Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “proteome stability”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3Linked to original sources
PubMed2004

[DDS and Me].

With the success of the human genome project, the focus of life science research has shifted to the functional and structural analyses of proteins, such as proteomics and structural genomics. These analyses of proteins including newly identified proteins are expected to contribute to the identification of therapeutically applicable proteins for various diseases. Thus, pharmaco-proteomic-based drug discovery and development for protein therapies, including gene therapy, cell therapy, and vaccine therapy, is attracting current attention. However, there is clinical difficulty in using almost all bioactive proteins, because of their very low stability and pleiotropic actions in vivo. To promote pharmaco-proteomic-based drug discovery and development, we have attempted to develop drug delivery systems (DDSs), such as the protein-drug innovation system and the optimal cell therapeutic system. In this review, we introduce our original DDSs.

Animals↗
PubMed2026

Multidimensional Proteomics Reveals the Pro-apoptotic Mechanism of Platycodin D: Targeting RFC4 to Regulate the Notch Signaling Axis in Non-Small Cell Lung Cancer.

Platycodin D (PD), a major bioactive saponin isolated from the traditional Chinese medicine Platycodon grandiflorus, has shown promising therapeutic potential against non-small cell lung cancer (NSCLC). However, the functional mechanisms of PD in NSCLC progression remains unclear. This study aimed to explore the pharmacological mechanism of PD against NSCLC. Thermal proteome profiling approach, molecular docking, cellular thermal shift assay and peptide-centric local stability assay were employed to identify the potential binding target of PD. Subsequent Western Blot and immunoprecipitation-Western Blot experiments were conducted to investigate the downstream signaling pathways of the target. Furthermore, proteomic and ubiquitinomic profiling of PD-treated cells were performed to investigate its functions on global. replication factor C subunit 4 (RFC4) was identified as a potential binding target of PD by thermal proteome profiling and their binding sites were further exposed by peptide-centric local stability assay. PD-RFC4 complex promotes the degradation of Notch1 and Notch3 by reducing nuclear entry of their domains. Compared with control treatment, the differentially expressed proteins induced by PD were found to be primarily involved in ferroptosis, ubiquitination, platinum drug resistance, and ribosome-related processes. The ubiquitin proteome analysis revealed that proteins associated with the Notch pathway underwent ubiquitin modifications. PD binds to RFC4 and inhibits its activity, leading to downregulation of the Notch signaling pathway, ultimately triggering cancer cell apoptosis. PD is a natural product with potential therapeutic value for NSCLC.

Saponins↗
PubMed2006

Proteomic analysis of adaptor protein 1A coats selectively assembled on liposomes.

Coat components localize to specific membrane domains, where they sort selected transmembrane proteins. To study how clathrin coats are stabilized on such domains and to identify the protein networks involved, we combined proteomic screens and in vitro liposome-based assays that recapitulate the fidelity of protein sorting in vivo. Our study identifying approximately 40 proteins on AP-1A-coated liposomes revealed that AP-1A coat assembly triggers the concomitant recruitment of Rac1, its effectors, and the Wave/Scar complex as well as that of Rab11 and Rab14. The coordinated recruitment of these different machineries requires a mosaic of membrane components comprising the GTPase ADP-ribosylation factor 1, sorting signals in selected transmembrane proteins, and phosphatidylinositol 4-phosphate. These results demonstrate that the combinatorial use of low-affinity binding sites present on the same membrane domain accounts not only for a selective coat assembly but also for the coordinated assembly of selected machineries required for actin polymerization and subsequent membrane fusion.

Actins↗
PubMed2026

Elevated 5-oxoproline levels and adverse outcomes in heart failure: Association with renal cortical OPLAH loss in a multi-comorbidity model.

BACKGROUND: Heart failure (HF) progression is closely linked to oxidative stress. 5-Oxoproline (5-OP), a product of glutathione degradation, is normally metabolized by 5-oxoprolinase (OPLAH) but accumulates when the gamma-glutamyl cycle is disrupted. Here, we investigated the clinical characteristics of circulating 5-OP, its proteomic correlates, and the associations to outcome in HF. METHODS: In serum of 823 BIOSTAT-CHF patients, 5-OP was quantified by validated liquid chromatography-mass spectrometry and analyzed for associations with clinical outcomes. Proteomic correlates were identified across 355 OLINK proteins using stability selection with Minimax Concave Penalty regression. Mechanistic context was evaluated in a multi-comorbidity, large-animal cardio-kidney-metabolic (CKM) model with regional OPLAH assessment. RESULTS: Higher 5-OP was associated with worse renal function (eGFR declining across 5-OP tertiles, 67.9 to 60.2 mL/min/1.73 m2; p = 0.0012) and higher all-cause mortality (HR 1.55, 95% CI 1.11-2.17, p = 0.010). Per SD increase in log-5-OP, risk for the 2-year composite endpoint increased (HR 1.27, 95% CI 1.05-1.53), with broadly similar associations across CKD strata (interaction p = 0.63). TGF-α was the most robust proteomic correlate (π = 0.70; empirical permutation p = 0.001). In CKM swine, circulating 5-OP was elevated and renal cortical OPLAH protein, but not cardiac OPLAH, was selectively reduced, consistent with a renal contribution to systemic 5-OP elevation. CONCLUSION: Circulating 5-OP identifies HF patients at higher risk and is robustly associated with TGF-α. In a translational swine model, selective loss of renal cortical OPLAH provides tissue context supporting a renal contribution to systemic 5-OP elevation in cardiorenal syndrome.

Heart Failure↗
PubMed2026

A Robust, Self-Digestion-Resistant LysN with Superior Activity and Cleavage Fidelity for Advanced Proteomic Workflows.

LysN is a valuable protease in proteomics because it cleaves peptide bonds N-terminal to lysine, generating peptides with physicochemical properties complementary to those produced by LysC and trypsin. However, the broader adoption of LysN in proteomic workflows has been limited by the lack of commercially available enzymes that combine high activity, low missed-cleavage rates, and sufficient stability under practical sample-processing conditions. Here, we report the recombinant production and proteomic characterization of a self-digestion-resistant and highly active LysN from Shewanella loihica (SL-LysN). Using terminomics, we mapped the mature N- and C-termini of the enzyme and established the primary structure of the active protease. We further developed a high-density fermentation, refolding, and purification workflow to obtain highly purified recombinant SL-LysN. Biochemical and proteomic benchmarking showed that SL-LysN displayed 3.3-fold higher specific activity than commercial LysN and reduced missed cleavages by approximately 80%. Notably, SL-LysN retained high activity in the presence of 8 M urea or 1% SDS and showed strong resistance to autolysis, indicating exceptional robustness for proteomic sample preparation. In complex mammalian proteome digests, SL-LysN achieved >95% cleavage specificity and a missed-cleavage rate of only 5.9%. These features address a long-standing bottleneck in N-terminal proteolysis and establish SL-LysN as a high-performance enzymatic tool for advanced proteomic workflows, including deep protein sequencing, quantitative proteomics, terminomics, de novo sequencing and analyses requiring efficient digestion under denaturing conditions.

Shewanella↗
PubMed2024

Mass Spectrometry-Based Proteomics for Assessing Epitranscriptomic Regulations.

Epitranscriptomics is a rapidly evolving field that explores chemical modifications in RNA and how they contribute to dynamic and reversible regulations of gene expression. These modifications, for example, N6-methyladenosine (m6A), are crucial in various RNA metabolic processes, including splicing, stability, subcellular localization, and translation efficiency of mRNAs. Mass spectrometry-based proteomics has become an indispensable tool in unraveling the complexities of epitranscriptomics, offering high-throughput, precise protein identification, and accurate quantification of differential protein expression. Over the past two decades, advances in mass spectrometry, including the improvement of high-resolution mass spectrometers and innovative sample preparation methods, have allowed researchers to perform in-depth analyses of epitranscriptomic regulations. This review focuses on the applications of bottom-up proteomics in the field of epitranscriptomics, particularly in identifying and quantifying epitranscriptomic reader, writer, and eraser (RWE) proteins and in characterizing their functions, posttranslational modifications, and interactions with other proteins. Together, by leveraging modern proteomics, researchers can gain deep insights into the intricate regulatory networks of RNA modifications, advancing fundamental biology, and fostering potential therapeutic applications.

Proteomics↗
PubMed2006

Proteomic analysis and comparison of the biopsy and autopsy specimen of human brain temporal lobe.

The proteomic study on human temporal lobe can help us to understand the physiological function of CNS in normal as well as in pathological state. Proteomic tools are potent for the assessment of protein stability post mortem. In this pilot study, the human temporal lobe biopsy specimen with chronic pharmacoresistant temporal lobe epilepsy (TLE) and autopsy specimen in control were separated by 2-DE. Using MALDI-TOF-MS and MS/MS, 375 protein spots were identified which were the products of 267 genes. Six down-regulated and 23 up-regulated protein spots in the autopsy specimen were ascertained after the gel image analysis with the ImageMaster software. A number of proteins that include neurotransmitter metabolic and glycolytic enzymes, cytoprotective proteins and cytoskeleton were found decreased while the precursor of apolipoprotein A-I increased in the TLE brain. We tried several methods to prepare the protein samples and found that DNase and RNase treatment, ultracentrifugation and Amersham clean-up kit purification can improve gel separation quality. This work optimized the sample preparation method and constructed a primary protein database of human temporal lobe and found some proteins with remarkable level change probably involved in the post-mortem process and chronic pharmacoresistant TLE pathogenesis.

Autopsy↗
PubMed2004

Markovian Backbone Negentropies: Molecular descriptors for protein research. I. Predicting protein stability in Arc repressor mutants.

As more and more protein structures are determined and applied to drug manufacture, there is increasing interest in studying their stability. In this sense, developing novel computational methods to predict and study protein stability in relation to their amino acid sequences has become a significant goal in applied Proteomics. In the study described here, Markovian Backbone Negentropies (MBN) have been introduced in order to model the effect on protein stability of a complete set of alanine substitutions in the Arc repressor. A total of 53 proteins were studied by means of Linear Discriminant Analysis using MBN as molecular descriptors. MBN are molecular descriptors based on a Markov chain model of electron delocalization throughout the protein backbone. The model correctly classified 43 out of 53 (81.13%) proteins according to their thermal stability. More specifically, the model classified 20/28 (71.4%) proteins with near wild-type stability and 23/25 (92%) proteins with reduced stability. Moreover, the model presented a good Mathew's regression coefficient of 0.643. Validation of the model was carried out by several Jackknife procedures. The method compares favorably with surface-dependent and thermodynamic parameter stability scoring functions. For instance, the D-FIRE potential classification function shows a level of good classification of 76.9%. On the other hand, surface, volume, logP, and molar refractivity show accuracies of 70.7, 62.3, 59.0, and 60.0%, respectively.

Alanine↗
PubMed2026

Body mass index-specific nanoparticle protein corona signatures in late pregnancy.

The protein corona (PC) formed on the surface of nanoparticles (NPs) upon exposure to human biofluids is a dynamic interface that reflects the physiological and pathological status of the host. In this study, we investigated how the maternal body mass index (BMI) influences the composition of the NPs' PC during late pregnancy. Polystyrene NPs were incubated with plasma samples collected from third-trimester pregnant individuals across normal weight, overweight, and obese BMI categories. Comprehensive characterization using dynamic light scattering (DLS), zeta potential measurements, and transmission electron microscopy (TEM) confirmed BMI-dependent differences in PC thickness and colloidal stability. SDS-PAGE and label-free quantitative proteomics revealed distinct molecular compositions: PCs from obese individuals were enriched in inflammatory and lipid metabolism-associated proteins (e.g., APOE and CRP), while normal weight-derived PCs showed higher levels of complementary regulators and extracellular matrix proteins. Principal component analysis (PCA) demonstrated clear clustering of proteomic profiles by the BMI group, suggesting BMI-specific PC fingerprints. These findings indicate that the maternal metabolic phenotype shapes nano-bio interactions at the proteomic level and highlight the potential of PC profiling as a non-invasive approach for assessing maternal health and metabolic status. This work lays the foundation for integrating NP-based proteomics into precision nanomedicine for maternal-fetal health monitoring.

Female↗
PubMed2026

Systematic differences in protein stability underlie species-specific developmental tempo.

Human embryonic development proceeds more slowly than in mice. The segmentation clock offers a tractable model for studying species-specific developmental tempo, as its oscillation period in human induced presomitic mesoderm (iPSM) cells is approximately twice that of mouse. While the core clock gene HES7 exhibits slower protein degradation in human cells, it remains unclear whether such cross-species differences in protein stability reflect a general principle. Here, we perform a dynamic stable isotope labeling of amino acids in cell culture (SILAC)-based proteomic analysis of ∼5,000 proteins in human and mouse iPSM, and we uncover a broad trend of slower protein degradation in human cells, regardless of subcellular localization or degradation pathways. Moreover, inhibition of glycolysis in mouse iPSM partially phenocopies the human protein stability profile, and modulation of protein stability alters the tempo of both the segmentation clock and cellular differentiation. Our findings establish protein stability, with systematic differences across species, as a key mediator linking metabolism to developmental tempo.

Animals↗
PubMed2003

Granular gland transcriptomes in stimulated amphibian skin secretions.

Amphibian defensive skin secretions are complex, species-specific cocktails of biologically active molecules, including many uncharacterized peptides. The study of such secretions for novel peptide discovery is time-limited, as amphibians are in rapid global decline. While secretion proteome analysis is non-lethal, transcriptome analysis has until now required killing of specimens prior to skin dissection for cDNA library construction. Here we present the discovery that polyadenylated mRNAs encoding dermal granular gland peptides are present in defensive skin secretions, stabilized by endogenous nucleic acid-binding amphipathic peptides. Thus parallel secretory proteome and transcriptome analyses can be performed without killing the specimen in this model amphibian system--a finding that has important implications in conservation of biodiversity within this threatened vertebrate taxon and whose mechanistics may have broader implications in biomolecular science.

Alternative Splicing↗
PubMed2024

Revealing novel protein interaction partners of glyphosate in Escherichia coli.

Despite all debates about its safe use, glyphosate remains the most widely applied active ingredient in herbicide products, with renewed approval in the European Union until 2033. Non-target organisms are commonly exposed to glyphosate as a matter of its mode of application, with its broader environmental and biological impacts remaining under investigation. Glyphosate displays structural similarity to phosphoenolpyruvate (PEP), thereby competitively inhibiting the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), crucial for the synthesis of aromatic amino acids in plants, fungi, bacteria, and archaea. Most microbes, including the gut bacterium Escherichia coli (E. coli), possess a glyphosate-sensitive class I EPSPS, making them vulnerable to glyphosate's effects. Yet, little is known about glyphosate's interactions with other bacterial proteins or its broader modes of action at the proteome level. Here, we employed a quantitative proteomics and thermal proteome profiling (TPP) approach to identify novel protein binding partners of glyphosate in the E. coli proteome. Glyphosate exposure significantly altered amino acid synthesizing pathways. The abundance of shikimate pathway proteins was increased, suggesting a compensatory mechanism. Extracellular riboflavin concentrations were elevated upon glyphosate exposure, while intracellular levels remained stable. Beyond the target enzyme EPSPS, thermal proteome profiling indicated an effect of glyphosate on the thermal stability of certain proteins, including AroH and ProA, indicating interactions. Similar to the competitive binding between PEP and glyphosate at EPSPS, one reason for the interaction of AroH and ProA with the herbicide could be a high structural similarity between their substrates and glyphosate. Overall, glyphosate induced metabolic disturbances in E. coli, extending beyond its primary target, thereby providing new insights into glyphosate's broader impact on microbial systems.

Glyphosate↗
PubMed2026

The proteomic origin of the genetic code.

INTRODUCTION: The origin and evolution of the genetic code is a central problem in molecular biology. Classical models have emphasized stereochemistry, frozen accidents, or adaptive optimization, often treating proteins as passive products of preexisting codes. More recent views instead portray the code as a dynamic, coevolving system shaped by reciprocal interactions among amino acids, RNA, and early catalysts. AREAS COVERED: Here, I review efforts of phylogeny reconstruction of the history of tRNA, protein structural domains, and dipeptide sequences in proteomes. These complementary approaches allow exploration of the entry of amino acids and codons into the code, and the transition from an operational RNA code in the tRNA acceptor arm to the canonical code in the anticodon loop. Evidence for ancestral synthetase enzymes with dual functions in aminoacylation and peptide-bond formation, as well as early bidirectional (sense-antisense) coding reflected in dipeptide-antidipeptide emergence is also discussed. EXPERT OPINION: The genetic code is best viewed as a proteome-driven, evolvable system in which early peptides actively shaped coding rules by stabilizing structure, expanding chemical diversity, and enhancing catalysis. This perspective connects origin-of-life studies with modern efforts of code expansion, translational engineering, and peptide-based therapeutics, highlighting the impact of the code's proteomic origin.

Genetic Code↗
PubMed2003

A high-yield method to extract peptides from rat brain tissue.

A process to extract and enrich extracellular peptides and proteins from tissues should have broad utility in the burgeoning proteomics field. To address this need, a novel three-step protocol was developed to extract polypeptides from whole tissue samples and enrich the extracellular components. The initial homogenization of rat brain was carried out at neutral pH to optimize protein and peptide stability and solubility. Subsequent covalent chromatography on an activated thiopropyl resin was employed to debulk the tissue extract by selectively removing a substantial fraction of the intracellular protein component under nondenaturing conditions. Finally, extraction with 0.1% trifluoroacetic acid was used to selectively precipitate large proteins while enhancing the solubility of smaller proteins and peptides. The fractions from each step in the process were compared to a single extract obtained by homogenization in 0.5 M acetic acid. The recovery and yields of endogenous neuropeptides and an exogenously added peptide were evaluated by enzyme immunoassay and Western blotting, respectively. In summary, the three-step protocol was superior to the extraction of tissue with 0.5 M acetic acid in terms of peptide recovery, enrichment, and sample stability. Enrichment of the extracellular protein compartment from tissues should be valuable in proteomics experiments aimed at identifying biomarkers that can partition into serum.

Animals↗
PubMed2003

Protein micro- and macroarrays: digitizing the proteome.

The early applications of microarrays and detection technologies have been centered on DNA-based applications. The application of array technologies to proteomics is now occurring at a rapid rate. Numerous researchers have begun to develop technologies for the creation of microarrays of protein-based screening tools. The stability of antibody molecules when bound to surfaces has made antibody arrays a starting point for proteomic microarray technology. To minimize disadvantages due to size and availability, some researchers have instead opted for antibody fragments, antibody mimics or phage display technology to create libraries for protein chips. Even further removed from antibodies are libraries of aptamers, which are single-stranded oligonucleotides that express high affinity for protein molecules. A variation on the theme of protein chips arrayed with antibody mimics or other protein capture ligand is that of affinity MS where the protein chips are directly placed in a mass spectrometer for detection. Other approaches include the creation of intact protein microarrays directly on glass slides or chips. Although many of the proteins may likely be denatured, successful screening has been demonstrated. The investigation of protein-protein interactions has formed the basis of a technique called yeast two-hybrid. In this method, yeast "bait" proteins can be probed with other yeast "prey" proteins fused to DNA binding domains. Although the current interpretation of protein arrays emphasizes microarray grids of proteins or ligands on glass slides or chips, 2-D gels are technically macroarrays of authentic proteins. In an innovative departure from the traditional concept of protein chips, some researchers are implementing microfluidic printing of arrayed chemistries on individual protein spots blotted onto membranes. Other researchers are using in-jet printing technology to create protein microarrays on chips. The rapid growth of proteomics and the active climate for new technology is driving a new generation of companies and academic efforts that are developing novel protein microarray techniques for the future.

Protein Array Analysis↗
PubMed2025

Multicompartment Quantitative Proteomics Revealing Potential Mechanisms Underlying the Treatment Effects of Mesenchymal-Derived Extracellular Vesicles in a Monkey Model of Cortical Injury.

Previous studies have demonstrated that mesenchymal stromal cell-derived extracellular vesicles (MSC-EVs) enhance functional recovery after cortical injury in rhesus monkeys by reducing chronic microglial inflammation, neuronal damage, and myelination deficits. However, the signaling pathways underlying these therapeutic effects remain largely unexplored. In this study, employing a reliable quantitative proteomics platform UHR-IonStar, we identified the protein cargo of MSC-EVs infused intravenously to rhesus monkeys 24 h and 2 weeks post-injury to the motor cortex. We then analyzed global protein expression changes across cerebrospinal fluid (CSF), plasma, and brain tissue of MSC-EV-treated versus vehicle-treated female, aged rhesus monkeys. A total of 1241/431/4124 monkey proteins were reliably quantified in CSF/plasma/tissue samples, respectively. Longitudinal analysis of CSF and plasma samples highlighted a shift from MSC-EV modulation of inflammatory and metabolic proteins in plasma at early recovery (2 weeks), toward modulation of plasticity-related proteins in CSF and brain tissue at later stages (4 weeks). Further protein-protein interaction analysis identified potential MSC-EV targets related to complementary signaling, proteolysis, and aminoglycan stability, which aligned with our previous findings. This comprehensive, multicompartment monkey proteomics study advances understanding of MSC-EV contents and treatment effects, paving the way for novel treatment of cortical injury.

Animals↗
PubMed2006

Collection, processing, and storage of biological samples in epidemiologic studies: sex hormones, carotenoids, inflammatory markers, and proteomics as examples.

The measurement of biomarkers in blood specimens has become an integral component of many epidemiologic studies and introduces several decision points about specimen collection, processing, and storage for the investigator. We briefly discuss the current state of knowledge for four commonly assessed biomarkers: estrogens and other sex hormones, ascorbic acid and carotenoids, cytokines involved in the inflammatory response, and proteomics. Sex hormones are relatively robust to type of sample collected, delayed processing (if chilled), and long-term storage at <-70 degrees C. Ascorbic acid and carotenoids also are relatively robust to sample type and delayed processing (if chilled); however, the blood sample should not be exposed to sunlight and must be stored at <-70 degrees C to prevent substantial degradation. If ascorbic acid is of primary interest, an acid stabilizer should be added during processing. Less is known for cytokines and proteomics, although initial research suggests that these assays are sensitive to varying collection, processing, and storage methods. Overall, we recommend conducting pilot studies if any nonstandard collection, processing, or storage procedure is used. Finally, decisions about these issues depend primarily on the scientific questions of most interest, cost, flexibility, and resources.

Ascorbic Acid↗
PubMed2005

Detecting protein-protein interactions with a green fluorescent protein fragment reassembly trap: scope and mechanism.

Identification of protein binding partners is one of the key challenges of proteomics. We recently introduced a screen for detecting protein-protein interactions based on reassembly of dissected fragments of green fluorescent protein fused to interacting peptides. Here, we present a set of comaintained Escherichia coli plasmids for the facile subcloning of fusions to the green fluorescent protein fragments. Using a library of antiparallel leucine zippers, we have shown that the screen can detect very weak interactions (K(D) approximately 1 mM). In vitro kinetics show that the reassembly reaction is essentially irreversible, suggesting that the screen may be useful for detecting transient interactions. Finally, we used the screen to discriminate cognate from noncognate protein-ligand interactions for tetratricopeptide repeat domains. These experiments demonstrate the general utility of the screen for larger proteins and elucidate mechanistic details to guide the further use of this screen in proteomic analysis. Additionally, this work gives insight into the positional inequivalence of stabilizing interactions in antiparallel coiled coils.

Amino Acid Sequence↗