Search Results (705)

The ZC4H2 gene is the site of congenital mutations linked to neurodevelopmental and musculoskeletal pathologies collectively termed ZARD (ZC4H2-Associated Rare Disorders). ZC4H2 consists of a coiled coil and a single novel zinc finger with four cysteines and two histidines, from which the protein obtains its name. Alpha Fold 3 confidently predicts a structure for the zinc finger but also for similarly sized random sequences, providing equivocal information on its folding status. We show using synthetic peptide fragments that the zinc finger of ZC4H2 is genuine and folds upon binding a zinc ion with picomolar affinity. NMR pH titration of histidines and UV–Vis of a cobalt complex of the peptide indicate its four cysteines coordinate zinc, while two histidines do not participate in binding. The experimental NMR structure of the zinc finger has a novel structural motif similar to RANBP2 zinc fingers, in which two orthogonal hairpins each contribute two cysteines to coordinate zinc. Most of the nine ZARD mutations that occur in the ZC4H2 zinc finger are likely to perturb this structure. While the ZC4H2 zinc finger shares the folding motif and cysteine-ligand spacing of the RANBP2 family, it is missing key substrate-binding residues. Unlike the NZF branch of the RANBP2 family, the ZC4H2 zinc finger does not bind ubiquitin. Since the ZC4H2 zinc finger occurs in a single copy, it is also unlikely to bind DNA. Based on sequence homology to the VAB-23 protein, the ZC4H2 zinc finger may bind RNA of a currently undetermined sequence or have alternative functions. Full article

Methionine residues in proteins and peptides are frequently oxidized by losing one electron. The presence of nearby amide groups is crucial for this process, enabling methionine to participate in long-range electron transfer. Hydroxyl radical (HO^•) plays an important role being generated in aerobic organisms by cellular metabolisms as well as by exogenous sources such as ionizing radiations. The reaction of HO^• with methionine mainly affords the one-electron oxidation of the thioether moiety through two consecutive steps (HO^• addition to the sulfur followed by HO⁻ elimination). We recently investigated the reaction of HO^• with model peptides mimicking methionine and its cysteine-methylated counterpart, i.e., CH₃C(O)NHCHXC(O)NHCH₃, where X = CH₂CH₂SCH₃ or CH₂SCH₃ at pH 7. The reaction mechanism varied depending on the distance between the sulfur atom and the peptide backbone, but, for a better understanding of various suggested equilibria, the analysis of the flux of protons is required. We extended the previous study to the present work at pH 4 using pulse radiolysis techniques with conductivity and optical detection of transient species, as well as analysis of final products by LC-MS and high-resolution MS/MS following γ-radiolysis. Comparing all the data provided a better understanding of how the presence of nearby amide groups influences the one-electron oxidation mechanism. Full article

Proper subcellular localization is essential to exert the designated function of a protein, not only for endogenous proteins but also transgene-encoded proteins. Post-translational modification is a frequently used method to regulate the subcellular localization of a specific protein. While there are a number of tags that are widely used to direct the target protein to a specific location within a cell, these tags often fail to emulate the dynamics of protein trafficking, necessitating an alternative approach to the direct subcellular localization of transgene-encoded proteins. Here, we report the development of a new synthetic polypeptide protein tag comprised of ten amino acids, which promotes membrane localization of a target protein. This short synthetic peptide tag, named “Palmito-Tag”, induces ectopic palmitoylation on the cysteine residue within the tag, thereby promoting membrane localization of the target proteins without affecting their innate function. We show that the target proteins with the Palmito-Tag are incorporated into the membranous organelles within the cells, including the endosomes, as well as extracellular vesicles. Given the reversible nature of palmitoylation, the Palmito-Tag may allow us to shift the subcellular localization of the target protein in a context-dependent manner. With the advent of therapeutic applications of exosomes and other extracellular vesicles, we believe that the ability to reversibly modify a target protein and direct its deposition to the specific subcellular milieu will help us explore more effective venues to harness the potential of extracellular vesicle-based therapies. Full article

Redox signaling is central to plant adaptation, influencing metabolic regulation, stress responses, and developmental processes through thiol-based oxidative post-translational modifications (oxiPTMs) of redox-sensitive proteins. These modifications, particularly those involving cysteine (Cys) residues, act as molecular switches that alter protein function, structure, and interactions. Advances in mass spectrometry-based redox proteomics have greatly enhanced the identification and quantification of oxiPTMs, enabling a more refined understanding of redox dynamics in plant cells. In parallel, the emergence of computational modeling, artificial intelligence (AI), and machine learning (ML) has revolutionized the ability to predict redox-sensitive residues and characterize redox-dependent signaling networks. This review provides a comprehensive synthesis of methodological advancements in redox proteomics, including enrichment strategies, quantification techniques, and real-time redox sensing technologies. It also explores the integration of computational tools for predicting S-nitrosation, sulfenylation, S-glutathionylation, persulfidation, and disulfide bond formation, highlighting key models such as CysQuant, BiGRUD-SA, DLF-Sul, and Plant PTM Viewer. Furthermore, the functional significance of redox modifications is examined in plant development, seed germination, fruit ripening, and pathogen responses. By bridging experimental proteomics with AI-driven prediction platforms, this review underscores the future potential of integrated redox systems biology and emphasizes the importance of validating computational predictions, through experimental proteomics, for enhancing crop resilience, metabolic efficiency, and precision agriculture under climate variability. Full article

Background: The overwhelming majority of the antimicrobial peptides (AMPs) studied in mussels (Mytilus spp.) so far are specifically expressed by hemocytes and display compact disulfide-stabilized structures. However, gill-specific myticalins play a role in mucosal immunity and are one of the very few examples of known molluscan AMPs lacking cysteine residues. Methods: We investigate the molecular evolution of myticalins, compiling a collection of sequences obtained by carefully annotating 169 genome assemblies of different Mytilus species. We determine the gene presence/absence patterns and gene expression profiles for the five myticalin subfamilies, including the newly reported myticalin E. Results: All sequences are deposited in MyticalinDB, a novel database that includes a total of 100 unique mature myticalin peptides encoded by 215 protein precursors, greatly enriching the compendium of these molecules from previous reports. Among the five subfamilies, myticalin A and C are the most widespread and highly expressed across all Mytilus species. Interestingly, structural prediction reveals a previously unreported strong amphipathic nature for some myticalins, which may be highly relevant for their biological activity. Conclusions: The results reported in this work support the role of myticalins in gill-associated mucosal immunity and highlight the importance of inter-individual molecular diversity in establishing an efficient response to microbial infections. The newly established MyticalinDB provides a valuable resource for investigating the evolution and extraordinary molecular diversity of this AMP family. Full article

Calpain-5/CAPN5 is a calcium-activated, non-lysosomal cysteine (thiol) protease. The substrate repertoire of CAPN5 is not known. Calpains catalyze limited proteolysis of their substrates, generating neo-N-termini that correspond to internal residues of their nascent substrate proteins. To identify such neo-N-termini generated by CAPN5, we employed an N-terminomics approach called TAILS (Terminal amine isotopic labeling of substrates) to quantitatively compare the N-terminal peptides detected in parental and CAPN5-deficient SH-SY5Y neuroblastoma cells. Thirty neo-N-termini corresponding to 29 protein groups and 24 unique proteins were detected to be depleted in the CAPN5^−/− cells. A subset of the identified putative substrates was further studied with CAPN5 co-immunoprecipitation, in vitro calcium-induced CAPN5 proteolysis assay, and their cellular fragmentation patterns were compared in parental and CAPN5-deficient SH-SY5Y cells. Here, we provide evidence for CAPN5-mediated proteolysis of the synaptic proteins DLGAP4, IQSEC1 and MPDZ, the neurodegeneration-related EWS, hnRNPU, TFG and UGP2, the DNA replication regulator MCM3, and the neuronal differentiation regulator LMTK1. Our data provide new relevance for neovascular inflammatory vitreoretinopathy (NIV), a progressive eye disease caused by pathogenic mutations in CAPN5. Data are available via ProteomeXchange with identifier PXD064313. Full article

The ReAV enzyme from Rhizobium etli, a representative of Class 3 L-asparaginases, is sequentially and structurally different from other known L-asparaginases. This distinctiveness makes ReAV a candidate for novel antileukemic therapies. ReAV is a homodimeric protein, with each subunit containing a highly specific zinc-binding site created by two cysteines, a lysine, and a water molecule. Two Ser-Lys tandems (Ser48-Lys51, Ser80-Lys263) are located in the close proximity of the metal binding site, with Ser48 hypothesized to be the catalytic nucleophile. To further investigate the catalytic process of ReAV, site-directed mutagenesis was employed to introduce alanine substitutions at residues from the Ser-Lys tandems and at Arg47, located near the Ser48-Lys51 tandem. These mutational studies, along with enzymatic assays and X-ray structure determinations, demonstrated that substitution of each of these highly conserved residues abolished the catalytic activity, confirming their essential role in enzyme mechanism. Full article

The tomato leaf miner, Tuta absoluta (Lepidoptera: Gelechiidae), is a destructive pest of Solanaceae crops worldwide. Its olfactory system plays an important role in locating mating partners and recognizing host plants. Understanding its olfactory recognition mechanism, particularly the function of odorant-binding proteins (OBPs), may reveal potential targets for pest management. In this study, we characterized two antenna-specific OBPs, TabsOBP45 and TabsOBP46, which were identified from the T. absoluta genome. Sequence analysis revealed that both TabsOBPs belong to the classic OBP subfamily, which is characterized by the presence of six conserved cysteine residues and an N-terminal signal peptide. Both TabsOBPs showed predominant antennal expression in quantitative real-time PCR (qRT-PCR) assays, suggesting their key roles in olfactory perception. Fluorescence competitive binding assays with a total of 63 tested volatiles revealed that 13 compounds exhibited strong binding affinities (Ki < 22 µM) to TabsOBP45, with the highest binding affinity to β-ionone, β-caryophyllene, terpinolene, and cinnamaldehyde. Nine compounds showed strong binding affinities to TabsOBP46, with the strongest binding to 4-anisaldehyde, 4-methoxybenzaldehyde, cinnamaldehyde, and β-ionone. Molecular docking analysis revealed the key residues involved in β-ionone binding: TabsOBP45 interacted with ILE8, ALA9, PHE12, TRP37, ILE92, PHE94, THR115, and PHE118, while TabsOBP46 interacted with ILE8, PHE12, PHE36, TRP37, ILE92, LEU94, PHE118, and VAL134. These results provide new insights into the olfactory mechanism of T. absoluta and potential molecular targets for the development of olfactory-based pest control strategies. Full article

TRPA1 (Transient Receptor Potential Ankyrin 1), a cation channel predominantly expressed in sensory neurons, plays a critical role in detecting noxious stimuli and mediating pain signal transmission. As a key player in nociceptive signaling pathways, TRPA1 has emerged as a promising therapeutic target for the development of novel analgesics. Crotalphine (CRP), a 14-amino acid peptide, has been demonstrated to specifically activate TRPA1 and elicit potent analgesic effects. Previous cryo-EM (cryo-electron microscopy) studies have elucidated the structural mechanisms of TRPA1 activation by small-molecule agonists, such as iodoacetamide (IA), through covalent modification of N-terminal cysteine residues. However, the molecular interactions between TRPA1 and peptide ligands, including crotalphine, remain unclear. Here, we present the cryo-EM structure of ligand-free human TRPA1 consistent with the literature, as well as TRPA1 complexed with crotalphine, with resolutions of 3.1 Å and 3.8 Å, respectively. Through a combination of single-particle cryo-EM studies, patch-clamp electrophysiology, and microscale thermophoresis (MST), we have identified the cysteine residue at position 621 (Cys621) within the TRPA1 ion channel as the primary binding site for crotalphine. Upon binding to the reactive pocket containing C621, crotalphine induces rotational and translational movements of the transmembrane domain. This allosteric modulation coordinately dilates both the upper and lower gates, facilitating ion permeation. Full article

The escalating crisis of antimicrobial resistance in aquaculture, driven by the indiscriminate use of antibiotics, underscores the urgent need to develop novel anti-infective agents. This study addresses this requirement by investigating cysteine-rich antimicrobial peptides (AMPs) in understudied crustacean species. A cysteine-rich AMP, designated PpRcys1, was identified and characterized from the genome of Pollicipes pollicipes. PpRcys1 comprises 104 amino acids, with 85 residues forming the mature peptide region, and exhibits random coils, a CSαβ-fold, and one β-sheet. Our findings demonstrated that recombinant PpRcys1 (rPpRcys1) possesses broad-spectrum antimicrobial activity against three Gram-positive bacteria (Staphylococcus aureus, Bacillus sp. T2, and Streptococcus agalactiae) and four Gram-negative bacteria (Aeromonas hydrophila, Escherichia coli, Vibrio alginolyticus, and Acinetobacter sp. L3), with minimum inhibitory concentrations ranging from 8 to 32 μM. It exerts antimicrobial effects by inducing membrane disruption without impacting bacterial protease activity, DNA migration, or respiratory chain reductase activity. Further investigation is warranted to determine whether it can target and interfere with intracellular bacterial processes. Our discovery and characterization of this novel AMP provide a promising foundation for its development as an alternative to antibiotics. Full article

Protein prenylation is a crucial post-translational modification that involves the formation of a covalent bond between isoprenoid lipids and the cysteine residues of specific proteins. This modification plays a significant role in determining protein localization, facilitating protein–protein interactions, and ultimately influencing protein function within the cellular context. Prenylation is a conserved process observed across various kingdoms of life, including plants, animals, fungi, and protists. This review aims to consolidate existing knowledge regarding the mechanisms underlying protein prenylation, encompassing the biosynthetic pathways of isoprenoids in plants and the processing involved in the prenylation modification. Furthermore, it highlights the implications of alterations in protein prenylation on plant development, signaling pathways, and stress responses. The review also addresses the similarities in modification mechanisms between plants and animals, as well as the diversity of their functional implications. Finally, it outlines prospective research directions of the plant prenylation mechanisms and the potential applications in the field of biotechnology. Full article

This study investigated the effects of adding fermented mixed feed (FMF, composed of several unconventional protein feeds, such as brown rice, rice bran, rice bran meal, sunflower meal, cottonseed meal, and corn starch residue) into the diet of Longyan Shan-ma ducks on their egg quality and intestinal health. The ducks were randomly divided into two groups: one group served as the control and received a standard diet, while the other group received a diet in which 4% of the feed was substituted with FMF. Compared to unfermented feed, FMF had elevated lactic acid levels and reduced phytic acid and crude fiber, along with higher amounts of crude protein and a range of amino acids, including serine, histidine, arginine, alanine, valine, methionine, cysteine, isoleucine, and lysine. FMF significantly enhanced egg production and improved the overall egg quality, such as eggshell strength and thickness. It also enhanced total antioxidant capacity and glutathione peroxidase concentrations in serum while reducing serum urea nitrogen and interleukin-1β levels. Histological analysis showed that FMF supplementation improved the ileal villus height-to-crypt depth ratio. Microbiota analysis demonstrated that FMF had a significant impact on β-diversity by increasing Firmicutes, Actinobacteriota, and Desulfobacterota and decreasing Proteobacteria and Myxococcota at the phylum level. The abundance of Corynebacterium, Lactobacillus, and Gallicola was found to be elevated due to FMF at the genus level, whereas Kocuria, Rothia, Helicobacter, and Escherichia-Shigella were decreased. Additionally, diets supplemented with FMF resulted in higher intestinal valeric acid levels among ducks. Our findings indicate that incorporating FMF into laying duck diets can enhance production performance, egg quality, and gut health. Full article

Metabolic enzymes and cancer-driving transcriptions factors are often overexpressed in neoplastic cells, and their exposed cysteine residues are amenable to chemical modification. This review explores cysteine alkylation as a cancer treatment strategy, focusing on Michael acceptors like curcumin and helenalin, which interact with transcription factors NF-κB, STAT3 and HIF-1α. Molecular docking studies using AutoDockFR revealed distinct binding affinities: curcumin showed strong interactions with STAT3 and NF-κB, while helenalin exhibited high affinity for STAT3 and HIF-1α. Synthetic compounds like STAT3-IN-1 and CDDO-Me demonstrated superior binding in most targets, except for CDDO-Me with HIF-1α, suggesting unique structural incompatibilities. Natural products such as zerumbone and umbelliferone displayed moderate activity, while palbociclib highlighted synthetic-drug advantages. These results underscore the importance of ligand−receptor structural complementarity, particularly for HIF-1α’s confined binding site, where helenalin’s terminal Michael acceptor system proved optimal. The findings advocate for integrating computational and experimental approaches to develop cysteine-targeted therapies, balancing synthetic precision with natural product versatility for context-dependent cancer treatment strategies. Full article

Viral replicons are efficient tools to understand the mechanisms of viral replication and screen antiviral drugs. In this study, a viral-cDNA-based replicon of Japanese encephalitis virus (JEV), which is the causative agent of Japanese encephalitis, was constructed by replacing the viral structural proteins with a green fluorescent protein (JEV-GFP replicon). The resulting JEV-GFP replicon was used as a tool to screen antiviral drugs targeting JEV nonstructural proteins, and the five compounds JNJ-A07, HZ-1157, NITD-2, quinine, and NITD008 were obtained, which significantly inhibited the replication of the JEV-GFP replicon and JEV in vitro, and the properties of these five compounds were also analyzed. The CC₅₀, EC₅₀, and SI indices of these five compounds were analyzed. In addition, the JEV-GFP replicon was used as a tool to identify the residues of viral nonstructural proteins involved in RNA replication, and the cysteine residue at position 4 of nonstructural protein 1 was found to be essential for JEV RNA replication. These data suggested that the noninfectious JEV-GFP replicon could be used as tool for different purposes, such as antiviral drug screening and gene function studies. Full article

Keratins and keratin-associated proteins (KRTAPs) are the main components of mammalian nails and hair. Comparative genomics and gene expression studies have revealed that keratins are conserved in all vertebrates, whereas KRTAPs exist only in mammals. Recently, we found hair keratin-like cysteine-rich keratins in jawless vertebrates with confirmed expression in the cornified epithelial teeth of the sea lamprey (Petromyzon marinus). Here, we report that KRTAP-like proteins are also present in the horny teeth of the lamprey. Mass spectrometry-based proteomics identified proteins that share features with KRTAPs, such as high contents of cysteine and tyrosine residues, which support intermolecular interactions, and abundant glycine residues, which endow the proteins with flexibility. Genes encoding KRTAP-like proteins are arranged in a cluster in P. marinus, and the presence of at least one KRTAP-like protein is conserved in phylogenetically diverse species of lamprey, including Lampetra fluviatilis, Lethenteron reissneri, Geotria australis, and Mordacia mordax. The KRTAP-like genes of lampreys contain two exons, whereas mammalian KRTAPs have only a single exon. Although KRTAPs and KRTAP-like proteins are products of independent evolution, their common expression in cornified skin appendages suggests that they fulfill similar functions. Full article