Molecular Recognition Research Articles

Unraveling the impact of SARS-CoV-2 mutations on immunity: insights from innate immune recognition to antibody and T cell responses

Throughout the COVID-19 pandemic, the emergence of new viral variants has challenged public health efforts, often evading antibody responses generated by infections and vaccinations. This immune escape has led to waves of breakthrough infections, raising questions about the efficacy and durability of immune protection. Here we focus on the impact of SARS-CoV-2 Delta and Omicron spike mutations on ACE-2 receptor binding, protein stability, and immune response evasion. Delta and Omicron variants had 3–5 times higher binding affinities to ACE-2 than the ancestral strain (KDwt = 23.4 nM, KDDelta = 8.08 nM, KDBA.1 = 4.77 nM, KDBA.2 = 4.47 nM). The pattern recognition molecule mannose-binding lectin (MBL) has been shown to recognize the spike protein. Here we found that MBL binding remained largely unchanged across the variants, even after introducing mutations at single glycan sites. Although MBL binding decreased post-vaccination, it increased by 2.6-fold upon IgG depletion, suggesting a compensatory or redundant role in immune recognition. Notably, we identified two glycan sites (N717 and N801) as potentially essential for the structural integrity of the spike protein. We also evaluated the antibody and T cell responses. Neutralization by serum immunoglobulins was predominantly mediated by IgG rather than IgA and was markedly impaired against the Delta (5.8-fold decrease) and Omicron variants BA.1 (17.4-fold) and BA.2 (14.2-fold). T cell responses, initially conserved, waned rapidly within 3 months post-Omicron infection. Our data suggests that immune imprinting may have hindered antibody and T cell responses toward the variants. Overall, despite decreased antibody neutralization, MBL recognition and T cell responses were generally unaffected by the variants. These findings extend our understanding of the complex interplay between viral adaptation and immune response, underscoring the importance of considering MBL interactions, immune imprinting, and viral evolution dynamics in developing new vaccine and treatment strategies.

Bioavailability and molecular recognition between secondary metabolites of Euphorbia hirta L. and 5-lipoxygenase using fragment molecular orbital method and pair interaction energy decomposition analysis

Is presented the bioavailability analysis for seven secondary metabolites from Euphorbia hirta L. (Euphorbiaceae). The bioactivity score, the molecular similarity analysis for each secondary metabolite, and the molecular docking 5-LOX/metabolite complex are also presented. For the similarity analysis, it is referenced the structure of allosteric LOX-5 inhibitor 3-acetyl-11-keto-beta-boswellic acid (AKBA). The fragment molecular orbital method (FMO) and pair interaction energy decomposition analysis (PIEDA) were applied to evaluate the interaction energy between secondary metabolites and the 5-LOX active site. Log P values of all the secondary metabolites studied were found to be higher than 5, contrary to what was expected with Lipinski’s rules of five. The reference LOX-5 ligand has a high electrostatic potential similarity with most secondary metabolites studied, with values from 0.667 to 0.730. Both AKBA and metabolites ligands were wedged between the two domains of LOX-5, and the main residues contact were LEU-66, ARG-68, VAL-110, HIS-130, ILE-126, GLN, 129, and LYS-133. The PIEDA analysis showed that stabilization in the 5-LOX active site is mainly dominated by hydrophobic interactions, with values up to -35 Kcal/mol. Due to the low presence of terminal-OH groups, electrostatic origin, and charge transfer interaction energies are also important but have values of less than 20 Kcal/mol.

Host-in-Host Complexation: Activating Classical Hosts through Complete Encapsulation within an M9L6 Coordination Cage.

This study reports a method for enhancing the functions and properties of traditional organic macrocyclic hosts by fully encapsulating them within a large M9L6 cage to form host-in-host complexes. Within the cage host, the macrocyclic organic hosts with electron-rich aromatic rings, such as cyclotriveratrylene and calix[8]arene, adopt specific orientations enhancing their inherent molecular recognition abilities. Due to the high crystallinity of the M9L6 cage, the guest encapsulation behavior of the host-in-host complexes can be observed by X-ray structural analysis.

Broad-Spectrum Detoxification of Snake Venoms With Supramolecular Materials Integrated via Molecular Recognition and Coassembly.

Snakebite is a medical emergency that often leads to high mortality and morbidity in tropical and subtropical regions. The diversity in venom composition between various types of snakes necessitates the use of different specific antivenom treatments, which presents clinical and financial challenges in the management of snakebites. Therefore, developing a broad-spectrum antidote to neutralize complex and diverse snake venoms has assumed critical importance. Herein, a broad-spectrum antidote is developed through molecular recognition and coassembly to neutralize four kinds of snake venom toxins, those are three-finger toxin (3FTx), snake venom metalloproteinase (SVMP), phospholipase A2 (PLA2), and snake venom serine protease (SVSP), which have high abundance and toxicity. The coassembly of sulfonate-modified amphiphilic calixarene (SCA) and amphiphilic cyclodextrin (CD) is employed to neutralize the toxicity of 3FTx, 1,2-dodecanedithiol (DDT) and thioetheramide phosphorylcholine (TEAPC) are introduced through coassembly to neutralize toxicity of SVMP and PLA2, respectively, and the nafamostat (NT), which can be loaded through the host-guest complexation, is employed to neutralize toxicity of SVSP. The broad-spectrum antidote, NT@SCA/CD/DDT/TEAPC, effectively neutralizes key toxins from the most medically important cobra and vipers, significantly improving survival rates of poisoned mice. This study conceptually validated the feasibility of broad-spectrum detoxification and also offers a conveniently integrated supramolecular strategy.

Scalable Photonic Nose Development through Corona Phase Molecular Recognition.

Breath sensors promise early disease diagnosis through noninvasive, rapid analysis, but have struggled to reach clinical use due to challenges in scalability and multivariate data extraction. The current breath sensor design necessitates various channel materials and surface functionalization methods, which delays the process. Additionally, the limited options for channel materials that provide optimum sensitivity and selectivity further restrict the array size to a maximum of only 10 to 20 channels. To address these limitations, we propose a breath sensing array design process based on Corona Phase Molecular Recognition (CoPhMoRe), which enables the creation of an expansive library of nanoparticle interfaces and broad fingerprints for multiple analytes in the breath. Although CoPhMoRe has predominantly been utilized for liquid-phase sensing, its recent application to gas-phase sensing has shown significant potential for breath sensing. We introduce the recent demonstrations in the field and present the concept of a CoPhMoRe-based photonic-nose sensor array, leveraging fluorescent nanomaterials such as near-infrared single-walled carbon nanotubes. Additionally, we identified four critical milestones for translating CoPhMoRe into breath sensors for practical clinical applications.

Genomic Insights into Host Susceptibility to Periprosthetic Joint Infections: A Comprehensive Literature Review

Periprosthetic joint infection (PJI) is a multifactorial disease, and the risk of contracting infection is determined by the complex interplays between environmental and host-related factors. While research has shown that certain individuals may have a genetic predisposition for PJI, the existing literature is scarce, and the heterogeneity in the assessed genes limits its clinical applicability. Our review on genetic susceptibility for PJI has the following two objectives: (1) Explore the potential risk of developing PJI based on specific genetic polymorphisms or allelic variations; and (2) Characterize the regulatory cascades involved in the risk of developing PJI. This review focused on clinical studies investigating the association between genetic mutations or variations with the development of PJI. The genes investigated in these studies included toll-like receptors and humoral pattern recognition molecules, cytokines, chemokines, mannose-binding lectin (MBL), bone metabolism molecules, and human leukocyte antigen. Among these genes, polymorphisms in IL-1, MBL, vitamin D receptors, HLA-C, and HLA-DQ might have a relevant impact on the development of PJI. The literature surrounding this topic is limited, but emerging transcriptomic and genome-wide association studies hold promise for identifying at-risk genes. This advancement could pave the way for incorporating genetic testing into preoperative risk stratification, enhancing personalized patient care.

Biomimetic Cell Membrane Layers for the Detection of Insulin and Glucagon.

The growing need for reliable and rapid insulin testing to enhance glycemic management has spurred intensive exploration of new insulin-binding bioreceptors and innovative biosensing platforms for detecting this hormone, along with glucagon, in biological samples. Here, by leveraging the native protein receptors on the HepG2 cell membrane, we construct a simple and chemical-free biomimetic molecular recognition layer for the detection of insulin and glucagon. Unlike traditional affinity sensors, which require lengthy surface modifications on the electrochemical transducers and use of two different capture antibodies to recognize each analyte, this new biomimetic sensing strategy employs a simple drop-casting of a natural cell membrane recognition layer onto the electrochemical transducer. This approach allows for the concurrent capture and detection of both insulin and glucagon. We investigate the presence of insulin and glucagon receptors on the HepG2 cell membrane and demonstrate its multiplexing bioelectronic sensing capabilities through the binding of the captured insulin and glucagon to enzyme-tagged signaling antibodies. This new molecular recognition layer offers highly sensitive simultaneous detection of insulin and glucagon under decentralized conditions, holding considerable promise for the management of diabetes and the development of diverse biomimetic diagnostic platforms.

Investigating Interaction Dynamics of an Enantioselective Peptide‐Catalyzed Acylation Reaction

Modern nuclear magnetic resonance (NMR) methods like carbon relaxation dispersion in the rotating frame (13C‐R1ρ) and proton chemical exchange saturation transfer (1H‐CEST) are key methods to investigate molecular recognition in biomacromolecules and to detect molecular motions on the µs to s timescale, revealing transient conformational states. Changes in kinetics can be linked to binding, folding, or catalytic events. Here, we investigated whether these methods allow detection of changes in the dynamics of a small, highly selective peptide catalyst during recognition of its enantiomeric substrates. The flexible tetrapeptide Boc‐l‐(π‐Me)‐His‐AGly‐l‐Cha‐l‐Phe‐OMe, used for the monoacetylation of cycloalkane‐diols, is probed at natural abundance using 13C‐R1ρ and 1H‐CEST. Indeed, we detected differences in dynamics of the peptide upon interaction with the diol. Importantly, these differ depending on the enantiomer of the substrate used. These enantiospecific influences of the substrates on the dynamics of the peptide are rationalized using computational techniques. We find that even though one enantiomer reacts faster, as confirmed by reaction monitoring, the other is more tightly bound in DCM (as confirmed by 1H‐saturation transfer difference (STD) measurements). These findings provide insights into the recognition of the substrates and explain the selectivity differences observed between the solvents toluene and DCM.

Sequentially amplified integration of catalytic DNA circuits for high-performance intracellular imaging of miRNA and interpretation of mRNA-miRNA signalling pathway

The cascaded catalytic circuits are viable tools for improving the signal gain of biosensors, yet their sensing performance is still limited by the signal leakage from complex biological environment and unsatisfying reaction efficiency from inter-reactants steric hindrance. Herein, we proposed a catalytically localized DNA (CLD) circuit for the accurate and high-efficiency imaging of microRNA (miRNA) in living cells by virtue of the sequentially and successively amplified integration of catalytic DNA circuits. The compact CLD circuit was constructed by integrating two elemental catalytic circuits, cell-responsive EDR module and analyte-sensing CHA module, where CHA module was initially caged in EDR module for eliminating the unwanted off-site and off-target signal leakage. Only by cell-specific messenger RNA (mRNA)-activated EDR operation then the elemental CHA circuit could be successively connected to facilitate the highly efficient intramolecular reaction with low steric hindrance, thus leading to accelerated reaction efficiency for miRNA analyte. The multiple molecular recognition and the spatial self-confinement of the smart CLD circuit enable the accurate and high-efficiency imaging of intracellular miRNA. The interaction network of mRNA and miRNA was then investigated in situ through our CLD circuit, which provides a powerful tool for discovering the underlying signal pathways between these different RNAs in living cells.

Entropy Driven Binding of 2-(4-Aminophenyl)benzothiazole with DNA: An Experimental and Theoretical Insights

Molecular recognition driven by molecular interactions is an intricate part of drug discovery and targeted drug delivery systems due to the dependence of thetherapeutic properties of drugs on interaction with desired target biomolecules as receptors. 2-(4-Aminophenyl) benzothiazole (APB), a heterocyclic molecule containing a benzothiazole nucleus, is known to induce apoptosis besides inhibiting cancer cell development and has been found effective against different microorganisms. This study highlights the spectroscopic and theoretical investigation of binding interactions of APB and ct-DNA. The UV-vis experiments indicate a binding constant of 9.73 ± 0.4 × 105 M-1. The measured binding constants of 1.0 ± 0.2 × 105, 2.4 ± 0.3 × 105 and 3.5 ± 0.3 × 105 at 298, 303 and 308 K, respectively, from fluorescence experiments indicated a dynamic quenching type. The binding was driven by hydrophobic forces with positive ΔHº (64.8467 ± 2 KJ mol–1) and ΔSº (317.12 ± 2 J mol–1 K–1) values besides spontaneity of the process with negative ΔGº values. The binding of APB molecule in the minor groove of ct-DNA was demonstrated by DNA melting tests, viscosity measurements and site marker displacement using ethidium bromide and Hoechst. Additional studies conducted by KI provided support for minor groove binding and NaCl has no impact on the binding electrostatic interactions, while the CD investigations showed no DNA structural alterations. Molecular docking studies also confirmed the experimental findings placing APB in the ct-DNA minor groove.

Coordination-Based Site-Specific Labeling Strategy for Electrogenerated Chemiluminescence Biosensing of Matrix Metalloproteinase 2.

Matrix metalloproteinase 2 (MMP-2) is an important biomarker for some diseases. Herein, one first-case coordination-based site-specific labeling strategy is proposed for electrogenerated chemiluminescence (ECL) biosensing of MMP-2 by employing an iridium(III) solvent complex as a signal reagent and a histidine (His)-containing peptide as a molecular recognition substrate. One ECL probe was prepared via coordination labeling of the His-containing peptide with one iridium(III) solvent complex ([(3-(2-pyridyl)benzoic acid)2Ir(DMSO)Cl], Ir1-DMSO). High ECL efficiency and good cleavage ability by MMP-2 were obtained for the ECL probe. By combining the high sensitivity of the ECL method, the good specificity of the peptide, and the simpleness of the magnetic bead-based assay, one "cleavage-magnetic enrichment type" ECL biosensing method was developed to detect MMP-2. MMP-2 can be sensitively detected in the linear range of 1.0-10 ng/mL with a limit of quantification of 1.0 ng/mL and a limit of detection of 0.3 ng/mL. Moreover, the ECL biosensing method was successfully applied for the determination of MMP-2 in serum samples with recoveries from 98.0% ± 8.0% to 108.0% ± 6.0%. Further, high affinity (Kd = 0.11 nM) was obtained for the Ir1-DMSO-labeled His-containing peptide and MMP-2. This work may pave the way for the labeling of His-containing biomolecules with an iridium(III) solvent complex and provides a promising method in point-of-care testing of MMP-2.

Circular Engineered Sortase for Interrogating Histone H3 in Chromatin.

Reversible modification of the histone H3 N-terminal tail is critical in regulating the chromatin structure, gene expression, and cell states, while its dysregulation contributes to disease pathogenesis. Understanding the crosstalk between H3 tail modifications in nucleosomes constitutes a central challenge in epigenetics. Here, we describe an engineered sortase transpeptidase, cW11, that displays highly favorable properties for introducing scarless H3 tails onto nucleosomes. This approach significantly accelerates the production of both symmetrically and asymmetrically modified nucleosomes. We demonstrate the utility of asymmetrically modified nucleosomes produced in this way in dissecting the impact of multiple modifications on eraser enzyme processing and molecular recognition by a reader protein. Moreover, we show that cW11 sortase is very effective at cutting and tagging histone H3 tails from endogenous histones, facilitating multiplex "cut-and-paste" middle-down proteomics with tandem mass tags. This cut-and-paste proteomics approach permits the quantitative analysis of histone H3 modification crosstalk after treatment with different histone deacetylase inhibitors. We propose that these chemoenzymatic tail isolation and modification strategies made possible with cW11 sortase will broadly power epigenetic discovery and therapeutic development.

Beyond DAD: proposing a one-letter code for nucleobase-mediated molecular recognition.

Nucleobase binding is a fundamental molecular recognition event central to modern biological and bioinspired supramolecular research. Underpinning this recognition is a deceptively simple hydrogen-bonding code, primarily based on the canonical nucleobases in DNA and RNA. Inspired by these biotic structures, chemists and biologists have designed abiotic hydrogen-bonding motifs that can interact with, augment, and reshape native molecular recognition, for applications ranging from genetic code expansion and nucleic acid recognition to supramolecular materials utilizing mono- and bifacial nucleobases. However, as the number of nucleobase-inspired motifs expands, the absence of a standard vocabulary to describe hydrogen bond (HB) patterns has led to a haphazard mixture of shorthand descriptors that are confusing and inconsistent. Alternative notations that specify individual HB sites (such as DAD for donor-acceptor-donor) are cumbersome for biological and supramolecular constructs that contain many such patterns. This situation creates a barrier to sharing and interpreting nucleobase-related research across sub-disciplines, hindering collaboration and innovation. In this perspective, we aim to initiate discourse on this issue by considering what would be needed to formulate a concise one-letter code for the HB patterns associated with synthetic nucleobases. We first summarize some of the issues caused by the current absence of a consistent naming scheme. Subsequently, we discuss some key considerations in designing a coherent naming system. Finally, we leverage chemical rationale and pedagogical mnemonic considerations to propose a succinct and intuitive one-letter code for supramolecular two- and three-HB motifs. We hope that this discussion will spark conversations within our interdisciplinary community, thereby facilitating collaboration and easing communication among researchers engaged in synthetic nucleobase design.

Molecular Determinants for Guanine Binding in GTP-Binding Proteins: A Data Mining and Quantum Chemical Study.

GTP-binding proteins are essential molecular switches that regulate a wide range of cellular processes. Their function relies on the specific recognition and binding of guanine within their binding pockets. This study aims to elucidate the molecular determinants underlying this recognition. A large-scale data mining of the Protein Data Bank yielded 298 GTP-binding protein complexes, which provided a structural foundation for a systematic analysis of the intermolecular interactions that are responsible for the molecular recognition of guanine in proteins. It was found that multiple modes of non-bonded interactions including hydrogen bonding, cation-π interactions, and π-π stacking interactions are employed by GTP-binding proteins for binding. Subsequently, the strengths of non-bonded interaction energies between guanine and its surrounding protein residues were quantified by means of the double-hybrid DFT method B2PLYP-D3/cc-pVDZ. Hydrogen bonds, particularly those involving the N2 and O6 atoms of guanine, confer specificity to guanine recognition. Cation-π interactions between the guanine ring and basic residues (Lys and Arg) provide significant electrostatic stabilization. π-π stacking interactions with aromatic residues (Phe, Tyr, and Trp) further contribute to the overall binding affinity. This synergistic interplay of multiple interaction modes enables GTP-binding proteins to achieve high specificity and stability in guanine recognition, ultimately underpinning their crucial roles in cellular signaling and regulation. Notably, the NKXD motif, while historically considered crucial for guanine binding in GTP-binding proteins, is not universally required. Our study revealed significant variability in hydrogen bonding patterns, with many proteins lacking the NKXD motif but still effectively binding guanine through alternative arrangements of interacting residues.

Electroanalytical Quantification of DNA Chirality.

Although chirality is critical for molecular properties and functions, experimental quantification of chirality is lacking. Herein, we performed cyclic voltammetry (CV) under polarized magnetic fields to provide a unified scale to quantify and compare DNA chirality. We observed the largest electron spin polarization in DNA structures with opposite chiral senses, which is consistent with the effect of chiral-induced spin selectivity (CISS). Spin polarization is weaker among DNA topologies of the same chiral arrangement, with DNA triplexes exhibiting the strongest CISS. Within DNA duplexes, spin polarization is further reduced depending on the sequence, with fewer guanine-cytosine (GC) pairs displaying a weaker CISS likely due to localized variations in chirality. Surprisingly, spin polarization is vectorial along the DNA duplex while presenting the smallest variation when the transportation directions of electrons become opposite. The four factors, chiral sense, topology, sequence, and directionality of electron transportation, delineate hierarchical contributions to molecular chirality, with profound implications ranging from spintronics to molecular recognitions.

Template and Solid-State-Assisted Assembly of an M9L6 Expanded Coordination Cage for Medium-Sized Molecule Encapsulation.

The M6L4 cage, self-assembling from six Pd(II) or Pt(II) 90-degree blocks and four triazine-cored triangular ligands, has an effective hydrophobic cavity of about 450 Å3 capable of encapsulating one or more small molecules. Here, from the same components, we successfully constructed an M9L6 cage with an internal volume expanded to 1540 Å3 via the self-assembly of an M8L6 precursor using pillar[5]arene as a template. This cage retains the high molecular recognition ability of the M6L4 cage while recognizing medium-sized guest molecules with molecular weights of up to ∼1600.

A polydopamine coated magnetic spiral switchable composite material for photothermal sterilization and dual-color fluorescence detection of food-borne pathogens

A multifunctional magnetic composite material (MSp@PDA) featuring with helical structure, superparamagnetism, photothermal properties, and fluorescence quenching capability was synthesized through sequential magnetization and in-situ polydopamine coating on the Spirulina surface, then applied for multi-scenario application of pathogens capture, sterilization, and sensitive detection. The pathogens capture and sterilization was investigated by loading bacterial broad-spectrum recognition molecule (MPBA) on MSp@PDA, the capture efficiencies of 91.6 % and 94.2 % were obtained for Escherichia coli and Staphylococcus aureus in 15 minutes, respectively, with complete photothermal sterilization achieved within 4 minutes. The fluorescence real-time detection of E. coli and S. aureus was realized by connecting dual-color fluorescent carbon dots to MSp@PDA through specific aptamers (dCD-apt-MSp@PDA), the corresponding detection limits were 2 and 3 cfu·mL−1, respectively, with linear ranges of 101∼107 cfu·mL−1. The spiked recovery rates of target bacteria in actual samples were 97.4∼101.1 % and 98.2∼101.4 % for E. coli and S. aureus, respectively. The constructed capture, sterilization, and fluorescence detection methods demonstrated promising application value for on-site monitoring of food-borne pathogens in complex matrices.

End Group Effects on Anion Binding in Tetraglycine Peptide: A Computational Study.

The importance of anions in various processes has led to a search for molecules that can effectively recognize and interact with these anions. This study explores how the tetraglycine [(Gly)4] peptide in its zwitterionic, neutral, and terminally capped forms acts as a receptor for H2PO4 - and HSO4 - anions within the framework of supramolecular host-guest chemistry. Using molecular dynamics (MD) simulations, we obtained the conformations of the receptor-anion complexes. Density functional theory (DFT), quantifies the complexes' interaction energies in both gas and solvent phases. Proton transfer within the zwitterionic complex with H2PO4 - anion alters peptide charge distribution, affecting its conformation and binding site arrangement, as analysed by quantum mechanics/molecular mechanics (QM/MM) methods. Symmetry-adapted perturbation theory (SAPT) and noncovalent interactions analysis highlight the role of electrostatic interactions in these receptor-anion complexes. It emphasizes the key interactions such as N-H⋅⋅⋅⋅O and O-H⋅⋅⋅O=C between the peptide backbone and anions and elucidates the molecular recognition mechanism driven by crucial noncovalent interactions. The termination of the peptide's end groups modulates anion binding sites from the backbone to the charged N-terminal, resulting in distinct binding sites. Our findings provide insights for designing peptides tailored to function as anion receptors in diverse supramolecular chemistry applications.

A Ni4O4-cubane-squarate coordination framework for molecular recognition

Molecular recognition is a fundamental function of natural systems that ensures biological activity. This is achieved through the sieving effect, host-guest interactions, or both in biological environments. Recent advancements in multifunctional proteins reveal a new dimension of functional organization that goes beyond single-function molecular recognition, emphasizing the need for artificial multifunctional materials in industrial applications. Herein, we have designed a porous Ni4O4-cubane squarate coordination polymer as an artificial molecular recognition host, drawing inspiration from the structural and functional features of natural enzymes. A comprehensive assessment of the material’s ability to distinguish target species under different operating conditions was carried out. The results confirm its sieving function through hexane isomers separation, host-guest interaction function via xenon/krypton separation, and dual presence of sieving and interaction through carbon dioxide/nitrogen separation. Additionally, the material demonstrates good stability and feasibility for large-scale production, indicating its practical potential. Our findings provide a bio-inspired multifunctional recognition material for chemical separations as proof-of-concept while offering solutions to advance artificial multifunctional materials adaptable to other applications beyond chemical separations.

Diversification of molecular pattern recognition in bacterial NLR-like proteins

Antiviral STANDs (Avs) are bacterial anti-phage proteins evolutionarily related to immune pattern recognition receptors of the NLR family. Type 2 Avs proteins (Avs2) were suggested to recognize the phage large terminase subunit as a signature of phage infection. Here, we show that Avs2 from Klebsiella pneumoniae (KpAvs2) can recognize several different phage proteins as signature for infection. While KpAvs2 recognizes the large terminase subunit of Seuratvirus phages, we find that to protect against Dhillonvirus phages, KpAvs2 recognizes a different phage protein named KpAvs2-stimulating protein 1 (Ksap1). KpAvs2 directly binds Ksap1 to become activated, and phages mutated in Ksap1 escape KpAvs2 defense despite encoding an intact terminase. We further show that KpAvs2 protects against a third group of phages by recognizing another protein, Ksap2. Our results exemplify the evolutionary diversification of molecular pattern recognition in bacterial Avs2, and show that a single pattern recognition receptor evolved to recognize different phage-encoded proteins.