GPS-PAIL: prediction of lysine acetyltransferase-specific modification sites from protein sequences

Integrated Multiomics Analyses of the Molecular Landscape of Sarcopenia in Alcohol-Related Liver Disease

BACKGROUND

Skeletal muscle is a major target for ethanol-induced perturbations, leading to sarcopenia in alcohol-related liver disease (ALD). The complex interactions and pathways involved in adaptive and maladaptive responses to ethanol in skeletal muscle are not well understood. Unlike hypothesis-driven experiments, an integrated multiomics-experimental validation approach provides a comprehensive view of these interactions.

METHODS

We performed multiomics analyses with experimental validation to identify novel regulatory mechanisms of sarcopenia in ALD. Studies were done in a comprehensive array of models including ethanol-treated (ET) murine and human-induced pluripotent stem cell-derived myotubes (hiPSCm), skeletal muscle from a mouse model of ALD (mALD) and human patients with alcohol-related cirrhosis and controls. We generated 13 untargeted datasets, including chromatin accessibility (assay for transposase accessible chromatin), RNA sequencing, proteomics, phosphoproteomics, acetylomics and metabolomics, and conducted integrated multiomics analyses using UpSet plots and feature extraction. Key findings were validated using immunoblots, redox measurements (NAD+/NADH ratio), imaging and senescence-associated molecular phenotype (SAMP) assays. Mechanistic studies included mitochondrial-targeted Lactobacillus brevis NADH oxidase (MitoLbNOX) to increase redox ratio and MitoTempo as a mitochondrial free radical scavenger.

RESULTS

Multiomics analyses revealed enrichment in mitochondrial oxidative function, protein synthesis and senescence pathways consistent with the known effects of hypoxia-inducible factor 1α (HIF1α) during normoxia. Across preclinical and clinical models, HIF1α targets (n = 32 genes) and signalling genes (n > 100 genes) (n = 3 ATACseq, n = 65 phosphoproteomics, n = 10 acetylomics, n = 6 C2C12 proteomics, n = 106 C2C12 RNAseq, n = 64 hiPSC RNAseq, n = 30 hiPSC proteomics, n = 3 mouse proteomics, n = 25 mouse RNAseq, n = 8 human RNAseq, n = 3 human proteomics) were increased. Stabilization of HIF1α (C2C12, 6hEtOH 0.24 ± 0.09; p = 0.043; mALD 0.32 ± 0.074; p = 0.005; data shown as mean difference ± standard error mean) was accompanied by enrichment in the early transient and late change clusters, -log(p-value) = 1.5-3.8, of the HIF1α signalling pathway. Redox ratio was reduced in ET myotubes (C2C12: 15512 ± 872.1, p < 0.001) and mALD muscle, with decreased expression of electron transport chain components (CI-V, p < 0.05) and Sirt3 (C2C12: 0.067 ± 0.023, p = 0.025; mALD: 0.41 ± 0.12, p = 0.013). Acetylation of mitochondrial proteins was increased in both models (C2C12: 107364 ± 4558, p = 0.03; mALD: 40036 ± 18 987, p = 0.049). Ethanol-induced SAMP was observed across models (P16: C2C12: 0.2845 ± 0.1145, p < 0.05; hiPSCm: 0.2591, p = 0.041). MitoLbNOX treatment reversed redox imbalance, HIF1α stabilization, global acetylation and myostatin expression (p < 0.05).

CONCLUSIONS

An integrated multiomics approach, combined with experimental validation, identifies HIF1α stabilization and accelerated post-mitotic senescence as novel mechanisms of sarcopenia in ALD. These findings show the complex molecular interactions leading to mitochondrial dysfunction and progressive sarcopenia in ALD.

Intratumoral Brevibacillus parabrevis enhances antitumor immunity by inhibiting NK cell ferroptosis in hepatocellular carcinoma

It is known that intestinal flora affects the number and function of NK cells through metabolites, thereby regulating the response of tumors to chemotherapy or immunotherapy. However, little is known about whether intratumoral bacteria are involved in NK cell-mediated antitumor immunity. In this study, 2bRAD-M analysis was performed on patient hepatocellular carcinoma and paired tissues to determine the composition of the intratumoral microbiota. Mass cytometry, flow cytometry, co-immunoprecipitation, immunoblotting, immunofluorescence, and DNA pull-down assays were used to evaluate the relationship between intratumoral bacteria, ferroptosis, and NK cell activity in Hu-SRC mice. Here, we found that the intratumoral B. parabrevis inhibited NK cell ferroptosis by promoting lipolysis into acetyl-CoA. Mechanistically, B. parabrevis catalyzed the acetylation of RORC, enhancing its binding to the NEDD4L promoter. NEDD4L induced ubiquitination of iron transporters SLC39A14, SLC39A8, and STEAP3. Functionally, B. parabrevis induced NK cells to differentiate into adaptability, cytotoxicity, and heat shock phenotypes, inhibiting the terminal phenotype and changing the tumor microenvironment from "cold" to "hot". In conclusion, B. parabrevis enhanced the antitumor response of NK cells by regulating post-translational modifications. Our study identified a new strategy for utilizing intratumor bacteria for clinical treatment.

Biochemical Impact of p300-Mediated Acetylation of Replication Protein A: Implications for DNA Metabolic Pathway Choice

Replication Protein A (RPA), a single-stranded DNA (ssDNA) binding protein, is vital for various aspects of genome maintenance such as replication, recombination, repair and cell cycle checkpoint activation. Binding of RPA to ssDNA protects it from degradation by cellular nucleases, prevents secondary structure formation and suppresses illegitimate recombination. In our current study, we identified the acetyltransferase p300 to be capable of acetylating the 70kDa subunit of RPA in vitro and within cells. The acetylation status of RPA changes throughout the cell cycle, increasing during the S and G2/M phases, and after UV-induced damage. Furthermore, we were able to specifically identify RPA directly associated with the replication fork during the S phase and UV damage to be acetylated. Based on these observations, we evaluated the impact of lysine acetylation on the biochemical properties of RPA. Investigation of binding properties of RPA revealed that acetylation of RPA increased its binding affinity to ssDNA compared to unmodified RPA. The improvement in binding efficiency was a function of DNA length with the greatest increases observed on shorter length ssDNA oligomers. Enzymatic assays further revealed that upon acetylation RPA governs the switch between the short and long flap pathway for Okazaki fragment processing. Our findings demonstrate that p300-dependent, site-specific acetylation enhances RPA's DNA binding properties, potentially regulating its function during various DNA transactions.

Identification and Functional Analysis of a Key Gene in the CHH Gene Family for Glucose Metabolism in the Pacific White Shrimp Litopenaeus vannamei

The crustacean hyperglycemic hormone (CHH) is a unique multifunctional neuroendocrine hormone superfamily in crustaceans, crucial for maintaining physiological homeostasis and stress adaptation. To explore the role of CHHs in shrimp metabolism and growth, we identified LvCHH Ia, a CHH family member who regulates glucose metabolism in the Pacific white shrimp (Litopenaeus vannamei), through CHH family gene classification, phylogenetic analysis, gene structure analysis, and transcription factor binding site (TFBS) prediction. Subsequently, we cloned two alternative splicing variants of this gene, LvCHH Ia-1 and LvCHH Ia-2, both expressed in the nervous system but with different expression levels, and LvCHH Ia-2 exhibiting a broader tissue distribution. Using interference (RNAi)-mediated gene silencing and recombinant protein injection, we investigated the functional similarities and differences between the two variants. Our results show that both variants affect glucose metabolism by modulating the expression of key enzyme genes involved in gluconeogenesis/glycolysis, such as HK, TPI, PCK1, ALD. Specifically, they likely regulate hemolymph glucose levels via the Wnt and PI3K-AKT signaling pathways, with LvCHH Ia-1 exerting a more sustained effect on glucose metabolism compared to LvCHH Ia-2. Furthermore, LvCHH Ia may also act as a molting inhibitory hormone by suppressing the expression of ecdysone synthesis-related genes, where LvCHH Ia-2 plays a more significant role. These findings deepen our understanding of CHH regulatory mechanisms in crustaceans and provide potential applications for shrimp physiological research and aquaculture.

In Silico-Based Investigation of the Immunogenicity and Biochemical Attributes of Toxoplasma gondii Apical Membrane Antigen 1 (TgAMA1)

Background: Apical membrane antigen 1 (AMA1) is a highly conserved microneme protein in apicomplexan parasites. In this study, immunoinformatics tools and in silico protein structure prediction were used to characterize the structure, physicochemical properties, posttranslational modification sites, immunogenic epitopes, allergenicity, and immune simulation of the Toxoplasma gondii AMA1 (TgAMA1) protein. Methods: A comprehensive analysis was performed using multiple bioinformatics web servers to analyze the antigenicity, physicochemical features, secondary and tertiary structures, B and T cell epitopes, and in silico immune simulation of TgAMA1. Results: The analysis revealed that the AMA1 protein consists of 569 amino acid residues and has a molecular weight of approximately 63 kDa. The grand average of hydropathicity (GRAVY) was -0.531 and the aliphatic index was calculated as 64.62. Based on the GOR IV server, TgAMA1 contained 20.21% alpha helices, 58.52% random coils, and 21.27% extended strands. The Ramachandran plot of the refined model revealed that over 97% of the residues were located in the favored region. The AMA1 protein was highly immunogenic and nonallergenic in nature. In silico immune simulation using the C-ImmSim server suggested that three doses of TgAMA1 would elicit potent humoral and cell-mediated immune responses. Conclusion: These findings provide valuable insights for further in vitro and in vivo investigations of TgAMA1's potential as a vaccine candidate against toxoplasmosis.

Toxoplasma gondii (GRA10): A Closer Glance Into Immunogenic and Biochemical Characteristics Using In Silico Approach

Toxoplasma gondii, an obligate, intracellular, protozoan parasite, is known to infect a wide range of warm-blooded animals, including livestock, marine mammals and humans leading to the development of toxoplasmosis. The dense granule antigens (GRAs) have garnered crucial role in parasite survival, virulence and the formation of the parasitophorous vacuole. The study focusing on the GRA10 protein of T. gondii aims to elucidate its features further to support its potential inclusion in future vaccine formulations. The present study provided an exhaustive elucidation of the key characteristics of the GRA10 protein, encompassing its presence of a transmembrane domain, physico-chemical properties, subcellular localization, potential epitopes recognised by B-cells and T-cells, secondary and tertiary structures, as well as other significant attributes of this protein. The results indicated that the GRA10 protein possesses a total of 192 possible post-translational modification sites, with no transmembrane domains being detected within its structure. In terms of secondary structure, the GRA10 protein is composed of 27.74% alpha-helix, 13.53% extended strand and 58.72% random coil elements. Additionally, various potential B- and T-cell epitopes were pinpointed for the GRA10 protein, suggesting its immunogenic properties. The assessment of antigenicity and allergenicity further confirmed that GRA10 is immunogenic but non-allergenic, making it a promising candidate for further study. Furthermore, the induction of IFN-γ and IL-4 highlighted the ability of related MHC-II molecules to interact with GRA10, indicating its potential role in immune responses. These findings shed light on the multifaceted nature of the GRA10 protein and its significance in immunological processes. The study presented crucial fundamental and theoretical information regarding GRA10 in order to facilitate the creation of a potent vaccine against both acute and chronic toxoplasmosis, warranting additional in vivo examinations.

Giardia fibrillarin: a bioinformatics exploration of sequence and structure

Fibrillarin is a key nucleolar S-adenosyl-L-methionine (SAM)-dependent methyltransferase, highly conserved among species in both sequence and function. It is actively involved in numerous cellular processes, particularly in the early stages of pre-ribosomal RNA processing. Although a fibrillarin orthologue has been identified in Giardia, an intestinal protozoan parasite responsible for numerous infections worldwide, its functional and structural features in this parasite remain largely unexplored. In this study, bioinformatics tools were used to analyze the sequence and structure of Giardia fibrillarin to provide insights that could aid future experimental and therapeutic investigations. Taking advantage of the protein sequence of Giardia fibrillarin, multiple bioinformatics tools were employed to estimate its domains, nuclear and nucleolar localization signals (NLS and NoLS), post-translational modifications, phylogeny, and three-dimensional structure. The analysis revealed significant conservation of Giardia fibrillarin, showing close relationships with archaeal and parasitic amoeba orthologs. It retains essential features such as the SAM-dependent methyltransferase domain, a glycine- and arginine-rich domain, and both NLS and NoLS. While the core region of the protein is structurally conserved, the N-terminal region exhibits notable divergence. The potential for inhibition of Giardia fibrillarin by SAM competitors suggests that it could be a promising target for drug development, particularly for strains resistant to current treatments.

Evolutionary and Structural Insights into the RNA Polymerase I A34 Protein Family: A Focus on Intrinsic Disorder and Phase Separation

BACKGROUND

Eukaryotic RNA polymerase I consists of 12 or 11 core subunits and three dissociable subunits, Rrn3, A34, and A49. The A34 and A49 subunits exist as a heterodimer. In silico analysis of the A34 family of transcription factors demonstrates a commonly shared domain structure despite a lack of sequence conservation, as well as N-terminal and C-terminal disordered regions. The common structure of A34 has an N-terminal disordered region followed by a dimerization domain that, in conjunction with A49, contributes to a fold that resembles the TFIIF core. This in turn is followed by a short region that cryo-EM demonstrates resembles an arm and intimately interacts with the PolR1A, PolR1B, and PolR1C subunits of Pol I.

ANALYSES

This Pol I-binding domain is then followed by a region that is not resolved in cryo-EM and is predicted to be intrinsically disordered. Interestingly, the size/length of this disordered structure increases from yeast to humans, and is composed of repeats with unique sequence and biochemical features that also increase in number. Further analyses of the A34 CTD (carboxy-terminal domain) indicate that it has a high probability of undergoing liquid-liquid phase separation.

CONCLUSIONS

We suggest that this intrinsically disordered domain found in the A34 family of Pol I transcription factors serves a function similar to the CTD of the PolR2A subunit in coordinating transcription initiation and elongation and RNA processing. Lastly, we propose that dynamic acetylation of PAF49 may regulate interactions of the intrinsically disordered CTD and thereby specify liquid-liquid phase separations. Overall, we propose a new paradigm for a repeat-containing CTD in Pol I transcription.

Insight into Protein Engineering: From In silico Modelling to In vitro Synthesis

Protein engineering alters the polypeptide chain to obtain a novel protein with improved functional properties. This field constantly evolves with advanced in silico tools and techniques to design novel proteins and peptides. Rational incorporating mutations, unnatural amino acids, and post-translational modifications increases the applications of engineered proteins and peptides. It aids in developing drugs with maximum efficacy and minimum side effects. Currently, the engineering of peptides is gaining attention due to their high stability, binding specificity, less immunogenic, and reduced toxicity properties. Engineered peptides are potent candidates for drug development due to their high specificity and low cost of production compared with other biologics, including proteins and antibodies. Therefore, understanding the current perception of designing and engineering peptides with the help of currently available in silico tools is crucial. This review extensively studies various in silico tools available for protein engineering in the prospect of designing peptides as therapeutics, followed by in vitro aspects. Moreover, a discussion on the chemical synthesis and purification of peptides, a case study, and challenges are also incorporated.

In silico analysis and structural vaccinology prediction of Toxoplasma gondii ROP41 gene via immunoinformatics methods as a vaccine candidate

INTRODUCTION

Toxoplasma gondii (T. gondii) infects all warm-blooded animals, including humans. Currently, no effective treatments exist to prevent the generation of chronic tissue cysts in infected hosts. Therefore, developing a vaccine to protect to deal with toxoplasmosis is a promising strategy, as a single immunization could provide lifelong protective immunity. Rhoptry proteins (ROPs) play a vital role for the parasite's survival within host cells and perform critical functions during different phases of parasite invasion. Little is known about ROP41 gene. Nevertheless, Understanding the characteristics of ROP41 will enhance diagnostic and vaccine research.

MATERIALS AND METHODS

The current article provides a comprehensive analysis of the essential components of the ROP41 protein, including its transmembrane domain, physico-chemical properties, subcellular location, tertiary and secondary structures, and potential T- and B-cell epitopes. These features were determined by many bioinformatics approaches to identify possible epitopes for developing a highly effective vaccine.

RESULTS

ROP41 protein showed 36 possible post-translational modification regions. The ROP41 protein secondary structure contains 17.35 % extended strand, 33.47 % alpha-helix, and 49.18 % random coil. Also, ROP41 showed many possible B- and T-cell epitopes. According to the Ramachandran plot, 90.78 % of amino acid residues had been placed in favored, 3.28 % in outlier, and 5.94 % in allowed areas. Also, the allergenicity and antigenicity evaluation indicated that ROP41 is non-allergenic and immunogenic.

CONCLUSION

The current study offered critical basic and conceptual information on ROP41 to increase a successful vaccine in opposition to continual and acute toxoplasmosis for in addition in vivo assessments. Further research is necessary for the development of vaccines utilizing ROP41 alone or combined with various antigens.

Deciphering a profiling based on multiple post-translational modifications functionally associated regulatory patterns and therapeutic opportunities in human hepatocellular carcinoma

BACKGROUND

Posttranslational modifications (PTMs) play critical roles in hepatocellular carcinoma (HCC). However, the locations of PTM-modified sites across protein secondary structures and regulatory patterns in HCC remain largely uncharacterized.

METHODS

Total proteome and nine PTMs (phosphorylation, acetylation, crotonylation, ubiquitination, lactylation, N-glycosylation, succinylation, malonylation, and β-hydroxybutyrylation) in tumor sections and paired normal adjacent tissues derived from 18 HCC patients were systematically profiled by 4D-Label free proteomics analysis combined with PTM-based peptide enrichment.

RESULTS

We detected robust preferences in locations of intrinsically disordered protein regions (IDRs) with phosphorylated sites and other site biases to locate in folded regions. Integrative analyses revealed that phosphorylated and multiple acylated-modified sites are enriched in proteins containing RRM1 domain, and RNA splicing is the key feature of this subset of proteins, as indicated by phosphorylation and acylation of splicing factor NCL at multiple residues. We confirmed that NCL-S67, K398, and K646 cooperate to regulate RNA processing.

CONCLUSION

Together, this proteome profiling represents a comprehensive study detailing regulatory patterns based on multiple PTMs of HCC.

Sirt1 Mitigates Hepatic Lipotoxic Injury Induced by High-Fat-Diet in Fish Through Ire1α Deacetylation

BACKGROUND

Silent information regulator protein 1 (Sirt1) is crucial in regulating lipid metabolism, but its specific role and mechanism in fish hepatic lipotoxic injury remain undefined.

OBJECTIVES

This study aimed to elucidate the regulatory role of Sirt1 and the underlying mechanisms in dietary lipid-induced hepatic lipotoxic injury in a marine teleost black seabream.

METHODS

Black seabream were fed a control diet (12% lipid level), high-fat diet (HFD) [18% lipid level, oleic acid (OA)-rich], or HFD supplemented with 0.25%, 0.50%, or 1.00% resveratrol (RSV) for 8 wk. The cultured hepatocytes were stimulated by OA (200 μM), OA supplemented with RSV (20 μM), or transfection with sirt1-small interfering RNA (sisirt1). Biochemical indices, gene expression (qPCR), histology, transmission electron microscope, immunofluorescence, Western blot, flow cytometry, and immunoprecipitation assays were conducted to evaluate hepatic lipid deposition, lipid metabolism, endoplasmic reticulum stress, inflammation and apoptosis, and determine protein interactions between Sirt1 and Ire1α.

RESULTS

In vivo, RSV supplementation increased mRNA and protein expression levels of sirt1 (236.2% ± 16.1% and 53.1% ± 14.3%) and downregulated the mRNA and phosphorylated protein expression levels of ire1α/Ire1α (46.0% ± 7.6% and 38.6% ± 7.0%), jnk/Jnk (57.6% ± 7.3% and 122.1%), and nuclear factor κ B (nf-κb/Nf-κb) p65 (41.7% ± 7.1% and 24.6% ± 0.8%) compared with the HFD group. Similar patterns were found in the in vitro experiments; however, after knockdown of sirt1, although the cells were incubated with RSV, the expression levels of ire1α/ Ire1α, jnk/Jnk, and nf-κb/Nf-κb p65 showed no significant differences compared with the OA treatment. Moreover, we found that mutation of K61 to arginine to mimic Ire1α deacetylation confers protection against Ire1α-mediated OA-rich HFD-induced inflammation and apoptosis.

CONCLUSIONS

The findings revealed that Sirt1 protects against OA-rich HFD-induced hepatic lipotoxic injury via the deacetylation of Ire1α on K61, hence reducing Ire1α autophosphorylation level, and suppressing Jnk and Nf-κb p65 activation. This mechanism is elucidated for the first time in fish.

Acetylation of p53 in the Cerebral Cortex after Photothrombotic Stroke

p53 expression and acetylation are crucial for the survival and death of neurons in penumbra. At the same time, the outcome of ischemia for penumbra cells depends largely on the histone acetylation status, but the effect of histone acetyltransferases and deacetylases on non-histone proteins like p53 is largely understudied. With combined in silico and in vitro approach, we have identified enzymes capable of acetylation/deacetylation, distribution, stability, and pro-apoptotic activity of p53 in ischemic penumbra in the course of post-stroke recovery, and also detected involved loci of acetylation in p53. The dynamic regulation of the acetylation of p53 at lysine 320 is controlled by acetyltransferase PCAF and histone deacetylases HDAC1 and HDAC6. The in silico simulation have made it possible to suggest the acetylation of p53 at lysine 320 acetylation may facilitate the shuttling of p53 between the nucleus and cytoplasm in penumbra neurons. Acetylation of p53 at lysine 320 is more preferable than acetylation at lysine 373 and probably promotes survival and repair of penumbra neurons after stroke. Strategies to increase p53 acetylation at lysine 320 via increasing PCAF activity, inhibiting HDAC1 or HDAC6, inhibiting p53, or a combination of these interventions may have therapeutic benefits for stroke recovery and would be promising for neuroprotective therapy of stroke.

Current computational tools for protein lysine acylation site prediction

As a main subtype of post-translational modification (PTM), protein lysine acylations (PLAs) play crucial roles in regulating diverse functions of proteins. With recent advancements in proteomics technology, the identification of PTM is becoming a data-rich field. A large amount of experimentally verified data is urgently required to be translated into valuable biological insights. With computational approaches, PLA can be accurately detected across the whole proteome, even for organisms with small-scale datasets. Herein, a comprehensive summary of 166 in silico PLA prediction methods is presented, including a single type of PLA site and multiple types of PLA sites. This recapitulation covers important aspects that are critical for the development of a robust predictor, including data collection and preparation, sample selection, feature representation, classification algorithm design, model evaluation, and method availability. Notably, we discuss the application of protein language models and transfer learning to solve the small-sample learning issue. We also highlight the prediction methods developed for functionally relevant PLA sites and species/substrate/cell-type-specific PLA sites. In conclusion, this systematic review could potentially facilitate the development of novel PLA predictors and offer useful insights to researchers from various disciplines.

Post-translational modification prediction via prompt-based fine-tuning of a GPT-2 model

Post-translational modifications (PTMs) are pivotal in modulating protein functions and influencing cellular processes like signaling, localization, and degradation. The complexity of these biological interactions necessitates efficient predictive methodologies. In this work, we introduce PTMGPT2, an interpretable protein language model that utilizes prompt-based fine-tuning to improve its accuracy in precisely predicting PTMs. Drawing inspiration from recent advancements in GPT-based architectures, PTMGPT2 adopts unsupervised learning to identify PTMs. It utilizes a custom prompt to guide the model through the subtle linguistic patterns encoded in amino acid sequences, generating tokens indicative of PTM sites. To provide interpretability, we visualize attention profiles from the model's final decoder layer to elucidate sequence motifs essential for molecular recognition and analyze the effects of mutations at or near PTM sites to offer deeper insights into protein functionality. Comparative assessments reveal that PTMGPT2 outperforms existing methods across 19 PTM types, underscoring its potential in identifying disease associations and drug targets.

In-silico screening of missense nsSNPs in Delta-opioid receptor protein and their restoring tendency on MCRT interaction; focusing on dynamic nature

Delta-opioid receptor protein (OPRD1) is one of the potential targets for treating pain. The presently available opioid agonists are known to cause unnecessary side effects. To discover a novel opioid agonist, our research group has synthesized a chimeric peptide MCRT and proved its potential activity through in vivo analysis. Non-synonymous SNPs (nsSNPs) missense mutations affect the functionality and stability of proteins leading to diseases. The current research was focused on understanding the role of MCRT in restoring the binding tendency of OPRD1 nsSNPs missense mutations on dynamic nature in comparison with Deltorphin-II and morphiceptin. The deleterious effects of nsSNPs were analyzed using various bioinformatics tools for predicting structural, functional, and oncogenic influence. The shortlisted nine nsSNPs were predicted for allergic reactions, domain changes, post-translation modification, multiple sequence alignment, secondary structure, molecular dynamic simulation (MDS), and peptide docking influence. Further, the docked complex of three shortlisted deleterious nsSNPs was analyzed using an MDS study, and the highly deleterious shortlisted nsSNP A149T was further analyzed for higher trajectory analysis. MCRT restored the binding tendency influence caused by nsSNPs on the dynamics of stability, functionality, binding affinity, secondary structure, residues connection, motion, and folding of OPRD1 protein.

Computational screening of pathogenic missense nsSNPs in heme oxygenase 1 (HMOX1) gene and their structural and functional consequences

Heme Oxygenase 1 (HMOX1) is a cytoprotective enzyme, exhibiting the highest activity in the spleen, catalyzing the heme ring breakdown into products of biological significance- biliverdin, CO, and Fe2+. In vascular cells, HMOX1 possesses strong anti-apoptotic, antioxidant, anti-proliferative, anti-inflammatory, and immunomodulatory actions. The majority of these activities are crucial for the prevention of atherogenesis. Single amino acid substitutions in proteins generated by missense non-synonymous single nucleotide polymorphism (nsSNPs) in the protein-encoding regions of genes are potent enough to cause significant medical challenges due to the alteration of protein structure and function. The current study aimed at characterizing and analyzing high-risk nsSNPs associated with the human HMOX1 gene. Preliminary screening of the total available 288 missense SNPs was performed through the lens of deleteriousness and stability prediction tools. Finally, a total of seven nsSNPs (Y58D, A131T, Y134H, F166S, F167S, R183S and M186V) were found to be most deleterious by all tools that are present at highly conserved positions. Molecular dynamics simulations (MDS) analysis explained the mutational effects on the dynamic action of the wild-type and mutant proteins. In a nutshell, R183S (rs749644285) was identified as a highly detrimental mutation that could significantly render the enzymatic activity of HMOX1. The finding of this computational analysis might help subject the experimental confirmatory analysis to characterize the role of nsSNPs in HMOX1.Communicated by Ramaswamy H. Sarma.

Genetic determinants of host- and virus-derived insertions for hepatitis E virus replication

Hepatitis E virus (HEV) is a long-neglected RNA virus and the major causative agent of acute viral hepatitis in humans. Recent data suggest that HEV has a very heterogeneous hypervariable region (HVR), which can tolerate major genomic rearrangements. In this study, we identify insertions of previously undescribed sequence snippets in serum samples of a ribavirin treatment failure patient. These insertions increase viral replication while not affecting sensitivity towards ribavirin in a subgenomic replicon assay. All insertions contain a predicted nuclear localization sequence and alanine scanning mutagenesis of lysine residues in the HVR influences viral replication. Sequential replacement of lysine residues additionally alters intracellular localization in a fluorescence dye-coupled construct. Furthermore, distinct sequence patterns outside the HVR are identified as viral determinants that recapitulate the enhancing effect. In conclusion, patient-derived insertions can increase HEV replication and synergistically acting viral determinants in and outside the HVR are described. These results will help to understand the underlying principles of viral adaptation by viral- and host-sequence snatching during the clinical course of infection.

TransPTM: a transformer-based model for non-histone acetylation site prediction

Protein acetylation is one of the extensively studied post-translational modifications (PTMs) due to its significant roles across a myriad of biological processes. Although many computational tools for acetylation site identification have been developed, there is a lack of benchmark dataset and bespoke predictors for non-histone acetylation site prediction. To address these problems, we have contributed to both dataset creation and predictor benchmark in this study. First, we construct a non-histone acetylation site benchmark dataset, namely NHAC, which includes 11 subsets according to the sequence length ranging from 11 to 61 amino acids. There are totally 886 positive samples and 4707 negative samples for each sequence length. Secondly, we propose TransPTM, a transformer-based neural network model for non-histone acetylation site predication. During the data representation phase, per-residue contextualized embeddings are extracted using ProtT5 (an existing pre-trained protein language model). This is followed by the implementation of a graph neural network framework, which consists of three TransformerConv layers for feature extraction and a multilayer perceptron module for classification. The benchmark results reflect that TransPTM has the competitive performance for non-histone acetylation site prediction over three state-of-the-art tools. It improves our comprehension on the PTM mechanism and provides a theoretical basis for developing drug targets for diseases. Moreover, the created PTM datasets fills the gap in non-histone acetylation site datasets and is beneficial to the related communities. The related source code and data utilized by TransPTM are accessible at https://www.github.com/TransPTM/TransPTM.

Crosstalk of HDAC4, PP1, and GSDMD in controlling pyroptosis

Gasdermin D (GSDMD) functions as a pivotal executor of pyroptosis, eliciting cytokine secretion following cleavage by inflammatory caspases. However, the role of posttranslational modifications (PTMs) in GSDMD-mediated pyroptosis remains largely unexplored. In this study, we demonstrate that GSDMD can undergo acetylation at the Lysine 248 residue, and this acetylation enhances pyroptosis. We identify histone deacetylase 4 (HDAC4) as the specific deacetylase responsible for mediating GSDMD deacetylation, leading to the inhibition of pyroptosis both in vitro and in vivo. Deacetylation of GSDMD impairs its ubiquitination, resulting in the inhibition of pyroptosis. Intriguingly, phosphorylation of HDAC4 emerges as a critical regulatory mechanism promoting its ability to deacetylate GSDMD and suppress GSDMD-mediated pyroptosis. Additionally, we implicate Protein phosphatase 1 (PP1) catalytic subunits (PP1α and PP1γ) in the dephosphorylation of HDAC4, thereby nullifying its deacetylase activity on GSDMD. This study reveals a complex regulatory network involving HDAC4, PP1, and GSDMD. These findings provide valuable insights into the interplay among acetylation, ubiquitination, and phosphorylation in the regulation of pyroptosis, offering potential targets for further investigation in the field of inflammatory cell death.

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

BACKGROUND

Cutaneous leishmaniasis (CL) is a parasitic disease with a significant burden in the Old World countries.

OBJECTIVE

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.

METHODS

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.

RESULTS

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.

CONCLUSION

This paper provides insights into the bioinformatics characteristics of the L. major gp46 protein as a promising vaccine candidate.

HOOKLESS1 acetylates AUTOPHAGY-RELATED PROTEIN18a to promote autophagy during nutrient starvation in Arabidopsis

Acetylation is an important posttranslational modification (PTM) that regulates almost all core processes of autophagy in yeast and mammals. However, the role of protein acetylation in plant autophagy and the underlying regulatory mechanisms remain unclear. Here, we show the essential role of the putative acetyltransferase HOOKLESS1 (HLS1) in acetylation of the autophagy-related protein ATG18a, a key autophagy component that regulates autophagosome formation in Arabidopsis (Arabidopsis thaliana). Loss of HLS1 function suppressed starvation-induced autophagy and increased plant susceptibility to nutrient deprivation. We discovered that HLS1 physically interacts with and directly acetylates ATG18a both in vitro and in vivo. In contrast, mutating putative active sites in HLS1 inhibited ATG18a acetylation and suppressed autophagy upon nutrient deprivation. Accordingly, overexpression of ATG18a mutant variants with lower acetylation levels inhibited the binding activity of ATG18a to PtdIns(3)P and autophagosome formation under starvation conditions. Moreover, HLS1-modulated autophagy was uncoupled from its function in hook development. Taken together, these findings shed light on a key regulator of autophagy and further elucidate the importance of PTMs in modulating autophagy in plants.

Mof plays distinct roles in hepatic lipid metabolism under healthy or non-alcoholic fatty liver conditions

The disturbance of hepatic lipid metabolism has a strong association with non-alcoholic fatty liver disease (NAFLD) and diabetes. Mof, an acetyltransferase involved in obesity and carbon metabolism, has not been thoroughly examined in its connection to hepatic metabolism. We aimed to explore the impact of Mof on hepatic lipid metabolism. The alteration of Mof expression was found in both obese mice and NAFLD human liver. The genes regulated by Mof were closely associated with lipid metabolism. In normal mice or hepatic cells, the down-regulation or inhibition of Mof resulted in increased lipid accumulation due to decreased PPARα expression. Conversely, in diet-induced obesity (DIO) mice or hepatic cells treated with palmitic acid, the inhibition of Mof led to improved lipid metabolism, attributed to the reduction in p-mTOR/mTOR levels. In summary, Mof exhibited distinct roles in lipid metabolism under different conditions. The inhibition of Mof may hold potential as a therapeutic target for hepatic lipid metabolism disturbances.

An insight into Pisum sativum HSF gene family-Genome-wide identification, phylogenetic, expression, and analysis of transactivation potential of pea heat shock transcription factor

Field pea (Pisum sativum L, 2n = 14) is a popular temperate legume with high economic value. Heat shock factors (HSFs) are the core element in the regulatory mechanism of heat stress responses. HSFs in pea (P. sativum) have not been characterized and their role remains unclear in different abiotic stresses. To address this knowledge gap, the current study aimed to characterize the HSF gene family in pea. We identified 38 PsHsf members in P. sativum, which are distributed on the seven chromosomes, and based on phylogenetic analysis, we classified them into three representative classes i.e. A, B, and C. Conserved motif and gene structure analysis confirmed a high degree of similarity among the members of the same class. Additionally, identified cis-acting regulatory elements (CAREs) related to abiotic responses, development, growth, and hormone signaling provides crucial insights into the regulatory mechanisms of PsHsfs. Our research revealed instances of gene duplication in PsHsf gene family, suggesting that this mechanism could be driving the expansion of the PsHsf gene family. Moreover, Expression analysis of PsHsfs exhibited upregulation under heat stress (HS), salt stress (SS), and drought stress (DS) showing their phenomenal role in stress conditions. PsHsfs protein interaction network suggested their involvement in stress-responsive mechanisms. Further transactivation potential was checked for spliced variant of PsHsfA2a (PsHsfA2aI, PsHsfA2aII, and PsHsfA2aIII), PsHsfA3, PsHsfA6b, PsHsfA9, PsHsfB1a, and PsHsfB2a. Overall, these findings provide valuable insight into the evolutionary relationship of PsHsf gene family and their role in abiotic stress responses.

Identification and characterization of putative biomarkers and therapeutic axis in Glioblastoma multiforme microenvironment

Non-cellular secretory components, including chemokines, cytokines, and growth factors in the tumor microenvironment, are often dysregulated, impacting tumorigenesis in Glioblastoma multiforme (GBM) microenvironment, where the prognostic significance of the current treatment remains unsatisfactory. Recent studies have demonstrated the potential of post-translational modifications (PTM) and their respective enzymes, such as acetylation and ubiquitination in GBM etiology through modulating signaling events. However, the relationship between non-cellular secretory components and post-translational modifications will create a research void in GBM therapeutics. Therefore, we aim to bridge the gap between non-cellular secretory components and PTM modifications through machine learning and computational biology approaches. Herein, we highlighted the importance of BMP1, CTSB, LOX, LOXL1, PLOD1, MMP9, SERPINE1, and SERPING1 in GBM etiology. Further, we demonstrated the positive relationship between the E2 conjugating enzymes (Ube2E1, Ube2H, Ube2J2, Ube2C, Ube2J2, and Ube2S), E3 ligases (VHL and GNB2L1) and substrate (HIF1A). Additionally, we reported the novel HAT1-induced acetylation sites of Ube2S (K211) and Ube2H (K8, K52). Structural and functional characterization of Ube2S (8) and Ube2H (1) have identified their association with protein kinases. Lastly, our results found a putative therapeutic axis HAT1-Ube2S(K211)-GNB2L1-HIF1A and potential predictive biomarkers (CTSB, HAT1, Ube2H, VHL, and GNB2L1) that play a critical role in GBM pathogenesis.

Mitochondrial general control of amino acid synthesis 5 like 1 promotes nonalcoholic steatohepatitis development through ferroptosis-induced formation of neutrophil extracellular traps

BACKGROUND

Mitochondria play central roles in metabolic diseases including nonalcoholic steatohepatitis (NASH). However, how mitochondria regulate NASH progression remains largely unknown. Our previous findings demonstrate that mitochondrial general control of amino acid synthesis 5 like 1 (GCN5L1) is associated with mitochondrial metabolism. Nevertheless, the roles of GCN5L1 in NASH are unclear.

AIMS AND METHODS

The GCN5L1 expression was detected in the fatty livers of NASH patients and animals. Hepatocyte-specific GCN5L1 deficiency or overexpression mice were used to induce NASH models by feeding with a high-fat/high-cholesterol or methionine-choline deficient diet. The molecular mechanisms underlying GCN5L1-regulated NASH were further explored and verified in mice.

RESULTS AND CONCLUSIONS

GCN5L1 expression was increased in NASH patients. Upregulated GCN5L1 level was also illustrated in NASH mice. Mice with hepatocyte-specific GCN5L1 conditional knockout improved the inflammatory response compared to GCN5L1flox/flox mice. However, overexpression of mitochondrial GCN5L1 augmented the inflammatory response. Mechanically, GCN5L1 acetylated CypD and enhanced its binding with ATP5B, which induced the opening of mitochondrial permeability transition pores and the release of mitochondrial ROS into the cytoplasm. The increased ROS promoted ferroptosis of hepatocytes and induced accumulation of high mobility group box 1 in the microenvironment, which recruited neutrophils and induced the generation of neutrophil extracellular traps (NETs). NETs block impaired GCN5L1-induced NASH progression. Furthermore, the upregulation of GCN5L1 in NASH was contributed by lipid overload-induced endoplasmic reticulum stress. Together, mitochondrial GCN5L1 has a vital function in promoting NASH progression by regulating oxidative metabolism and the hepatic inflammatory microenvironment. Thus, GCN5L1 might be a potential intervention target in NASH treatment.

In Silico Characterization of an Important Metacyclogenesis Marker in Leishmania donovani, HASPB1, as a Potential Vaccine Candidate

Visceral leishmaniasis is a life-threatening infectious disease worldwide. Extensive experiments have been done to introduce potential vaccine candidates to combat leishmaniasis. The present study was done to evaluate Leishmania donovani hydrophilic acylated surface protein B1 as a potential vaccine candidate using in silico methods. For this aim, server-based predictions were performed regarding physicochemical characteristics, solubility, antigenicity, allergenicity, signal peptide, transmembrane domain, and posttranslational modifications (PTMs). Also, secondary and tertiary structures were predicted using NetSurfP-3.0 and I-TASSER, respectively. The 3D model was further subjected to refinement and validation, and promising B-cell, cytotoxic T-lymphocyte (CTL; human, dog), and helper T-lymphocyte (HTL; human) epitopes were predicted. The protein had a molecular weight of 42.19 kDa, with high solubility (0.749), stability (instability index: 21.34), and hydrophilicity (GRAVY: -2.322). No signal peptide or transmembrane domain was predicted, and the most abundant PTMs were phosphorylation, O-glycosylation, and acetylation. Many coils and disordered regions existed in the secondary structure analysis, and the tertiary model had a good confidence score (-0.79). Next, the ProSA-web and PROCHECK tools showed adequate improvements in the refined model compared to the crude model. Only 4 shared B-cell epitopes among three web servers (ABCpred, BepiPred 2.0, and SVMTriP) were shown to be antigenic, nonallergenic, and with good water solubility. Also, five potent CTL epitopes in dogs and five in humans were predicted. Notably, two HTL epitopes were found to be potential IFN-γ inducers. In conclusion, our results demonstrated several immunogenic epitopes in this protein, which could be directed towards multiepitope vaccine design.

Orchestration of Mitochondrial Function and Remodeling by Post-Translational Modifications Provide Insight into Mechanisms of Viral Infection

The regulation of mitochondria structure and function is at the core of numerous viral infections. Acting in support of the host or of virus replication, mitochondria regulation facilitates control of energy metabolism, apoptosis, and immune signaling. Accumulating studies have pointed to post-translational modification (PTM) of mitochondrial proteins as a critical component of such regulatory mechanisms. Mitochondrial PTMs have been implicated in the pathology of several diseases and emerging evidence is starting to highlight essential roles in the context of viral infections. Here, we provide an overview of the growing arsenal of PTMs decorating mitochondrial proteins and their possible contribution to the infection-induced modulation of bioenergetics, apoptosis, and immune responses. We further consider links between PTM changes and mitochondrial structure remodeling, as well as the enzymatic and non-enzymatic mechanisms underlying mitochondrial PTM regulation. Finally, we highlight some of the methods, including mass spectrometry-based analyses, available for the identification, prioritization, and mechanistic interrogation of PTMs.

Combined inhibition of histone deacetylase and cytidine deaminase improves epigenetic potency of decitabine in colorectal adenocarcinomas

BACKGROUND

Targeting the epigenome of cancerous diseases represents an innovative approach, and the DNA methylation inhibitor decitabine is recommended for the treatment of hematological malignancies. Although epigenetic alterations are also common to solid tumors, the therapeutic efficacy of decitabine in colorectal adenocarcinomas (COAD) is unfavorable. Current research focuses on an identification of combination therapies either with chemotherapeutics or checkpoint inhibitors in modulating the tumor microenvironment. Here we report a series of molecular investigations to evaluate potency of decitabine, the histone deacetylase inhibitor PBA and the cytidine deaminase (CDA) inhibitor tetrahydrouridine (THU) in patient derived functional and p53 null colon cancer cell lines (CCCL). We focused on the inhibition of cell proliferation, the recovery of tumor suppressors and programmed cell death, and established clinical relevance by evaluating drug responsive genes among 270 COAD patients. Furthermore, we evaluated treatment responses based on CpG island density.

RESULTS

Decitabine caused marked repression of the DNMT1 protein. Conversely, PBA treatment of CCCL recovered acetylation of histone 3 lysine residues, and this enabled an open chromatin state. Unlike single decitabine treatment, the combined decitabine/PBA treatment caused > 95% inhibition of cell proliferation, prevented cell cycle progression especially in the S and G2-phase and induced programmed cell death. Decitabine and PBA differed in their ability to facilitate re-expression of genes localized on different chromosomes, and the combined decitabine/PBA treatment was most effective in the re-expression of 40 tumor suppressors and 13 genes typically silenced in cancer-associated genomic regions of COAD patients. Furthermore, this treatment repressed expression of 11 survival (anti-apoptotic) genes and augmented expression of X-chromosome inactivated genes, especially the lncRNA Xist to facilitate p53-mediated apoptosis. Pharmacological inhibition of CDA by THU or its gene knockdown prevented decitabine inactivation. Strikingly, PBA treatment recovered the expression of the decitabine drug-uptake transporter SLC15A1, thus enabling high tumor drug-loads. Finally, for 26 drug responsive genes we demonstrated improved survival in COAD patients.

CONCLUSION

The combined decitabine/PBA/THU drug treatment improved drug potency considerably, and given their existing regulatory approval, our findings merit prospective clinical trials for the triple combination in COAD patients.

Proteomics profiling for the global and acetylated proteins of papillary thyroid cancers

BACKGROUND

Papillary thyroid carcinoma (PTC) is the most common endocrine malignancy cancer among the malignancies of thyroid. Despite of wide usages of proteomics in PTC, the profile of acetylated proteins in PTC remains unsettled, which is helpful for understanding the carcinogenesis mechanism and identifying useful biomarkers for PTC.

METHODS

The surgically removed specimens of cancer tissues (Ca-T) and adjacent normal tissues (Ca-N) from 10 female patients pathological diagnosed as PTC (TNM stage III) were enrolled in the study. After preparing the pooled extracts of the whole proteins and the acetylated proteins from 10 cases, TMT labeling and LC/MS/MS methods were applied to the assays of global proteomics and acetylated proteomics separately. Bioinformatics analysis, including KEGG, gene ontology (GO) and hierarchical clustering were performed. Some differentially expressed proteins (DEPs) and differentially expressed acetylated proteins (DEAPs) were validated by individual Western blots.

RESULTS

Controlled with the normal tissues adjacent to the lesions, 147 out of 1923 identified proteins in tumor tissues were considered as DEPs in global proteomics, including 78 up-regulated and 69 down-regulated ones, while 57 out of 311 identified acetylated proteins in tumor tissues were DEAPs in acetylated proteomics, including 32 up-regulated and 25 down-regulated, respectively. The top 3 up- and down-regulated DEPs were fibronectin 1, KRT1B protein and chitinase-3-like protein 1, as well as keratin, type I cytoskeletal 16, A-gamma globin Osilo variant and Huntingtin interacting protein-1. The top 3 up- and down-regulated DEAPs were ribosomal protein L18a-like protein, alpha-1-acid glycoprotein 2 and eukaryotic peptide chain release factor GTP-binding subunit ERF3A, as well as trefoil factor 3, thyroglobulin and histone H2B. Functional GO annotation and KEGG pathway analysis based on the DEPs and DEAPs showed completely different changing pictures. Contrary to the top 10 up- and -down regulated DEPs, most of which were addressed in PTC and other types of carcinomas, changes of the majority DEAPs were not mentioned in the literatures.

CONCLUSIONS

Taken the profiling of the global and acetylated proteomics together will provide more broad view of protein alterations on the carcinogenesis and new direction for selecting biomarker for diagnosis of PTC.

Insertions and deletions in the hypervariable region of the hepatitis E virus genome in individuals with acute and chronic infection

BACKGROUND AND AIMS

Hepatitis E virus is a major cause of acute hepatitis worldwide and can progress to chronicity in immunocompromised individuals. Various virus-host recombination events have been reported in the hypervariable region of the hepatitis E virus genome, but the patterns of assembly and selection remain unclear.

METHODS

To gain further insight into viral evolution, we assessed the presence of low abundance variants in 16 samples from individuals with acute or chronic infection using a targeted next-generation sequencing approach.

RESULTS

In seven samples, different variants with insertions and/or deletions were identified. Among them, eight insertions originating either from human genes or from the hepatitis E virus genome. Five different deletions could be identified. The amino acid composition of sequences with insertions showed a higher frequency of lysine and a lower abundance of proline, and additionally acetylation and ubiquitination sites were more frequent than in hepatitis E virus wild-type sequences.

CONCLUSIONS

These findings suggest that the nucleotide composition of insertions and sites for post-translational modification may contribute to recombination events. Although the impact of low-level hepatitis E virus variants is uncertain, our results highlight the importance of a highly sensitive next-generation sequencing approach to capture the full diversity of hypervariable region.

An inclusive study of deleterious missense PAX9 variants using user-friendly tools reveals structural, functional alterations, as well as potential therapeutic targets

Mutations in the PAX9 are responsible for non-syndromic tooth agenesis in humans, although their structural and functional consequences on protein phenotype, stability, and posttranslational modifications (PTMs) have not yet been adequately investigated. This in silico study focuses on retrieving the six most deleterious mutations (L21P, R26W, R28P, G51S, I87F, and K91E) of PAX9 that has been linked to severe oligodontia. Several computational algorithm methods were used to determine the deleterious effects of PAX9 mutations. Analysis of gene ontology, protein interactions, and PTMs indicated significant functional changes caused by PAX9 mutations. The structural superimposition of the wild-type and mutant PAX9 variants revealed structural changes in locations that were present in the structures of all six variations. The conserved domain analysis revealed that the areas shared by all six variations contained unique sections that lacked DNA binding or protein-protein interaction sites, suggesting prospective drug target sites for functional restoration. The protein-protein interaction network showed KDM5B as PAX9's strongest interacting partner similar to MSX1. The PAX9 protein's structural conformations, compactness, stiffness, and function may all be impacted by changes, according to MD simulations. In addition, research on cell lines and animal models may be valuable in establishing their specific roles in functional annotations.

MIND-S is a deep-learning prediction model for elucidating protein post-translational modifications in human diseases

We present a deep-learning-based platform, MIND-S, for protein post-translational modification (PTM) predictions. MIND-S employs a multi-head attention and graph neural network and assembles a 15-fold ensemble model in a multi-label strategy to enable simultaneous prediction of multiple PTMs with high performance and computation efficiency. MIND-S also features an interpretation module, which provides the relevance of each amino acid for making the predictions and is validated with known motifs. The interpretation module also captures PTM patterns without any supervision. Furthermore, MIND-S enables examination of mutation effects on PTMs. We document a workflow, its applications to 26 types of PTMs of two datasets consisting of ∼50,000 proteins, and an example of MIND-S identifying a PTM-interrupting SNP with validation from biological data. We also include use case analyses of targeted proteins. Taken together, we have demonstrated that MIND-S is accurate, interpretable, and efficient to elucidate PTM-relevant biological processes in health and diseases.

PPICT: an integrated deep neural network for predicting inter-protein PTM cross-talk

Post-translational modifications (PTMs) fine-tune various signaling pathways not only by the modification of a single residue, but also by the interplay of different modifications on residue pairs within or between proteins, defined as PTM cross-talk. As a challenging question, less attention has been given to PTM dynamics underlying cross-talk residue pairs and structural information underlying protein-protein interaction (PPI) graph, limiting the progress in this PTM functional research. Here we propose a novel integrated deep neural network PPICT (Predictor for PTM Inter-protein Cross-Talk), which predicts PTM cross-talk by combining protein sequence-structure-dynamics information and structural information for PPI graph. We find that cross-talk events preferentially occur among residues with high co-evolution and high potential in allosteric regulation. To make full use of the complex associations between protein evolutionary and biophysical features, and protein pair features, a heterogeneous feature combination net is introduced in the final prediction of PPICT. The comprehensive test results show that the proposed PPICT method significantly improves the prediction performance with an AUC value of 0.869, outperforming the existing state-of-the-art methods. Additionally, the PPICT method can capture the potential PTM cross-talks involved in the functional regulatory PTMs on modifying enzymes and their catalyzed PTM substrates. Therefore, PPICT represents an effective tool for identifying PTM cross-talk between proteins at the proteome level and highlights the hints for cross-talk between different signal pathways introduced by PTMs.

Identification and Characterization of p300-Mediated Lysine Residues in Cardiac SERCA2a

Impaired calcium uptake resulting from reduced expression and activity of the cardiac sarco-endoplasmic reticulum Ca²⁺ ATPase (SERCA2a) is a hallmark of heart failure (HF). Recently, new mechanisms of SERCA2a regulation, including post-translational modifications (PTMs), have emerged. Our latest analysis of SERCA2a PTMs has identified lysine acetylation as another PTM which might play a significant role in regulating SERCA2a activity. SERCA2a is acetylated, and that acetylation is more prominent in failing human hearts. In this study, we confirmed that p300 interacts with and acetylates SERCA2a in cardiac tissues. Several lysine residues in SERCA2a modulated by p300 were identified using in vitro acetylation assay. Analysis of in vitro acetylated SERCA2a revealed several lysine residues in SERCA2a susceptible to acetylation by p300. Among them, SERCA2a Lys514 (K514) was confirmed to be essential for SERCA2a activity and stability using an acetylated mimicking mutant. Finally, the reintroduction of an acetyl-mimicking mutant of SERCA2a (K514Q) into SERCA2 knockout cardiomyocytes resulted in deteriorated cardiomyocyte function. Taken together, our data demonstrated that p300-mediated acetylation of SERCA2a is a critical PTM that decreases the pump's function and contributes to cardiac impairment in HF. SERCA2a acetylation can be targeted for therapeutic aims for the treatment of HF.

In Silico Examination of Single Nucleotide Missense Mutations in NHLH2, a Gene Linked to Infertility and Obesity

Continual advances in our understanding of the human genome have led to exponential increases in known single nucleotide variants. The characterization of each of the variants lags behind. For researchers needing to study a single gene, or multiple genes in a pathway, there must be ways to narrow down pathogenic variants from those that are silent or pose less pathogenicity. In this study, we use the NHLH2 gene which encodes the nescient helix-loop-helix 2 (Nhlh2) transcription factor in a systematic analysis of all missense mutations to date in the gene. The NHLH2 gene was first described in 1992. Knockout mice created in 1997 indicated a role for this protein in body weight control, puberty, and fertility, as well as the motivation for sex and exercise. Only recently have human carriers of NHLH2 missense variants been characterized. Over 300 missense variants for the NHLH2 gene are listed in the NCBI single nucleotide polymorphism database (dbSNP). Using in silico tools, predicted pathogenicity of the variants narrowed the missense variants to 37 which were predicted to affect NHLH2 function. These 37 variants cluster around the basic-helix-loop-helix and DNA binding domains of the transcription factor, and further analysis using in silico tools provided 21 SNV resulting in 22 amino acid changes for future wet lab analysis. The tools used, findings, and predictions for the variants are discussed considering the known function of the NHLH2 transcription factor. Overall use of these in silico tools and analysis of these data contribute to our knowledge of a protein which is both involved in the human genetic syndrome, Prader-Willi syndrome, and in controlling genes involved in body weight control, fertility, puberty, and behavior in the general population, and may provide a systematic methodology for others to characterize variants for their gene of interest.

EhSir2c, a Sir2 homolog from the human pathogen Entamoeba histolytica interacts with a DNA repair protein, EhRAD23: Protein-protein interaction, docking and functional study

Chromosome segregation is a crucial phenomenon in the cell cycle and defects in genome segregation result in an abnormality in various cellular events. Unlike higher eukaryotes, chromosome segregation and a number of cell cycle events are unusual in the protozoan parasite Entamoeba histolytica (E. histolytica). Characterization of Sir2 proteins from E. histolytica may reveal its unique cellular events as they play role in diverse cellular processes including chromosome segregation. E. histolytica has four homologs of Sir2 proteins. EhSir2a and EhSir2b show sequence similarity towards eukaryotic Sir2 homologs, whereas EhSir2c and EhSir2d are more like prokaryotic sirtuins. Using both computational and experimental methods, EhSir2c has been characterized in this study. The three-dimensional structure of EhSir2c is predicted by homology modelling. The protein interactors of EhSir2c have been identified by yeast-two-hybrid screening against the cDNA library of E. histolytica. We have identified a novel interactor, EhRAD23 which is a homolog of UV excision repair protein RAD23. The interaction of EhSir2c and EhRAD23 was validated by pull-down assay. UV-C irradiation up-regulates the relative expression of EhSir2c, suggesting the necessity of EhSir2c in UV-induced stress in this parasite.Communicated by Ramaswamy H. Sarma.

Protein acylation: mechanisms, biological functions and therapeutic targets

Metabolic reprogramming is involved in the pathogenesis of not only cancers but also neurodegenerative diseases, cardiovascular diseases, and infectious diseases. With the progress of metabonomics and proteomics, metabolites have been found to affect protein acylations through providing acyl groups or changing the activities of acyltransferases or deacylases. Reciprocally, protein acylation is involved in key cellular processes relevant to physiology and diseases, such as protein stability, protein subcellular localization, enzyme activity, transcriptional activity, protein-protein interactions and protein-DNA interactions. Herein, we summarize the functional diversity and mechanisms of eight kinds of nonhistone protein acylations in the physiological processes and progression of several diseases. We also highlight the recent progress in the development of inhibitors for acyltransferase, deacylase, and acylation reader proteins for their potential applications in drug discovery.

Thirty years of molecular dynamics simulations on posttranslational modifications of proteins

Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements.

Mini-review: Recent advances in post-translational modification site prediction based on deep learning

Post-translational modifications (PTMs) are closely linked to numerous diseases, playing a significant role in regulating protein structures, activities, and functions. Therefore, the identification of PTMs is crucial for understanding the mechanisms of cell biology and diseases therapy. Compared to traditional machine learning methods, the deep learning approaches for PTM prediction provide accurate and rapid screening, guiding the downstream wet experiments to leverage the screened information for focused studies. In this paper, we reviewed the recent works in deep learning to identify phosphorylation, acetylation, ubiquitination, and other PTM types. In addition, we summarized PTM databases and discussed future directions with critical insights.

Leveraging Protein Dynamics to Identify Functional Phosphorylation Sites using Deep Learning Models

Accurate prediction of post-translational modifications (PTMs) is of great significance in understanding cellular processes, by modulating protein structure and dynamics. Nowadays, with the rapid growth of protein data at different "omics" levels, machine learning models largely enriched the prediction of PTMs. However, most machine learning models only rely on protein sequence and little structural information. The lack of the systematic dynamics analysis underlying PTMs largely limits the PTM functional predictions. In this research, we present two dynamics-centric deep learning models, namely, cDL-PAU and cDL-FuncPhos, by incorporating sequence, structure, and dynamics-based features to elucidate the molecular basis and underlying functional landscape of PTMs. cDL-PAU achieved satisfactory area under the curve (AUC) scores of 0.804-0.888 for predicting phosphorylation, acetylation, and ubiquitination (PAU) sites, while cDL-FuncPhos achieved an AUC value of 0.771 for predicting functional phosphorylation (FuncPhos) sites, displaying reliable improvements. Through a feature selection, the dynamics-based coupling and commute ability show large contributions in discovering PAU sites and FuncPhos sites, suggesting the allosteric propensity for important PTMs. The application of cDL-FuncPhos in three oncoproteins not only corroborates its strong performance in FuncPhos prioritization but also gains insight into the physical basis for the functions. The source code and data set of cDL-PAU and cDL-FuncPhos are available at https://github.com/ComputeSuda/PTM_ML.

DeepDA-Ace: A Novel Domain Adaptation Method for Species-Specific Acetylation Site Prediction

Protein lysine acetylation is an important type of post-translational modification (PTM), and it plays a crucial role in various cellular processes. Recently, although many researchers have focused on developing tools for acetylation site prediction based on computational methods, most of these tools are based on traditional machine learning algorithms for acetylation site prediction without species specificity, still maintained as a single prediction model. Recent studies have shown that the acetylation sites of distinct species have evident location-specific differences; however, there is currently no integrated prediction model that can effectively predict acetylation sites cross all species. Therefore, to enhance the scope of species-specific level, it is necessary to establish a framework for species-specific acetylation site prediction. In this work, we propose a domain adaptation framework DeepDA-Ace for species-specific acetylation site prediction, including Rattus norvegicus, Schistosoma japonicum, Arabidopsis thaliana, and other types of species. In DeepDA-Ace, an attention based densely connected convolutional neural network is designed to capture sequence features, and the semantic adversarial learning strategy is proposed to align features of different species so as to achieve knowledge transfer. The DeepDA-Ace outperformed both the general prediction model and fine-tuning based species-specific model across most types of species. The experiment results have demonstrated that DeepDA-Ace is superior to the general and fine-tuning methods, and its precision exceeds 0.75 on most species. In addition, our method achieves at least 5% improvement over the existing acetylation prediction tools.

Possible Regulation of Toll-Like Receptor 4 By Lysine Acetylation Through LPCAT2 Activity in RAW264.7 Cells

Inflammation is central to several diseases. TLR4 mediates inflammation by recognising and binding to bacterial lipopolysaccharides and interacting with other proteins in the TLR4 signalling pathway. Although there is extensive research on TLR4-mediated inflammation, there are gaps in understanding its mechanisms. Recently, TLR4 co-localised with LPCAT2, a lysophospholipid acetyltransferase. LPCAT2 is already known to influence lipopolysaccharide-induced inflammation; however, the mechanism of LPCAT2 influencing lipopolysaccharide-mediated inflammation is not understood.

The present study combined computational analysis with biochemical analysis to investigate the influence of LPCAT2 on lysine acetylation in LPS-treated RAW264.7 cells.

The results suggest for the first time that LPCAT2 influences lysine acetylation in LPS-treated RAW264.7 cells. Moreover, we detected acetylated lysine residues on TLR4. The present study lays a foundation for further research on the role of lysine acetylation on TLR4 signalling. Moreover, further research is required to characterise LPCAT2 as a protein acetyltransferase.

Non-canonical vs. Canonical Functions of Heme Oxygenase-1 in Cancer

Heme oxygenase-1 (HO-1) is a critical stress-responsive enzyme that has antioxidant and anti-inflammatory functions. HO-1 catalyzes heme degradation, which gives rise to the formation of carbon monoxide (CO), biliverdin, and iron. The upregulation of HO-1 under pathological conditions associated with cellular stress represents an important cytoprotective defense mechanism by virtue of the anti-oxidant properties of the bilirubin and the anti-inflammatory effect of the CO produced. The same mechanism is hijacked by premalignant and cancerous cells. In recent years, however, there has been accumulating evidence supporting that the upregulation of HO-1 promotes cancer progression, independently of its catalytic activity. Such non-canonical functions of HO-1 are associated with its interaction with other proteins, particularly transcription factors. HO-1 also undergoes post-translational modifications that influence its stability, functional activity, cellular translocation, etc. HO-1 is normally present in the endoplasmic reticulum, but distinct subcellular localizations, especially in the nucleus, are observed in multiple cancers. The nuclear HO-1 modulates the activation of various transcription factors, which does not appear to be mediated by carbon monoxide and iron. This commentary summarizes the non-canonical functions of HO-1 in the context of cancer growth and progression and underlying regulatory mechanisms.

Non-canonical vs. Canonical Functions of Heme Oxygenase-1 in Cancer

Heme oxygenase-1 (HO-1) is a critical stress-responsive enzyme that has antioxidant and anti-inflammatory functions. HO-1 catalyzes heme degradation, which gives rise to the formation of carbon monoxide (CO), biliverdin, and iron. The upregulation of HO-1 under pathological conditions associated with cellular stress represents an important cytoprotective defense mechanism by virtue of the anti-oxidant properties of the bilirubin and the anti-inflammatory effect of the CO produced. The same mechanism is hijacked by premalignant and cancerous cells. In recent years, however, there has been accumulating evidence supporting that the upregulation of HO-1 promotes cancer progression, independently of its catalytic activity. Such non-canonical functions of HO-1 are associated with its interaction with other proteins, particularly transcription factors. HO-1 also undergoes post-translational modifications that influence its stability, functional activity, cellular translocation, etc. HO-1 is normally present in the endoplasmic reticulum, but distinct subcellular localizations, especially in the nucleus, are observed in multiple cancers. The nuclear HO-1 modulates the activation of various transcription factors, which does not appear to be mediated by carbon monoxide and iron. This commentary summarizes the non-canonical functions of HO-1 in the context of cancer growth and progression and underlying regulatory mechanisms.

Impact of deleterious missense PRKCI variants on structural and functional dynamics of protein

Protein kinase C iota (PKCɩ) is a novel protein containing 596 amino acids and is also a member of atypical kinase family. The role of PKCɩ has been explored in neurodegenerative diseases, neuroblastoma, ovarian and pancreatic cancers. Single nucleotide polymorphisms (SNPs) have not been studied in PKCɩ till date. The purpose of the current study is to scrutinize the deleterious missense variants in PKCɩ and determine the effect of these variants on stability and dynamics of the protein. The structure of protein PKCɩ was predicted for the first time and post translational modifications were determined. Genetic variants of PKCɩ were retrieved from ENSEMBL and only missense variants were further analyzed because of its linkage with diseases. The pathogenicity of missense variants, effect on structure and function of protein, association with cancer and conservancy of the protein residues were determined through computational approaches. It is observed that C1 and the pseudo substrate region has the highest number of pathogenic SNPs. Variations in the kinase domain of the protein are predicted to alter overall phosphorylation of the protein. Molecular dynamic simulations predicted noteworthy change in structural and functional dynamics of the protein because of these variants. The study revealed that nine deleterious variants can possibly contribute to malfunctioning of the protein and can be associated with diseases. This can be useful in diagnostics and developing therapeutics for diseases related to these polymorphisms.