVA Antigen Conjugates into DEC‐Positive Dendritic Cells and Subsequent T‐Cell Activation

To achieve specific cell targeting by various receptors for oligosaccharides or antibodies, a carrier must not be taken up by any of the very many different cells and needs functional groups prone to clean conjugation chemistry to derive well‐defined structures with a high biological specificity. A polymeric nanocarrier is presented that consists of a cylindrical brush polymer with poly‐2‐oxazoline side chains carrying an azide functional group on each of the many side chain ends. After click conjugation of dye and an anti‐DEC205 antibody to the periphery of the cylindrical brush polymer, antibody‐mediated specific binding and uptake into DEC205⁺‐positive mouse bone marrow‐derived dendritic cells (BMDC) was observed, whereas binding and uptake by DEC205^? negative BMDC and non‐DC was essentially absent. Additional conjugation of an antigen peptide yielded a multifunctional polymer structure with a much stronger antigen‐specific T‐cell stimulatory capacity of pretreated BMDC than application of antigen or polymer–antigen conjugate.     

Solid-Phase Synthesis and Purification of Protein–DNA Origami Nanostructures

We present a facile method for the combined synthesis and purification of protein-decorated DNA origami nanostructures (DONs). DONs bearing reductively cleavable biotin groups in addition to ligands for ligation of recombinant proteins are bound to magnetic beads. Protein immobilization is conducted with a large protein excess to achieve high ligation yields. Subsequent to cleavage from the solid support, pure sample solutions are obtained which are suitable for direct AFM analysis of occupation patterns. We demonstrate the method's utility using three different orthogonal ligation methods, the “halo-based oligonucleotide binder” (HOB), a variant of Halo-tag, the “SpyTag/SpyCatcher” (ST/SC) system, and the enzymatic “ybbR tag” coupling. We find surprisingly low efficiency for ST/SC ligation, presumably due to electrostatic repulsion and steric hindrance, whereas the ybbR method, despite its ternary nature, shows good ligation yields. Our method is particularly useful for the development of novel ligation methods and the synthesis of mechanically fragile DONs that present protein patterns for surface-based cell assays.     

Native conjugation between proteins and [60]fullerene derivatives using SpyTag as a reactive handle

Herein,we report the facile conjugation between proteins and water-soluble [60]fullerene derivatives(DC₆₀) under native conditions using SpyTag as a reactive handle.Water-soluble [60] fullerene derivatives were first prepared via sequential Bingel-Hirsch reaction and "clicked" with SpyTag to give DC₆₀-SpyTag for native conjugation with proteins by the highly efficient SpyTag-SpyCatcher chemistry.The bioconjugation was confirmed by MALDI-TOF MS spectra and SDS-PAGE analysis.The TEM and UVvis spectroscopic study further revealed that the DC₆₀ could alter the optical performance and induce aggregation of the target proteins.It thus provides a general and robust method for modifying proteins with C₆₀ derivatives and could potentially be adapted for native conjugation between proteins and other nonbiological motifs as well.     

Structure-activity-based design of a synthetic malaria peptide eliciting sporozoite inhibitory antibodies in a virosomal formulation

The circumsporozoite protein (CSP) of Plasmodium falciparum is a leading candidate antigen for inclusion in a malaria subunit vaccine. We describe here the design of a conformationally constrained synthetic peptide, designated UK-39, which has structural and antigenic similarity to the NPNA-repeat region of native CSP. NMR studies on the antigen support the presence of helical turn-like structures within consecutive NPNA motifs in aqueous solution. Intramuscular delivery of UK-39 to mice and rabbits on the surface of reconstituted influenza virosomes elicited high titers of sporozoite crossreactive antibodies. Influenza virus proteins were crucially important for the immunostimulatory activity of the virosome-based antigen delivery system, as a liposomal formulation of UK-39 was not immunogenic. IgG antibodies elicited by UK-39 inhibited invasion of hepatocytes by P. falciparum sporozoites, but not by antigenically distinct P. yoelii sporozoites. Our approach to optimized virosome-formulated synthetic peptide vaccines should be generally applicable for other infectious and noninfectious diseases.     

Projected Hartree-Fock theory

Projected Hartree-Fock (PHF) theory has a long history in quantum chemistry. PHF is here understood as the variational determination of an N-electron broken symmetry Slater determinant that minimizes the energy of a projected state with the correct quantum numbers. The method was actively pursued for several decades but seems to have been abandoned. We here derive and implement a "variation after projection" PHF theory using techniques different from those previously employed in quantum chemistry. Our PHF methodology has modest mean-field computational cost, yields relatively simple expressions, can be applied to both collinear and non-collinear spin cases, and can be used in conjunction with deliberate symmetry breaking and restoration of other molecular symmetries like complex conjugation and point group. We present several benchmark applications to dissociation curves and singlet-triplet energy splittings, showing that the resulting PHF wavefunctions are of high quality multireference character. We also provide numerical evidence that in the thermodynamic limit, the energy in PHF is not lower than that of broken-symmetry HF, a simple consequence of the lack of size consistency and extensivity of PHF.     

Sugar–Protein Connectivity Impacts on the Immunogenicity of Site‐Selective Salmonella O‐Antigen Glycoconjugate Vaccines

A series of glycoconjugates with defined connectivity were synthesized to investigate the impact of coupling Salmonella typhimurium O‐antigen to different amino acids of CRM₁₉₇ protein carrier. In particular, two novel methods for site‐selective glycan conjugation were developed to obtain conjugates with single attachment site on the protein, based on chemical modification of a disulfide bond and pH‐controlled transglutaminase‐catalyzed modification of lysine, respectively. Importantly, conjugation at the C186‐201 bond resulted in significantly higher anti O‐antigen bactericidal antibody titers than coupling to K37/39, and in comparable titers to conjugates bearing a larger number of saccharides. This study demonstrates that the conjugation site plays a role in determining the immunogenicity in mice and one single attachment point may be sufficient to induce high levels of bactericidal antibodies.