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1
Larson, Megan E., Susan J. Greimel, Fatou Amar та ін. "Selective lowering of synapsins induced by oligomeric α-synuclein exacerbates memory deficits". Proceedings of the National Academy of Sciences 114, № 23 (2017): E4648—E4657. http://dx.doi.org/10.1073/pnas.1704698114.
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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.
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Dalgėdienė, Indrė, Asta Lučiūnaitė, and Aurelija Žvirblienė. "Activation of Macrophages by Oligomeric Proteins of Different Size and Origin." Mediators of Inflammation 2018 (November 18, 2018): 1–13. http://dx.doi.org/10.1155/2018/7501985.
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Activation of macrophages is one of the key processes in generating the immune response against pathogens or misfolded/aggregated otherwise unharmful host’s proteins. Antigens and their immune complexes (IC) may shape macrophage phenotype in various directions. Data on the impact of protein structure during inflammation are evident; however, some separate steps of this process involving changes in macrophage phenotype are not fully understood. Our aim was to investigate the phenotype of macrophages after activation with different oligomeric proteins and their IC. We have used amyloid beta (Aβ1–42) that plays a role in neurodegenerative inflammation as a model of host-associated protein and three oligomeric viral antigens as pathogen-associated proteins. Murine cell lines J774, BV-2, and macrophage primary cell culture were treated with oligomeric proteins and their IC. After 48 h, expression of surface markers F4/80, CD68, CD86, and CD206 and secreted cytokines IL-10, IL-12, IL-23, and TNF-αwas analysed. Aβ1–42oligomers stimulated expression of both inflammatory and anti-inflammatory molecules; however, fibrils induced less intense expression of markers investigated as compared to small and large oligomers. Two out of three viral oligomeric proteins induced the inflammatory response of macrophages. Data suggest that macrophage activation pattern depends on the origin, size, and structure of oligomeric proteins.
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Sudipa, Saha. "Oligomeric structure and molecular chaperone function of eye lens protein α-crystallin – A Review". Journal of Indian Chemical Society Vol. 93, Nov 2016 (2016): 1233–42. https://doi.org/10.5281/zenodo.5639119.
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Department of Biotechnology, St. Xavier’s College, Kolkata-700 016, India <em>E-mail </em>: sahasudipa74@yahoo.co.in <em>Manuscript received 03 August 2016, accepted 26 August 2016</em> α-Crystallin, the major eye lens protein, exists as a large oligomer of two subunits, αA- and αB-crystallin. α-Crystallin exists in solution as a polydisperse high molecular mass aggregate with a molecular weight distribution ranging from 300,000 to over 1 million. Crystallization attempts of both the natural and recombinant α-crystallin of vertebrate were not fruitful so far because of the polydispersed nature of the protein oligomer. It is seen that despite the enormous number of studies on the structure of α-crystallin, the oligomeric sructure of α-crystallin is still the subject of much debate and speculation. It is generally believed that large oligomeric structure of α-crystallin or other sHSPs is prerequisite for their chaperone-like function. Although most chaperones are oligomers, whether oligomerization is absolutely required for protein stability or for chaperone function is not yet established.
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Pokrajac, Lisa, Clara Baik, J. Robin Harris, Naghmeh S. Sarraf, and Michael Palmer. "Partial oligomerization of pyolysin induced by a disulfide-tethered mutant." Biochemistry and Cell Biology 90, no. 6 (2012): 709–17. http://dx.doi.org/10.1139/o2012-029.
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The bacterial toxin pyolysin (PLO) belongs to the family of cholesterol-dependent cytolysins (CDCs), which form large, ring-shaped oligomeric pores in cholesterol-containing membranes. Monomeric CDC molecules have a structure of four domains, with domains 2 and 3 packed against each other. After binding to target membranes containing cholesterol, toxin monomers oligomerize into pre-pore complexes. Trans-membrane pores form when the pre-pores insert into the lipid bilayer. Membrane insertion requires each subunit in the pre-pore to undergo a significant change in conformation, including the separation of domains 2 and 3. We here characterize a pyolysin mutant with an engineered disulfide bond between domains 2 and 3. The disulfide-tethered mutant binds to membranes but does not form oligomers. When mixed with wild type PLO, the two proteins form hybrid oligomers, which are reduced in size and arc-shaped rather than ring-shaped. With equimolar mixtures or the disulfide mutant in slight excess, the hybrid oligomers retain pore-forming activity, while a larger excess of the mutant suppresses pore formation. These results support a “partially cooperative” mode of protein activity, in which a limited number of functional subunits within an oligomer have to cooperate to initiate membrane insertion and pore formation.
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Gurevich, Vsevolod V. "Do arrestin oligomers have specific functions?" Cell Signaling 1, no. 1 (2023): 42–46. http://dx.doi.org/10.46439/signaling.1.009.
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Arrestins are a small family of versatile regulators of cell signaling. Arrestins regulate signaling and trafficking of G protein-coupled receptors, regulate and direct to particular subcellular compartments numerous protein kinases, ubiquitin ligases, etc. Three out of four arrestin subtypes expressed in vertebrates self-associate, each forming oligomers of a distinct size and shape. While the structures of the solution oligomers of arrestin-1, -2, and -3 have been elucidated, no function specific for the oligomeric form of either of these three subtypes has been identified thus far. Considering how multi-functional average-sized (~45 kDa) arrestin proteins were found to be, it appears likely that certain functions are predominantly or exclusively fulfilled by monomeric and oligomeric forms of each subtype.
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Sanganna Gari, Raghavendar Reddy, Patrick Seelheim, Brendan Marsh, Volker Kiessling, Carl E. Creutz, and Lukas K. Tamm. "Quaternary structure of the small amino acid transporter OprG from Pseudomonas aeruginosa." Journal of Biological Chemistry 293, no. 44 (2018): 17267–77. http://dx.doi.org/10.1074/jbc.ra118.004461.
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Pseudomonas aeruginosa is an opportunistic human pathogen that causes nosocomial infections. The P. aeruginosa outer membrane contains specific porins that enable substrate uptake, with the outer membrane protein OprG facilitating transport of small, uncharged amino acids. However, the pore size of an eight-stranded β-barrel monomer of OprG is too narrow to accommodate even the smallest transported amino acid, glycine, raising the question of how OprG facilitates amino acid uptake. Pro-92 of OprG is critically important for amino acid transport, with a P92A substitution inhibiting transport and the NMR structure of this variant revealing that this substitution produces structural changes in the barrel rim and restricts loop motions. OprG may assemble into oligomers in the outer membrane (OM) whose subunit interfaces could form a transport channel. Here, we explored the contributions of the oligomeric state and the extracellular loops to OprG's function. Using chemical cross-linking to determine the oligomeric structures of both WT and P92A OprG in native outer membranes and atomic force microscopy, and single-molecule fluorescence of the purified proteins reconstituted into lipid bilayers, we found that both protein variants form oligomers, supporting the notion that subunit interfaces in the oligomer could provide a pathway for amino acid transport. Furthermore, performing transport assays with loop-deleted OprG variants, we found that these variants also can transport small amino acids, indicating that the loops are not solely responsible for substrate transport. We propose that OprG functions as an oligomer and that conformational changes in the barrel–loop region might be crucial for its activity.
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Melotto, Eunice, L. Carl Greve, and John M. Labavitch. "PECTIN OLIGOMERS - POTENTIAL ENDOGENOUS REGULATORS OF RIPENING?" HortScience 27, no. 6 (1992): 653g—653. http://dx.doi.org/10.21273/hortsci.27.6.653g.
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Acid hydrolysis-generated pectic oligomers have been shown to affect ripening of tomato fruit by inducing both acceleration of reddening and increased ethylene biosynthesis (Campbell & Labavitch, 1991 Plant Physiol 97:706-713). In the present work, homogeneous size classes of these oligomers were demonstrated to have different impacts on ethylene production of tomato fruit pericarp discs. Endogenous oligomeric material of the same size classes was isolated from ripening tomato tissues and also tested for biological activity. They promoted some aspects of ripening as shown by increased ACC and ethylene production, which suggests that pectic oligomers are potential regulators of the ripening process in tomatoes. A metabolic origin for these oligomers is suggested by the fact that they are produced by in vitro polygalacturonase I treatment of polygalacturonic acid or tomato pectin.
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Wojciechowska, Daria, Michał Taube, Karolina Rucińska, Joanna Maksim, and Maciej Kozak. "Oligomerization of Human Cystatin C—An Amyloidogenic Protein: An Analysis of Small Oligomeric Subspecies." International Journal of Molecular Sciences 23, no. 21 (2022): 13441. http://dx.doi.org/10.3390/ijms232113441.
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Human cystatin C (HCC), an amyloidogenic protein, forms dimers and higher oligomers (trimers, tetramers and donut like large oligomers) via a domain-swapping mechanism. The aim of this study was the characterization of the HCC oligomeric states observed within the pH range from 2.2 to 10.0 and also in conditions promoting oligomerization. The HCC oligomeric forms obtained in different conditions were characterized using size exclusion chromatography, dynamic light scattering and small-angle X-ray scattering. The marked ability of HCC to form tetramers at low pH (2.3 or 3.0) and dimers at pH 4.0–5.0 was observed. HCC remains monomeric at pH levels above 6.0. Based on the SAXS data, the structure of the HCC tetramer was proposed. Changes in the environment (from acid to neutral) induced a breakdown of the HCC tetramers to dimers. The tetrameric forms of human cystatin C are formed by the association of the dimers without a domain-swapping mechanism. These observations were confirmed by their dissociation to dimers at pH 7.4.
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Stoneman, Michael R., Naomi Raicu, Gabriel Biener, and Valerică Raicu. "Fluorescence-based Methods for the Study of Protein-Protein Interactions Modulated by Ligand Binding." Current Pharmaceutical Design 26, no. 44 (2020): 5668–83. http://dx.doi.org/10.2174/1381612826666201116120934.
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Background: The growing evidence that G protein-coupled receptors (GPCRs) not only form oligomers but that the oligomers also may modulate the receptor function provides a promising avenue in the area of drug design. Highly selective drugs targeting distinct oligomeric sub-states offer the potential to increase efficacy while reducing side effects. In this regard, determining the various oligomeric configurations and geometric sub-states of a membrane receptor is of utmost importance. Methods: In this report, we have reviewed two techniques that have proven to be valuable in monitoring the quaternary structure of proteins in vivo: Fӧrster resonance energy transfer (FRET) spectrometry and fluorescence intensity fluctuation (FIF) spectrometry. In FRET spectrometry, distributions of pixel-level FRET efficiency are analyzed using theoretical models of various quaternary structures to determine the geometry and stoichiometry of protein oligomers. In FIF spectrometry, spatial fluctuations of fluorescent molecule intensities are analyzed to reveal quantitative information on the size and stability of protein oligomers. Results: We demonstrate the application of these techniques to a number of different fluorescence-based studies of cells expressing fluorescently labeled membrane receptors, both in the presence and absence of various ligands. The results show the effectiveness of using FRET spectrometry to determine detailed information regarding the quaternary structure receptors form, as well as FIF and FRET for determining the relative abundance of different-sized oligomers when an equilibrium forms between such structures. Conclusion: FRET and FIF spectrometry are valuable techniques for characterizing membrane receptor oligomers, which are of great benefit to structure‐based drug design.
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BÖDE, Csaba, Ferenc G. TÖLGYESI, László SMELLER, Karel HEREMANS, Sergiy V. AVILOV, and Judit FIDY. "Chaperone-like activity of alpha-crystallin is enhanced by high-pressure treatment." Biochemical Journal 370, no. 3 (2003): 859–66. http://dx.doi.org/10.1042/bj20021097.
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α-Crystallin, an oligomeric protein in vertebrate eye lens, is a member of the small heat-shock protein family. Several papers pointed out that its chaperone-like activity could be enhanced by increasing the temperature. We demonstrate in the present study that structural perturbations by high hydrostatic pressures up to 300MPa also enhance this activity. In contrast with temperature-induced changes, the pressure-induced enhancement is reversible. After pressure release, the extra activity is lost with a relaxation time of 2.0±0.5h. Structural alterations contributing to the higher activity were studied with IR and fluorescence spectroscopy, and light-scattering measurements. The results suggest that while the secondary structure barely changes under pressure, the interactions between the subunits weaken, the oligomers dissociate, the area of accessible hydrophobic surfaces significantly increases and the environment of tryptophan residues becomes slightly more polar. It seems that structural flexibility and the total surface area of the oligomers are the key factors in the chaperone capacity, and that the increase in the chaperone activity does not require the increase in the oligomer size as was assumed previously [Burgio, Kim, Dow and Koretz (2000) Biochem. Biophys. Res. Commun. 268, 426—432]. After pressure release, the structure of subunits are reorganized relatively quickly, whereas the oligomer size reaches its original value slowly with a relaxation time of 33±4 h. In our interpretation, both the fast and slow structural rearrangements have an impact on the functional relaxation.
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Herczeg, Mihály, Fruzsina Demeter, Tibor Nagy, et al. "Block Synthesis and Step-Growth Polymerization of C-6-Sulfonatomethyl-Containing Sulfated Malto-Oligosaccharides and Their Biological Profiling." International Journal of Molecular Sciences 25, no. 1 (2024): 677. http://dx.doi.org/10.3390/ijms25010677.
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Highly sulfated malto-oligomers, similar to heparin and heparan-sulfate, have good antiviral, antimetastatic, anti-inflammatory and cell growth inhibitory effects. Due to their broad biological activities and simple structure, sulfated malto-oligomer derivatives have a great therapeutic potential, therefore, the development of efficient synthesis methods for their production is of utmost importance. In this work, preparation of α-(1→4)-linked oligoglucosides containing a sulfonatomethyl moiety at position C-6 of each glucose unit was studied by different approaches. Malto-oligomeric sulfonic acid derivatives up to dodecasaccharides were prepared by polymerization using different protecting groups, and the composition of the product mixtures was analyzed by MALDI-MS methods and size-exclusion chromatography. Synthesis of lower oligomers was also accomplished by stepwise and block synthetic methods, and then the oligosaccharide products were persulfated. The antiviral, anti-inflammatory and cell growth inhibitory activity of the fully sulfated malto-oligosaccharide sulfonic acids were determined by in vitro tests. Four tested di- and trisaccharide sulfonic acids effectively inhibited the activation of the TNF-α-mediated inflammatory pathway without showing cytotoxicity.
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LIBONATI, Massimo, and Giovanni GOTTE. "Oligomerization of bovine ribonuclease A: structural and functional features of its multimers." Biochemical Journal 380, no. 2 (2004): 311–27. http://dx.doi.org/10.1042/bj20031922.
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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.
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Caldwell, Brian J., Andrew Norris, Ekaterina Zakharova та ін. "Oligomeric complexes formed by Redβ single strand annealing protein in its different DNA bound states". Nucleic Acids Research 49, № 6 (2021): 3441–60. http://dx.doi.org/10.1093/nar/gkab125.
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Abstract Redβ is a single strand annealing protein from bacteriophage λ that binds loosely to ssDNA, not at all to pre-formed dsDNA, but tightly to a duplex intermediate of annealing. As viewed by electron microscopy, Redβ forms oligomeric rings on ssDNA substrate, and helical filaments on the annealed duplex intermediate. However, it is not clear if these are the functional forms of the protein in vivo. We have used size-exclusion chromatography coupled with multi-angle light scattering, analytical ultracentrifugation and native mass spectrometry (nMS) to characterize the size of the oligomers formed by Redβ in its different DNA-bound states. The nMS data, which resolve species with the highest resolution, reveal that Redβ forms an oligomer of 12 subunits in the absence of DNA, complexes ranging from 4 to 14 subunits on 38-mer ssDNA, and a much more distinct and stable complex of 11 subunits on 38-mer annealed duplex. We also measure the concentration of Redβ in cells active for recombination and find it to range from 7 to 27 μM. Collectively, these data provide new insights into the dynamic nature of the complex on ssDNA, and the more stable and defined complex on annealed duplex.
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Potier, M., J. F. Villemure, and L. Thauvette. "Radiation inactivation of proteins: temperature-dependent inter-protomeric energy transfer in ox liver catalase." Biochemical Journal 298, no. 3 (1994): 571–74. http://dx.doi.org/10.1042/bj2980571.
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The radiation-inactivation method is widely used to determine the oligomeric structure of enzymes without need for solubilization or purification. We have used purified ox liver catalase, a tetrameric enzyme in solution, to study energy transfer between associated promoters responsible for oligomer inactivation. However, after freeze-drying the tetramer dissociates into an asymmetric dimer. In the present paper we compare both the radiation-inactivation size (obtained by following the activity decay) and the target size (obtained by measuring the amount of remaining protein by SDS/PAGE) of catalase under various states of aggregation and temperature. At −78 degrees C, only one promoter was fragmented after being hit by a gamma-ray and, as expected, this protomer was also inactivated. This result was obtained when either catalase was in tetrameric or in dimeric forms. However, at 38 degrees C, even though a single monomer was fragmented as at −78 degrees C, the whole dimer was inactivated. This result suggests that, at the higher temperature, there is a transfer of energy from the fragmented protomer to the other associated protomer, causing inactivation of the whole dimer. The inactivation of oligomeric enzymes is a two-step mechanism involving: (1) fragmentation of the hit monomer, followed by (2) temperature-dependent energy transfer from the fragmented towards the associated protomer. Thus we conclude that the radiation-inactivation size reflects the transfer of absorbed energy inside the oligomer which causes inactivation of one or several monomers.
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Szigyártó, Imola Cs, Judith Mihály, András Wacha та ін. "Membrane active Janus-oligomers of β3-peptides". Chemical Science 11, № 26 (2020): 6868–81. http://dx.doi.org/10.1039/d0sc01344g.
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Self-assembly of an acyclic β<sup>3</sup>-hexapeptide with alternating side chain chirality, into nanometer size oligomeric bundles showing membrane activity and hosting capacity for hydrophobic small molecules.
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Nugent, J. H. A. "Molecular-size standards for use in radiation-inactivation studies on proteins." Biochemical Journal 239, no. 2 (1986): 459–62. http://dx.doi.org/10.1042/bj2390459.
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The accuracy of the radiation-inactivation technique for estimating molecular size was investigated with a range of proteins of known molecular mass. With the use of irradiation with a 16 MeV electron beam, inactivation was examined both in frozen samples at 77 K and in freeze-dried samples at room temperature. The effect of the presence of detergents and chloroplast membrane preparations was also measured. It was demonstrated that proteins added as internal standards, including malate dehydrogenase, glucose-6-phosphate dehydrogenase and cytochrome c, can provide an accurate calibration of molecular size. However, a disadvantage of the technique was that the target size of oligomeric enzymes could be that of either the monomers, dimers or higher oligomers. The detergent Triton X-100 increased the rate of inactivation of the proteins investigated.
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Tang, Ping, Kai Xiang, Huijie Wei, Shuhong Li, and Caihong Xu. "A high-emissive and stable luminescent silafluorene hybrid constructed by hydrosilylation." Journal of Chemical Research 43, no. 3-4 (2019): 144–48. http://dx.doi.org/10.1177/1747519819857504.
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Under Karstedt’s catalyst, an organic–inorganic hybrid fluorescent nano-molecular dendrimer has been synthesized by grafting silafluorene units onto the polyhedral oligomeric silsesquioxane core through hydrosilylation reaction. The new hybrid molecule exhibits high solid fluorescence quantum efficiency because of the nano-size and large steric hindrance of the polyhedral oligomeric silsesquioxane core. Thermogravimetric analysis shows that the thermal stability of the target compound is effectively improved by the presence of polyhedral oligomeric silsesquioxane.
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Pokrajac, Lisa, J. Robin Harris, Naghmeh Sarraf, and Michael Palmer. "Oligomerization and hemolytic properties of the C-terminal domain of pyolysin, a cholesterol-dependent cytolysin." Biochemistry and Cell Biology 91, no. 2 (2013): 59–66. http://dx.doi.org/10.1139/bcb-2012-0065.
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Pyolysin (PLO) belongs to the homologous family of the cholesterol-dependent cytolysins (CDCs), which bind to cell membranes containing cholesterol to form oligomeric pores of large size. The CDC monomer structure consists of 4 domains. Among these, the C-terminal domain 4 has been implicated in membrane binding of the monomer, while the subsequent processes of oligomerization and membrane insertion have primarily been assigned to other domains of the molecule. Recombinantly expressed or proteolytic fragments that span domain 4 of the CDCs streptolysin O and perfringolysin O bind to membranes but fail to oligomerize, and they inhibit the activity of the respective wild-type toxins. We report here that the isolated domain 4 of pyolysin (PLO-D4) not only binds to membranes but also forms oligomers with itself, as well as hybrid oligomers with the full-length toxin. As expected, the pure PLO-D4 oligomers are devoid of pore-forming activity. Surprisingly, however, within hybrid oligomers, PLO-D4 not only fails to inhibit, but even amplifies the hemolytic activity of the full-length toxin, to an extent similar to that of doubling the amount of the full-length toxin alone. We propose that this amplification may be related to the kinetics of the oligomerization reaction. Overall, our findings indicate a greater role of domain 4 in the oligomerization of CDCs than previously demonstrated.
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Celej, María Soledad, Rabia Sarroukh, Erik Goormaghtigh, Gerardo D. Fidelio, Jean-Marie Ruysschaert та Vincent Raussens. "Toxic prefibrillar α-synuclein amyloid oligomers adopt a distinctive antiparallel β-sheet structure". Biochemical Journal 443, № 3 (2012): 719–26. http://dx.doi.org/10.1042/bj20111924.
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Parkinson's disease is an age-related movement disorder characterized by the presence in the mid-brain of amyloid deposits of the 140-amino-acid protein AS (α-synuclein). AS fibrillation follows a nucleation polymerization pathway involving diverse transient prefibrillar species varying in size and morphology. Similar to other neurodegenerative diseases, cytotoxicity is currently attributed to these prefibrillar species rather than to the insoluble aggregates. Nevertheless, the underlying molecular mechanisms responsible for cytotoxicity remain elusive and structural studies may contribute to the understanding of both the amyloid aggregation mechanism and oligomer-induced toxicity. It is already recognized that soluble oligomeric AS species adopt β-sheet structures that differ from those characterizing the fibrillar structure. In the present study we used ATR (attenuated total reflection)–FTIR (Fourier-transform infrared) spectroscopy, a technique especially sensitive to β-sheet structure, to get a deeper insight into the β-sheet organization within oligomers and fibrils. Careful spectral analysis revealed that AS oligomers adopt an antiparallel β-sheet structure, whereas fibrils adopt a parallel arrangement. The results are discussed in terms of regions of the protein involved in the early β-sheet interactions and the implications of such conformational arrangement for the pathogenicity associated with AS oligomers.
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Zurlo, Enrico, Pravin Kumar, Georg Meisl та ін. "In situ kinetic measurements of α-synuclein aggregation reveal large population of short-lived oligomers". PLOS ONE 16, № 1 (2021): e0245548. http://dx.doi.org/10.1371/journal.pone.0245548.
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Knowledge of the mechanisms of assembly of amyloid proteins into aggregates is of central importance in building an understanding of neurodegenerative disease. Given that oligomeric intermediates formed during the aggregation reaction are believed to be the major toxic species, methods to track such intermediates are clearly needed. Here we present a method, electron paramagnetic resonance (EPR), by which the amount of intermediates can be measured over the course of the aggregation, directly in the reacting solution, without the need for separation. We use this approach to investigate the aggregation of α-synuclein (αS), a synaptic protein implicated in Parkinson’s disease and find a large population of oligomeric species. Our results show that these are primary oligomers, formed directly from monomeric species, rather than oligomers formed by secondary nucleation processes, and that they are short-lived, the majority of them dissociates rather than converts to fibrils. As demonstrated here, EPR offers the means to detect such short-lived intermediate species directly in situ. As it relies only on the change in size of the detected species, it will be applicable to a wide range of self-assembling systems, making accessible the kinetics of intermediates and thus allowing the determination of their rates of formation and conversion, key processes in the self-assembly reaction.
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Jayaraman, Bhargavi, Amber M. Smith, Jason D. Fernandes, and Alan D. Frankel. "Oligomeric viral proteins: small in size, large in presence." Critical Reviews in Biochemistry and Molecular Biology 51, no. 5 (2016): 379–94. http://dx.doi.org/10.1080/10409238.2016.1215406.
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Rousseau, Karine, Sara Kirkham, Shaun McKane, Richard Newton, Peter Clegg, and David J. Thornton. "Muc5b and Muc5ac are the major oligomeric mucins in equine airway mucus." American Journal of Physiology-Lung Cellular and Molecular Physiology 292, no. 6 (2007): L1396—L1404. http://dx.doi.org/10.1152/ajplung.00444.2006.
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Horses frequently suffer from respiratory diseases, which, irrespective of etiology, are often associated with airway mucus accumulation. Studies on human airways have shown that the key structural components of the mucus layer are oligomeric mucins, which can undergo changes of expression and properties in disease. However, there is little information on these gel-forming glycoproteins in horse airways mucus. Therefore, the aims of this study were to isolate equine airways oligomeric mucins, characterize their macromolecular properties, and identify their gene products. To this end, pooled tracheal washes, collected from healthy horses and horses suffering from respiratory diseases, were solubilized with 6 M guanidinium chloride (GdmCl). The oligomeric mucins were purified by density gradient centrifugation followed by size exclusion chromatography. Biochemical and biophysical analyses showed the mucins were stiffened random coils in solution that were polydisperse in size ( Mr = 6–20 MDa, average Mr = 14 MDa) and comprised of disulfide-linked subunits (average Mr = 7 MDa). Agarose gel electrophoresis showed that the pooled mucus sample contained at least two populations of oligomeric mucins. Electrospray ionization tandem mass spectrometry of tryptic digests of the unfractionated mucin preparation showed that the oligomeric mucins Muc5b and Muc5ac were present. In summary, we have shown that equine airways mucus is a mixture of Muc5b and Muc5ac mucins that have a similar macromolecular organization to their human counterparts. This study will form the basis for future studies to analyze the contribution of these two mucins to equine airways pathology associated with mucus accumulation.
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Gerganova, Veneta, and Sophie G. Martin. "Dynamic visits of cortical structures probe for cell size." Journal of Cell Biology 217, no. 5 (2018): 1559–61. http://dx.doi.org/10.1083/jcb.201803079.
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All cells show size homeostasis owing to coordination of division with growth. In this issue, Allard et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201709171) establish that transient inhibitory visits of a negative regulator of Cdk1 to cortical oligomeric platforms increase in number and duration with cell growth, suggesting how Cdk1 activation is coupled to cell size.
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Silva, Alexandra, Zsuzsa Sárkány, Joana Fraga, Pablo Taboada, Sandra Macedo-Ribeiro, and Pedro Martins. "Probing the Occurrence of Soluble Oligomers through Amyloid Aggregation Scaling Laws." Biomolecules 8, no. 4 (2018): 108. http://dx.doi.org/10.3390/biom8040108.
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Drug discovery frequently relies on the kinetic analysis of physicochemical reactions that are at the origin of the disease state. Amyloid fibril formation has been extensively investigated in relation to prevalent and rare neurodegenerative diseases, but thus far no therapeutic solution has directly arisen from this knowledge. Other aggregation pathways producing smaller, hard-to-detect soluble oligomers are increasingly appointed as the main reason for cell toxicity and cell-to-cell transmissibility. Here we show that amyloid fibrillation kinetics can be used to unveil the protein oligomerization state. This is illustrated for human insulin and ataxin-3, two model proteins for which the amyloidogenic and oligomeric pathways are well characterized. Aggregation curves measured by the standard thioflavin-T (ThT) fluorescence assay are shown to reflect the relative composition of protein monomers and soluble oligomers measured by nuclear magnetic resonance (NMR) for human insulin, and by dynamic light scattering (DLS) for ataxin-3. Unconventional scaling laws of kinetic measurables were explained using a single set of model parameters consisting of two rate constants, and in the case of ataxin-3, an additional order-of-reaction. The same fitted parameters were used in a discretized population balance that adequately describes time-course measurements of fibril size distributions. Our results provide the opportunity to study oligomeric targets using simple, high-throughput compatible, biophysical assays.
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Long, Jaclyn S., Nigel J. Pyne, and Susan Pyne. "Lipid phosphate phosphatases form homo- and hetero-oligomers: catalytic competency, subcellular distribution and function." Biochemical Journal 411, no. 2 (2008): 371–77. http://dx.doi.org/10.1042/bj20071607.
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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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Simonov-Emelyanov, I. D., and K. I. Kharlamova. "Technological classification of dispersed fillers by size and design of polymer composites with different types of structures." Plasticheskie massy, no. 9-10 (November 28, 2022): 3–6. http://dx.doi.org/10.35164/0554-2901-2022-9-10-3-6.
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The paper presents data on the determination of oil capacity and oligomer capacity of dispersed fillers based on silica with different particle sizes (from 50 nm to 250 microns). It is shown that using the oil absorption and oligomeric capacity data, it is possible to carry out a complete technological classification of dispersed particles by size and use it to create disperse filled polymer composite materials (DFPCM) with a given composition, type and structure parameters, as well as a set of operational properties. The values of the maximum disperse filler content (parameter φm) in DFPCM for particles of different sizes (from 50 nm to 250 microns) obtained by oil and oligomer adsorption and other methods are presented. For the first time, an algorithm for designing DFPCM compositions with different types of structures based on oil and oligomer capacity data of disperse fillers with different particle sizes and particle size distributions is proposed. The methods are simple, accessible and effective, which will allow solving problems of creating DFPCM with a given structure and a set of required properties quickly, reliably and with minimum costs. Compositions of DFPCM with different particle sizes of fillers, types of structures that cover the practical whole spectrum of modern polymer composites are given.
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Fernández, Guzmán, Ramos, and Fernández. "Effect of Alkyl Chain Length in POSS Nanocage on Non-Isothermal Crystallization Behavior of PCL/Amino-POSS Nanocomposites." Polymers 11, no. 10 (2019): 1719. http://dx.doi.org/10.3390/polym11101719.
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The study of the non-isothermal crystallization behavior of polymers is of great importance due to the effect of degree of crystallinity and crystallization process on the polymer properties. The effect of aminopropylisobutyl polyhedral oligomeric silsesquioxane (APIBPOSS) and aminopropylisooctyl polyhedral oligomeric silsesquioxane (APIOPOSS) on poly(ε-caprolactone) (PCL) crystallization is studied by differential scanning calorimetry (DSC) under non-isothermal conditions and polarized optical microscopy (POM). The crystallization kinetics is analyzed using the Avrami and Mo models, and effective activation energies are evaluated by the Friedman isoconversional method. The results show that the compatibility between polyhedral oligomeric silsesquioxanes (POSS) and PCL and POSS loading affect the crystallization process. A higher crystallization temperature, a narrower size distribution of crystallite, and a faster crystallization rate are obtained in the presence of all the studied contents of APIBPOSS and at lower contents of APIOPOSS. At APIOPOSS contents higher than 2 wt %, the crystallization temperature is lowered, the size distribution of crystallite is broadened, and the crystallization process is retarded. The presence of POSS leads to an increase in the number of nucleation sites, and a reduction in the size of the crystallite and the overall degree of crystallinity, as a result of the confinement of PCL chains caused by POSS nanoparticles.
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Kapsali, Ioanna, Maria-Evgenia Brinia, and Vasilios C. Constantinides. "Cerebrospinal Fluid Total, Phosphorylated and Oligomeric A-Synuclein in Parkinson’s Disease: A Systematic Review, Meta-Analysis and Meta-Regression Study." Biomedicines 12, no. 10 (2024): 2266. http://dx.doi.org/10.3390/biomedicines12102266.
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Background: The diagnostic accuracy for Parkinson’s disease (PD), a synucleinopathy, based on diagnostic criteria is suboptimal. A biomarker for synucleinopathies is pivotal both from a clinical and from a research point of view. CSF a-synuclein has been extensively studied over the past two decades as a candidate biomarker of synucleinopathies. Herein, we present data on studies focusing on total, phosphorylated and oligomeric CSF a-synuclein in PD. Methods: Pubmed, Scopus and Web of Science were searched for studies with >10 PD patients and control subjects, with data (mean, SD) on total, phosphorylated or oligomeric a-synuclein. Cohen’s d, as a measure of effect size, was calculated for all a-synuclein forms. Subgroup analysis and meta-regression were performed in an effort to explain between-study heterogeneity. Results: Thirty studies on total, six studies on oligomeric and one study on phosphorylated a-synuclein were included. Total a-synuclein was decreased and oligomeric a-synuclein increased in PD patients vs. controls. The effect size was medium for total and high for oligomeric a-synuclein. A-syn forms provided suboptimal combined sensitivity/specificity for the differentiation of PD from controls. There was significant between-study heterogeneity. The PD cohort characteristics (sex, age, disease duration, UPDRS, H & Y) and study characteristics (study design, healthy vs. neurological controls, control for CSF blood contamination, method of a-syn measurement) could not account for between-study heterogeneity. Publication bias was limited. Conclusions: CSF a-synuclein levels lack sufficient accuracy to be used as biomarkers for PD. The standardization of (pre)analytical variables may improve the discriminatory power of a-synuclein forms in the future.
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Sudipa, Saha, та P. Das K. "Effect of thermal treatment on the oligomeric size and chaperone activity of α-crystallin". Journal of Indian Chemical Society Vol. 92, Oct 2015 (2015): 1531–36. https://doi.org/10.5281/zenodo.5700970.
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Department of Biotechnology, St. Xavier’s College, Kolkata-700 016, India <em>E-mail</em> : sahasudipa74@yahoo.co.in Department of Chemistry, Bose Institute, Kolkata-700 009, India <em>E-mail</em> : kalipada@jcboseinst.ac.in, daskp25@gmail.com <em>Manuscript received 17 February 2015, accepted 26 March 2015</em> α-Crystallin is the major structural protein of eye lens of vertebrates. The intricacy of quaternary association of α-crystallin still remains vague because of its high molecular mass and polydispersity. It is generally believed that oligomerization is pre-requisite for chaperone function, although there is no hard data available on this subject. We therefore undertook a study using temperature as a tool for examining the relationship between oligomeric size and chaperone activity of α-crystallin. Gel filtration experiment showed that α-crystallin existed as low and high molecular mass species. Progressive pre-incubation to higher temperatures dissociated the high molecular mass species to the low molecular mass species. Both light scattering and gel filtration experiment revealed the same finding. Our results also indicate that apart from other age related reasons, simple storage of α-crystallin may lead to formation of high molecular weight aggregated α-crystallin which has very low chaperone activity. One way to prevent the loss of chaperone activity of α-crystallin would be to prevent its further association into larger oligomer.
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Kakuta, Takahiro, Kazuo Tanaka, and Yoshiki Chujo. "Synthesis of emissive water-soluble network polymers based on polyhedral oligomeric silsesquioxane and their application as optical sensors for discriminating the particle size." Journal of Materials Chemistry C 3, no. 48 (2015): 12539–45. http://dx.doi.org/10.1039/c5tc03139g.
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We report organic–inorganic hybrid gels composed of polyhedral oligomeric silsesquioxane (POSS)-based network polymers and their variable emission properties depending on the size of coexisting silica particles (SPs).
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Ponstingl, Hannes, Thomas Kabir, and Janet M. Thornton. "Automatic inference of protein quaternary structure from crystals." Journal of Applied Crystallography 36, no. 5 (2003): 1116–22. http://dx.doi.org/10.1107/s0021889803012421.
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The arrangement of the subunits in an oligomeric protein often cannot be inferred without ambiguity from crystallographic studies. The annotation of the functional assembly of protein structures in the Protein Data Bank (PDB) is incomplete and frequently inconsistent. Instructions for the reconstruction, by symmetry, of the functional assembly from the deposited coordinates are often absent. An automatic procedure is proposed for the inference of assembly structures that are likely to be physiologically relevant. The method scores crystal contacts by their contact size and chemical complementarity. The subunit assembly is then inferred from these scored contacts by a clustering procedure involving a single adjustable parameter. When predicting the oligomeric state for a non-redundant set of 55 monomeric and 163 oligomeric proteins from dimers up to hexamers, a classification error rate of 16% was observed.
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Lolli, Graziano, Denise Naressi, Stefania Sarno та Roberto Battistutta. "Characterization of the oligomeric states of the CK2 α2β2 holoenzyme in solution". Biochemical Journal 474, № 14 (2017): 2405–16. http://dx.doi.org/10.1042/bcj20170189.
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The regulatory mechanism of protein kinase CK2 has still to be fully clarified. The prevailing hypothesis is that CK2 is controlled by a self-polymerisation mechanism leading to inactive supramolecular assemblies that, when needed, can be disassembled into the α2β2 monomer, the active form of the holoenzyme. In vitro, monomeric α2β2 seems present only at high ionic strengths, typically 0.35–0.50 M NaCl, while at lower salt concentrations oligomers are formed. In the present study, size-exclusion chromatography (SEC), dynamic light scattering (DLS), small-angle X-ray scattering (SAXS) and mutagenesis have been employed for the characterization of the oligomeric states of CK2 in solution. SAXS measurements at 0.35 M NaCl show for the first time the shape of the α2β2 active monomer in solution. At 0.25 M salt, despite single average properties indicating an aggregated holoenzyme, deconvolution analysis of SAXS data reveals an equilibrium involving not only circular trimeric and linear oligomeric (3–4 units) forms of α2β2, but also considerable amounts of the monomer. Together SAXS and mutagenesis confirm the presence in solution of the oligomers deduced by crystal structures. The lack of intermediate species such as αβ2, α or β2 indicates that the holoenzyme is a strong complex that does not spontaneously dissociate, challenging what was recently proposed on the basis of mass spectrometry data. A significant novel finding is that a considerable amount of monomer, the active form of CK2, is present also at low salt. The solution properties of CK2 shown in the present study complement the model of regulation by polymerization.
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Markina, Anastasia A., Maria A. Frolkina, Alexander D. Muratov, Vladislav S. Petrovskii, Alexander F. Valov, and Vladik A. Avetisov. "Spontaneous Synchronization of Two Bistable Pyridine-Furan Nanosprings Connected by an Oligomeric Bridge." Nanomaterials 14, no. 1 (2023): 3. http://dx.doi.org/10.3390/nano14010003.
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The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose long-term conformational dynamics are similar to the dynamics of bistable mechanical systems such as Euler arches and Duffing oscillators. Collective synchrony in bistable dynamics of molecular-sized systems has attracted immense attention as a potential pathway to amplify the output signals of molecular nanodevices. Recently, pyridine-furan oligomers of helical shape that are a few nanometers in size and exhibit bistable dynamics similar to a Duffing oscillator have been identified through molecular dynamics simulations. In this article, we present the case of dynamical synchronization of these bistable systems. We show that two pyridine-furan springs connected by a rigid oligomeric bridge spontaneously synchronize vibrations and stochastic resonance enhances the synchronization effect.
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Mahalingam, Sundararajan, Goutham Shankar, Brian P. Mooney, Kamal Singh, Puttur Santhoshkumar та Krishna K. Sharma. "Deletion of Specific Conserved Motifs from the N-Terminal Domain of αB-Crystallin Results in the Activation of Chaperone Functions". International Journal of Molecular Sciences 23, № 3 (2022): 1099. http://dx.doi.org/10.3390/ijms23031099.
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Smaller oligomeric chaperones of α-crystallins (αA- and αB-) have received increasing attention due to their improved therapeutic potential in preventing protein aggregating diseases. Our previous study suggested that deleting 54–61 residues from the N-terminal domain (NTD) of αB-crystallin (αBΔ54–61) decreases the oligomer size and increases the chaperone function. Several studies have also suggested that NTD plays a significant role in protein oligomerization and chaperone function. The current study was undertaken to assess the effect of deleting conserved 21–28 residues from the activated αBΔ54–61 (to get αBΔ21–28, Δ54–61) on the structure–function of recombinant αBΔ21–28, Δ54–61. The αBΔ21–28, Δ54–61 mutant shows an 80% reduction in oligomer size and 3- to 25-fold increases in chaperone activity against model substrates when compared to αB-WT. Additionally, the αB∆21–28, ∆54–61 was found to prevent β-amyloid (Aβ1–42) fibril formation in vitro and suppressed Aβ1–42-induced cytotoxicity in ARPE-19 cells in a more effective manner than seen with αB-WT or αB∆54–61. Cytotoxicity and reactive oxygen species (ROS) detection studies with sodium iodate (SI) showed that the double mutant protein has higher anti-apoptotic and anti-oxidative activities than the wild-type or αB∆54–61 in oxidatively stressed cells. Our study shows that the residues 21–28 and 54–61 in αB-crystallin contribute to the oligomerization and modulate chaperone function. The deletion of conserved 21–28 residues further potentiates the activated αBΔ54–61. We propose that increased substrate affinity, altered subunit structure, and assembly leading to smaller oligomers could be the causative factors for the increased chaperone activity of αBΔ21–28, Δ54–61.
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Muranova, Lydia K., Vladislav M. Shatov, Andrey V. Slushchev, and Nikolai B. Gusev. "Quaternary Structure and Hetero-Oligomerization of Recombinant Human Small Heat Shock Protein HspB7 (cvHsp)." International Journal of Molecular Sciences 22, no. 15 (2021): 7777. http://dx.doi.org/10.3390/ijms22157777.
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In this study, a reliable and simple method of untagged recombinant human HspB7 preparation was developed. Recombinant HspB7 is presented in two oligomeric forms with an apparent molecular weight of 36 kDa (probably dimers) and oligomers with an apparent molecular weight of more than 600 kDa. By using hydrophobic and size-exclusion chromatography, we succeeded in preparation of HspB7 dimers. Mild oxidation promoted the formation of large oligomers, whereas the modification of Cys 126 by iodoacetamide prevented it. The deletion of the first 13 residues or deletion of the polySer motif (residues 17–29) also prevented the formation of large oligomers of HspB7. Cys-mutants of HspB6 and HspB8 containing a single-Cys residue in the central part of the β7 strand in a position homologous to that of Cys137 in HspB1 can be crosslinked to the wild-type HspB7 through a disulfide bond. Immobilized on monoclonal antibodies, the wild-type HspB6 interacted with the wild-type HspB7. We suppose that formation of heterodimers of HspB7 with HspB6 and HspB8 may be important for the functional activity of these small heat shock proteins.
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Janin, Joël, Ranjit P. Bahadur, and Pinak Chakrabarti. "Protein–protein interaction and quaternary structure." Quarterly Reviews of Biophysics 41, no. 2 (2008): 133–80. http://dx.doi.org/10.1017/s0033583508004708.
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AbstractProtein–protein recognition plays an essential role in structure and function. Specific non-covalent interactions stabilize the structure of macromolecular assemblies, exemplified in this review by oligomeric proteins and the capsids of icosahedral viruses. They also allow proteins to form complexes that have a very wide range of stability and lifetimes and are involved in all cellular processes. We present some of the structure-based computational methods that have been developed to characterize the quaternary structure of oligomeric proteins and other molecular assemblies and analyze the properties of the interfaces between the subunits. We compare the size, the chemical and amino acid compositions and the atomic packing of the subunit interfaces of protein–protein complexes, oligomeric proteins, viral capsids and protein–nucleic acid complexes. These biologically significant interfaces are generally close-packed, whereas the non-specific interfaces between molecules in protein crystals are loosely packed, an observation that gives a structural basis to specific recognition. A distinction is made within each interface between a core that contains buried atoms and a solvent accessible rim. The core and the rim differ in their amino acid composition and their conservation in evolution, and the distinction helps correlating the structural data with the results of site-directed mutagenesis and in vitro studies of self-assembly.
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A, Goldlust, Oxender D.O, and Werber M.M. "Determination of the Functional Size of Superoxide Dismutases by Radiation Inactivation Analysis." Protein & Peptide Letters 3, no. 2 (1996): 125–32. http://dx.doi.org/10.2174/092986650302220614122659.
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Abstract: Five different superoxide dismutases (SODs) representing the three classes of SODs (FeSOD, MnSOD and CuZnSOD) were analyzed by the radiation inactivation technique, which is a unique method for the determination of the functional mass of oligomeric proteins. All SODs showed a single exponential inactivation curve, with a radiation target size corresponding to the dimer of each of the enzymes, suggesting that the dimer is the functional unit of SODs.
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Buchert, J., A. Mustranta, T. Tamminen, P. Spetz, and B. Holmbom. "Modification of Spruce Lignans with Trametes hirsuta Laccase." Holzforschung 56, no. 6 (2002): 579–84. http://dx.doi.org/10.1515/hf.2002.088.
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Summary The effect of Trametes hirsuta laccase on isolated spruce wood lignans was evaluated. Lignans were isolated from the heartwood of spruce branches and treated with different laccase dosages and treatment times. The effect of the treatment was monitored by gas chromatography, size exclusion chromatography and ionization difference UV spectroscopy. Lignans were efficiently oxidized by T. hirsuta laccase. About half of the phenolic groups present in lignans remained intact during the treatment. The oxidation of phenolic groups in lignans produced oligomeric structures containing approximately 4–5 lignan units (i.e., 8–10 phenyl propane units). Precipitation of the formed oligomeric structures probably prevented further polymerization.
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Hickling, Timothy P., Rajneesh Malhotra, and Robert B. Sim. "Human Lung Surfactant Protein A Exists in Several Different Oligomeric States: Oligomer Size Distribution Varies between Patient Groups." Molecular Medicine 4, no. 4 (1998): 266–75. http://dx.doi.org/10.1007/bf03401923.
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Batiste, Suzanne M., and Jeffrey N. Johnston. "Rapid synthesis of cyclic oligomeric depsipeptides with positional, stereochemical, and macrocycle size distribution control." Proceedings of the National Academy of Sciences 113, no. 52 (2016): 14893–97. http://dx.doi.org/10.1073/pnas.1616462114.
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Macrocyclic small molecules are attractive tools in the development of sensors, new materials, and therapeutics. Within early-stage drug discovery, they are increasingly sought for their potential to interact with broad surfaces of peptidic receptors rather than within their narrow folds and pockets. Cyclization of linear small molecule precursors is a straightforward strategy to constrain conformationally mobile motifs, but forging a macrocycle bond typically becomes more difficult at larger ring sizes. We report the development of a general approach to discrete collections of oligomeric macrocyclic depsipeptides using an oligomerization/macrocyclization process governed by a series of Mitsunobu reactions of hydroxy acid monomers. Ring sizes of 18, 24, 30, and 36 are formed in a single reaction from a didepsipeptide, whereas sizes of 24, 36, and 60 result from a tetradepsipeptide. The ring-size selectivity inherent to the approach can be modulated by salt additives that enhance the formation of specific ring sizes. Use of chemical synthesis to prepare the monomers suggests broad access to functionally and stereochemically diverse collections of natural product-like oligodepsipeptide macrocycles. Two cyclodepsipeptide natural products were prepared along with numerous unnatural oligomeric congeners to provide rapid access to discrete collections of complex macrocyclic small molecules from medium (18) to large (60) ring sizes.
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Zhou, Dai‐Lin, Jiang‐Hui Li, Qing‐Yun Guo, et al. "Polyhedral Oligomeric Silsesquioxanes Based Ultralow‐ k Materials: The Effect of Cage Size." Advanced Functional Materials 31, no. 31 (2021): 2102074. http://dx.doi.org/10.1002/adfm.202102074.
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Bayon, Chloé, Gonzague Agez, and Michel Mitov. "Size-effect of oligomeric cholesteric liquid-crystal microlenses on the optical specifications." Optics Letters 40, no. 20 (2015): 4763. http://dx.doi.org/10.1364/ol.40.004763.
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Delbecq, Scott P., та Rachel E. Klevit. "One size does not fit all: The oligomeric states of αB crystallin". FEBS Letters 587, № 8 (2013): 1073–80. http://dx.doi.org/10.1016/j.febslet.2013.01.021.
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Burford, Neil T., Tom Wehrman, Daniel Bassoni та ін. "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, № 9 (2014): 1255–65. http://dx.doi.org/10.1177/1087057114542975.
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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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Hanack, Michael, A. Hirsch, A. Lange, M. Rein, G. Renz, and P. Vermehren. "Bridged macrocyclic transition metal complexes, a new type of semiconducting materials." Journal of Materials Research 6, no. 2 (1991): 385–92. http://dx.doi.org/10.1557/jmr.1991.0385.
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Bridged quasi–one-dimensional macrocyclic transition metal complexes [MacM(L)]n using phthalocyanine (Pc), tetrabenzoporphyrine (TBP), 1,2- and 2,3-naphthalocyanines (1,2-Nc; 2,3-Nc) as macrocycles (Mac) with M = e.g., Fe, Ru, Co and L = e.g., pyrazine (pyz), 1,4-diisocyanobenzene (dib), tetrazine (tz) exhibit interesting electrical properties. Regardless of the size of the bridging ligand after either chemical or electrochemical doping stable semiconducting compounds [MacM(L)Xy]n (X = e.g., I2 BF4−, ClO4−…) are formed. For the first time the complete characterization of soluble oligomers [MacM(L)]n (Mac = t-Bu4Pc, M = Ru, L = dib, me4dib) by 1H-NMR spectroscopy is reported. Some of these shish kebab complexes, e.g., [PcM(tz)]n, (M = Fe, Ru) or [MacMCN]n; (Mac = Pc, TBP; M = Co, Fe) exhibit good semiconducting properties without additional external doping. Whether or not these compounds are intrinsic semiconductors will be discussed. The synthesis of oligomeric bridged mixed valence compounds [PcM(III)LPcM(II)L]n, (M = e.g., Fe) is another target of our work. We report here on first results of these oligomers.
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Liu, Ying, Chang Ping Wei, and Li Dan Dong. "Preparation and Properties of Oligomeric Sulfonated Chitosan." Advanced Materials Research 624 (December 2012): 274–78. http://dx.doi.org/10.4028/www.scientific.net/amr.624.274.
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In the homogeneous system, the low molecular weight Chitosan is obtained by H2O2 oxidation degradation method. Acetyl Sulface reacted by the mixture of Acetic Anhydride and Concentrated Sulfuric Acid at equal proportion is the reagent. low molecular weight Chitosan being as raw materials, Vulcanized Oligomer Chitosan is sulfonated with good water-solubility and high sulfur content under certain conditions. It has been tested for the influence of the usage of sulfonated reagent, reaction temperature and reaction time on Sulfer content. The best condition for preparation Vulcanized Oligomer Chitosan is 5ml of Acetyl Sulface with the reaction temperature of 25°C and time of 5 Hours. It’s a new potential heparin with around 100 nm particale size tested by spectral analysis and SEM measurements, which could be a new reagent in other fields.
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Schlie, Katrin, Anna Maisa, Frank Lennartz, Ute Ströher, Wolfgang Garten, and Thomas Strecker. "Characterization of Lassa Virus Glycoprotein Oligomerization and Influence of Cholesterol on Virus Replication." Journal of Virology 84, no. 2 (2009): 983–92. http://dx.doi.org/10.1128/jvi.02039-09.
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ABSTRACT Mature glycoprotein spikes are inserted in the Lassa virus envelope and consist of the distal subunit GP-1, the transmembrane-spanning subunit GP-2, and the signal peptide, which originate from the precursor glycoprotein pre-GP-C by proteolytic processing. In this study, we analyzed the oligomeric structure of the viral surface glycoprotein. Chemical cross-linking studies of mature glycoprotein spikes from purified virus revealed the formation of trimers. Interestingly, sucrose density gradient analysis of cellularly expressed glycoprotein showed that in contrast to trimeric mature glycoprotein complexes, the noncleaved glycoprotein forms monomers and oligomers spanning a wide size range, indicating that maturation cleavage of GP by the cellular subtilase SKI-1/S1P is critical for formation of the correct oligomeric state. To shed light on a potential relation between cholesterol and GP trimer stability, we performed cholesterol depletion experiments. Although depletion of cholesterol had no effect on trimerization of the glycoprotein spike complex, our studies revealed that the cholesterol content of the viral envelope is important for the infectivity of Lassa virus. Analyses of the distribution of viral proteins in cholesterol-rich detergent-resistant membrane areas showed that Lassa virus buds from membrane areas other than those responsible for impaired infectivity due to cholesterol depletion of lipid rafts. Thus, derivation of the viral envelope from cholesterol-rich membrane areas is not a prerequisite for the impact of cholesterol on virus infectivity.
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Jung, Kyoung Ho, Sunghark Kwon, Chang Min Kim, Jun Hyuck Lee, and Hyun Ho Park. "Putative hexameric glycosyltransferase functional unit revealed by the crystal structure of Acinetobacter baumannii MurG." IUCrJ 8, no. 4 (2021): 574–83. http://dx.doi.org/10.1107/s2052252521003729.
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Lipid II, the main component of the bacterial cell wall, is synthesized by the addition of UDP-N-acetylglucosamine to the UDP-N-acetylmuramic acid pentapeptide catalyzed by the glycosyltransferase MurG. Owing to its critical role in cell-wall biosynthesis, MurG is considered to be an attractive target for antibacterial agents. Although the Mur family ligases have been extensively studied, the molecular mechanism of the oligomeric scaffolding assembly of MurG remains unclear. In this study, MurG from Acinetobacter baumannii (abMurG), a human pathogen, was characterized and its hexameric crystal structure was unveiled; this is the first homo-oligomeric structure to be described in the MurG family and the Mur family. Homogeneous protein samples were produced for structural studies using size-exclusion chromatography, the absolute molecular mass was calculated via multi-angle light scattering, and protein–protein interactions were analyzed using the PDBePISA server. abMurG was found to form homo-oligomeric complexes in solution, which might serve as functional units for the scaffolding activity of MurG. Furthermore, analysis of this structure revealed the molecular assembly mechanism of MurG. This structural and biochemical study elucidated the homo-oligomerization mechanism of MurG and suggests a new potential antibiotic target on MurG.
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NORDMAN, Henrik, Julia R. DAVIES, Gert LINDELL, Carme de BOLÓS, Francisco REAL, and Ingemar CARLSTEDT. "Gastric MUC5AC and MUC6 are large oligomeric mucins that differ in size, glycosylation and tissue distribution." Biochemical Journal 364, no. 1 (2002): 191–200. http://dx.doi.org/10.1042/bj3640191.
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Gastric MUC5AC and MUC6 mucins were studied using polyclonal antibodies. Immunohistochemistry showed MUC5AC to originate from the surface epithelium, whereas MUC6 was produced by the glands. Mucins from the surface epithelium or glands of corpus and antrum were purified using CsCl/4M guanidinium chloride density-gradient centrifugation. MUC5AC appeared as two distinct populations at 1.4 and 1.3g/ml, whereas MUC6, which was enriched in the gland tissue, appeared at 1.45g/ml. Reactivity with antibodies against the Leb structure (where Le represents the Lewis antigen) followed the MUC5AC distribution, whereas antibodies against the Ley structure and reactivity with the GlcNAc-selective Solanum tuberosum lectin coincided with MUC6, suggesting that the two mucins are glycosylated differently. Rate-zonal centrifugation of whole mucins and reduced subunits showed that both gastric MUC5AC and MUC6 are oligomeric glycoproteins composed of disulphide-bond linked subunits and that oligomeric MUC5AC was apparently smaller than MUC6. A heterogeneous population of ‘low-density’ MUC5AC mucins, which were smaller than the ‘high-density’ ones both before and after reduction, reacted with an antibody against a variable number tandem repeat sequence within MUC5AC, suggesting that they represent precursor forms of this mucin. Following ion-exchange HPLC, both MUC5AC and MUC6 appeared as several distinct populations, probably corresponding to ‘glycoforms’ of the mucins, the most highly charged of which were found in the gland tissue.
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Bürgy, Heribert, and Gion Calzaferri. "Separation of the oligomeric silsesquioxanes (HSiO3/2)8–18 by size-exclusion chromatography." Journal of Chromatography A 507 (May 1990): 481–86. http://dx.doi.org/10.1016/s0021-9673(01)84227-8.
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