Probing aggrephagy using chemically-induced protein aggregates.
Ontology highlight
ABSTRACT:
SUBMITTER: Janssen AFJ
PROVIDER: S-EPMC6185936 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Characterization of amorphous protein aggregates may offer insights into the process of aggregation. Eleven single amino acid mutants of lipase (LipA of Bacillus subtilis) were subjected to temperature-induced aggregation, and the resultant aggregates were characterized for recovery of activity in the presence of guanidinium chloride (GdmCl). Based on activity recovery profiles of the aggregates, the mutants could be broadly assigned into four groups. By including at least one mutation from each group, a mutant was generated that showed an increase of ~ 10 °C in melting temperature (T m) compared to the wild-type and did not aggregate even at 75 °C. This method explores characterization of amorphous protein aggregates in the presence of GdmCl and helps in identifying mutations involved in protein aggregation.
| S-EPMC4821347 | biostudies-literature
Project description:Trions, charged excitons that are reminiscent of hydrogen and positronium ions, have been intensively studied for energy harvesting, light-emitting diodes, lasing, and quantum computing applications because of their inherent connection with electron spin and dark excitons. However, these quasi-particles are typically present as a minority species at room temperature making it difficult for quantitative experimental measurements. Here, we show that by chemically engineering the well depth of sp3 quantum defects through a series of alkyl functional groups covalently attached to semiconducting carbon nanotube hosts, trions can be efficiently generated and localized at the trapping chemical defects. The exciton-electron binding energy of the trapped trion approaches 119 meV, which more than doubles that of "free" trions in the same host material (54 meV) and other nanoscale systems (2-45 meV). Magnetoluminescence spectroscopy suggests the absence of dark states in the energetic vicinity of trapped trions. Unexpectedly, the trapped trions are approximately 7.3-fold brighter than the brightest previously reported and 16 times as bright as native nanotube excitons, with a photoluminescence lifetime that is more than 100 times larger than that of free trions. These intriguing observations are understood by an efficient conversion of dark excitons to bright trions at the defect sites. This work makes trions synthetically accessible and uncovers the rich photophysics of these tricarrier quasi-particles, which may find broad implications in bioimaging, chemical sensing, energy harvesting, and light emitting in the short-wave infrared.
| S-EPMC6891859 | biostudies-literature
Project description:Although the development of chemically induced, self-assembled protein-based materials is rapidly expanding, methods for directing their assembly in solution are sparse, and problems of population heterogeneity remain. By exerting control over the assembly of advanced protein structures, new classes of ordered protein nanomaterials become feasible, affecting numerous applications ranging from therapeutics to nanostructural engineering. Focusing on a protein-based method for modulating the stability of a chemically induced dihydrofolate reductase (DHFR) dimer, we demonstrate the sensitivity of a methotrexate competition assay in determining the change in DHFR-DHFR binding cooperativity via interfacial mutations over a 1.3 kcal/mol range. This represents a change of more than 40% of the dimer complex binding energy conferred from protein-protein cooperativity (~3.1 kcal/mol). With the development of this investigative system and refinement of protein-based techniques for complex stability modulation, the directed assembly of protein nanomaterials into heterocomplexes and a concomitant decrease in population heterogeneity becomes a realizable goal.
| S-EPMC5568899 | biostudies-literature
Project description:Understanding the role of biomolecular dynamics in cellular processes leading to human diseases and the ability to rationally manipulate these processes is of fundamental importance in scientific research. The last decade has witnessed significant progress in probing biophysical behavior of proteins. However, we are still limited in understanding how changes in protein dynamics and inter-protein interactions occurring in short length- and time-scales lead to aberrations in their biological function. Bridging this gap in biology probed using computer simulations marks a challenging frontier in computational biology. Here we examine hypothesis-driven simplified protein models in conjunction with discrete molecular dynamics in the study of protein aggregation, implicated in series of neurodegenerative diseases, such as Alzheimer's and Huntington's diseases. Discrete molecular dynamics simulations of simplified protein models have emerged as a powerful methodology with its ability to bridge the gap in time and length scales from protein dynamics to aggregation, and provide an indispensable tool for probing protein aggregation.
| S-EPMC2497428 | biostudies-literature
Project description:The triploid block, which prevents interploidy hybridizations in flowering plants, is characterized by a failure in endosperm development, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed genes (PEGs), which are upregulated in tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed collapse is bypassed in Arabidopsis plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early growth. We identified strong suppressor lines showing stable transgenerational inheritance of hypomethylation in the CG context, as well as normalized expression of PEGs in triploid seeds. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow epialleles involved in the triploid block response to be identified in future studies. Finally, we demonstrate that chemically induced epimutagenesis facilitates hybridization between different Capsella species, thus potentially emerging as a strategy for producing triploids and interspecific hybrids with high agronomic interest.
| S-EPMC8894923 | biostudies-literature
Project description:Confinement and surface effects provided by nanoparticles have been shown to produce changes in polymer molecules affecting their macroscopic viscosity. Nanoparticles may induce rearrangements in polymer conformation with an increase in free volume significantly lowering the viscosity. This phenomenon is generally attributed to the selective adsorption of the polymer high molar mass fraction onto nanoparticles surface when the polymer radius of gyration is comparable to the nanoparticles characteristic dimensions. Carbon nanotubes seem to be the ideal candidate to induce viscosity reduction of polymer due to both their high surface-to-volume ratio and their nanometric sizes, comparable to the gyration radius of polymer chains. However, the amount of nanotube in a polymer system is limited by the percolation threshold as, above this limit, the formation of a nanotubes network hinders the viscosity reduction effect. Based on these findings, we have used multiwalled carbon nanotubes MWCNT "aggregates" as viscosity reducers. Our results reveal both that the use of nanotube clusters reduce significantly the viscosity of the final system and strongly increase the nanotube limiting concentration for viscosity hindering. By using hydroxyl and carboxyl functionalized nanotubes, this effect has been rather maximized likely due to the hydrogen bridged stabilization of nanotube aggregates.
| S-EPMC5453357 | biostudies-other
Project description:Impact statementThe paper presents a comprehensive review of integral membrane protein studies utilizing droplet interface bilayers. Droplet interface bilayers are a novel method of constructing artificial lipid bilayers with enhanced stability and physicochemical complexity compared to existing methods. Their unique morphology also suggests applications in the construction of synthetic biological systems and protocells. As well as serving as a guide to in vitro membrane protein functional studies using droplet interface bilayers in the literature to date, a novel in vitro study of a flippase protein in a droplet interface bilayer is presented.
| S-EPMC6552395 | biostudies-literature
Project description:RationaleBunyaviruses have become a major threat to both humans and livestock in Europe and the Americas. The nucleocapsid (N) protein of these viruses is key to the replication cycle and knowledge of the N oligomerisation state is central to understanding the viral lifecycle and for development of therapeutic strategies.MethodsBunyamwera virus and Schmallenberg virus N proteins (BUNV-N and SBV-N) were expressed recombinantly in E. coli as hexahistidine-SUMO-tagged fusions, and the tag removed subsequently. Noncovalent nano-electrospray ionisation mass spectrometry was conducted in the presence and absence of short RNA oligonucleotides. Instrumental conditions were optimised for the transmission of intact protein complexes into the gas phase. The resulting protein-protein and protein-RNA complexes were identified and their stoichiometries verified by their mass. Collision-induced dissociation tandem mass spectrometry was used in cases of ambiguity.ResultsBoth BUNV-N and SBV-N proteins reassembled into N-RNA complexes in the presence of RNA; however, SBV-N formed a wider range of complexes with varying oligomeric states. The N:RNA oligomers observed were consistent with a model of assembly via stepwise addition of N proteins. Furthermore, upon mixing the two proteins in the presence of RNA no heteromeric complexes were observed, thus revealing insights into the specificity of oligomerisation.ConclusionsNoncovalent mass spectrometry has provided the first detailed analysis of the co-populated oligomeric species formed by these important viral proteins and revealed insights into their assembly pathways. Using this technique has also enabled comparisons to be made between the two N proteins.
| S-EPMC4377080 | biostudies-literature
Project description:Despite major successes of biophysical theories in predicting the effects of electrical shocks within the heart, recent optical mapping studies have revealed two major discrepancies between theory and experiment: 1), the presence of negative bulk polarization recorded during strong shocks; and 2), the unexpectedly small surface polarization under shock electrodes. There is little consensus as to whether these differences result from deficiencies of experimental techniques, artifacts of tissue damage, or deficiencies of existing theories. Here, we take advantage of recently developed near-infrared voltage-sensitive dyes and transillumination optical imaging to perform, for the first time that we know of, noninvasive probing of field effects deep inside the intact ventricular wall. This technique removes some of the limitations encountered in previous experimental studies. We explicitly demonstrate that deep inside intact myocardial tissue preparations, strong electrical shocks do produce considerable negative bulk polarization previously inferred from surface recordings. We also demonstrate that near-threshold diastolic field stimulation produces activation of deep myocardial layers 2-6 mm away from the cathodal surface, contrary to theory. Using bidomain simulations we explore factors that may improve the agreement between theory and experiment. We show that the inclusion of negative asymmetric current can qualitatively explain negative bulk polarization in a discontinuous bidomain model.
| S-EPMC3042586 | biostudies-literature
Project description:Liver injuries due to ingestion or exposure to chemicals and industrial toxicants pose a serious health risk that may be hard to assess due to a lack of non-invasive diagnostic tests. Mapping chemical injuries to organ-specific damage and clinical outcomes via biomarkers or biomarker panels will provide the foundation for highly specific and robust diagnostic tests. Here, we have used DrugMatrix, a toxicogenomics database containing organ-specific gene expression data matched to dose-dependent chemical exposures and adverse clinical pathology assessments in Sprague Dawley rats, to identify groups of co-expressed genes (modules) specific to injury endpoints in the liver. We identified 78 such gene co-expression modules associated with 25 diverse injury endpoints categorized from clinical pathology, organ weight changes, and histopathology. Using gene expression data associated with an injury condition, we showed that these modules exhibited different patterns of activation characteristic of each injury. We further showed that specific module genes mapped to 1) known biochemical pathways associated with liver injuries and 2) clinically used diagnostic tests for liver fibrosis. As such, the gene modules have characteristics of both generalized and specific toxic response pathways. Using these results, we proposed three gene signature sets characteristic of liver fibrosis, steatosis, and general liver injury based on genes from the co-expression modules. Out of all 92 identified genes, 18 (20%) genes have well-documented relationships with liver disease, whereas the rest are novel and have not previously been associated with liver disease. In conclusion, identifying gene co-expression modules associated with chemically induced liver injuries aids in generating testable hypotheses and has the potential to identify putative biomarkers of adverse health effects.
| S-EPMC4165895 | biostudies-literature