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SpyCatcher

SpyCatcher is a 15 kDa protein engineered from the CnaB2 domain of the fibronectin-binding protein FbaB in the bacterium Streptococcus pyogenes, designed to form a rapid, irreversible isopeptide bond with its complementary 13-amino-acid peptide partner, SpyTag, upon simple mixing without the need for additional catalysts or cofactors.^[1] This covalent linkage occurs spontaneously in high yield (>99%) across a wide range of conditions, including pH 5–8, temperatures from 4–37 °C, and diverse buffers, making it a robust tool for protein ligation in biological systems.^[2] The reaction proceeds via a nucleophilic attack by a lysine residue in SpyCatcher on an aspartate in SpyTag, resulting in a stable β-strand-locked structure that withstands mechanical forces exceeding 1 nN and remains intact even under denaturing conditions like boiling.^[1] Developed in 2012 by splitting the intramolecular isopeptide-forming domain of FbaB, the original SpyTag/SpyCatcher system has undergone iterative improvements to enhance reaction kinetics and solubility.^[1] Subsequent variants, such as SpyTag003 and SpyCatcher003 introduced in 2019,^[3] achieve reaction rates up to 400-fold faster (5.5 × 10⁵ M⁻¹ s⁻¹) while maintaining biocompatibility and enabling reactions in cellular environments, including the E. coli cytosol and on mammalian cell surfaces.^[2] These optimizations address limitations like slower initial kinetics and aggregation in the prototype, positioning the system as a cornerstone of modular protein engineering.^[2] Reversible and split variants have further expanded its utility, allowing controlled assembly and disassembly for dynamic applications.^[2] The SpyCatcher system has found broad applications in biotechnology, including the construction of protein nanomaterials, enzyme immobilization, and vaccine design through irreversible multimerization of antigens into nanoparticles or arrays, as demonstrated in developments for malaria, HIV, and cancer immunotherapies.^[2] As of 2025, the system continues to evolve with applications in programmable cell surface engineering and novel nanoparticle vaccines for tuberculosis.^[4] It facilitates site-specific labeling for live-cell imaging, hydrogel formation for tissue engineering, and retargeting of viral vectors or CAR-T cells by covalently attaching targeting moieties to cell surfaces.^[1]^[2] Additionally, SpyCatcher enables purification strategies like SpyDock for one-step affinity tagging and has been integrated into synthetic biology for creating resilient enzyme cascades and responsive biomaterials.^[2] Its genetic encodability and orthogonality to other ligation chemistries underscore its versatility in advancing protein-based therapeutics and diagnostics.^[2]

Overview and Development

Discovery and Initial Design

The SpyCatcher system was derived from the CnaB2 domain, the second immunoglobulin-like domain in the FbaB fibronectin-binding protein of the Gram-positive bacterium Streptococcus pyogenes. This bacterial adhesin domain naturally forms an internal isopeptide bond between a lysine and an aspartate residue, which contributes to its mechanical stability during host cell invasion.^[1] In a 2012 study by the Howarth laboratory, researchers split the CnaB2 domain to create two complementary components: SpyTag, a 13-amino-acid peptide corresponding to the reactive N-terminal region, and SpyCatcher, a 138-amino-acid (~15 kDa) protein encompassing the remainder of the domain. This design enabled the intermolecular formation of an irreversible isopeptide bond between a lysine on SpyCatcher and the aspartate on SpyTag, replicating the intramolecular linkage of the original domain but in a controlled, user-directed manner.^[1] The initial publication demonstrated that SpyTag and SpyCatcher react rapidly, forming the covalent bond in minutes at physiological conditions (pH 5–8, 4–37°C) without needing exogenous catalysts, enzymes, or specific cofactors. An early proof-of-concept experiment showed efficient covalent linkage upon mixing green fluorescent protein (GFP) fused to SpyTag with maltose-binding protein (MBP) fused to SpyCatcher, yielding nearly complete reaction in high-purity preparations as confirmed by SDS-PAGE.^[1] This genetically encodable tool provided a foundation for protein ligation in biotechnology.^[1]

Variants and Improvements

Following the initial discovery of the SpyTag/SpyCatcher system, iterative engineering efforts from 2017 onward focused on accelerating reaction rates, enhancing specificity, and improving protein stability to broaden utility in protein ligation. In 2017, phage display selection yielded SpyTag002 and SpyCatcher002, which exhibited a 12-fold faster second-order rate constant for isopeptide bond formation compared to the original pair, primarily through targeted mutations that reduced SpyCatcher's self-reactivity and optimized the peptide-protein interface.^[5] These variants maintained high specificity while enabling applications such as live-cell imaging of bacterial membrane dynamics.^[6] Building on this, the 2019 development of SpyTag003 and SpyCatcher003 achieved a 400-fold acceleration over the original system's rate constant, approaching diffusion-limited kinetics and effectively creating "infinite affinity" through rational redesign of the non-covalent interface and catalytic residues.^[3] This third-generation pair demonstrated backward compatibility, reacting efficiently with earlier SpyTags while minimizing off-target interactions, thus facilitating modular protein assembly without redesigning existing constructs.^[3] In the 2020s, SpyCatcher2.1 emerged as a stabilized variant of SpyCatcher002, incorporating mutations like E77A to abolish intrinsic reactivity while preserving tight binding to SpyTag, which improved solubility, thermal stability, and performance in affinity purification systems such as Spy&Go.^[7] This variant's enhanced biophysical properties reduced aggregation and supported scalable expression in E. coli.^[7] For orthogonal reactivity, additional mutations were introduced: I3W in SpyTag (termed AW) paired with F77V/F94A in SpyCatcher (BVA), enabling selective ligation between mutant pairs with minimal cross-reactivity to wild-type components.^[8]^[9] As of 2025, reviews continue to emphasize the system's strengths while noting persistent challenges such as industrial scalability and immunogenicity that may guide future optimizations.^[10]

Reaction Mechanism

Isopeptide Bond Formation

The SpyTag/SpyCatcher system enables rapid formation of a covalent isopeptide bond between the 13-residue SpyTag peptide and the 138-residue SpyCatcher protein, derived from splitting the CnaB2 domain of the Streptococcus pyogenes adhesin FbaB. This bond links the side chain of a lysine residue in SpyCatcher to the side chain of an aspartate residue in SpyTag, mimicking the intramolecular isopeptide linkages that stabilize bacterial pili.^[1] The reaction begins with non-covalent docking of SpyTag into SpyCatcher's β-sandwich fold, where SpyTag's C-terminal β-strand aligns parallel to SpyCatcher's β-strand 1 via hydrogen bonds, positioning the reactive residues in proximity. This structural mimicry of the intact CnaB2 domain ensures specificity and stability prior to covalent linkage. The catalytic glutamate residue (Glu77 in SpyCatcher) deprotonates the ε-amine of the lysine (Lys31 in SpyCatcher), enabling its nucleophilic attack on the carboxylate of the aspartate (Asp7 in SpyTag) to form a tetrahedral intermediate. This intermediate collapses, expelling water to yield the irreversible isopeptide bond.^[1]^[11] The process occurs spontaneously under mild conditions, including pH 5–8 and temperatures from 4°C to 37°C, with optimal performance near physiological pH 7–8 and room temperature; no enzymes, metals, or other cofactors are required. Crystal structures of the ligated complex, such as PDB entry 4MLI (resolved at 2.1 Å), confirm the β-sheet docking and the geometry of the isopeptide bond, with the catalytic glutamate hydrogen-bonded to the aspartate carbonyl in the transition state.^[1]^[11]

Kinetics and Engineering Enhancements

The SpyTag/SpyCatcher system exhibits a second-order rate constant of $1.4 \times 10^{3} \ \mathrm{M^{-1} s^{-1}} for isopeptide bond formation at 25 °C and pH 7, enabling efficient protein ligation under physiological conditions.^[12] This rate supports applications such as rapid vaccine antigen display, where timely covalent assembly is critical for immunogenicity.^[1] Engineering efforts have significantly accelerated the reaction kinetics through iterative optimization of the peptide and protein partners. The SpyTag002/SpyCatcher002 pair achieves a rate constant of $2.0 \pm 0.2 \times 10^{4} \ \mathrm{M^{-1} s^{-1}}, representing a 12-fold improvement over the original system by enhancing the initial non-covalent association.^[6] Further refinements yielded the SpyTag003/SpyCatcher003 variant, with a rate constant of $5.5 \pm 0.6 \times 10^{5} \ \mathrm{M^{-1} s^{-1}}, approximately 400-fold faster than the progenitor pair, approaching the diffusion-limited rate for biomolecular interactions.^[3] These enhancements stem from targeted mutations that stabilize the reactive intermediate, reducing the energy barrier for nucleophilic attack.^[2] Specificity in the SpyCatcher system is bolstered by minimal cross-reactivity among engineered variants, particularly in orthogonal tag/catcher pairs such as SpyTag003/SpyCatcher003 alongside SnoopTag/SnoopCatcher.^[9] Mutant pairs exhibit encrypted reactivity profiles, where substitutions in the reactive glutamate or lysine residues prevent unintended ligation while preserving efficiency within matched components.^[8] For non-covalent intermediates, dissociation constants inform binding affinity; for instance, the SpyTag/SpyDock complex has a K_d of 750 nM, facilitating reversible capture prior to covalent locking.^[7] A 2025 development, the SMART-SpyCatcher system, enables programmable protein ligation on cell surfaces using blue light-activated photocatalytic labeling with SpyTag conjugates, achieving up to 2.5-fold enhancements in recruitment efficiency while preserving orthogonality.^[4]

Core Applications

Vaccine Antigen Display

SpyCatcher enables modular antigen presentation on virus-like particles (VLPs) by fusing the SpyTag peptide to target antigens and incorporating SpyCatcher into the VLP scaffold, allowing spontaneous and irreversible isopeptide bond formation upon simple mixing. This plug-and-display approach facilitates rapid decoration of VLPs, such as the bacteriophage-derived AP205 particles or the engineered Mi3 nanoscaffolds, with antigens at high densities without the need for chemical cross-linkers or genetic refusion. For instance, SpyCatcher fused to the AP205 coat protein forms stable 20 nm VLPs in E. coli, enabling efficient conjugation of diverse antigens like malarial proteins or viral epitopes. Similarly, SpyCatcher003-mi3 VLPs, derived from thermophilic bacterial aldolases, support the display of 38-56 antigens per particle, enhancing multivalent presentation for immune targeting.^[13] In vaccine development, this system has been pivotal for COVID-19 prototypes, where the SARS-CoV-2 spike receptor-binding domain (RBD) fused to SpyTag is covalently linked to SpyCatcher-mi3 VLPs, creating a nanoparticle vaccine candidate. Reported in 2021, this design assembles RBD multimers on the VLP surface, mimicking viral geometry to boost immunogenicity while avoiding full spike protein complexities. The resulting conjugates elicit potent humoral responses, with preclinical studies demonstrating superior neutralization compared to soluble RBD antigens.^[14] Key advantages include site-specific conjugation that preserves antigen structure and orientation, enabling high-density display (often exceeding 90% efficiency) for amplified B-cell activation. The covalent bonds also confer storage stability, with Mi3-RBD VLPs retaining activity post-lyophilization and elevated temperatures, mitigating cold-chain requirements for global distribution. Preclinical evaluations in 2021 confirmed enhanced outcomes, such as neutralizing antibody titers (ND50 up to 2095 in mice and 11,000 in pigs) surpassing convalescent human levels after low-dose prime-boost regimens, alongside robust ELISA-detected anti-RBD responses.^[14] These results underscore SpyCatcher's role in accelerating VLP-based vaccine platforms for rapid pandemic response. As of 2025, extensions include mosaic nanoparticles displaying multiple sarbecovirus RBDs on SpyCatcher-mi3, inducing cross-reactive neutralizing antibodies against diverse variants.^[15]

Enzyme Stabilization and Cyclization

The SpyTag/SpyCatcher system enables intramolecular ligation for enzyme cyclization by genetically fusing SpyTag to the N-terminus and SpyCatcher to the C-terminus of the target enzyme, resulting in spontaneous formation of a covalent isopeptide bond that creates a closed-loop structure known as a SpyRing.^[16] This approach mimics the structural rigidity of naturally occurring cyclic peptides, which are prevalent in antimicrobial and bioactive compounds, by constraining the protein backbone and limiting conformational flexibility.^[17] The cyclization occurs efficiently in vivo or in vitro under mild conditions, typically achieving 70-90% yield without requiring additional catalysts or harsh reagents.^[18] The primary benefit of SpyRing cyclization lies in its enhancement of enzyme stability against thermal and proteolytic stress, primarily through reduction in entropy loss during unfolding and improved refolding kinetics after denaturation. By forming a covalent backbone link, the system minimizes the entropic penalty associated with linear protein unfolding, allowing the enzyme to more readily regain its native conformation upon cooling or stress removal.^[17] This mechanism does not significantly alter the unfolding temperature (T_m) but dramatically increases resistance to aggregation and proteolysis, as demonstrated in differential scanning calorimetry studies where cyclized variants show refolding signals absent in linear counterparts.^[16] Proteolytic stability can be bolstered by up to 10-fold in some cases, though thermal resilience improvements are more pronounced.^[19] A seminal example is the cyclization of mesophilic β-lactamase (TEM-1), where the SpyRing construct remained soluble and retained nearly full catalytic activity after incubation at 100°C, representing a greater than 60°C increase in aggregation resistance compared to the wild-type enzyme, which aggregates at 37°C.^[16] Similarly, cyclization of phytase, an industrially relevant enzyme for animal feed processing, preserved solubility and activity following heating to 100°C, with over 80% activity retention after 90°C exposure, outperforming alternative cyclization methods like PilinRing or SnoopRing in resilience.^[17] These enhancements have been extended to other enzymes, such as lichenase from Bacillus subtilis, where SpyRing formation increased the optimum temperature by 5°C (from 55°C to 60°C), with enhanced thermal stability including retention of ~80% activity after 10 min at 100°C compared to near-total loss for the linear form, underscoring the method's broad applicability for stabilizing biocatalysts in harsh industrial conditions.^[19]

Hydrogel Formation and Biomaterials

SpyCatcher-mediated hydrogel formation relies on the covalent isopeptide bond between multivalent SpyCatcher fusions and SpyTag-bearing peptides or proteins, enabling the creation of branched, crosslinked protein networks under physiological conditions. For instance, tandem modular proteins such as (GB1-SpyCatcher)₃ and (GB1-SpyTag)₄ undergo rapid gelation in less than 5 minutes at room temperature when mixed at concentrations of 5-15 wt%, forming stable viscoelastic hydrogels suitable for biomedical use.^[20] These networks mimic extracellular matrices through genetically encoded elastin-like or globular domains, providing a modular platform for incorporating bioactive motifs without chemical crosslinkers.^[21] The mechanical properties of these SpyCatcher-crosslinked hydrogels are tunable, with shear storage moduli (G') ranging from approximately 0.06 kPa at lower concentrations to 0.6 kPa at higher ones, and potential extension to 1-10 kPa through optimized multivalency and protein density.^[20] Biocompatibility is a key attribute, as demonstrated by over 90% cell viability in encapsulated human lung fibroblasts over 96 hours and minimal erosion rates of 5-25% over extended periods in aqueous environments.^[20]^[21] Swelling ratios up to 3,000% in water further support their use in hydrated, tissue-like applications.^[21] In applications for 3D cell culture, these hydrogels facilitate encapsulation of fibroblasts and stem cells, maintaining pluripotency and promoting colony formation when bioactive factors like leukemia inhibitory factor (LIF) are integrated, yielding up to 41 colonies per microliter compared to 6 without.^[21] Photo-responsive variants incorporate light-sensitive domains such as the CarH_C photoreceptor fused to SpyTag/SpyCatcher constructs, allowing reversible gel-sol transitions upon white light exposure (30-90 klux), with G' around 0.66 kPa and controlled release of encapsulated proteins or cells (e.g., 45% mCherry release in 10 minutes).^[22] Studies from the 2010s highlighted enzyme-loaded gels for biocatalysis, where SpyTag/SpyCatcher enabled self-assembling networks of multiple enzymes, such as phenolic acid decarboxylases, supporting continuous flow reactions with high stability and activity retention.^[23] More recent 2025 advances involve modifying supramolecular polymers like ureidopyrimidinone (UPy) fibers with SpyCatcher-fused functional proteins, achieving 100% conjugation efficiency and tunable viscoelasticity for enhanced bioactive hybrid materials in tissue engineering.^[24]

Advanced and Emerging Uses

Affinity Purification Systems

The Spy&Go system represents an affinity purification method that leverages engineered variants of SpyCatcher to enable reversible capture of proteins fused to SpyTag peptides, facilitating efficient isolation without the need for harsh denaturing conditions. This approach, developed in 2019, utilizes SpyDock, a pseudo-SpyCatcher derived from SpyCatcher2.1, which is immobilized on resin to bind target proteins non-covalently while preventing irreversible isopeptide bond formation. SpyDock incorporates specific mutations—E77A to abolish the catalytic residue responsible for ligation and S49C to introduce a cysteine for site-specific attachment to solid supports such as SulfoLink or epoxy resins—allowing for stable immobilization and repeated use of the resin.^[7] SpyDock exhibits high-affinity binding to SpyTag fusions, with a dissociation constant (Kd) of 750 ± 50 nM for the original SpyTag and an improved 73 ± 13 nM for the SpyTag002 variant, which benefits from enhanced electrostatic interactions. These affinities enable sensitive capture of low-abundance proteins from complex mixtures like E. coli lysates, with binding occurring rapidly at neutral pH and physiological salt concentrations. The SpyCatcher2.1 backbone of SpyDock further includes mutations A89P, Q97D, and K108E to optimize the binding interface, reducing flexibility and improving specificity for the SpyTag peptide.^[7] In the purification protocol, cell lysates containing SpyTag-fused proteins are incubated with SpyDock-resin, followed by washing with 500 mM imidazole to remove unbound material, and elution using 2.5 M imidazole at neutral pH, which disrupts the non-covalent interaction without denaturing the target protein. The resin can then be regenerated by washing with buffer, maintaining functionality for multiple cycles without the need for denaturation or harsh chemicals, thus extending its reusability. This process achieves yields comparable to traditional methods while yielding proteins with authentic termini if combined with self-cleaving tags.^[7] Compared to nickel-nitrilotriacetic acid (Ni-NTA) purification of His-tagged proteins, the Spy&Go system offers advantages including covalent capture options via reactive SpyCatcher if desired, lower non-specific binding (resulting in >98% purity versus ~66% for Ni-NTA), and versatility in tag placement at N- or C-termini or internally. It also avoids metal ion contamination, making it suitable for downstream applications sensitive to nickel, such as structural biology or therapeutics.^[7]

Protein Ubiquitination and Delivery

In 2025, researchers developed a method utilizing the SpyTag/SpyCatcher system to achieve site-specific ubiquitination of target proteins, enabling detailed studies of proteasomal degradation. This approach combines chemical synthesis of ubiquitin chains bearing SpyTag with recombinant expression of SpyCatcher-fused proteins, such as enhanced green fluorescent protein (eGFP), to form covalent isopeptide bonds that mimic Lys48-linked polyubiquitin chains of 1 to 4 units. The technique addresses challenges in preparing homogeneous ubiquitinated substrates by integrating solid-phase peptide synthesis (SPPS) and native chemical ligation (NCL) for ubiquitin variants with expressed protein components, yielding high-purity conjugates suitable for in vitro assays.^[25] SpyTag/SpyCatcher has also facilitated cytosolic delivery of therapeutic proteins by ligating cargo to toxin-based carriers. For instance, in a 2025 study, SpyCatcher003 was fused to the translocation domain of AIP56 (a bacterial toxin from Aeromonas hydrophila), enabling rapid covalent attachment of SpyTag-bearing β-lactamase as a model cargo; this chimera successfully delivered the enzyme into the cytosol of J774.A1 macrophages at nanomolar concentrations, confirming endosomal escape and enzymatic activity. Such toxin-mediated delivery leverages the Spy system's bioorthogonal reactivity to couple proteins to carriers that exploit natural cellular uptake pathways, often in combination with sortase A for sequential or proximity-enhanced ligations that improve yield and specificity in complex environments.^[26] These applications extend to proteomics by enabling chemical ubiquitination alongside expression systems for investigating protein stability and turnover, as demonstrated by the degradation of SpyCatcher-ubiquitin conjugates by the 20S proteasome, where efficiency increased with chain length (e.g., 65% degradation of tetra-ubiquitinated eGFP after 8 hours). In contrast, the 26S proteasome primarily trims ubiquitin chains without full substrate degradation, highlighting the system's utility in dissecting proteasomal mechanisms. Outcomes include selective induction of protein turnover in cellular contexts, which advances drug discovery by providing tools to modulate degradation pathways for targeted therapies, such as in cancer or neurodegeneration research.^[25]

Viral Vector Retargeting and Cell Surface Ligation

Viral vector retargeting leverages the SpyTag/SpyCatcher system to modify adeno-associated virus (AAV) and adenoviral vectors post-assembly, enabling precise conjugation of targeting ligands to enhance specificity in gene therapy. In AAV retargeting, SpyTag is genetically inserted into surface-exposed sites on the capsid proteins, such as positions 453 and 587 in AAV2 variable regions IV and VIII, allowing covalent bonding with SpyCatcher-fused targeting molecules like designed ankyrin repeat proteins (DARPins) under physiological conditions.^[27] This modular approach facilitates rapid exchange of ligands, such as those targeting EGFR, EpCAM, or HER2, to redirect AAV transduction to specific cell types, including cancer cell lines like A-431 and SK-OV-3, with transduction efficiencies achieving up to 100% at low multiplicities of infection (MOI 190) and minimal off-target activity below 6.2%.^[27] For adenoviral vectors, post-assembly modifications involve incorporating SpyTag into the fiber protein's HI loop, followed by conjugation of SpyCatcher-nanobody fusions to retarget the vector to desired receptors without altering viral production yields.^[28] This method has been applied to generate bionanoparticles specific to target cells in vitro, improving delivery selectivity and reducing unintended interactions with native receptors like coxsackievirus and adenovirus receptor (CAR).^[28] Such enhancements in viral vectors minimize off-target effects, such as liver tropism in AAV or broad tissue uptake in adenoviruses, thereby increasing therapeutic efficacy and safety in gene delivery applications.^[27]^[28] Cell surface ligation using SpyCatcher enables convergent assembly of proteins on live cells, programming selective targeting through logic-gated mechanisms. The SMART-SpyCatcher platform splits SpyCatcher003 with caged NrdJ-1 inteins, activating only upon recognition of dual antigens (e.g., HER2 and EGFR on K562 cells), which triggers covalent ligation of SpyTag-labeled effectors like fluorescent dyes or enzymes.^[4] This AND-gated system achieves high selectivity in mixed cell populations, with dose-dependent responses from 1 µM to 1 nM and up to 92% targeted cell depletion in multi-dose regimens, supporting applications in proximity labeling and proteomics.^[4] In tissue engineering, SpyCatcher-based programmable actuators facilitate dynamic protein assembly on cell surfaces, mimicking natural signaling to guide tissue morphogenesis and repair.^[4] By integrating diverse targeting modalities—such as antibody fragments, peptide mimetics, or small molecules—the system ensures conditional activation, enhancing specificity and reducing non-specific binding in complex extracellular environments.^[4] Overall, these advances in viral retargeting and cell surface ligation via SpyCatcher provide robust tools for engineering therapeutic interfaces with improved precision and minimized immunogenicity in gene therapy and regenerative medicine.^[27]^[4]

Orthogonal Tag/Catcher Pairs

Orthogonal tag/catcher pairs enable the independent and selective assembly of multiple protein components, allowing complex multi-ligation reactions without cross-reactivity. These systems, derived from bacterial pilin proteins, form isopeptide bonds via mechanisms analogous to SpyTag/SpyCatcher but with distinct reactive residues and structures, facilitating applications in protein engineering where simultaneous orthogonal couplings are required.^[29] The SnoopTag/SnoopCatcher pair, split from the D4 domain of the RrgA adhesin in Streptococcus pneumoniae, reacts orthogonally to SpyTag/SpyCatcher, showing no detectable cross-reaction even after prolonged incubation at equimolar concentrations. SnoopTag is a 12-residue peptide that forms an isopeptide bond with SnoopCatcher (15 kDa protein partner) through a lysine-asparagine reaction, achieving near-quantitative yields under physiological conditions with a second-order rate constant of approximately 1.3 × 10³ M⁻¹ s⁻¹. This orthogonality stems from sequence divergence in the reactive loops, enabling dual or multi-component assemblies.^[29]^[29] Isopeptag/Pilin-C represents an earlier orthogonal system, derived from the C-terminal pilin domain (Spy0128) of Streptococcus pyogenes, predating SpyTag/SpyCatcher and offering a similar isopeptide-forming mechanism but with improved reactivity over the unsplit pilin domains. Isopeptag (16 residues) reacts with Pilin-C (~20 kDa) via an asparagine-lysine linkage, proceeding robustly across pH 5–8 and temperatures 4–37 °C, though at a slower rate than later pairs (second-order rate constant ~1–10 M⁻¹ s⁻¹), making it suitable for applications tolerant of longer reaction times. Its orthogonality to subsequent systems like Spy and Snoop arises from unique residue positioning, allowing independent use in hybrid constructs.^[30] DogTag/DogCatcher provides a compact orthogonal alternative, engineered from the RrgA D4 domain of S. pneumoniae with a β-hairpin structure in the DogTag peptide (23 residues) to enhance reactivity when inserted into protein loops. Paired with DogCatcher (~14 kDa), it forms an isopeptide bond (lysine-aspartate) orthogonal to both SpyTag/SpyCatcher and SnoopTag/SnoopCatcher families, with no cross-reactivity observed over 24 hours. The system exhibits a second-order rate constant of 760 ± 20 M⁻¹ s⁻¹ under standard conditions, outperforming SpyTag003/SpyCatcher003 in loop contexts due to the hairpin's flexibility.^[31]^[31]^[31] These orthogonal pairs have been applied in dual-ligation strategies for building complex protein architectures, such as polyproteams and modular cascades, in studies from the 2010s to 2020s; for instance, combining Spy and Snoop systems enabled the covalent assembly of enzyme chains for metabolic pathway engineering and vaccine multimers.^[29]^[32]

Alternative Bond-Forming Variants

The SdyTag/SdyCatcher system, derived from the CnaB domain of Streptococcus dysgalactiae fibronectin-binding protein, represents a variant that maintains isopeptide bond formation but introduces altered specificity for controlled protein assembly.^[33] SdyTag exhibits 75-fold higher specificity for SdyCatcher compared to SpyCatcher, while showing minimal reactivity with the latter, enabling kinetic control in directed covalent interactions.^[33] This cross-reactivity with the Spy system allows for tunable preferences, such as SdyCatcher's efficient reaction with SdyTag but limited engagement with SpyTag, facilitating selective ligation in complex mixtures.^[33] In contrast, the Cpe0147 Tag/Catcher pair, engineered from the C1 domain of Clostridium perfringens adhesin Cpe0147, forms a Thr-Gln ester bond rather than an isopeptide linkage, providing a hydrolyzable alternative for reversible protein conjugation.^[34] This ester bond enables spontaneous assembly of protein nanomaterials under mild conditions, with hydrolysis allowing disassembly, unlike the permanent nature of isopeptide bonds in traditional systems.^[34] Developed in the 2010s, this variant expands SpyCatcher-inspired technologies to applications requiring transient linkages, such as dynamic biomaterial scaffolds.^[34] Mutant variants of the SpyTag/SpyCatcher pair, such as SpyTag I3W (denoted AW) paired with SpyCatcher F77V/F94A (BVA), offer tuned reactivity for partial orthogonality while preserving isopeptide bond formation.^[9] The I3W mutation in SpyTag reduces yield with wild-type SpyCatcher to approximately 39% under standard conditions, but pairing with BVA restores reactivity to about 60%, enabling selective functionalization with minimal cross-talk.^[9] These double mutations in SpyCatcher (F77V and F94A) maintain full reactivity with wild-type SpyTag while favoring the AW variant, supporting applications in multiplexed protein engineering.^[9] By 2025, SpyTag/SpyCatcher systems have been adapted for self-assembling peptides in food applications, particularly for creating edible materials with enhanced stability and functionality.^[35] These peptides enable covalent immobilization of enzymes, such as trehalose synthase, retaining over 85% activity at elevated temperatures for scalable production of food-grade additives like trehalose.^[35] In antimicrobial packaging and preservation, the system's orthogonality supports high-sensitivity detection of contaminants, such as aflatoxin B1 with 7.3-fold improved limits, promoting safer edible structures.^[35]

References

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Jan 19, 2016 · To enable synthesis of polyproteams, here we first developed a covalent peptide/protein pair (SnoopTag/SnoopCatcher) orthogonal to SpyTag/ ...
[27]
Insider information on successful covalent protein coupling with help ...
The SpyTag/SpyCatcher system uses a peptide SpyTag that irreversibly reacts with SpyCatcher on another protein, forming a spontaneous isopeptide bond.
[28]
https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2022.1039324/full
[29]
SnoopLigase peptide-peptide conjugation enables modular vaccine ...
Mar 15, 2019 · IMX was fused at the N-terminus to SpyCatcher and at the C-terminus to SnoopCatcher, allowing oligomerization of both SpyTag-fused antigen and ...
[30]
Kinetic Controlled Tag-Catcher Interactions for Directed Covalent ...
Oct 26, 2016 · SdyTag also has a 75-fold specificity for SdyCatcher versus SpyCatcher while SpyTag has minimal preference for SpyCatcher and SdyCatcher. Our ...
[31]
Harnessing ester bond chemistry for protein ligation
**Summary:**
[32]
Research Progress Based on SpyTag/SpyCatcher Self‐Assembling ...
Sep 14, 2025 · The SpyTag/SpyCatcher system has demonstrated unique application potential in the food industry due to its efficient covalent combination, mild ...<|control11|><|separator|>