Search Results (676)

Alpha-Synuclein (α-Syn) is a presynaptic neuronal protein implicated in the pathogenesis of Parkinson’s disease (PD) and other synucleinopathies, primarily through its aggregation into insoluble fibrils. The extended α-Syn half-life necessitates treatment durations that are incompatible with efficient high-throughput drug screening, can risk compound stability or cause cellular toxicity. To address this, we inserted a PEST sequence, a motif known to promote rapid protein degradation, at the C-terminus of the SNCA gene using CRISPR/Cas9 to create a novel cell line with reduced α-Syn half-life. This modification accelerates α-Syn turnover, providing a robust model for studying α-Syn dynamics and offering a platform that is applicable to other long-lived proteins. Our results demonstrate a six-fold reduction in α-Syn half-life, enabling the rapid detection of changes in protein levels and facilitating the identification of molecules that modulate α-Syn production and degradation pathways. Using inhibitors of the proteasome, transcription, and translation further validated the model’s utility in examining various mechanisms that impact protein levels. This novel cell line represents a significant advancement for studying α-Syn dynamics and offers promising avenues to develop therapeutics for α-synucleinopathies. Future research should focus on validating this model in diverse experimental settings and exploring its potential in high-throughput screening applications. Full article

Incorporating health-promoting resveratrol into food products is challenging, primarily due to its poor solubility. Covalent conjugation is a promising, low-energy, and environmentally friendly strategy to overcome this limitation. This study compared the effectiveness of free radical grafting and alkaline methods for covalently conjugating whey protein isolate (WPI) with resveratrol. Conjugates were evaluated for molecular weight, structural characteristics, functional properties, and antioxidant activities. Both methods yielded conjugates with enhanced solubility relative to native resveratrol, with fold increases from 7.6 to 21.7 for the free radical grafting and from 8.1 to 23.6 for the alkaline method. Conjugates prepared via free radical grafting exhibited greater increases in molecular weight (10–100 kDa range), higher resveratrol incorporation (up to 17.6%), and superior functional properties compared to the alkaline conjugates (p < 0.05). Specifically, emulsifying activity, foaming capacity, and foaming stability improved by up to 64.7%, 45.8%, and 220.9%, respectively, compared to WPI. The antioxidant activities of the free radical grafting conjugates were 1.3- to 3.6-fold higher than those of alkaline conjugates. These findings highlight free radical grafting of WPI as a promising approach for incorporating resveratrol and improving the functionality of protein-based ingredients in functional food products. Full article

The mechanical stability and deformability of erythrocytes are vital for their function as they traverse capillaries, where shear stress can reach up to 10 Pa under physiological conditions. Human serum albumin (HSA) is known to help maintain erythrocyte stability by influencing cell shape, membrane integrity, and resistance to hemolysis. However, the precise mechanisms by which albumin exerts these effects remain debated, with some studies indicating a stabilizing role and others suggesting the opposite. This review highlights that under high shear rates, albumin molecules may undergo unfolding due to normal stress differences. Such structural changes can significantly alter albumin’s interactions with the erythrocyte membrane, thereby affecting cell mechanical stability. We discuss two potential scenarios explaining how albumin influences erythrocyte mechanics under shear stress, considering both the viscoelastic properties of blood and those of the erythrocyte membrane. Based on theoretical analyses and experimental evidence from the literature, we propose that albumin’s effect on erythrocyte mechanical stability depends on (i) the transition between unfolded and folded states of the protein and (ii) the impact of shear stress on the erythrocyte membrane’s ζ-potential. Understanding these factors is essential for elucidating the complex relationship between albumin and erythrocyte mechanics in physiological and pathological conditions. Full article

Methods such as AlphaFold have revolutionized protein structure prediction, making quantitative prediction of the thermodynamic stability of individual proteins and their complexes one of the next frontiers in computational protein modeling. Here, we develop methods for using protein language models (PLMs) with protein mutational datasets related to protein tertiary and quaternary stability. First, we demonstrate that fine-tuning of a ProtT5 PLM enables accurate prediction of the largest protein mutant stability dataset available. Next, we show that mutational impacts on protein function can be captured by fine-tuning PLMs, using green fluorescent protein (GFP) brightness as a readout of folding and stability. In our final case study, we observe that PLMs can also be extended to protein complexes by identifying mutations that are stabilizing or destabilizing. Finally, we confirmed that state-of-the-art simulation methods (free energy perturbation) can refine the accuracy of predictions made by PLMs. This study highlights the versatility of PLMs and demonstrates their application towards the prediction of protein and complex stability. Full article

The mevalonate pathway is crucial for synthesizing isopentenyl pyrophosphate (IPP), the universal precursor of terpenoids, with 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) serving as the rate-determining enzyme that catalyzes the reduction of 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) to mevalonate, requiring NAD(P)H as an electron donor. Improving the cofactor promiscuity of HMGR can facilitate substrate utilization and terpenoid production by overcoming cofactor specificity limitations. In this study, we heterologously expressed rpHMGR from Ruegeria pomeroyi in Escherichia coli BL21(DE3) for the first time and established that it predominantly utilizes NADH. To broaden its cofactor usage, we employed Molecular Operating Environment (MOE)-assisted design to engineer the cofactor binding site, creating a dual-cofactor-utilizing mutant, D154K (the substitution of aspartic acid with lysine at residue 154). This mutant exhibited a significant 53.7-fold increase in activity toward NADPH, without compromising protein stability at physiological temperatures. The D154K mutant displayed an optimal pH of 6, maintaining over 80% of its catalytic activity across the pH range of 6–8, regardless of whether NADH or NADPH was the cofactor. These findings highlight the value of rational design, enhance our understanding of HMGR-cofactor recognition mechanisms, and provide a foundation for future efforts to optimize and engineer HMGR for broader cofactor flexibility. Full article

In the present investigation, an eco-friendly biocatalyst was developed using Pleurotus eryngii laccase (PeLac) through a copper (Cu)-based protein–inorganic hybrid system for the degradation of bisphenol A, a representative xenobiotic. After partial purification, the specific activity of crude PeLac was 92.6 U/mg of total protein. Immobilization of PeLac as Cu₃(PO₄)₂–Lac (Cu–PeLac) nanoflowers (NFs) at 4 °C resulted in a relative activity 333% higher than that of the free enzyme. The Cu–PeLac NFs exhibited greater pH and temperature stability and enhanced catalytic activity compared to free laccase. This enhanced activity was validated through improved electrochemical properties. After immobilization, Cu–PeLac NFs retained up to 8.7-fold higher residual activity after storage at 4 °C for 30 days. Free and immobilized laccase degraded bisphenol A by 41.6% and 99.8%, respectively, after 2 h of incubation at 30 °C. After ten cycles, Cu–PeLac NFs retained 91.2% degradation efficiency. In the presence of potent laccase inhibitors, Cu–PeLac NFs exhibited a 47.3-fold improvement in bisphenol A degradation compared to free PeLac. Additionally, the synthesized Cu–PeLac NFs demonstrated lower acute toxicity against Vibrio fischeri than Cu nanoparticles. This study presents the first report of PeLac immobilization through an eco-friendly protein–inorganic hybrid system, with promising potential for degrading bisphenol A in the presence of inhibitors to support sustainable development. Full article

The 26S proteasome is a large, ATP-dependent proteolytic complex responsible for degrading ubiquitinated proteins in eukaryotic cells. It plays a crucial role in maintaining cellular protein homeostasis by selectively eliminating misfolded, damaged, or regulatory proteins marked for degradation. In this study, whole-exome sequencing (WES) was performed on an individual presenting with developmental delay and mild intellectual disability, as well as on both of his unaffected parents. This analysis identified a de novo variant, c.959C>G (p.Pro320Arg), in the PSMC5 gene. As predicted, this gene shows a very likely autosomal dominant inheritance pattern. Notably, PSMC5 has not previously been associated with any phenotype in the OMIM database. This variant was recently submitted to the ClinVar database as a variant of uncertain significance (VUS) and remains absent in both gnomAD and dbSNP. Notably, it has been identified in six unrelated individuals presenting with clinical features comparable to those observed in the patient described in this study. Multiple in silico prediction tools classified the variant as pathogenic, and a PhyloP conservation score supports strong evolutionary conservation of the mutated nucleotide. Protein structure predictions using the AlphaFold3 algorithm revealed notable structural differences between the mutant and wild-type PSMC5 proteins. We hypothesize that the p.Pro320Arg substitution alters the structure and function of PSMC5 as a regulatory subunit of the 26S proteasome, potentially impairing the stability and activity of the entire complex. Although functional studies are imperative, this study contributes to a deeper understanding of PSMC5, expands the spectrum of associated neurodevelopmental phenotypes, and highlights its potential as a therapeutic target. Furthermore, this study resulted in the submission of the identified variant to the ClinVar database (SCV006083352), where it was classified as pathogenic. Full article

Tomato chlorosis virus (ToCV) is a highly infectious plant virus that poses a significant threat to the Solanaceae family worldwide. Despite its widespread impact, effective control remains challenging due to its vector-borne transmission by whiteflies. To facilitate early detection and potential therapeutic intervention, this study aimed to identify diagnostic epitopes through a comprehensive bioinformatics approach combining comparative genomics and artificial intelligence-based structural modeling. We analyzed forty-four complete ToCV genomes to identify highly conserved regions and uncovered an orphan clade, indicating evolutionary divergence. Subcellular localization and transmembrane domain predictions revealed viral proteins with extracellularly exposed peptide regions. Structural modeling using AlphaFold3 further validated the stability and accessibility of these domains. By integrating these findings with epitope prediction algorithms, this study identified four highly promising epitope candidates, which are suitable for the development of antibody-based diagnostic kits and antiviral therapeutics targeting ToCV. These epitopes provide a strong foundation for the development of antibody-based diagnostic kits or antiviral therapeutics targeting ToCV. Full article

Direct stochastic optical reconstruction microscopy (dSTORM) circumvents the diffraction limit of light, emerging as a powerful superresolution technique for visualizing subcellular structures with a nanoscale resolution of 10–20 nm. Yet achieving ultrastructural resolution using dSTORM alone remains challenging, despite its advantage of requiring only minimal modifications to the imaging setup and sample preparation compared to conventional fluorescence microscopy. A recent advancement that integrates expansion microscopy (ExM), which embeds specimens in a swellable polymer gel, with dSTORM holds promise for attaining imaging resolutions below 10 nm. The combined resolution, however, is governed by the expansion factor of samples, and prior studies have primarily focused on integrations involving approximately 4-fold gel expansion, as dSTORM imaging of high-fold-expanded specimens is still technically demanding. Here, we propose a pragmatic expansion strategy—post-labeling ten-fold robust expansion microscopy (plTREx)—and outline a workflow to facilitate its compatibility with dSTORM, collectively termed plTREx-dSTORM. Specifically, this workflow enhances the mechanical stability of the expansion hydrogel and improves fluorescence signal density across both widefield and dSTORM imaging platforms. Furthermore, we optimize the re-embedding protocol to integrate hydrogel expansion with dSTORM while preventing gel shrinkage. Together, plTREx-dSTORM enables highly refined imaging capable of ultrastructural interpretation of cellular proteins, effectively bridging the resolution gap between electron microscopy and optical microscopy. Full article

Fabry disease is a rare genetic disorder caused by deficient activity of the lysosomal enzyme alpha-galactosidase A (AGAL), resulting in the accumulation of globotriaosylceramides (Gb3) in tissues and organs. This buildup leads to progressive, multi-systemic complications that severely impact quality of life and can be life-threatening. Interpreting the functional consequences of missense variants in the GLA gene remains a significant challenge, especially in rare diseases where experimental evidence is scarce. In this study, we present an integrative computational framework that combines structural, interaction, pathogenicity, and stability data from both in silico tools and experimental sources, enriched through expert curation and structural analysis. Given the clinical relevance of pharmacological chaperones in Fabry disease, we focus in particular on the structural characteristics of variants classified as “amenable” to such treatments. Our multidimensional analysis—using tools such as AlphaMissense, EVE, FoldX, and ChimeraX—identifies key molecular features that distinguish amenable from non-amenable variants. We find that amenable mutations tend to preserve protein stability, while non-amenable ones are associated with structural destabilisation. By comparing AlphaMissense with alternative predictors rooted in evolutionary (EVE) and thermodynamic (FoldX) models, we explore the relative contribution of different biological paradigms to variant classification. Additionally, the investigation of outlier variants—where AlphaMissense predictions diverge from clinical annotations—highlights candidates for further experimental validation. These findings demonstrate how combining structural bioinformatics with machine learning–based predictions can improve missense variant interpretation and support precision medicine in rare genetic disorders. Full article

Phosphomannomutase 2 (PMM2) catalyzes the interconversion of mannose-6-phosphate and mannose-1-phosphate, a key step in the biosynthesis of GDP-mannose for N-glycosylation. Its deficiency is the most common cause of congenital disorders of glycosylation (CDGs), accounting for the subtype known as PMM2-CDG. PMM2-CDG is a rare autosomal recessive disease characterized by multisystemic dysfunction, including cerebellar atrophy, peripheral neuropathy, developmental delay, and coagulation abnormalities. The disease is associated with a spectrum of pathogenic missense mutations, particularly at residues involved in dimerization and catalytic function (i.e., p.Phe119Leu and p.Arg141His). The dimerization of PMM2 is considered essential for enzymatic activity, although it remains unclear whether this supports structural stability alone, or whether both subunits are catalytically active—a distinction that may affect how mutations in each monomer contribute to overall enzyme function and disease phenotype. PMM2 has a paralog, phosphomannomutase 1 (PMM1), which shares substantial structural similarity—including obligate dimerization—and displays mutase activity in vitro, but does not compensate for PMM2 deficiency in vivo. To investigate potential heterodimerization between PMM1 and PMM2 and the effect of interface mutations over PMM2 dimer stability, we first assessed the likelihood of their co-expression using data from GTEx and the Human Protein Atlas. Building on this expression evidence, we modeled all possible dimeric combinations between the two paralogs using AlphaFold3. Models of the PMM2 and PMM1 homodimers were used as internal controls and aligned closely with their respective reference biological assemblies (RMSD < 1 Å). In contrast, the PMM2/PMM1 heterodimer model, the primary result of interest, showed high overall confidence (pLDDT > 90), a low inter-chain predicted alignment error (PAE∼1 Å), and robust interface confidence scores (iPTM = 0.80). Then, we applied PISA, PRODIGY, and mmCSM-PPI to assess interface energetics and evaluate the impact of missense variants specifically at the dimerization interface. Structural modeling suggested that PMM2/PMM1 heterodimers were energetically viable, although slightly less stable than PMM2 homodimers. Interface mutations were predicted to reduce dimer stability, potentially contributing to the destabilizing effects of disease-associated variants. These findings offer a structural framework for understanding PMM2 dimerization, highlighting the role of interface stability, paralogs co-expression, and sensitivity to disease-associated mutations. Full article

The endoplasmic reticulum mediates essential processes such as protein folding, transport, and post-translational modifications. Disruptions in endoplasmic reticulum function can lead to the accumulation of unfolded or misfolded proteins, initiating endoplasmic reticulum stress. This stress activates the unfolded protein response, a multifaceted signaling pathway aimed at restoring proteostasis, which is crucial for cellular survival and fate determination. This review summarizes the current knowledge of three major branches of the unfolded protein response: the IRE1, PERK, and ATF6 signaling pathways. A key novel component in endoplasmic reticulum stress adaptation is the redox-sensitive enzyme glutathione peroxidase 8 (GPX8), which plays a dual role in detoxifying hydrogen peroxide and supporting proper protein folding. By connecting unfolded protein response branches, GPX8 reduces oxidative damage while maintaining redox homeostasis, emphasizing its importance in endoplasmic reticulum stability. Furthermore, plant glutathione peroxidases exhibit parallel functions in endoplasmic reticulum redox homeostasis and unfolded protein response activation, highlighting the evolutionary conservation of this protective mechanism across kingdoms. Understanding the intricate relationship between GPX8, endoplasmic reticulum stress, and unfolded protein response signaling provides novel insights into therapeutic strategies for diseases characterized by protein folding defects and oxidative stress. Full article

The ongoing threat of viral pandemics such as COVID-19 highlights the urgent need for novel antiviral therapeutics targeting conserved viral proteins. In this study, peptides of 10–30 kDa derived from the marine diatom Phaeodactylum tricornutum were identified as potential inhibitors of SARS-CoV-2 main protease (Mpro), a key enzyme in viral replication. Peptides less than 60 amino acids in length were retrieved from the UniProt database and aligned with reference antiviral sequences using the Biopython pairwise2 algorithm. Six candidates were selected for structural modeling using AlphaFold2 and Swiss-Model, followed by molecular docking using ClusPro2. LigPlot+ was used to assess molecular interactions, while NetMHCpan 4.1 and AVPpred evaluated immunogenicity and antiviral potential, respectively. Molecular dynamics simulations over 100 ns were conducted using OpenMM. These peptides demonstrated stable binding interactions with key catalytic residues of Mpro. Specifically, peptide A0A8J9SA87 interacted with Cys145 and Glu166, while peptide A0A8J9SDW0 exhibited interactions with His41 and Phe140, both of which are known to be essential for Mpro inhibition. Although peptide A0A8J9X3P8 also interacted with catalytic residues, it exhibited greater structural fluctuations during molecular dynamics simulations and achieved lower AVPpred scores, suggesting lower overall antiviral potential. Therefore, A0A8J9SA87 and A0A8J9SDW0 were identified as the most promising candidates. Molecular dynamics simulations further supported the high structural stability of these peptide-Mpro complexes over a 100 ns timescale, reinforcing their potential as effective inhibitors. These findings support P. tricornutum as a valuable source of antiviral peptides and demonstrate the feasibility of in silico pipelines for identifying therapeutic candidates against SARS-CoV-2. Full article

Preparative protein crystallization is regarded as an economically sustainable protein purification alternative to chromatography in biotechnological downstream processing. However, protein crystallization is a not-well-understood process that is usually slow and poorly reproducible. A promising strategy for enhancing protein crystallization is exploiting the metastable liquid–liquid phase separation (LLPS) of protein solutions. Here, we report an enhancement of lysozyme-crystallization yield by using a combination of two additives under LLPS conditions. The first additive, NaCl (0.15 M), is necessary to introduce protein–protein attractive interactions and induce LLPS by lowering temperature. The second additive, 4-(2-hydroxyethyl)-1-piperazineethanesulfonate (HEPES, 0.10 M, pH 7.4), accumulates in the metastable protein-rich liquid phase and thermodynamically stabilizes lysozyme crystals. We found that this combination of additives leads to crystallization yields of higher than 90% under LLPS conditions at a lysozyme concentration of 5% by weight and a fairly low ionic strength (0.2 M) within an operational time of the order of one hour. This crystallization yield is more than three-fold larger than that obtained from samples containing NaCl without HEPES at the same pH and ionic strength. Moreover, we determined crystallization yield as a function of incubation time, and temperature below and above the LLPS boundary. As crystallization temperature intersects with LLPS temperature, a significant increase in crystallization yield is observed. This is consistent with LLPS boosting protein crystallization. Our work suggests a possible strategy for increasing the crystallization success of other proteins, with applications in protein purification. Full article

Rhodopsin, a G-protein-coupled receptor (GPCR) comprising the protein opsin covalently linked to the chromophore 11-cis retinal, is pivotal in visual phototransduction. Mutations in the gene encoding rhodopsin (RHO) can cause opsin misfolding or reduce its stability, resulting in retinal degenerative disorders such as retinitis pigmentosa (RP). Current therapeutic strategies employing retinoid-based chaperones partially rescue the folding and trafficking of mutant rhodopsin, but are limited by inherent toxicity and instability due to photoinduced isomerization. In the present work, a pharmacophore-based virtual screening protocol combined with molecular docking and molecular dynamics simulations was employed, leading to the identification of a novel non-retinoid opsin ligand that can potentially act as a pharmacological chaperone. Biological validation confirmed that the compound VS1 binds opsin effectively, representing a valuable starting point for structure-based optimization studies aimed at identifying new opsin stabilizers. Full article