Post-translational Modification Sites Research Articles

Structural impact, ligand–protein interactions, and molecular phenotypic effects of TGF-β1 gene variants: In silico analysis with implications for idiopathic pulmonary fibrosis

BackgroundIdiopathic Pulmonary Fibrosis (IPF) is a chronic interstitial lung disease resulting in progressively deteriorating lung function. Transforming growth factor-β1 (TGF-β1) belongs to the TGF superfamily and exerts a profibrotic role in promoting lung fibrosis by facilitating fibroblast infiltration and activity, extracellular matrix deposition, and inhibition of collagen breakdown, thus promoting tissue remodelling and IPF. Materials and MethodsWe evaluated the link between pathogenic TGF-β1 SNPs and IPF pathogenesis and the structure–activity functional consequences of those SNPs on the TGF-β1 protein. Several computational algorithms were merged to address the functional consequences of TGF-β1 gene mutations to protein stability, putative post-translational modification sites, ligand–protein interactions, and molecular phenotypic effects. These included FATHMM, POLYPHEN2, PROVEAN, and SIFT tools (identifying deleterious nsSNPs in the TGF-β1 gene), along with Pmut, PhD-SNP, SNAP, MutPred and the related TMHMM, MARCOIL, and DisProt algorithms (predicting structural disorders). INPS-MD was also used to evaluate the mutation-induced TGF-β1 protein’s stability and MODPRED for recognition of post-translational TGF-β1 modification. ResultsIn total, 14 major pathogenic variants markedly impact the destabilization of the TGF-β1 protein, with most of these high-risk mutations associated with decreased stability of the TGF-β1 protein as per the I-Mutant, MUpro, and INPS-MD tools. R205W, R185W, R180Q, D86Y, and I300T variants were proposed to participate in the post-translational modifications, thus affecting affect protein–ligand interactions. Furthermore, at-risk genetic variants appear to target conserved regions in the alpha helices, random coils, and extracellular loops, resulting in a varied composition of amino acids, charge, hydrophobicity, and spatial architecture. ConclusionsThis study manuscript comprehensively analyzes gene variants within the TGF-β1 gene, offering novel insights into their structural and functional implications in interacting with target sites. This study is significant for the development of targeted therapeutic strategies and personalized treatment approaches for patients with inflammatory lung diseases such as IPF.

Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput.

Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here we describe the high-throughput, functional assessment of phosphorylation sites through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of PHLPP1, which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.

An Integrated Analytical Approach for Screening Functional Post-Translational Modification Sites in Metabolic Enzymes.

Post-translational modifications (PTMs) are pivotal in the orchestration of diverse physiological and pathological processes. Despite this, the identification of functional PTM sites within the vast amount of data remains challenging. Conventionally, those PTM sites are discerned through labor-intensive and time-consuming experiments. Here, we developed an integrated analytical approach for the identification of functional PTM sites on metabolic enzymes via a screening process. Through gene ontology (GO) analysis, we identified 269 enzymes with lysine 2-hydroxyisobutyrylation (Khib) from our proteomics data set of Escherichia coli. The first round of screening was performed based on the enzyme structures/predicted structures using the TM-score engineer, a tool designed to evaluate the impact of PTM on the protein structure. Subsequently, we examined the influence of Khib on the enzyme-substrate interactions through both static and dynamic analyses, molecular docking, and molecular dynamics simulation. Ultimately, we identified NfsB K181hib and ThiF K83hib as potential functional sites. This work has established a novel analytical approach for the identification of functional protein PTM sites, thereby contributing to the understanding of Khib functions.

Characterization of Phosphorylated Peptides by Electron-Activated and Ultraviolet Dissociation Mass Spectrometry: A Comparative Study with Collision-Induced Dissociation.

Mass-spectrometry-based methods have made significant progress in the characterization of post-translational modifications (PTMs) in peptides and proteins; however, room remains to improve fragmentation methods. Ideal MS/MS methods are expected to simultaneously provide extensive sequence information and localization of PTM sites and retain labile PTM groups. This collection of criteria is difficult to meet, and the various activation methods available today offer different capabilities. In order to examine the specific case of phosphorylation on peptides, we investigate electron transfer dissociation (ETD), electron-activated dissociation (EAD), and 193 nm ultraviolet photodissociation (UVPD) and compare all three methods with classical collision-induced dissociation (CID). EAD and UVPD show extensive backbone fragmentation, comparable in scope to that of CID. These methods provide diverse backbone fragmentation, producing a/x, b/y, and c/z ions with substantial sequence coverages. EAD displays a high retention efficiency of the phosphate modification, attributed to its electron-mediated fragmentation mechanisms, as observed in ETD. UVPD offers reasonable retention efficiency, also allowing localization of the PTM site. EAD experiments were also performed in an LC-MS/MS workflow by analyzing phosphopeptides spiked in human plasma, and spectra allow accurate identification of the modified sites and discrimination of isomers. Based on the overall performance, EAD and 193 nm UVPD offer alternative options to CID and ETD for phosphoproteomics.

Effect of α-tubulin acetylation on the doublet microtubule structure

Acetylation of α-tubulin at the lysine 40 residue (αK40) by αTAT1/MEC-17 acetyltransferase modulates microtubule properties and occurs in most eukaryotic cells. Previous literatures suggest that acetylated microtubules are more stable and damage resistant. αK40 acetylation is the only known microtubule luminal post-translational modification site. The luminal location suggests that the modification tunes the lateral interaction of protofilaments inside the microtubule. In this study, we examined the effect of tubulin acetylation on the doublet microtubule (DMT) in the cilia of Tetrahymena thermophila using a combination of cryo-electron microscopy, molecular dynamics, and mass spectrometry. We found that αK40 acetylation exerts a small-scale effect on the DMT structure and stability by influencing the lateral rotational angle. In addition, comparative mass spectrometry revealed a link between αK40 acetylation and phosphorylation in cilia.

Effect of α-tubulin acetylation on the doublet microtubule structure.

Acetylation of α-tubulin at the lysine 40 residue (αK40) by αTAT1/MEC-17 acetyltransferase modulates microtubule properties and occurs in most eukaryotic cells. Previous literatures suggest that acetylated microtubules are more stable and damage resistant. αK40 acetylation is the only known microtubule luminal post-translational modification site. The luminal location suggests that the modification tunes the lateral interaction of protofilaments inside the microtubule. In this study, we examined the effect of tubulin acetylation on the doublet microtubule (DMT) in the cilia of Tetrahymena thermophila using a combination of cryo-electron microscopy, molecular dynamics, and mass spectrometry. We found that αK40 acetylation exerts a small-scale effect on the DMT structure and stability by influencing the lateral rotational angle. In addition, comparative mass spectrometry revealed a link between αK40 acetylation and phosphorylation in cilia.

Genetic insights into the ‘sandwich fusion’ subtype of Klippel–Feil syndrome: novel FGFR2 mutations identified by 21 cases of whole-exome sequencing

BackgroundKlippel–Feil syndrome (KFS) is a rare congenital disorder characterized by the fusion of two or more cervical vertebrae during early prenatal development. This fusion results from a failure of segmentation during the first trimester. Although six genes have previously been associated with KFS, they account for only a small proportion of cases. Among the distinct subtypes of KFS, “sandwich fusion” involving concurrent fusion of C0-1 and C2-3 vertebrae is particularly noteworthy due to its heightened risk for atlantoaxial dislocation. In this study, we aimed to investigate novel candidate mutations in patients with “sandwich fusion.”MethodsWe collected and analyzed clinical data from 21 patients diagnosed with “sandwich fusion.” Whole-exome sequencing (WES) was performed, followed by rigorous bioinformatics analyses. Our focus was on the six known KFS-related genes (GDF3, GDF6, MEOX1, PAX1, RIPPLY2, and MYO18). Suspicious mutations were subsequently validated through in vitro experiments.ResultsOur investigation revealed two novel exonic mutations in the FGFR2 gene, which had not previously been associated with KFS. Notably, the c.1750A > G variant in Exon 13 of FGFR2 was situated within the tyrosine kinase domain of the protein, in close proximity to several established post-translational modification sites. In vitro experiments demonstrated that this certain mutation significantly impacted the function of FGFR2. Furthermore, we identified four heterozygous candidate variants in two genes (PAX1 and MYO18B) in two patients, with three of these variants predicted to have potential clinical significance directly linked to KFS.ConclusionsThis study encompassed the largest cohort of patients with the unique “sandwich fusion” subtype of KFS and employed WES to explore candidate mutations associated with this condition. Our findings unveiled novel variants in PAX1, MYO18B, and FGFR2 as potential risk mutations specific to this subtype of KFS.

Improving PTM Site Prediction by Coupling of Multi-Granularity Structure and Multi-Scale Sequence Representation

Protein post-translational modification (PTM) site prediction is a fundamental task in bioinformatics. Several computational methods have been developed to predict PTM sites. However, existing methods ignore the structure information and merely utilize protein sequences. Furthermore, designing a more fine-grained structure representation learning method is urgently needed as PTM is a biological event that occurs at the atom granularity. In this paper, we propose a PTM site prediction method by Coupling of Multi-Granularity structure and Multi-Scale sequence representation, PTM-CMGMS for brevity. Specifically, multigranularity structure-aware representation learning is designed to learn neighborhood structure representations at the amino acid, atom, and whole protein granularity from AlphaFold predicted structures, followed by utilizing contrastive learning to optimize the structure representations. Additionally, multi-scale sequence representation learning is used to extract context sequence information, and motif generated by aligning all context sequences of PTM sites assists the prediction. Extensive experiments on three datasets show that PTM-CMGMS outperforms the state-of-the-art methods. Source code can be found at https://github.com/LZY-HZAU/PTM-CMGMS.

Discovery of a Covalent Inhibitor Selectively Targeting the Autophosphorylation Site of c-Src Kinase.

Nonreceptor tyrosine kinase c-Src plays a crucial role in cell signaling and contributes to tumor progression. However, the development of selective c-Src inhibitors turns out to be challenging. In our previous study, we performed posttranslational modification-inspired drug design (PTMI-DD) to provide a plausible way for designing selective kinase inhibitors. In this study, after identifying a unique pocket comprising a less conserved cysteine and an autophosphorylation site in c-Src as well as a promiscuous covalent inhibitor, chemical optimization was performed to obtain (R)-LW-Srci-8 with nearly 75-fold improved potency (IC50 = 35.83 ± 7.21 nM). Crystallographic studies revealed the critical C-F···C═O interactions that may contribute to tight binding. The kinact and Ki values validated the improved binding affinity and decreased warhead reactivity of (R)-LW-Srci-8 for c-Src. Notably, in vitro tyrosine kinase profiling and cellular activity-based protein profiling (ABPP) cooperatively indicated a specific inhibition of c-Src by (R)-LW-Srci-8. Intriguingly, (R)-LW-Srci-8 preferentially binds to inactive c-Src with unphosphorylated Y419 both in vitro and in cells, subsequently disrupting the autophosphorylation. Collectively, our study demonstrated the feasibility of developing selective kinase inhibitors by cotargeting a nucleophilic residue and a posttranslational modification site and providing a chemical probe for c-Src functional studies.

Biochemical Properties and Immunogenic Epitopes of Echinococcus granulosus Glutathione S-Transferase as a Vaccine Target: In-Silico Study.

The current in silico study was done to determine the primary biochemical features and immunogenic epitopes of Echinococcus granulosus glutathione S-transferase protein as a potential vaccine candidate. Several web tools were employed to predict physico-chemical properties, antigenicity, allergenicity, solubility, post-translational modification (PTM) sites, subcellular localization, signal peptide, transmembrane domain, secondary and tertiary structure followed by refinement and validations. In addition, B-cell epitopes were predicted and were screened using various web servers, while MHC-binding and CTL epitopes were predicted using IEDB and NetCTL servers, respectively. The protein had 219 residues with a molecular weight of 25.55 kDa and alkaline isoelectric pH (7.5). This protein was stable, thermo-tolerant (aliphatic index: 78.04) and hydrophilic (GRAVY: -0.440). The predicted antigenicity scores were low and the protein was nonallergenic in nature. There were no transmembrane domain and signal peptide in the sequence. Moreover, several B-cell, MHC-binding and CTL epitopes were found in the EgGST protein, which could be further used in multi-epitope vaccines. Further studies are needed on the development of vaccines in vivo using EgGST alone or in combination with other antigens in the future.

Post-translational modification sites are present in hydrophilic cavities of alpha-synuclein, tau, FUS, and TDP-43 fibrils: A molecular dynamics study.

Hydration plays a crucial role in the refolding of intrinsically disordered proteins into amyloid fibrils; however, the specific interactions between water and protein that may contribute to this process are still unknown. In our previous studies of alpha-synuclein (aSyn), we have shown that waters confined in fibril cavities are stabilizing features of this pathological fold; and that amino acids that hydrogen bond with these confined waters modulate primary and seeded aggregation. Here, we extend our aSyn molecular dynamics (MD) simulations with three new polymorphs and correlate MD trajectory information with known post-translational modifications (PTMs) and experimental data. We show that cavity residues are more evolutionarily conserved than non-cavity residues and are enriched with PTM sites. As expected, the confinement within hydrophilic cavities results in more stably hydrated amino acids. Interestingly, cavity PTM sites display the longest protein-water hydrogen bond lifetimes, three-fold greater than non-PTM cavity sites. Utilizing the deep mutational screen dataset by Newberry et al. and the Thioflavin T aggregation review by Pancoe et al. parsed using a fibril cavity/non-cavity definition, we show that hydrophobic changes to amino acids in cavities have a larger effect on fitness and aggregation rate than residues outside cavities, supporting our hypothesis that these sites are involved in the inhibition of aSyn toxic fibrillization. Finally, we expand our study to include analysis of fibril structures of tau, FUS, TDP-43, prion, and hnRNPA1; all of which contained hydrated cavities, with tau, FUS, and TDP-43 recapitulating our PTM results in aSyn fibril cavities.

Immunological lectins in shrimp Penaeus vannamei challenged with infectious myonecrosis virus (IMNV) under low-salinity conditions

Lectins are proteins capable of recognizing and binding to glycan in a specific way. In invertebrates, lectins are a crucial group of Pattern Recognition Proteins (PRRs), activating cellular and humoral responses in the innate immune system. The shrimp Penaeus vannamei is the main crustacean cultivated worldwide, however, the productivity of cultures is strongly affected by diseases, mainly viral ones, such as Infectious Myonecrosis (IMN). Thus, we investigated the participation of five lectins (LvAV, LvCTL4, LvCTL5, LvCTLU, and LvLdlrCTL) in IMNV-challenged shrimp. We verified upregulation gene profiles of lectins after IMNV-challenge, especially in hepatopancreas and gills, in addition to an increase in total hemocytes count (THC) after to 12 h post-infection (hpi). The bioinformatics characterization also revealed several sites of post-translational modification (PTM), such as phosphorylation and glycosylation, which possibly influence the action and stabilization of these lectins. We conclude that LvLdlrCTL and LvCTL5 are the lectins with greater participation in the activation of the immune system against IMNV, showing the greatest potential for PTM, higher upregulation levels, and overlapping with the THC and IMNV viral load.

Post-translational modifications of proteins in cardiovascular diseases examined by proteomic approaches.

Over 400 different types of post-translational modifications (PTMs) have been reported and over 200 various types of PTMs have been discovered using mass spectrometry (MS)-based proteomics. MS-based proteomics has proven to be a powerful method capable of global PTM mapping with the identification of modified proteins/peptides, the localization of PTM sites and PTM quantitation. PTMs play regulatory roles in protein functions, activities and interactions in various heart related diseases, such as ischemia/reperfusion injury, cardiomyopathy and heart failure. The recognition of PTMs that are specific to cardiovascular pathology and the clarification of the mechanisms underlying these PTMs at molecular levels are crucial for discovery of novel biomarkers and application in a clinical setting. With sensitive MS instrumentation and novel biostatistical methods for precise processing of the data, low-abundance PTMs can be successfully detected and the beneficial or unfavorable effects of specific PTMs on cardiac function can be determined. Moreover, computational proteomic strategies that can predict PTM sites based on MS data have gained an increasing interest and can contribute to characterization of PTM profiles in cardiovascular disorders. More recently, machine learning- and deep learning-based methods have been employed to predict the locations of PTMs and explore PTM crosstalk. In this review article, the types of PTMs are briefly overviewed, approaches for PTM identification/quantitation in MS-based proteomics are discussed and recently published proteomic studies on PTMs associated with cardiovascular diseases are included.

IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data.

Proteoforms, the different forms of a protein with sequence variations including post-translational modifications (PTMs), execute vital functions in biological systems, such as cell signaling and epigenetic regulation. Advances in top-down mass spectrometry (MS) technology have permitted the direct characterization of intact proteoforms and their exact number of modification sites, allowing for the relative quantification of positional isomers (PI). Protein positional isomers refer to a set of proteoforms with identical total mass and set of modifications, but varying PTM site combinations. The relative abundance of PI can be estimated by matching proteoform-specific fragment ions to top-down tandem MS (MS2) data to localize and quantify modifications. However, the current approaches heavily rely on manual annotation. Here, we present IsoForma, an open-source R package for the relative quantification of PI within a single tool. Benchmarking IsoForma's performance against two existing workflows produced comparable results and improvements in speed. Overall, IsoForma provides a streamlined process for quantifying PI, reduces the analysis time, and offers an essential framework for developing customized proteoform analysis workflows. The software is open source and available at https://github.com/EMSL-Computing/isoforma-lib.

Full-length single-molecule protein fingerprinting.

Proteins are the primary functional actors of the cell. While proteoform diversity is known to be highly biologically relevant, current protein analysis methods are of limited use for distinguishing proteoforms. Mass spectrometric methods, in particular, often provide only ambiguous information on post-translational modification sites, and sequences of co-existing modifications may not be resolved. Here we demonstrate fluorescence resonance energy transfer (FRET)-based single-molecule protein fingerprinting to map the location of individual amino acids and post-translational modifications within single full-length protein molecules. Our data show that both intrinsically disordered proteins and folded globular proteins can be fingerprinted with a subnanometer resolution, achieved by probing the amino acids one by one using single-molecule FRET via DNA exchange. This capability was demonstrated through the analysis of alpha-synuclein, an intrinsically disordered protein, by accurately quantifying isoforms in mixtures using a machine learning classifier, and by determining the locations of two O-GlcNAc moieties. Furthermore, we demonstrate fingerprinting of the globular proteins Bcl-2-like protein 1, procalcitonin and S100A9. We anticipate that our ability to perform proteoform identification with the ultimate sensitivity may unlock exciting new venues in proteomics research and biomarker-based diagnosis.

Immunoinformatic Analysis of Leishmania Major gp46 Protein and Potential Targets for Vaccination against Leishmaniasis.

Cutaneous leishmaniasis (CL) is a parasitic disease with a significant burden in the Old World countries. In the current study, some of the primary biochemical properties and IFN-γ inducing epitopes with specific binding capacity to human and mouse MHC alleles were predicted for Leishmania major gp46 antigenic protein. Several online servers were used to predict physico-chemical traits, allergenicity, antigenicity, transmembrane domain and signal peptide, subcellular localization, post-translational modifications (PTMs), secondary and tertiary structures, tertiary model refining with validations. Also, IEDB web server was used to predict mouse/human cytotoxic T-lymphocyte (CTL) and helper T-lymphocyte (HTL) epitopes. The 33.25 kDa protein was stable, hydrophilic, antigenic, while non-allergenic, with enhanced thermotolerance and 45 PTM sites. The secondary structure encompassed a random coil, followed by extended strands and helices. Ramachandran-based analysis of the refined model showed 73.1%, 21.6%, 3.4% and 1.9% of residues in the most favored, additional allowed, generously-allowed and disallowed regions, respectively. Epitope screening demonstrated 4 HTL epitopes against seemingly protective HLA alleles, 5 HTL epitopes against the HLA reference set, 3 human CTL epitopes and a number of mouse MHC-restricted epitopes. This paper provides insights into the bioinformatics characteristics of the L. major gp46 protein as a promising vaccine candidate.

Post-translational modification sites are present in hydrophilic cavities of alpha-synuclein, tau, FUS, and TDP-43 fibrils: A molecular dynamics study

Post-translational modification sites are present in hydrophilic cavities of alpha-synuclein, tau, FUS, and TDP-43 fibrils: A molecular dynamics study

DeepPTM: Protein Post-translational Modification Prediction from Protein Sequences by Combining Deep Protein Language Model with Vision Transformers

Introduction:: More recent self-supervised deep language models, such as Bidirectional Encoder Representations from Transformers (BERT), have performed the best on some language tasks by contextualizing word embeddings for a better dynamic representation. Their proteinspecific versions, such as ProtBERT, generated dynamic protein sequence embeddings, which resulted in better performance for several bioinformatics tasks. Besides, a number of different protein post-translational modifications are prominent in cellular tasks such as development and differentiation. The current biological experiments can detect these modifications, but within a longer duration and with a significant cost. Methods:: In this paper, to comprehend the accompanying biological processes concisely and more rapidly, we propose DEEPPTM to predict protein post-translational modification (PTM) sites from protein sequences more efficiently. Different than the current methods, DEEPPTM enhances the modification prediction performance by integrating specialized ProtBERT-based protein embeddings with attention-based vision transformers (ViT), and reveals the associations between different modification types and protein sequence content. Additionally, it can infer several different modifications over different species. Results:: Human and mouse ROC AUCs for predicting Succinylation modifications were 0.988 and 0.965 respectively, once 10-fold cross-validation is applied. Similarly, we have obtained 0.982, 0.955, and 0.953 ROC AUC scores on inferring ubiquitination, crotonylation, and glycation sites, respectively. According to detailed computational experiments, DEEPPTM lessens the time spent in laboratory experiments while outperforming the competing methods as well as baselines on inferring all 4 modification sites. In our case, attention-based deep learning methods such as vision transformers look more favorable to learning from ProtBERT features than more traditional deep learning and machine learning techniques. Conclusion:: Additionally, the protein-specific ProtBERT model is more effective than the original BERT embeddings for PTM prediction tasks. Our code and datasets can be found at https://github.com/seferlab/deepptm.

Acetylated tau exacerbates apoptosis by disturbing mitochondrial dynamics in HEK293 cells.

An increase in tau acetylation at K274 and K281 and abnormal mitochondrial dynamics have been observed in the brains of Alzheimer's disease (AD) patients. Here, we constructed three types of tau plasmids, TauKQ (acetylated tau mutant, by mutating its K274/K281 into glutamine to mimic disease-associated lysine acetylation), TauKR (non-acetylated tau mutant, by mutating its K274/K281 into arginine), and TauWT (wild-type human full-length tau). By transfecting these tau plasmids in HEK293 cells, we found that TauWT and TauKR induced mitochondrial fusion by increasing the level of mitochondrial fusion proteins. Conversely, TauKQ induced mitochondrial fission by reducing mitochondrial fusion proteins, exacerbating mitochondrial dysfunction and apoptosis. BGP-15 ameliorated TauKQ-induced mitochondrial dysfunction and apoptosis by improving mitochondrial dynamics. Our findings suggest that acetylation of K274/281 represents an important post-translational modification site regulating mitochondrial dynamics, and that BGP-15 holds potential as a therapeutic agent for mitochondria-associated diseases such as AD.

MERITS: a web-based integrated Mycobacterial PE/PPE protein database.

PE/PPE proteins, highly abundant in the Mycobacterium genome, play a vital role in virulence and immune modulation. Understanding their functions is key to comprehending the internal mechanisms of Mycobacterium. However, a lack of dedicated resources has limited research into PE/PPE proteins. Addressing this gap, we introduce MycobactERIal PE/PPE proTeinS (MERITS), a comprehensive 3D structure database specifically designed for PE/PPE proteins. MERITS hosts 22 353 non-redundant PE/PPE proteins, encompassing details like physicochemical properties, subcellular localization, post-translational modification sites, protein functions, and measures of antigenicity, toxicity, and allergenicity. MERITS also includes data on their secondary and tertiary structure, along with other relevant biological information. MERITS is designed to be user-friendly, offering interactive search and data browsing features to aid researchers in exploring the potential functions of PE/PPE proteins. MERITS is expected to become a crucial resource in the field, aiding in developing new diagnostics and vaccines by elucidating the sequence-structure-functional relationships of PE/PPE proteins. MERITS is freely accessible at http://merits.unimelb-biotools.cloud.edu.au/.