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1
Vaikath, Nishant, Indulekha Sudhakaran, Ilham Abdi, Vijay Gupta, Nour Majbour, Simona Ghanem, Houari Abdesselem, Kostas Vekrellis e Omar El-Agnaf. "Structural and Biophysical Characterization of Stable Alpha-Synuclein Oligomers". International Journal of Molecular Sciences 23, n. 23 (23 novembre 2022): 14630. http://dx.doi.org/10.3390/ijms232314630.
Testo completoAbstract (sommario):
The aggregation of α-synuclein (α-syn) into neurotoxic oligomers and fibrils is an important pathogenic feature of synucleinopatheis, including Parkinson’s disease (PD). A further characteristic of PD is the oxidative stress that results in the formation of aldehydes by lipid peroxidation. It has been reported that the brains of deceased patients with PD contain high levels of protein oligomers that are cross-linked to these aldehydes. Increasing evidence also suggests that prefibrillar oligomeric species are more toxic than the mature amyloid fibrils. However, due to the heterogenous and metastable nature, characterization of the α-syn oligomeric species has been challenging. Here, we generated and characterized distinct α-syn oligomers in vitro in the presence of DA and lipid peroxidation products 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-nonenal (ONE). HNE and ONE oligomer were stable towards the treatment with SDS, urea, and temperature. The secondary structure analysis revealed that only HNE and ONE oligomers contain β-sheet content. In the seeding assay, both DA and ONE oligomers significantly accelerated the aggregation. Furthermore, all oligomeric preparations were found to seed the aggregation of α-syn monomers in vitro and found to be cytotoxic when added to SH-SY5Y cells. Finally, both HNE and ONE α-syn oligomers can be used as a calibrator in an α-syn oligomers-specific ELISA.
2
Grewal, Annu, Deepak Sheokand, Vandana Saini e Ajit Kumar. "Molecular docking analysis of α-Synuclein aggregation with Anle138b". Bioinformation 20, n. 3 (31 marzo 2024): 217–22. http://dx.doi.org/10.6026/973206300200217.
Testo completoAbstract (sommario):
α-Synuclein aggregation into toxic oligomeric species is central to Parkinson痴 disease pathogenesis. Anle138b is a recently identified inhibitor of α-synuclein oligomerization showing promise in preclinical studies. This study employed computational approaches to elucidate Anle138b痴 mechanism of oligomer-specific action. The inhibitory potential of Anle138b against α-synuclein oligomers was evaluated by performing molecular docking studies using AutoDock Tools, followed by their binding pocket analysis. Further, protein-protein docking studies were performed using Hex8.0 to validate the aggregation inhibitory potential of Anle138b. Molecular docking revealed increasing binding affinity of Anle138b against higher order α-synuclein oligomers (dimer to decamer). Anle138b occupied oligomeric cavity and interacted with residues Thr54, Gly73, Val74 and Thr75 across several oligomers. Protein-protein docking showed that Anle138b interferes with α-synuclein decamer formation. These results highlight the oligomer-directed inhibitory mechanism of Anle138b, without hindering the monomeric forms and provide molecular insights to advance its therapeutic development for Parkinson's and related synucleinopathies.
3
Wang, Yu, Karen S. L. Lam, Ming-hon Yau e Aimin Xu. "Post-translational modifications of adiponectin: mechanisms and functional implications". Biochemical Journal 409, n. 3 (15 gennaio 2008): 623–33. http://dx.doi.org/10.1042/bj20071492.
Testo completoAbstract (sommario):
Adiponectin is an insulin-sensitizing adipokine with anti-diabetic, anti-atherogenic, anti-inflammatory and cardioprotective properties. This adipokine is secreted from adipocytes into the circulation as three oligomeric isoforms, including trimeric, hexameric and the HMW (high-molecular-mass) oligomeric complex consisting of at least 18 protomers. Each oligomeric isoform of adiponectin exerts distinct biological properties in its various target tissues. The HMW oligomer is the major active form mediating the insulin-sensitizing effects of adiponectin, whereas the central actions of this adipokine are attributed primarily to the hexameric and trimeric oligomers. In patients with Type 2 diabetes and coronary heart disease, circulating levels of HMW adiponectin are selectively decreased due to an impaired secretion of this oligomer from adipocytes. The biosynthesis of the adiponectin oligomers is a complex process involving extensive post-translational modifications. Hydroxylation and glycosylation of several conserved lysine residues in the collagenous domain of adiponectin are necessary for the intracellular assembly and stabilization of its high-order oligomeric structures. Secretion of the adiponectin oligomers is tightly controlled by a pair of molecular chaperones in the ER (endoplasmic reticulum), including ERp44 (ER protein of 44 kDa) and Ero1-Lα (ER oxidoreductase 1-Lα). ERp44 inhibits the secretion of adiponectin oligomers through a thiol-mediated retention. In contrast, Ero1-Lα releases HMW adiponectin trapped by ERp44. The PPARγ (peroxisome-proliferator-activated receptor γ) agonists thiazolidinediones selectively enhance the secretion of HMW adiponectin through up-regulation of Ero1-Lα. In the present review, we discuss the recent advances in our understanding of the structural and biological properties of the adiponectin oligomeric isoforms and highlight the role of post-translational modifications in regulating the biosynthesis of HMW adiponectin.
4
Liu, Guang-Hui, Jing Qu, Anne E. Carmack, Hyun Bae Kim, Chang Chen, Hongmei Ren, Andrew J. Morris, Brian N. Finck e Thurl E. Harris. "Lipin proteins form homo- and hetero-oligomers". Biochemical Journal 432, n. 1 (25 ottobre 2010): 65–76. http://dx.doi.org/10.1042/bj20100584.
Testo completoAbstract (sommario):
Lipin family members (lipin 1, 2 and 3) are bi-functional proteins that dephosphorylate PA (phosphatidic acid) to produce DAG (diacylglycerol) and act in the nucleus to regulate gene expression. Although other components of the triacylglycerol synthesis pathway can form oligomeric complexes, it is unknown whether lipin proteins also exist as oligomers. In the present study, using various approaches, we revealed that lipin 1 formed stable homo-oligomers with itself and hetero-oligomers with lipin 2/3. Both the N- and C-terminal regions of lipin 1 mediate its oligomerization in a head-to-head/tail-to-tail manner. We also show that lipin 1 subcellular localization can be influenced through oligomerization, and the individual lipin 1 monomers in the oligomer function independently in catalysing dephosphorylation of PA. The present study provides evidence that lipin proteins function as oligomeric complexes and that the three mammalian lipin isoforms can form combinatorial units.
5
Prots, Iryna, Janina Grosch, Razvan-Marius Brazdis, Katrin Simmnacher, Vanesa Veber, Steven Havlicek, Christian Hannappel et al. "α-Synuclein oligomers induce early axonal dysfunction in human iPSC-based models of synucleinopathies". Proceedings of the National Academy of Sciences 115, n. 30 (10 luglio 2018): 7813–18. http://dx.doi.org/10.1073/pnas.1713129115.
Testo completoAbstract (sommario):
α-Synuclein (α-Syn) aggregation, proceeding from oligomers to fibrils, is one central hallmark of neurodegeneration in synucleinopathies. α-Syn oligomers are toxic by triggering neurodegenerative processes in in vitro and in vivo models. However, the precise contribution of α-Syn oligomers to neurite pathology in human neurons and the underlying mechanisms remain unclear. Here, we demonstrate the formation of oligomeric α-Syn intermediates and reduced axonal mitochondrial transport in human neurons derived from induced pluripotent stem cells (iPSC) from a Parkinson’s disease patient carrying an α-Syn gene duplication. We further show that increased levels of α-Syn oligomers disrupt axonal integrity in human neurons. We apply an α-Syn oligomerization model by expressing α-Syn oligomer-forming mutants (E46K and E57K) and wild-type α-Syn in human iPSC-derived neurons. Pronounced α-Syn oligomerization led to impaired anterograde axonal transport of mitochondria, which can be restored by the inhibition of α-Syn oligomer formation. Furthermore, α-Syn oligomers were associated with a subcellular relocation of transport-regulating proteins Miro1, KLC1, and Tau as well as reduced ATP levels, underlying axonal transport deficits. Consequently, reduced axonal density and structural synaptic degeneration were observed in human neurons in the presence of high levels of α-Syn oligomers. Together, increased dosage of α-Syn resulting in α-Syn oligomerization causes axonal transport disruption and energy deficits, leading to synapse loss in human neurons. This study identifies α-Syn oligomers as the critical species triggering early axonal dysfunction in synucleinopathies.
6
Di Gennaro, Patrizia, Valentina Sabatini, Silvia Fallarini, Roberto Pagliarin e Guido Sello. "Polyphenol Polymerization by an Alternative Oxidative Microbial Enzyme and Characterization of the Biological Activity of Oligomers". BioMed Research International 2018 (2018): 1–10. http://dx.doi.org/10.1155/2018/3828627.
Testo completoAbstract (sommario):
The recombinant catalase-peroxidase HPI from E. coli was used as an alternative enzyme in polymerization reactions for the production of (−) epicatechin oligomers and their biological activity was characterized. The enzyme was prepared in two forms: a purified and an immobilized form. Both were tested for their activity in oxidative polymerization reactions, and their stability and reusability were assessed. The polymerization reactions were followed by SEC-HPLC analyses, and the substrate was completely converted into one or more polymerization products depending on the reactions conditions. Results showed that the utilized conditions allowed for the isolation of some oligomers of different molecular weight: the oligomers containing 6 and 7 units of epicatechin substrate are the heaviest ones. Epicatechin was also used in reactions catalyzed by HRP in the same reaction conditions for comparison. In addition, one selected oligomer obtained by HPI enzyme catalysis was shown to act as in vitro inhibitor of tumor cell growth, like one oligomer deriving from epicatechin by HRP catalysis. These data confirm that epicatechin oligomeric form is more effective than its monomer in biological activity and suggest the use of HPI as an alternative enzyme in reactions for the production of epicatechin oligomers.
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Bazaco, Raúl Blanco, José L. Segura e Carlos Seoane. "Recent advances in the design, synthesis and study of covalent conjugated oligomer–C60 ensembles". Collection of Czechoslovak Chemical Communications 74, n. 6 (2009): 857–86. http://dx.doi.org/10.1135/cccc2008218.
Testo completoAbstract (sommario):
This review presents an overview of the most recent results in the field of conjugated oligomer covalently attached to the C60 sphere focusing mainly on donor–conjugated oligomer–C60 triads and conjugated oligomer–multifullerene materials. Well-defined monodisperse oligomers as new materials that exhibit interesting optoelectronic properties have been the subject of intense study during the last decade. In this regard, a huge amount of work has been devoted to the development of new synthetic strategies toward the synthesis of conjugated oligomeric materials with precise length and constitution and to their chemical functionalization in order to incorporate them into more complex molecular and supramolecular architectures. An important area of research in the field of conjugated oligomers involves the design and synthesis of donor–acceptor ensembles by combination of monodisperse π-conjugated oligomeric systems with C60 fullerene. Such hybrid systems have shown excited-state interactions making them excellent candidates for fundamental photophysical studies. In addition, these materials have found applications in the field of photovoltaic devices. A review with 70 references.
8
Burford, Neil T., Tom Wehrman, Daniel Bassoni, Jonathan O’Connell, Martyn Banks, Litao Zhang e Andrew Alt. "Identification of Selective Agonists and Positive Allosteric Modulators for µ- and δ-Opioid Receptors from a Single High-Throughput Screen". Journal of Biomolecular Screening 19, n. 9 (21 luglio 2014): 1255–65. http://dx.doi.org/10.1177/1087057114542975.
Testo completoAbstract (sommario):
Hetero-oligomeric complexes of G protein–coupled receptors (GPCRs) may represent novel therapeutic targets exhibiting different pharmacology and tissue- or cell-specific site of action compared with receptor monomers or homo-oligomers. An ideal tool for validating this concept pharmacologically would be a hetero-oligomer selective ligand. We set out to develop and execute a 1536-well high-throughput screen of over 1 million compounds to detect potential hetero-oligomer selective ligands using a β-arrestin recruitment assay in U2OS cells coexpressing recombinant µ- and δ-opioid receptors. Hetero-oligomer selective ligands may bind to orthosteric or allosteric sites, and we might anticipate that the formation of hetero-oligomers may provide novel allosteric binding pockets for ligand binding. Therefore, our goal was to execute the screen in such a way as to identify positive allosteric modulators (PAMs) as well as agonists for µ, δ, and hetero-oligomeric receptors. While no hetero-oligomer selective ligands were identified (based on our selection criteria), this single screen did identify numerous µ- and δ-selective agonists and PAMs as well as nonselective agonists and PAMs. To our knowledge, these are the first µ- and δ-opioid receptor PAMs described in the literature.
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Renaud, Justin, Abdulhrahman M. Alhazmi e Paul M. Mayer. "Comparing the fragmentation chemistry of gas-phase adducts of poly(dimethylsiloxane) oligomers with metal and organic ions". Canadian Journal of Chemistry 87, n. 2 (febbraio 2009): 453–59. http://dx.doi.org/10.1139/v08-184.
Testo completoAbstract (sommario):
Gas-phase ions of poly(dimethylsiloxane) oligomers were formed by electrospray ionization either by protonating them in solution with formic acid or by generating adducts of the oligomers with the metal ions Li+, Na+, K+, and Ag+ as well as with the organic cations NH4+, CH3CH2NH3+, and protonated glycine, aspartic acid, and 1,2-diphenylethylamine. The collision-induced fragmentation of the oligomeric ions was strongly dependent on the nature of the charging species. Ag+ adducts dissociated in a manner previously observed in secondary ion mass spectrometry experiments generating a series of linear and cyclic fragment ions, while Li+ adducts fragmented to form two ions: an adduct of the metal ion with the oligomer end-group and one with the remaining oligomer. Na+ and K+ adducts simply dissociate to form the bare metal ion. The organic species, to varying extents, transfer the proton to the oligomer to form a protonated poly(siloxane) ion. These protonated oligomers then dissociate at very low laboratory-frame collision energy along the siloxane backbone by loss of a silanol. These backbone fragments can then lose a methyl group to form a second series of fragment ions. Suggestions for probable mechanistic pathways for these processes are presented.
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Qing, Xiaoyu, Qian Wang, Hanyu Xu, Pei Liu e Luhua Lai. "Designing Cyclic-Constrained Peptides to Inhibit Human Phosphoglycerate Dehydrogenase". Molecules 28, n. 17 (4 settembre 2023): 6430. http://dx.doi.org/10.3390/molecules28176430.
Testo completoAbstract (sommario):
Although loop epitopes at protein-protein binding interfaces often play key roles in mediating oligomer formation and interaction specificity, their binding sites are underexplored as drug targets owing to their high flexibility, relatively few hot spots, and solvent accessibility. Prior attempts to develop molecules that mimic loop epitopes to disrupt protein oligomers have had limited success. In this study, we used structure-based approaches to design and optimize cyclic-constrained peptides based on loop epitopes at the human phosphoglycerate dehydrogenase (PHGDH) dimer interface, which is an obligate homo-dimer with activity strongly dependent on the oligomeric state. The experimental validations showed that these cyclic peptides inhibit PHGDH activity by directly binding to the dimer interface and disrupting the obligate homo-oligomer formation. Our results demonstrate that loop epitope derived cyclic peptides with rationally designed affinity-enhancing substitutions can modulate obligate protein homo-oligomers, which can be used to design peptide inhibitors for other seemingly intractable oligomeric proteins.
11
Barton, Jeremy, D. Sebastian Arias, Chamani Niyangoda, Gustavo Borjas, Nathan Le, Saefallah Mohamed e Martin Muschol. "Kinetic Transition in Amyloid Assembly as a Screening Assay for Oligomer-Selective Dyes". Biomolecules 9, n. 10 (27 settembre 2019): 539. http://dx.doi.org/10.3390/biom9100539.
Testo completoAbstract (sommario):
Assembly of amyloid fibrils and small globular oligomers is associated with a significant number of human disorders that include Alzheimer’s disease, senile systemic amyloidosis, and type II diabetes. Recent findings implicate small amyloid oligomers as the dominant aggregate species mediating the toxic effects in these disorders. However, validation of this hypothesis has been hampered by the dearth of experimental techniques to detect, quantify, and discriminate oligomeric intermediates from late-stage fibrils, in vitro and in vivo. We have shown that the onset of significant oligomer formation is associated with a transition in thioflavin T kinetics from sigmoidal to biphasic kinetics. Here we showed that this transition can be exploited for screening fluorophores for preferential responses to oligomer over fibril formation. This assay identified crystal violet as a strongly selective oligomer-indicator dye for lysozyme. Simultaneous recordings of amyloid kinetics with thioflavin T and crystal violet enabled us to separate the combined signals into their underlying oligomeric and fibrillar components. We provided further evidence that this screening assay could be extended to amyloid-β peptides under physiological conditions. Identification of oligomer-selective dyes not only holds the promise of biomedical applications but provides new approaches for unraveling the mechanisms underlying oligomer versus fibril formation in amyloid assembly.
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Long, Jaclyn S., Nigel J. Pyne e Susan Pyne. "Lipid phosphate phosphatases form homo- and hetero-oligomers: catalytic competency, subcellular distribution and function". Biochemical Journal 411, n. 2 (27 marzo 2008): 371–77. http://dx.doi.org/10.1042/bj20071607.
Testo completoAbstract (sommario):
Lipid phosphate phosphatases (LPP1–LPP3) have been topographically modelled as monomers (molecular mass of 31–36 kDa) composed of six transmembrane domains and with the catalytic site facing the extracellular side of the plasma membrane or the luminal side of intracellular membranes. The catalytic motif has three conserved domains, termed C1, C2 and C3. The C1 domain may be involved in substrate recognition, whereas C2 and C3 domains appear to participate in the catalytic dephosphorylation of the substrate. We have obtained three lines of evidence to demonstrate that LPPs exist as functional oligomers. First, we have used recombinant expression and immunoprecipitation analysis to demonstrate that LPP1, LPP2 and LPP3 form both homo- and hetero-oligomers. Secondly, large LPP oligomeric complexes that are catalytically active were isolated using gel-exclusion chromatography. Thirdly, we demonstrate that catalytically deficient guinea-pig FLAG-tagged H223L LPP1 mutant can form an oligomer with wild-type LPP1 and that wild-type LPP1 activity is preserved in the oligomer. These findings suggest that, in an oligomeric arrangement, the catalytic site of the wild-type LPP can function independently of the catalytic site of the mutant LPP. Finally, we demonstrate that endogenous LPP2 and LPP3 form homo- and hetero-oligomers, which differ in their subcellular localization and which may confer differing spatial regulation of phosphatidic acid and sphingosine 1-phosphate signalling.
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Lee, Young A., Eun Ju Cho e Takako Yokozawa. "Oligomeric proanthocyanidins improve memory and enhance phosphorylation of vascular endothelial growth factor receptor-2 in senescence-accelerated mouse prone/8". British Journal of Nutrition 103, n. 4 (13 ottobre 2009): 479–89. http://dx.doi.org/10.1017/s0007114509992005.
Testo completoAbstract (sommario):
Senescence-accelerated mouse prone/8 (SAMP8), a murine model of accelerated senescence, shows age-related deficits in learning and memory. We investigated the effect of oligomeric proanthocyanidins (oligomers) on memory impairment using the SAMP8 model involving the oral administration of oligomers for 5 weeks. To analyse memory improvement in SAMP8, we performed Morris water maze, object location and object recognition tests. The oral administration of oligomers improved spatial and object recognition impairment in SAMP8. Expressions of phosphorylated neurofilament-H (P-NF-H, axon marker), microtubule-associated proteins (MAP) 2a and 2b (MAP2; dendrite marker) and synaptophysin were increased in the brains of SAMP8-administered oligomers. In particular, the expression of P-NF-H was significantly elevated in the hippocampal CA1. This indicates that oligomers result in an increase in the densities of axons, dendrites and synapses. To investigate the protective mechanisms of oligomers against brain dysfunction with ageing, we carried out a receptor tyrosine kinase phosphorylation antibody array, and clarified that the administration of oligomers led to an increase in the phosphorylation of vascular endothelial growth factor receptor (VEGFR)-2, suggesting the neuroprotective role of oligomers. The phosphorylation of VEGFR-2 was more greatly increased in the hypothalamus and choroid plexus than in other brain regions of SAMP8. Memory in oligomer-treated mice was impaired by SU1498, a VEGFR-2-specific antagonist. Elucidating the relationship between memory impairment with ageing and VEGFR-2 signalling may provide new suggestions for protection against memory deficit in the ageing brain.
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RAMSAY, Douglas, Elaine KELLETT, Mary McVEY, Stephen REES e Graeme MILLIGAN. "Homo- and hetero-oligomeric interactions between G-protein-coupled receptors in living cells monitored by two variants of bioluminescence resonance energy transfer (BRET): hetero-oligomers between receptor subtypes form more efficiently than between less closely related sequences". Biochemical Journal 365, n. 2 (15 luglio 2002): 429–40. http://dx.doi.org/10.1042/bj20020251.
Testo completoAbstract (sommario):
Homo- and hetero-oligomerization of G-protein-coupled receptors (GPCRs) were examined in HEK-293 cells using two variants of bioluminescence resonance energy transfer (BRET). BRET2 (a variant of BRET) offers greatly improved separation of the emission spectra of the donor and acceptor moieties compared with traditional BRET. Previously recorded homo-oligomerization of the human δ-opioid receptor was confirmed using BRET2. Homo-oligomerization of the κ-opioid receptor was observed using both BRET techniques. Both homo- and hetero-oligomers, containing both δ- and κ-opioid receptors, were unaffected by the presence of receptor ligands. BRET detection of opioid receptor homo- and hetero-oligomers required expression of 50000–100000 copies of the receptor energy acceptor construct per cell. The effectiveness of δ—κ-opioid receptor hetero-oligomer formation was as great as for homomeric interactions. The capacity of the two opioid receptors to form oligomeric complexes with the β2-adrenoceptor was also assessed. Although such interactions were detected, at least 250000 copies per cell of the energy acceptor were required. Requirement for high levels of receptor expression was equally pronounced in attempts to measure hetero-oligomer formation between the κ-opioid receptor and the thyrotropin-releasing hormone receptor-1. These studies indicate that constitutively formed homo- and hetero-oligomers of opioid receptor subtypes can be detected in living cells containing less than 100000 copies of the receptors. However, although hetero-oligomeric interactions between certain less closely related GPCRs can be detected, they appear to be of lower affinity than homo- or hetero-oligomers containing closely related sequences. Interactions recorded between certain GPCR family members in heterologous expression systems are likely to be artefacts of extreme levels of overexpression.
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Larson, Megan E., Susan J. Greimel, Fatou Amar, Michael LaCroix, Gabriel Boyle, Mathew A. Sherman, Hallie Schley et al. "Selective lowering of synapsins induced by oligomeric α-synuclein exacerbates memory deficits". Proceedings of the National Academy of Sciences 114, n. 23 (22 maggio 2017): E4648—E4657. http://dx.doi.org/10.1073/pnas.1704698114.
Testo completoAbstract (sommario):
Mounting evidence indicates that soluble oligomeric forms of amyloid proteins linked to neurodegenerative disorders, such as amyloid-β (Aβ), tau, or α-synuclein (αSyn) might be the major deleterious species for neuronal function in these diseases. Here, we found an abnormal accumulation of oligomeric αSyn species in AD brains by custom ELISA, size-exclusion chromatography, and nondenaturing/denaturing immunoblotting techniques. Importantly, the abundance of αSyn oligomers in human brain tissue correlated with cognitive impairment and reductions in synapsin expression. By overexpressing WT human αSyn in an AD mouse model, we artificially enhanced αSyn oligomerization. These bigenic mice displayed exacerbated Aβ-induced cognitive deficits and a selective decrease in synapsins. Following isolation of various soluble αSyn assemblies from transgenic mice, we found that in vitro delivery of exogenous oligomeric αSyn but not monomeric αSyn was causing a lowering in synapsin-I/II protein abundance. For a particular αSyn oligomer, these changes were either dependent or independent on endogenous αSyn expression. Finally, at a molecular level, the expression of synapsin genes SYN1 and SYN2 was down-regulated in vivo and in vitro by αSyn oligomers, which decreased two transcription factors, cAMP response element binding and Nurr1, controlling synapsin gene promoter activity. Overall, our results demonstrate that endogenous αSyn oligomers can impair memory by selectively lowering synapsin expression.
16
Eisenberg, David, Arthur Laganowsky, Cong Liu, Michael Sawaya, Julian Whitelegge, Minglei Zhao, Angela Soriaga et al. "Structural Studies of the Amyloid State of Proteins". Acta Crystallographica Section A Foundations and Advances 70, a1 (5 agosto 2014): C797. http://dx.doi.org/10.1107/s205327331409202x.
Testo completoAbstract (sommario):
Amyloid diseases, including Alzheimer's, Parkinson's, and the prion conditions, are each associated with a particular protein in fibrillar form. At the morphological level, these fibers appear similar and are termed "amyloid." We found that the adhesive segments of amyloid fibers are short protein sequences which form pairs of interdigitated, in-register beta sheets. These amyloid fibrils were long suspected to be the disease agents, but evidence suggests that in the neurodegenerative diseases, smaller, often transient and polymorphic oligomers are the toxic entities. We have identified a segment of the amyloid-forming protein, alphaB crystallin, which forms an oligomeric complex exhibiting properties of other amyloid oligomers: beta-sheet-rich structure, cytotoxicity, and recognition by an anti-oligomer antibody. The X-ray-derived atomic structure of the oligomer reveals a cylindrical barrel, formed from six anti-parallel, out-of-register protein strands, which we term a cylindrin. The cylindrin structure is compatible with sequence segments from the Abeta protein of Alzheimer's disease and from other amyloid proteins. Cylindrins offer models for the hitherto elusive structures of amyloid oligomers, and are distinct in structure from amyloid fibrils.
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Dekker, J., A. van der Ende, P. H. Aelmans e G. J. Strous. "Rat gastric mucin is synthesized and secreted exclusively as filamentous oligomers". Biochemical Journal 279, n. 1 (1 ottobre 1991): 251–56. http://dx.doi.org/10.1042/bj2790251.
Testo completoAbstract (sommario):
Oligomeric gastric mucin was isolated from the fundic part of the rat stomach. Previously we have shown by biochemical analysis that this oligomeric mucin consists of disulphide-linked homo-oligomers, which contain no other covalently attached proteins [Dekker, Aelmans & Strous (1991) Biochem. J. 277, 423-427]. Electron-microscopic images of the oligomeric mucin revealed a heterogenous population of long filamentous molecules of 300-3000 nm length. After reduction and carboxymethylation the monomeric mucins displayed a length distribution with a single peak at about 279 nm. Length-distribution analysis of oligomeric molecules with length up to 1000 nm revealed three subpopulations with one, two or three times the length of the monomeric mucin. The oligomers displayed small globular domains of about 15 nm, which were equally spaced along the molecule's length. As the distance between these globular domains was similar to the monomer length, these domains most likely indicate attachment sites of the monomers. These results show that the mucin monomers attached end-to-end in the oligomer. Biosynthesis of the mucin oligomers was studied by labelling of stomach explants in vitro with [35S]methionine, [3H]galactose or [35S]sulphate and subsequent immunoprecipitation of the mucin with a specific antiserum. Analysis by electrophoresis and gel filtration revealed that the oligomerization takes place by formation of disulphide bonds between the 300 kDa mucin precursors. The mucin was exclusively synthesized and secreted as fully glycosylated oligomers, as neither precursor proteins nor monomeric mucin were detected in the culture medium. A model for the biosynthesis of rat gastric mucin is proposed in which the filamentous mucin monomers are linked end-to-end by disulphide bonds.
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Rodigast, Maria, Anke Mutzel e Hartmut Herrmann. "A quantification method for heat-decomposable methylglyoxal oligomers and its application on 1,3,5-trimethylbenzene SOA". Atmospheric Chemistry and Physics 17, n. 6 (23 marzo 2017): 3929–43. http://dx.doi.org/10.5194/acp-17-3929-2017.
Testo completoAbstract (sommario):
Abstract. Methylglyoxal forms oligomeric compounds in the atmospheric aqueous particle phase, which could establish a significant contribution to the formation of aqueous secondary organic aerosol (aqSOA). Thus far, no suitable method for the quantification of methylglyoxal oligomers is available despite the great effort spent for structure elucidation. In the present study a simplified method was developed to quantify heat-decomposable methylglyoxal oligomers as a sum parameter. The method is based on the thermal decomposition of oligomers into methylglyoxal monomers. Formed methylglyoxal monomers were detected using PFBHA (o-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine hydrochloride) derivatisation and gas chromatography–mass spectrometry (GC/MS) analysis. The method development was focused on the heating time (varied between 15 and 48 h), pH during the heating process (pH = 1–7), and heating temperature (50, 100 °C). The optimised values of these method parameters are presented. The developed method was applied to quantify heat-decomposable methylglyoxal oligomers formed during the OH-radical oxidation of 1,3,5-trimethylbenzene (TMB) in the Leipzig aerosol chamber (LEipziger AerosolKammer, LEAK). Oligomer formation was investigated as a function of seed particle acidity and relative humidity. A fraction of heat-decomposable methylglyoxal oligomers of up to 8 % in the produced organic particle mass was found, highlighting the importance of those oligomers formed solely by methylglyoxal for SOA formation. Overall, the present study provides a new and suitable method for quantification of heat-decomposable methylglyoxal oligomers in the aqueous particle phase.
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Chase, Anna R., Ethan Laudermilch, Jimin Wang, Hideki Shigematsu, Takeshi Yokoyama e Christian Schlieker. "Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1". Molecular Biology of the Cell 28, n. 21 (15 ottobre 2017): 2765–72. http://dx.doi.org/10.1091/mbc.e17-05-0281.
Testo completoAbstract (sommario):
TorsinA is an essential AAA+ ATPase requiring LAP1 or LULL1 as cofactors. The dynamics of the Torsin/cofactor system remain poorly understood, with previous models invoking Torsin/cofactor assemblies with fixed stoichiometries. Here we demonstrate that TorsinA assembles into homotypic oligomers in the presence of ATP. Torsin variants mutated at the “back” interface disrupt homo-oligomerization but still show robust ATPase activity in the presence of its cofactors. These Torsin mutants are severely compromised in their ability to rescue nuclear envelope defects in Torsin-deficient cells, suggesting that TorsinA homo-oligomers play a key role in vivo. Engagement of the oligomer by LAP1 triggers ATP hydrolysis and rapid complex disassembly. Thus the Torsin complex is a highly dynamic assembly whose oligomeric state is tightly controlled by distinctively localized cellular cofactors. Our discovery that LAP1 serves as a modulator of the oligomeric state of an AAA+ protein establishes a novel means of regulating this important class of oligomeric ATPases.
20
Schmid, J. A., H. Just e H. H. Sitte. "Impact of oligomerization on the function of the human serotonin transporter". Biochemical Society Transactions 29, n. 6 (1 novembre 2001): 732–36. http://dx.doi.org/10.1042/bst0290732.
Testo completoAbstract (sommario):
The formation of oligomeric structures has been proposed for a large number of membrane proteins, including G-protein-coupled receptors and ion channels. Biochemical studies employing gel filtration, cross-linking or co-immunoprecipitation techniques showed that the serotonin [5-hydroxytryptamine (5-HT)] transporter is also capable of forming oligomers. We investigated whether the human serotonin transporter (hSERT) can be visualized as an oligomer in the plasma membrane of intact cells. To test this working hypothesis, we generated fusion proteins of hSERT and spectral variants of green fluorescent protein [cyan and yellow fluorescent proteins (CFP and YFP, respectively)]. When expressed in HeLa or HEK-293 cells, the resulting fusion proteins (CFP-hSERT and YFP-hSERT) were inserted into the plasma membrane and were indistinguishable from wild-type hSERT on functional testing (5-HT uptake assays, inhibition of 5-HT uptake by blockers such as imipramine). Oligomers were visualized by fluorescence resonance energy transfer (FRET) microscopy in living cells using complementary methods. Interestingly, oligomerization was not confined to hSERT; FRET was also observed between CFP-and YFP-labelled rat γ-aminobutyric acid transporter. Gel filtration experiments showed that most of the protein was recovered as higher molecular weight complexes; almost no monomeric form was detected. This indicates that the homo-oligomeric form is the favoured state of hSERT in living cells. The formation of oligomers was not significantly affected by co-incubation with transporter substrates or blockers. Based on our observations, oligomer formation might not be essential for the physiological function of the transporter protein, the re-uptake of substrates. Furthermore, we conclude that constitutive oligomer formation might be a general property of Na+/Cl−-dependent neurotransmitter transporters.
21
Harrison, R. A. "Preliminary characterization of the multiple forms of ram sperm hyaluronidase". Biochemical Journal 252, n. 3 (15 giugno 1988): 875–82. http://dx.doi.org/10.1042/bj2520875.
Testo completoAbstract (sommario):
An investigation was made of the inter-relationships and characteristics of various hyaluronidase forms isolated from ram spermatozoa. They were shown to be members of an oligomeric series, apparently formed by intermolecular disulphide cross-linking. Two monomer species were detected, alpha (Mr 89,600) and beta (Mr 81,200). Although the alpha species predominated, the two were evenly distributed throughout the oligomer population, and they shared antigenic determinants; the beta species did not arise from the alpha species as a result of catabolism following cell disruption. The oligomeric series was of the form [Hyal]n, where n = 1, 2, 4, 5, 6, 7 etc.; no trimer was detectable. Though essentially cationic, part of the hyaluronidase population also had anionic characteristics, probably due to oxidation of free thiol groups. In the anionic subpopulation tetramers and higher oligomers predominated, whereas the non-anionic subpopulation was composed of monomers, dimers and tetramers. The pH optimum of the monomer was 4.3 in 0.2 M-NaCl/0.1 M-sodium citrate, whereas that of the anionic oligomers was 4.9. Both serum albumin and polylysine stimulated enzyme activity at pH 4.0 in the absence of NaCl; polylysine was particularly effective. NaCl diminished the stimulatory effects, and essentially suppressed them above the pH optimum. The specific activities of different oligomer populations were the same as that of the monomer, and conversion of oligomers into monomer by reduction had likewise no effect upon the specific activity. Low concentrations of poly(vinyl alcohol), poly(ethylene glycol) or polyvinylpyrrolidone stabilized soluble hyaluronidase activity by preventing the enzyme's binding to surfaces; solutions of anionic oligomers were further stabilized by NaCl. Enzyme preparations were stable for several months frozen in the presence of poly(vinyl alcohol) and salt.
22
Sokolov, Yuri, J. Ashot Kozak, Rakez Kayed, Alexandr Chanturiya, Charles Glabe e James E. Hall. "Soluble Amyloid Oligomers Increase Bilayer Conductance by Altering Dielectric Structure". Journal of General Physiology 128, n. 6 (13 novembre 2006): 637–47. http://dx.doi.org/10.1085/jgp.200609533.
Testo completoAbstract (sommario):
The amyloid hypothesis of Alzheimer's toxicity has undergone a resurgence with increasing evidence that it is not amyloid fibrils but a smaller oligomeric species that produces the deleterious results. In this paper we address the mechanism of this toxicity. Only oligomers increase the conductance of lipid bilayers and patch-clamped mammalian cells, producing almost identical current–voltage curves in both preparations. Oligomers increase the conductance of the bare bilayer, the cation conductance induced by nonactin, and the anion conductance induced by tetraphenyl borate. Negative charge reduces the sensitivity of the membrane to amyloid, but cholesterol has little effect. In contrast, the area compressibility of the lipid has a very large effect. Membranes with a large area compressibility modulus are almost insensitive to amyloid oligomers, but membranes formed from soft, highly compressible lipids are highly susceptible to amyloid oligomer-induced conductance changes. Furthermore, membranes formed using the solvent decane (instead of squalane) are completely insensitive to the presence of oligomers. One simple explanation for these effects on bilayer conductance is that amyloid oligomers increase the area per molecule of the membrane-forming lipids, thus thinning the membrane, lowering the dielectric barrier, and increasing the conductance of any mechanism sensitive to the dielectric barrier.
23
Oliva, A., H. Armas e J. B. Fariña. "HPLC determination of polyethylene glycol 400 in urine: oligomeric profile in healthy and celiac disease subjects". Clinical Chemistry 40, n. 8 (1 agosto 1994): 1571–74. http://dx.doi.org/10.1093/clinchem/40.8.1571.
Testo completoAbstract (sommario):
Abstract The absorption of orally administered polyethylene glycol (PEG) has been used to assess intestinal permeability. We describe a simple HPLC technique to determine the oligomeric profile of PEG excreted in urine. We measured the total (%) PEG excreted in 6 h and the ratio of the four smallest oligomers to the three largest oligomers (expressed as mean percentages). The proposed method differentiates distinct groups of subjects with varying degrees of intestinal permeability detected by intestinal biopsy. The percent of PEG excreted and the oligomer ratio values for healthy subjects were, respectively, 30.1 +/- 3.87 and 0.35 +/- 0.03; for celiac patients on a gluten-free diet, 24.5 +/- 6.65 and 0.45 +/- 0.16; and for celiac patients, 15.0 +/- 5.93 and 1.12 +/- 0.55.
24
Connell, J. W., J. G. Smith e P. M. Hergenrother. "Imide Oligomers Containing Pendent and Terminal Phenylethynyl Groups—II". High Performance Polymers 10, n. 3 (settembre 1998): 273–83. http://dx.doi.org/10.1088/0954-0083/10/3/005.
Testo completoAbstract (sommario):
As part of a programme to develop high-performance/high-temperature structural resins for aeronautical applications, imide oligomers containing pendent and terminal phenylethynyl groups were prepared, characterized and the cured resins evaluated as composite matrices. The oligomers were prepared at a calculated number-average molecular weight of 5000 g mol−1 and contained 15–20 mol% pendent phenylethynyl groups. In previous work, an oligomer containing pendent and terminal phenylethynyl groups exhibited a high glass transition temperature (∼313 °C), and laminates therefrom exhibited high compressive properties, but processability, fracture toughness, microcrack resistance and damage tolerance were less than desired. In an attempt to improve these deficiencies, modifications in the oligomeric backbone involving the incorporation of 1,3-bis(3-aminophenoxy)benzene were investigated as a means of improving processability and toughness without detracting from the high glass transition temperature and high compressive properties. The amide acid oligomeric solutions were prepared in N-methyl-2-pyrrolidinone and were subsequently processed into imide powder, thin films, adhesive tape and carbon fibre prepreg. Neat resin plaques were fabricated from imide powder by compression moulding. The maximum processing pressure was 1.4 MPa and the cure temperature ranged from 350 to 371 °C for 1 h for the mouldings, adhesives, films and composites. The properties of the 1,3-bis(3-aminophenoxy)benzene modified cured imide oligomers containing pendent and terminal phenylethynyl groups are compared with those of previously prepared oligomers containing pendent and terminal phenylethynyl groups of similar composition and molecular weight.
25
Thoms, Sven. "Import of proteins into peroxisomes: piggybacking to a new home away from home". Open Biology 5, n. 11 (novembre 2015): 150148. http://dx.doi.org/10.1098/rsob.150148.
Testo completoAbstract (sommario):
Peroxisomes are capable of importing folded and oligomeric proteins. However, it is a matter of dispute whether oligomer import by peroxisomes is the exception or the rule. Here, I argue for a clear distinction between homo-oligomeric proteins that are essentially peroxisomal, and dually localized hetero-oligomers that access the peroxisome by piggyback import, localizing there in limited number, whereas the majority remain in the cytosol. Homo-oligomeric proteins comprise the majority of all peroxisomal matrix proteins. There is evidence that binding by Pex5 in the cytosol can regulate their oligomerization state before import. The hetero-oligomer group is made up of superoxide dismutase and lactate dehydrogenase. These proteins have evolved mechanisms that render import inefficient and retain the majority of proteins in the cytosol.
26
Karunarathne, Kanchana, Teresa R. Kee, Hanna Jeon, Sara Cazzaro, Yasith I. Gamage, Jianjun Pan, Jung-A. A. Woo, David E. Kang e Martin Muschol. "Crystal Violet Selectively Detects Aβ Oligomers but Not Fibrils In Vitro and in Alzheimer’s Disease Brain Tissue". Biomolecules 14, n. 6 (23 maggio 2024): 615. http://dx.doi.org/10.3390/biom14060615.
Testo completoAbstract (sommario):
Deposition of extracellular Amyloid Beta (Aβ) and intracellular tau fibrils in post-mortem brains remains the only way to conclusively confirm cases of Alzheimer’s Disease (AD). Substantial evidence, though, implicates small globular oligomers instead of fibrils as relevant biomarkers of, and critical contributors to, the clinical symptoms of AD. Efforts to verify and utilize amyloid oligomers as AD biomarkers in vivo have been limited by the near-exclusive dependence on conformation-selective antibodies for oligomer detection. While antibodies have yielded critical evidence for the role of both Aβ and tau oligomers in AD, they are not suitable for imaging amyloid oligomers in vivo. Therefore, it would be desirable to identify a set of oligomer-selective small molecules for subsequent development into Positron Emission Tomography (PET) probes. Using a kinetics-based screening assay, we confirm that the triarylmethane dye Crystal Violet (CV) is oligomer-selective for Aβ42 oligomers (AβOs) grown under near-physiological solution conditions in vitro. In postmortem brains of an AD mouse model and human AD patients, we demonstrate that A11 antibody-positive oligomers but not Thioflavin S (ThioS)-positive fibrils colocalize with CV staining, confirming in vitro results. Therefore, our kinetic screen represents a robust approach for identifying new classes of small molecules as candidates for oligomer-selective dyes (OSDs). Such OSDs, in turn, provide promising starting points for the development of PET probes for pre-mortem imaging of oligomer deposits in humans.
27
Pils, Marlene, Alexandra Dybala, Fabian Rehn, Lara Blömeke, Tuyen Bujnicki, Victoria Kraemer-Schulien, Wolfgang Hoyer, Detlev Riesner, Dieter Willbold e Oliver Bannach. "Development and Implementation of an Internal Quality Control Sample to Standardize Oligomer-Based Diagnostics of Alzheimer’s Disease". Diagnostics 13, n. 10 (11 maggio 2023): 1702. http://dx.doi.org/10.3390/diagnostics13101702.
Testo completoAbstract (sommario):
Protein misfolding and aggregation are pathological hallmarks of various neurodegenerative diseases. In Alzheimer’s disease (AD), soluble and toxic amyloid-β (Aβ) oligomers are biomarker candidates for diagnostics and drug development. However, accurate quantification of Aβ oligomers in bodily fluids is challenging because extreme sensitivity and specificity are required. We previously introduced surface-based fluorescence intensity distribution analysis (sFIDA) with single-particle sensitivity. In this report, a preparation protocol for a synthetic Aβ oligomer sample was developed. This sample was used for internal quality control (IQC) to improve standardization, quality assurance, and routine application of oligomer-based diagnostic methods. We established an aggregation protocol for Aβ1–42, characterized the oligomers by atomic force microscopy (AFM), and assessed their application in sFIDA. Globular-shaped oligomers with a median size of 2.67 nm were detected by AFM, and sFIDA analysis of the Aβ1–42 oligomers yielded a femtomolar detection limit with high assay selectivity and dilution linearity over 5 log units. Lastly, we implemented a Shewhart chart for monitoring IQC performance over time, which is another important step toward quality assurance of oligomer-based diagnostic methods.
28
Obels, Daniela, Melanie Lievenbrück e Helmut Ritter. "From N-vinylpyrrolidone anions to modified paraffin-like oligomers via double alkylation with 1,8-dibromooctane: access to covalent networks and oligomeric amines for dye attachment". Beilstein Journal of Organic Chemistry 12 (6 luglio 2016): 1395–400. http://dx.doi.org/10.3762/bjoc.12.133.
Testo completoAbstract (sommario):
The double alkylation of N-vinylpyrrolidone (N-VP) with 1,8-dibromooctane yields paraffin-like oligomeric chains bearing polymerizable vinyl moieties. These oligomers were radically crosslinked in bulk with N-VP as co-monomer yielding swellable polymer disks. The vinylic side groups of the N-VP oligomers allow thiol–ene click reactions with 2-aminoethanethiol hydrochloride to obtain reactive amino-functionalized oligomers. Further modification of the free amino groups with 1,4-difluoro-9,10-anthraquinone (DFA) yields red-colored oligomeric anthraquinone dyes. The final reaction of DFA-substituted N-VP oligomers with Jeffamine® M 600 leads to blue-colored and branched oligomers with poly(ethylene glycol) side chains.
29
Iljina, Marija, Gonzalo A. Garcia, Mathew H. Horrocks, Laura Tosatto, Minee L. Choi, Kristina A. Ganzinger, Andrey Y. Abramov et al. "Kinetic model of the aggregation of alpha-synuclein provides insights into prion-like spreading". Proceedings of the National Academy of Sciences 113, n. 9 (16 febbraio 2016): E1206—E1215. http://dx.doi.org/10.1073/pnas.1524128113.
Testo completoAbstract (sommario):
The protein alpha-synuclein (αS) self-assembles into small oligomeric species and subsequently into amyloid fibrils that accumulate and proliferate during the development of Parkinson’s disease. However, the quantitative characterization of the aggregation and spreading of αS remains challenging to achieve. Previously, we identified a conformational conversion step leading from the initially formed oligomers to more compact oligomers preceding fibril formation. Here, by a combination of single-molecule fluorescence measurements and kinetic analysis, we find that the reaction in solution involves two unimolecular structural conversion steps, from the disordered to more compact oligomers and then to fibrils, which can elongate by further monomer addition. We have obtained individual rate constants for these key microscopic steps by applying a global kinetic analysis to both the decrease in the concentration of monomeric protein molecules and the increase in oligomer concentrations over a 0.5–140-µM range of αS. The resulting explicit kinetic model of αS aggregation has been used to quantitatively explore seeding the reaction by either the compact oligomers or fibrils. Our predictions reveal that, although fibrils are more effective at seeding than oligomers, very high numbers of seeds of either type, of the order of 104, are required to achieve efficient seeding and bypass the slow generation of aggregates through primary nucleation. Complementary cellular experiments demonstrated that two orders of magnitude lower numbers of oligomers were sufficient to generate high levels of reactive oxygen species, suggesting that effective templated seeding is likely to require both the presence of template aggregates and conditions of cellular stress.
30
Pandey, Rachit, e Brigita Urbanc. "Oligomer Formation by Physiologically Relevant C-Terminal Isoforms of Amyloid β-Protein". Biomolecules 14, n. 7 (28 giugno 2024): 774. http://dx.doi.org/10.3390/biom14070774.
Testo completoAbstract (sommario):
Alzheimer’s disease (AD) is a neurological disorder associated with amyloid β-protein (Aβ) assembly into toxic oligomers. In addition to the two predominant alloforms, Aβ1−40 and Aβ1−42, other C-terminally truncated Aβ peptides, including Aβ1−38 and Aβ1−43, are produced in the brain. Here, we use discrete molecular dynamics (DMD) and a four-bead protein model with amino acid-specific hydropathic interactions, DMD4B-HYDRA, to examine oligomer formation of Aβ1−38, Aβ1−40, Aβ1−42, and Aβ1−43. Self-assembly of 32 unstructured monomer peptides into oligomers is examined using 32 replica DMD trajectories for each of the four peptides. In a quasi-steady state, Aβ1−38 and Aβ1−40 adopt similar unimodal oligomer size distributions with a maximum at trimers, whereas Aβ1−42 and Aβ1−43 oligomer size distributions are multimodal with the dominant maximum at trimers or tetramers, and additional maxima at hexamers and unidecamers (for Aβ1−42) or octamers and pentadecamers (for Aβ1−43). The free energy landscapes reveal isoform- and oligomer-order specific structural and morphological features of oligomer ensembles. Our results show that oligomers of each of the four isoforms have unique features, with Aβ1−42 alone resulting in oligomers with disordered and solvent-exposed N-termini. Our findings help unravel the structure–function paradigm governing oligomers formed by various Aβ isoforms.
31
Eghiaian, Frederic, Thorsten Daubenfeld, Yann Quenet, Marieke van Audenhaege, Anne-Pascale Bouin, Guillaume van der Rest, Jeanne Grosclaude e Human Rezaei. "Diversity in prion protein oligomerization pathways results from domain expansion as revealed by hydrogen/deuterium exchange and disulfide linkage". Proceedings of the National Academy of Sciences 104, n. 18 (18 aprile 2007): 7414–19. http://dx.doi.org/10.1073/pnas.0607745104.
Testo completoAbstract (sommario):
The prion protein (PrP) propensity to adopt different structures is a clue to its biological role. PrP oligomers have been previously reported to bear prion infectivity or toxicity and were also found along the pathway of in vitro amyloid formation. In the present report, kinetic and structural analysis of ovine PrP (OvPrP) oligomerization showed that three distinct oligomeric species were formed in parallel, independent kinetic pathways. Only the largest oligomer gave rise to fibrillar structures at high concentration. The refolding of OvPrP into these different oligomers was investigated by analysis of hydrogen/deuterium exchange and introduction of disulfide bonds. These experiments revealed that, before oligomerization, separation of contacts in the globular part (residues 127–234) occurred between the S1–H1–S2 domain (residues 132–167) and the H2–H3 bundle (residues 174–230), implying a conformational change of the S2–H2 loop (residues 168–173). The type of oligomer to be formed depended on the site where the expansion of the OvPrP monomer was initiated. Our data bring a detailed insight into the earlier conformational changes during PrP oligomerization and account for the diversity of oligomeric entities. The kinetic and structural mechanisms proposed here might constitute a physicochemical basis of prion strain genesis.
32
de Klerk, G. J., e D. Engelen. "Assembly of Agrostemma githago (corn-cockle) storage proteins and their precursor proteins into oligomers". Biochemical Journal 230, n. 1 (15 agosto 1985): 269–72. http://dx.doi.org/10.1042/bj2300269.
Testo completoAbstract (sommario):
The major fraction of seed storage proteins of Agrostemma githago (corn-cockle), a non-leguminous dicot, occurs as material with S20,w values of approximately 11S and approximately 2S, and a minor fraction as oligomers with S20,w values of approximately 6.5S. The 11S proteins are of the legumin type and consist of disulphide-linked α- and β-subunits of Mr approximately 39 000 and approximately 23 000 respectively. The oligomeric assembly of the precursor polypeptides of the 11S proteins was examined. The approximately 65 000-Mr precursor polypeptides of two 11S proteins, which consist of 38 000-25 000-Mr subunits and 36 000-22 000-Mr subunits respectively, were assembled into oligomers of approximately 7S and subsequently cleaved. Thereafter the 11S oligomer was formed. The 88 000-Mr precursor of a third 11S protein, which consists of 41 000-23 000-Mr subunits, was assembled into an approximately 8S oligomer and then cleaved, yielding two disulphide-linked intermediates of Mr 59 000 and 24 000. Thereafter, the 11S oligomer was formed. Processing of the 59 000-Mr to the 41 000-Mr polypeptide occurred both in the 8S and in the 11S form.
33
LIBONATI, Massimo, e Giovanni GOTTE. "Oligomerization of bovine ribonuclease A: structural and functional features of its multimers". Biochemical Journal 380, n. 2 (1 giugno 2004): 311–27. http://dx.doi.org/10.1042/bj20031922.
Testo completoAbstract (sommario):
Bovine pancreatic RNase A (ribonuclease A) aggregates to form various types of catalytically active oligomers during lyophilization from aqueous acetic acid solutions. Each oligomeric species is present in at least two conformational isomers. The structures of two dimers and one of the two trimers have been solved, while plausible models have been proposed for the structures of a second trimer and two tetrameric conformers. In this review, these structures, as well as the general conditions for RNase A oligomerization, based on the well known 3D (three-dimensional) domain-swapping mechanism, are described and discussed. Attention is also focused on some functional properties of the RNase A oligomers. Their enzymic activities, particularly their ability to degrade double-stranded RNAs and polyadenylate, are summarized and discussed. The same is true for the remarkable antitumour activity of the oligomers, displayed in vitro and in vivo, in contrast with monomeric RNase A, which lacks these activities. The RNase A multimers also show an aspermatogenic action, but lack any detectable embryotoxicity. The fact that both activity against double-stranded RNA and the antitumour action increase with the size of the oligomer suggests that these activities may share a common structural requirement, such as a high number or density of positive charges present on the RNase A oligomers.
34
Vortman, M. Ya, Zh P. Kopteva, A. E. Kopteva, D. R. Abdulina, Yu B. Pysmenna, G. O. Iutynska, A. V. Rudenko, V. V. Tretyak, V. N. Lemeshko e V. V. Shevchenko. "Antibacterial and Fungicidal Activity of Guanidinium Oligomers". Mikrobiolohichnyi Zhurnal 83, n. 4 (17 agosto 2021): 86–97. http://dx.doi.org/10.15407/microbiolj83.04.086.
Testo completoAbstract (sommario):
Guanidinium oligomers are a poorly studied class of organic compounds and attract attention due to their antimicrobial properties. Strengthening the antimicrobial properties and simplifying and reducing the cost of the synthesis of these compounds is promising for obtaining functional guanidine-containing oligomers with alkyl radicals of different lengths in their composition. The aim of this work is to study the bactericidal and fungicidal activities of newly synthesized oligomeric guanidinium bromides with alkyl radicals of various lengths. Methods. The synthesis of tetraalkyl-substituted guanidine-containing oligomers with an aromatic and aliphatic oligoether component was carried out by the reaction of guanidine-containing oligomers with terminal guanidine fragments and alkyl bromides (Alk=-C3H7, -C7H15, -C10H21) at a molar ratio (1:4) of components. Different types of microorganisms (clinical isolates, gram-positive and gramnegative bacteria, microscopic fungi) were used as test cultures to determine the biocidal activity of the obtained compounds. The bacteria were grown on meat-peptone agar for 48 hours, micromycetes – on beer wort agar (6°B) for 14 days. The hydrocarbon-oxidizing bacteria and micromycetes were incubated at a temperature of 28±2°C, and clinical bacterial isolates – at a temperature of 37±2°C. Antimicrobial activity of oligomers was determined by the standard disco-diffusion method, and fungicidal – by the method of wells in agar. Results. Tetraalkyl-substituted guanidinium bromide oligomers with various radicals (-C3H7, -C7H15, -C10H21) were obtained and their bactericidal and fungicidal activity against various groups of microorganisms was shown. It was found that the obtained oligomers at a concentration of 1–3% in aqueous solution inhibited the growth of gram-negative and gram-positive bacteria. Antimicrobial and fungicidal properties depended on the length of the alkyl radical, and as its length increased, the diameter of growth inhibition zones of bacteria and micromycetes were increased. For 3% solutions of tetraalkyl-substituted guanidine oligomer with aromatic oligoepoxide (Alk=-C10H21), the growth inhibition zones of bacteria were 18–21 mm. The bactericidal effect of oligomer based on aromatic oligoepoxide with alkyl radicals Alk=-C7H15, -C10H21 was 20–25% higher than that for variants with aliphatic oligoepoxide. All the tetraalkyl-substituted (Alk=-C7H15, -C10H21) guanidine-containing oligomers at a concentration of 1% solution showed fungicidal activity to almost all micromycetes, the growth inhibition zones for microscopic fungi on the 7th day were 7–20 mm. The largest growth inhibition zones of micromycetes (in the range 15–20 mm) were observed for oligomers with aromatic oligoepoxide and radicals Alk=-C10H21 and -C7H15 and aliphatic oligoepoxide with radical Alk=-C10H21 (in the range 15–20 mm). Conclusions. The length of the alkyl radical and the nature of the oligoether component affected the bactericidal and fungicidal properties of newly synthesized oligomers. With an increase of the length of the alkyl radical of guanidine-containing oligomers, their bactericidal and fungicidal properties increase, tetralkyl-containing oligomers are promising for use as disinfectants for indoor treatment and as additives in polymer compositions to protect them from bio-damage.
35
Risti, Robert, Kathryn H. Gunn, Kristofer Hiis-Hommuk, Natjan-Naatan Seeba, Hamed Karimi, Ly Villo, Marko Vendelin, Saskia B. Neher e Aivar Lõokene. "Combined action of albumin and heparin regulates lipoprotein lipase oligomerization, stability, and ligand interactions". PLOS ONE 18, n. 4 (12 aprile 2023): e0283358. http://dx.doi.org/10.1371/journal.pone.0283358.
Testo completoAbstract (sommario):
Lipoprotein lipase (LPL), a crucial enzyme in the intravascular hydrolysis of triglyceride-rich lipoproteins, is a potential drug target for the treatment of hypertriglyceridemia. The activity and stability of LPL are influenced by a complex ligand network. Previous studies performed in dilute solutions suggest that LPL can appear in various oligomeric states. However, it was not known how the physiological environment, that is blood plasma, affects the action of LPL. In the current study, we demonstrate that albumin, the major protein component in blood plasma, has a significant impact on LPL stability, oligomerization, and ligand interactions. The effects induced by albumin could not solely be reproduced by the macromolecular crowding effect. Stabilization, isothermal titration calorimetry, and surface plasmon resonance studies revealed that albumin binds to LPL with affinity sufficient to form a complex in both the interstitial space and the capillaries. Negative stain transmission electron microscopy and raster image correlation spectroscopy showed that albumin, like heparin, induced reversible oligomerization of LPL. However, the albumin induced oligomers were structurally different from heparin-induced filament-like LPL oligomers. An intriguing observation was that no oligomers of either type were formed in the simultaneous presence of albumin and heparin. Our data also suggested that the oligomer formation protected LPL from the inactivation by its physiological regulator angiopoietin-like protein 4. The concentration of LPL and its environment could influence whether LPL follows irreversible inactivation and aggregation or reversible LPL oligomer formation, which might affect interactions with various ligands and drugs. In conclusion, the interplay between albumin and heparin could provide a mechanism for ensuring the dissociation of heparan sulfate-bound LPL oligomers into active LPL upon secretion into the interstitial space.
36
Yumura, Takashi, e Hiroki Yamashita. "Key factors in determining the arrangement of π-conjugated oligomers inside carbon nanotubes". Physical Chemistry Chemical Physics 17, n. 35 (2015): 22668–77. http://dx.doi.org/10.1039/c5cp03433g.
Testo completoAbstract (sommario):
Dispersion corrected DFT calculations found different arrangements of π-conjugated oligomers inside a carbon nanotube, dependent on the type of oligomer, which are responsible for determining the oligomers’ electronic properties.
37
Tariq, Mamoona, Rabia Khokhar, Arslan Javed, Muhammad Usman, Syed Muhammad Muneeb Anjum, Huma Rasheed, Nadeem Irfan Bukhari, Chao Yan e Hafiz Awais Nawaz. "Novel Hydrophilic Oligomer-Crosslinked Gelatin-Based Hydrogels for Biomedical Applications". Gels 9, n. 7 (11 luglio 2023): 564. http://dx.doi.org/10.3390/gels9070564.
Testo completoAbstract (sommario):
Gelatin-based hydrogels have shown good injectability and biocompatibility and have been broadly used for drug delivery and tissue regeneration. However, their low mechanical strengths and fast degradation rates must be modified for long-term implantation applications. With an aim to develop mechanically stable hydrogels, reactive anhydride-based oligomers were developed and used to fabricate gelatin-based crosslinked hydrogels in this study. A cascade of hydrophilic oligomers containing reactive anhydride groups was synthesized by free radical polymerization. These oligomers varied in degree of reactivity, comonomer composition, and showed low molecular weights (Mn < 5 kDa). The reactive oligomers were utilized to fabricate hydrogels that differed in their mechanical strengths and degradation profiles. These formulations exhibited good cytocompatibility with human adipose tissue-derived stem cells (hADCs). In conclusion, the reactive MA-containing oligomers were successfully synthesized and utilized for the development of oligomer-crosslinked hydrogels. Such oligomer-crosslinked gelatin-based hydrogels hold promise as drug or cell carriers in various biomedical applications.
38
De Rosa, Anna, Maria Ludovica Monaco, Mario Capasso, Pietro Forestieri, Vincenzo Pilone, Carmela Nardelli, Pasqualina Buono e Aurora Daniele. "Adiponectin oligomers as potential indicators of adipose tissue improvement in obese subjects". European Journal of Endocrinology 169, n. 1 (luglio 2013): 37–43. http://dx.doi.org/10.1530/eje-12-1039.
Testo completoAbstract (sommario):
ObjectiveAdiponectin is an adipocytokine that exerts beneficial effects on obesity and related disorders by two receptors (ADIPORs). Adiponectin is produced as a monomer that circulates in serum as different oligomers. The oligomerization state and the tissue expression of adiponectin and ADIPORs are linked to its biological activities. In this study, the levels of total adiponectin and its oligomers were evaluated in relation to obesity and surgical weight loss. The expression of adiponectin and ADIPORs was analyzed in visceral and subcutaneous adipose tissues of obese patients.Design and methodsIn 25 obese patients and 44 age- and sex-matched controls, the serum levels of adiponectin and its oligomers were measured and compared by ELISA, western blotting, and gel filtration. The expression of adiponectin and ADIPORs in both adipose tissues was evaluated by real-time quantitative PCR and western blotting.ResultsThe amount of each adiponectin oligomer, including the monomer, increases after weight loss. The reduced circulating levels of adiponectin and its oligomers are not associated with the adipose tissue depot-specific expression of adiponectin and ADIPORs.ConclusionsOur results suggest that in patients, adiposity is associated with the serum concentrations of adiponectin and its oligomers but not with adipose tissue depot-specific expression of adiponectin and ADIPORs. In particular, the increase in adiponectin monomer levels could probably be related to the improvement of the whole-body energy metabolism then being involved in the improvement of adipose tissue function after weight loss. This work indicates the importance of assessing the whole adiponectin oligomeric profile as further potential indicators of adipose tissue functions in obesity.
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Markina, Anastasia, Alexander Muratov, Vladislav Petrovskyy e Vladik Avetisov. "Detection of Single Molecules Using Stochastic Resonance of Bistable Oligomers". Nanomaterials 10, n. 12 (15 dicembre 2020): 2519. http://dx.doi.org/10.3390/nano10122519.
Testo completoAbstract (sommario):
Ultra-sensitive elements for nanoscale devices capable of detecting single molecules are in demand for many important applications. It is generally accepted that the inevitable stochastic disturbance of a sensing element by its surroundings will limit detection at the molecular level. However, a phenomenon exists (stochastic resonance) in which the environmental noise acts abnormally: it amplifies, rather than distorts, a weak signal. Stochastic resonance is inherent in non-linear bistable systems with criticality at which the bistability emerges. Our computer simulations have shown that the large-scale conformational dynamics of a short oligomeric fragment of thermosrespective polymer, poly-N-isopropylmethacrylamid, resemble the mechanical movement of nonlinear bistable systems. The oligomers we have studied demonstrate spontaneous vibrations and stochastic resonance activated by conventional thermal noise. We have observed reasonable shifts of the spontaneous vibrations and stochastic resonance modes when attaching an analyte molecule to the oligomer. Our simulations have shown that spontaneous vibrations and stochastic resonance of the bistable thermoresponsive oligomers are sensitive to both the analyte molecular mass and the binding affinity. All these effects indicate that the oligomers with mechanic-like bistability may be utilized as ultrasensitive operational units capable of detecting single molecules.
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Alberto Lopes, Joao, Fabiano Reniero, Claude Guillou e Emmanouil Tsochatzis. "Odd-Even Effect of Polyesters‘ Cyclic Oligomers and the Definition of Oligomers Based on Physicochemical Properties". Applied Sciences 14, n. 5 (1 marzo 2024): 2085. http://dx.doi.org/10.3390/app14052085.
Testo completoAbstract (sommario):
This work explores the definition and characterization of synthetic polymeric oligomers, chemical substances comprising a small number of repeated organic molecules. It highlights the lack of clarity surrounding the range of repeated units that can be classified as an oligomer, and how this definition is field-dependent. The present study focused on PET cyclic oligomers and revealed that the progression of the ring length from smaller to longer oligomers followed the well-known odd-even effect. This phenomenon affects the physical and chemical properties of oligomers and can also be observed with analytical techniques such as differential scanning calorimetry (DSC), high resolution mass spectrometry (HR-MS) and NMR. Similarities between PET and PBT oligomers were also observed, and an alternative potential definition for oligomers in the polymeric field is suggested based on physical behaviour of the longer cyclic oligomers.
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Aung-Htut, May T., Craig S. McIntosh, Kristin A. West, Sue Fletcher e Steve D. Wilton. "In Vitro Validation of Phosphorodiamidate Morpholino Oligomers". Molecules 24, n. 16 (12 agosto 2019): 2922. http://dx.doi.org/10.3390/molecules24162922.
Testo completoAbstract (sommario):
One of the crucial aspects of screening antisense oligonucleotides destined for therapeutic application is confidence that the antisense oligomer is delivered efficiently into cultured cells. Efficient delivery is particularly vital for antisense phosphorodiamidate morpholino oligomers, which have a neutral backbone, and are known to show poor gymnotic uptake. Here, we report several methods to deliver these oligomers into cultured cells. Although 4D-Nucleofector™ or Neon™ electroporation systems provide efficient delivery and use lower amounts of phosphorodiamidate morpholino oligomer, both systems are costly. We show that some readily available transfection reagents can be used to deliver phosphorodiamidate morpholino oligomers as efficiently as the electroporation systems. Among the transfection reagents tested, we recommend Lipofectamine 3000™ for delivering phosphorodiamidate morpholino oligomers into fibroblasts and Lipofectamine 3000™ or Lipofectamine 2000™ for myoblasts/myotubes. We also provide optimal programs for nucleofection into various cell lines using the P3 Primary Cell 4D-Nucleofector™ X Kit (Lonza), as well as antisense oligomers that redirect expression of ubiquitously expressed genes that may be used as positive treatments for human and murine cell transfections.
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YAMADA, TOMOYUKI, e SHINICHI MORISHITA. "COMPUTING HIGHLY SPECIFIC AND NOISE-TOLERANT OLIGOMERS EFFICIENTLY". Journal of Bioinformatics and Computational Biology 02, n. 01 (marzo 2004): 21–46. http://dx.doi.org/10.1142/s0219720004000454.
Testo completoAbstract (sommario):
The sequencing of the genomes of a variety of species and the growing databases containing expressed sequence tags (ESTs) and complementary DNAs (cDNAs) facilitate the design of highly specific oligomers for use as genomic markers, PCR primers, or DNA oligo microarrays. The first step in evaluating the specificity of short oligomers of about 20 units in length is to determine the frequencies at which the oligomers occur. However, for oligomers longer than about fifty units this is not efficient, as they usually have a frequency of only 1. A more suitable procedure is to consider the mismatch tolerance of an oligomer, that is, the minimum number of mismatches that allows a given oligomer to match a substring other than the target sequence anywhere in the genome or the EST database. However, calculating the exact value of mismatch tolerance is computationally costly and impractical. Therefore, we studied the problem of checking whether an oligomer meets the constraint that its mismatch tolerance is no less than a given threshold. Here, we present an efficient dynamic programming algorithm solution that utilizes suffix and height arrays. We demonstrated the effectiveness of this algorithm by efficiently computing a dense list of numerous oligo-markers applicable to the human genome. Experimental results show that the algorithm runs faster than well-known Abrahamson's algorithm by orders of magnitude and is able to enumerate 65%~76% of qualified oligomers.
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Trikha, Saurabh, e Aleksandar M. Jeremic. "Clustering and Internalization of Toxic Amylin Oligomers in Pancreatic Cells Require Plasma Membrane Cholesterol". Journal of Biological Chemistry 286, n. 41 (24 agosto 2011): 36086–97. http://dx.doi.org/10.1074/jbc.m111.240762.
Testo completoAbstract (sommario):
Self-assembly of the human pancreatic hormone amylin into toxic oligomers and aggregates is linked to dysfunction of islet β-cells and pathogenesis of type 2 diabetes mellitus. Recent evidence suggests that cholesterol, an essential component of eukaryotic cells membranes, controls amylin aggregation on model membranes. However, the pathophysiological consequence of cholesterol-regulated amylin polymerization on membranes and biochemical mechanisms that protect β-cells from amylin toxicity are poorly understood. Here, we report that plasma membrane (PM) cholesterol plays a key role in molecular recognition, sorting, and internalization of toxic amylin oligomers but not monomers in pancreatic rat insulinoma and human islet cells. Depletion of PM cholesterol or the disruption of the cytoskeleton network inhibits internalization of amylin oligomers, which in turn enhances extracellular oligomer accumulation and potentiates amylin toxicity. Confocal microscopy reveals an increased nucleation of amylin oligomers across the plasma membrane in cholesterol-depleted cells, with a 2-fold increase in cell surface coverage and a 3-fold increase in their number on the PM. Biochemical studies confirm accumulation of amylin oligomers in the medium after depletion of PM cholesterol. Replenishment of PM cholesterol from intracellular cholesterol stores or by the addition of water-soluble cholesterol restores amylin oligomer clustering at the PM and internalization, which consequently diminishes cell surface coverage and toxicity of amylin oligomers. In contrast to oligomers, amylin monomers followed clathrin-dependent endocytosis, which is not sensitive to cholesterol depletion. Our studies identify an actin-mediated and cholesterol-dependent mechanism for selective uptake and clearance of amylin oligomers, impairment of which greatly potentiates amylin toxicity.
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Jugl, Adam, e Miloslav Pekař. "Hyaluronan-Arginine Interactions—An Ultrasound and ITC Study". Polymers 12, n. 9 (12 settembre 2020): 2069. http://dx.doi.org/10.3390/polym12092069.
Testo completoAbstract (sommario):
High-resolution ultrasound spectroscopy and isothermal titration calorimetry were used to characterize interactions between hyaluronan and arginine oligomers. The molecular weight of arginine oligomer plays an important role in interactions with hyaluronan. Interactions were observable for arginine oligomers with eight monomer units and longer chains. The effect of the ionic strength and molecular weight of hyaluronan on interactions was tested. In an environment with increased ionic strength, the length of the arginine oligomer was crucial. Generally, sufficiently high ionic strength suppresses interactions between hyaluronan and arginine oligomers, which demonstrated interactions in water. From the point of view of the molecular weight of hyaluronan, the transition between the rod conformation and the random coil conformation appeared to be important.
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Finbloom, D. S. "Subcellular characterization of the endocytosis of small oligomers of mouse immunoglobulin G in murine macrophages." Journal of Immunology 136, n. 3 (1 febbraio 1986): 844–51. http://dx.doi.org/10.4049/jimmunol.136.3.844.
Testo completoAbstract (sommario):
Abstract To characterize the internalization and degradation of model immune complexes in murine macrophages, the endocytosis of well-defined radiolabeled IgG dimers and heavy oligomers (5 to 7 IgG molecules per complex), which were covalently cross-linked at the antigen-combining site, was studied. Of those heavy oligomers which were bound to the cell at 4 degrees C, 50 to 60% (400,000 molecules of IgG) were internalized within 30 min at 37 degrees C and, subsequently, were completely degraded over a period of 3 hr. Low pH had little effect on the dissociation of the oligomer from its receptor. The degradation of oligomers was markedly inhibited when macrophages were treated with monensin, a proton ionophore which raises organelle pH. Because this treatment did not prevent the delivery of oligomer into the lysosome, the transport of a soluble complex of IgG from the cell surface to the lysosome was not a pH-dependent event. On the other hand, 25 to 30% (50,000 molecules) of those dimers capable of binding to the cell entered the macrophage, but only 5000 molecules were degraded. When macrophages were studied by using density gradient centrifugation, within 15 min, heavy oligomers were found in a vesicle which sedimented at a density between that of the plasma membrane and lysosome. The density of this vesicle was similar to that of endosomes studied in other receptor-ligand systems. Heavy oligomers were within lysosomes shortly thereafter. Incubation of cells at 18 degrees C prevented the appearance of heavy oligomer within the lysosomes and resulted in the concentration of oligomers within an intracellular compartment of a density slightly heavier than that of plasma membrane. At 37 degrees C, dimers sedimented in a similar region of the gradient. But unlike heavy oligomers, dimers never entered lysosomes. These data suggest that the degree of Fc receptor clustering induced by oligomers of IgG influenced the intracellular fate of the ligand.
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Xue, Christine, Joyce Tran, Hongsu Wang, Giovanna Park, Frederick Hsu e Zhefeng Guo. "Aβ42 fibril formation from predominantly oligomeric samples suggests a link between oligomer heterogeneity and fibril polymorphism". Royal Society Open Science 6, n. 7 (luglio 2019): 190179. http://dx.doi.org/10.1098/rsos.190179.
Testo completoAbstract (sommario):
Amyloid-β (Aβ) oligomers play a central role in the pathogenesis of Alzheimer's disease. Oligomers of different sizes, morphology and structures have been reported in both in vivo and in vitro studies, but there is a general lack of understanding about where to place these oligomers in the overall process of Aβ aggregation and fibrillization. Here, we show that Aβ42 spontaneously forms oligomers with a wide range of sizes in the same sample. These Aβ42 samples contain predominantly oligomers, and they quickly form fibrils upon incubation at 37°C. When fractionated using ultrafiltration filters, the samples enriched with smaller oligomers form fibrils at a faster rate than the samples enriched with larger oligomers, with both a shorter lag time and faster fibril growth rate. This observation is independent of Aβ42 batches and hexafluoroisopropanol treatment. Furthermore, the fibrils formed by the samples enriched with larger oligomers are more readily solubilized by epigallocatechin gallate, a main catechin component of green tea. These results suggest that the fibrils formed by larger oligomers may adopt a different structure from fibrils formed by smaller oligomers, pointing to a link between oligomer heterogeneity and fibril polymorphism.
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Zheng, Weihua, Min-Yeh Tsai, Mingchen Chen e Peter G. Wolynes. "Exploring the aggregation free energy landscape of the amyloid-β protein (1–40)". Proceedings of the National Academy of Sciences 113, n. 42 (3 ottobre 2016): 11835–40. http://dx.doi.org/10.1073/pnas.1612362113.
Testo completoAbstract (sommario):
A predictive coarse-grained protein force field [associative memory, water-mediated, structure, and energy model for molecular dynamics (AWSEM)-MD] is used to study the energy landscapes and relative stabilities of amyloid-β protein (1–40) in the monomer and all of its oligomeric forms up to an octamer. We find that an isolated monomer is mainly disordered with a short α-helix formed at the central hydrophobic core region (L17-D23). A less stable hairpin structure, however, becomes increasingly more stable in oligomers, where hydrogen bonds can form between neighboring monomers. We explore the structure and stability of both prefibrillar oligomers that consist of mainly antiparallel β-sheets and fibrillar oligomers with only parallel β-sheets. Prefibrillar oligomers are polymorphic but typically take on a cylindrin-like shape composed of mostly antiparallel β-strands. At the concentration of the simulation, the aggregation free energy landscape is nearly downhill. We use umbrella sampling along a structural progress coordinate for interconversion between prefibrillar and fibrillar forms to identify a conversion pathway between these forms. The fibrillar oligomer only becomes favored over its prefibrillar counterpart in the pentamer where an interconversion bottleneck appears. The structural characterization of the pathway along with statistical mechanical perturbation theory allow us to evaluate the effects of concentration on the free energy landscape of aggregation as well as the effects of the Dutch and Arctic mutations associated with early onset of Alzheimer’s disease.
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Byrne, Patrick O., Kalina Hristova e Daniel J. Leahy. "EGFR forms ligand-independent oligomers that are distinct from the active state". Journal of Biological Chemistry 295, n. 38 (29 luglio 2020): 13353–62. http://dx.doi.org/10.1074/jbc.ra120.012852.
Testo completoAbstract (sommario):
The human epidermal growth factor receptor (EGFR/ERBB1) is a receptor tyrosine kinase (RTK) that forms activated oligomers in response to ligand. Much evidence indicates that EGFR/ERBB1 also forms oligomers in the absence of ligand, but the structure and physiological role of these ligand-independent oligomers remain unclear. To examine these features, we use fluorescence microscopy to measure the oligomer stability and FRET efficiency for homo- and hetero-oligomers of fluorescent protein-labeled forms of EGFR and its paralog, human epidermal growth factor receptor 2 (HER2/ERBB2) in vesicles derived from mammalian cell membranes. We observe that both receptors form ligand-independent oligomers at physiological plasma membrane concentrations. Mutations introduced in the kinase region at the active state asymmetric kinase dimer interface do not affect the stability of ligand-independent EGFR oligomers. These results indicate that ligand-independent EGFR oligomers form using interactions that are distinct from the EGFR active state.
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Kahraman, Gülten, Mustafa Türk, Zakir M. O. Rzayev, M. Elif Unsal e Ernur Söylemez. "Bioengineering functional copolymers. XV. Synthesis of organoboron amide-ester branched derivatives of oligo(maleic anhydride) and their interaction with HeLa and L929 fibroblast cells". Collection of Czechoslovak Chemical Communications 76, n. 8 (2011): 1013–31. http://dx.doi.org/10.1135/cccc2010080.
Testo completoAbstract (sommario):
Novel bioengineering functional organoboron oligomers were synthesized by (i) amidolysis of oligo(maleic anhydride) (OMA) with 2-aminoethyldiphenylborinate (2-AEPB), (ii) esterification of organoboron oligomer (OMA-B) with α-hydroxy-ω-methoxypoly(ethylene oxide) (PEO) as a compatibilizer and (iii) conjugation of organoboron PEO branches (OMA-B-PEO) with folic acid as a taggering agent. Structure and composition of the synthesized oligomers were characterized by FTIR-ART and 1H (13C) NMR spectroscopy, chemical and physical analysis methods. Interaction of functional oligomers and oligomer···FA complex (OMA-B-PEO-F) with HeLa and L929 fibroblast cells were investigated by using different biochemical methods such as cytotoxicity, statistical, apoptotic and necrotic cell indexes, double staining and caspase-3 immunostaining, light and fluorescence inverted microscope analyses. It was found that citotoxisity and apoptotic/necrotic effects of oligomers significantly depend on the structure and composition of studied oligomers, and increase the following raw: OMA << OMA-B < OMA-B-PEO < OMA-B-PEO-F. A folic acid complex (MA-PEG-B-F) at 400 μg ml–1 (2.36 μmol ml–1) concentration as a therapeutic drug exhibits minimal toxcisity toward the fibroblast cells, but influential for HeLa cells.
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Singh, Ratna, Jens Smiatek e Bruno M. Moerschbacher. "Unraveling the Impact of Acetylation Patterns in Chitosan Oligomers on Cu2+ Ion Binding: Insights from DFT Calculations". International Journal of Molecular Sciences 24, n. 18 (7 settembre 2023): 13792. http://dx.doi.org/10.3390/ijms241813792.
Testo completoAbstract (sommario):
Chitosans are partially acetylated polymers of glucosamine, structurally characterized by their degree of polymerization as well as their fraction and pattern of acetylation. These parameters strongly influence the physico-chemical properties and biological activities of chitosans, but structure-function relationships are only poorly understood. As an example, we here investigated the influence of acetylation on chitosan-copper complexation using density functional theory. We investigated the electronic structures of completely deacetylated and partially acetylated chitosan oligomers and their copper-bound complexes. Frontier molecular orbital theory revealed bonding orbitals for electrophiles and antibonding orbitals for nucleophiles in fully deacetylated glucosamine oligomers, while partially acetylated oligomers displayed bonding orbitals for both electrophiles and nucleophiles. Our calculations showed that the presence of an acetylated subunit in a chitosan oligomer affects the structural and the electronic properties of the oligomer by generating new intramolecular interactions with the free amino group of neighboring deacetylated subunits, thereby influencing its polarity. Furthermore, the band gap energy calculated from the fully and partially deacetylated oligomers indicates that the mobility of electrons in partially acetylated chitosan oligomers is higher than in fully deacetylated oligomers. In addition, fully deacetylated oligomers form more stable complexes with higher bond dissociation energies with copper than partially acetylated ones. Interestingly, in partially acetylated oligomers, the strength of copper binding was found to be dependent on the pattern of acetylation. Our study provides first insight into the influence of patterns of acetylation on the electronic and ion binding properties of chitosans. Depending on the intended application, the obtained results can serve as a guide for the selection of the optimal chitosan for a specific purpose.