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Journal articles on the topic 'Protein oligomers'

Author: Grafiati

Published: 10 March 2023

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1

Schmid, J. A., H. Just, and H. H. Sitte. "Impact of oligomerization on the function of the human serotonin transporter." Biochemical Society Transactions 29, no. 6 (2001): 732–36. http://dx.doi.org/10.1042/bst0290732.

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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 fluor

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2

Eisenberg, David, Arthur Laganowsky, Cong Liu, et al. "Structural Studies of the Amyloid State of Proteins." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C797. http://dx.doi.org/10.1107/s205327331409202x.

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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 segm

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Tanner, John J. "Empirical power laws for the radii of gyration of protein oligomers." Acta Crystallographica Section D Structural Biology 72, no. 10 (2016): 1119–29. http://dx.doi.org/10.1107/s2059798316013218.

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The radius of gyration is a fundamental structural parameter that is particularly useful for describing polymers. It has been known since Flory's seminal work in the mid-20th century that polymers show a power-law dependence, where the radius of gyration is proportional to the number of residues raised to a power. The power-law exponent has been measured experimentally for denatured proteins and derived empirically for folded monomeric proteins using crystal structures. Here, the biological assemblies in the Protein Data Bank are surveyed to derive the power-law parameters for protein oligomer

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Vaikath, Nishant, Indulekha Sudhakaran, Ilham Abdi, et al. "Structural and Biophysical Characterization of Stable Alpha-Synuclein Oligomers." International Journal of Molecular Sciences 23, no. 23 (2022): 14630. http://dx.doi.org/10.3390/ijms232314630.

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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 meta

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Kreiser, Ryan P., Aidan K. Wright, Natalie R. Block, et al. "Therapeutic Strategies to Reduce the Toxicity of Misfolded Protein Oligomers." International Journal of Molecular Sciences 21, no. 22 (2020): 8651. http://dx.doi.org/10.3390/ijms21228651.

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The aberrant aggregation of proteins is implicated in the onset and pathogenesis of a wide range of neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases. Mounting evidence indicates that misfolded protein oligomers produced as intermediates in the aggregation process are potent neurotoxic agents in these diseases. Because of the transient and heterogeneous nature of these elusive aggregates, however, it has proven challenging to develop therapeutics that can effectively target them. Here, we review approaches aimed at reducing oligomer toxicity, including (1) modulating

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de Klerk, G. J., and D. Engelen. "Assembly of Agrostemma githago (corn-cockle) storage proteins and their precursor proteins into oligomers." Biochemical Journal 230, no. 1 (1985): 269–72. http://dx.doi.org/10.1042/bj2300269.

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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 00

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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 qua

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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 huma

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Wang, Yu, Karen S. L. Lam, Ming-hon Yau, and Aimin Xu. "Post-translational modifications of adiponectin: mechanisms and functional implications." Biochemical Journal 409, no. 3 (2008): 623–33. http://dx.doi.org/10.1042/bj20071492.

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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 adipo

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NEMOTO, Takayuki, and Nobuko SATO. "Oligomeric forms of the 90-kDa heat shock protein." Biochemical Journal 330, no. 2 (1998): 989–95. http://dx.doi.org/10.1042/bj3300989.

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Two isoforms of the 90-kDa heat shock protein, HSP90α and HSP90β, are present in the cytosol of mammalian cells. Analysis by polyacrylamide gel electrophoresis under nondenaturing conditions (native PAGE) revealed that HSP90α predominantly exists as a homodimer and that HSP90β is present mainly as a monomer [Minami, Kawasaki, Miyata, Suzuki and Yahara (1991) J. Biol. Chem. 266, 10099-10103]. However, only the dimeric form has been observed under other analytical conditions such as gradient centrifugation. In this study, therefore, we investigated native forms of HSP90 by use of immunochemical

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Haataja, Leena, Tatyana Gurlo, Chang J. Huang, and Peter C. Butler. "Islet Amyloid in Type 2 Diabetes, and the Toxic Oligomer Hypothesis." Endocrine Reviews 29, no. 3 (2008): 303–16. http://dx.doi.org/10.1210/er.2007-0037.

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Abstract Type 2 diabetes (T2DM) is characterized by insulin resistance, defective insulin secretion, loss of β-cell mass with increased β-cell apoptosis and islet amyloid. The islet amyloid is derived from islet amyloid polypeptide (IAPP, amylin), a protein coexpressed and cosecreted with insulin by pancreatic β-cells. In common with other amyloidogenic proteins, IAPP has the propensity to form membrane permeant toxic oligomers. Accumulating evidence suggests that these toxic oligomers, rather than the extracellular amyloid form of these proteins, are responsible for loss of neurons in neurode

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Chia, Sean, Johnny Habchi, Thomas C. T. Michaels, et al. "SAR by kinetics for drug discovery in protein misfolding diseases." Proceedings of the National Academy of Sciences 115, no. 41 (2018): 10245–50. http://dx.doi.org/10.1073/pnas.1807884115.

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To develop effective therapeutic strategies for protein misfolding diseases, a promising route is to identify compounds that inhibit the formation of protein oligomers. To achieve this goal, we report a structure−activity relationship (SAR) approach based on chemical kinetics to estimate quantitatively how small molecules modify the reactive flux toward oligomers. We use this estimate to derive chemical rules in the case of the amyloid beta peptide (Aβ), which we then exploit to optimize starting compounds to curtail Aβ oligomer formation. We demonstrate this approach by converting an inactive

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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. Heter

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Weisz, OA, AM Swift, and CE Machamer. "Oligomerization of a membrane protein correlates with its retention in the Golgi complex." Journal of Cell Biology 122, no. 6 (1993): 1185–96. http://dx.doi.org/10.1083/jcb.122.6.1185.

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The first membrane-spanning domain (m1) of the M glycoprotein of avian coronavirus (formerly called E1) is sufficient to retain this protein in the cis-Golgi. When the membrane-spanning domain of a protein which is efficiently delivered to the plasma membrane (VSV G protein) is replaced with m1, the resulting chimera (Gm1) is retained in the Golgi (Swift, A. M., and C. E. Machamer. 1991. J. Cell Biol. 115:19-30). When assayed in sucrose gradients, we observed that Gm1 formed a large oligomer, and that much of this oligomer was SDS resistant and stayed near the top of the stacking gel of an SDS

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Wako, Hiroshi, and Shigeru Endo. "ProMode-Oligomer: Database of Normal Mode Analysis in Dihedral Angle Space for a Full-Atom System of Oligomeric Proteins." Open Bioinformatics Journal 6, no. 1 (2012): 9–19. http://dx.doi.org/10.2174/1875036201206010009.

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The database ProMode-Oligomer (http://promode.socs.waseda.ac.jp/promode_oligomer) was constructed by collecting normal-mode-analysis (NMA) results for oligomeric proteins including protein-protein complexes. As in the ProMode database developed earlier for monomers and individual subunits of oligomers (Bioinformatics vol. 20, pp. 2035–2043, 2004), NMA was performed for a full-atom system using dihedral angles as independent variables, and we released the results (fluctuations of atoms, fluctuations of dihedral angles, correlations between atomic fluctuations, etc.). The vibrating oligomer is v

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Milligan, G. "Oligomerisation of G-protein-coupled receptors." Journal of Cell Science 114, no. 7 (2001): 1265–71. http://dx.doi.org/10.1242/jcs.114.7.1265.

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A range of approaches have recently provided evidence that G-protein-coupled receptors can exist as oligomeric complexes. Both homo-oligomers, comprising multiple copies of the same gene product, and hetero-oligomers containing more than one receptor have been detected. In several, but not all, examples, the extent of oligomerisation is regulated by the presence of agonist ligands, and emerging evidence indicates that receptor hetero-oligomers can display distinct pharmacological characteristics. A chaperonin-like role for receptor oligomerisation in effective delivery of newly synthesised rec

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Zheng, Weihua, Min-Yeh Tsai, Mingchen Chen та Peter G. Wolynes. "Exploring the aggregation free energy landscape of the amyloid-β protein (1–40)". Proceedings of the National Academy of Sciences 113, № 42 (2016): 11835–40. http://dx.doi.org/10.1073/pnas.1612362113.

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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

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Eghiaian, Frederic, Thorsten Daubenfeld, Yann Quenet, et al. "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, no. 18 (2007): 7414–19. http://dx.doi.org/10.1073/pnas.0607745104.

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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

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Chase, Anna R., Ethan Laudermilch, Jimin Wang, Hideki Shigematsu, Takeshi Yokoyama, and Christian Schlieker. "Dynamic functional assembly of the Torsin AAA+ ATPase and its modulation by LAP1." Molecular Biology of the Cell 28, no. 21 (2017): 2765–72. http://dx.doi.org/10.1091/mbc.e17-05-0281.

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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, sugges

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Irumagawa, Shin, Keiko Hiemori, Sayoko Saito, Hiroaki Tateno, and Ryoichi Arai. "Self-Assembling Lectin Nano-Block Oligomers Enhance Binding Avidity to Glycans." International Journal of Molecular Sciences 23, no. 2 (2022): 676. http://dx.doi.org/10.3390/ijms23020676.

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Lectins, carbohydrate-binding proteins, are attractive biomolecules for medical and biotechnological applications. Many lectins have multiple carbohydrate recognition domains (CRDs) and strongly bind to specific glycans through multivalent binding effect. In our previous study, protein nano-building blocks (PN-blocks) were developed to construct self-assembling supramolecular nanostructures by linking two oligomeric proteins. A PN-block, WA20-foldon, constructed by fusing a dimeric four-helix bundle de novo protein WA20 to a trimeric foldon domain of T4 phage fibritin, self-assembled into seve

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Di Domizio, Jeremy, Ran Zhang, Ming Zhuo, et al. "A novel class of host-derived etiological agent for autoimmunity: oligomers of endogenous proteins bind to self-nucleic acids and trigger type I IFN production by plasmacytoid dendritic cells (44.2)." Journal of Immunology 186, no. 1_Supplement (2011): 44.2. http://dx.doi.org/10.4049/jimmunol.186.supp.44.2.

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Abstract Under certain conditions, some soluble endogenous proteins can form ordered oligomeric structures leading to the assembly of stable insoluble amyloids, a process that increases with age. The presence of such structures is associated with cellular toxicity and diseases development, e.g. Alzheimer disease, type II diabetes. Recent studies clearly show that the primary toxic species in such pathologies is the soluble oligomers of proteins, precursors of amyloids. Yet, it is unknown if such aberrant forms of proteins would elicit any immune reaction. Here we obtained oligomers derived fro

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Martellucci, Stefano, Letizia Clementi, Samantha Sabetta, et al. "Tau oligomers accumulation sensitizes prostate cancer cells to docetaxel treatment." Journal of Cancer Research and Clinical Oncology 147, no. 7 (2021): 1957–71. http://dx.doi.org/10.1007/s00432-021-03598-3.

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Abstract Purpose Human tau is a highly dynamic, multifunctional protein expressed in different isoforms and conformers, known to modulate microtubule turnover. Tau oligomers are considered pathologic forms of the protein able to initiate specific protein accumulation diseases, called tauopathies. In our study, we investigated the potential association between autophagy and tau oligomers accumulation and its role in the response of prostate cancer cells to docetaxel. Methods We evaluated in vitro the expression of tau oligomers in prostate cancer cell lines, PC3 and DU145, in presence of autoph

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Iljina, Marija, Gonzalo A. Garcia, Mathew H. Horrocks, et al. "Kinetic model of the aggregation of alpha-synuclein provides insights into prion-like spreading." Proceedings of the National Academy of Sciences 113, no. 9 (2016): E1206—E1215. http://dx.doi.org/10.1073/pnas.1524128113.

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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 involv

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RAMSAY, Douglas, Elaine KELLETT, Mary McVEY, Stephen REES, and 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, no. 2 (2002): 429–40. http://dx.doi.org/10.1042/bj20020251.

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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 unaffe

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Dey, Simli, Anirban Das, Arpan Dey, and Sudipta Maiti. "Membrane affinity of individual toxic protein oligomers determined at the single-molecule level." Physical Chemistry Chemical Physics 22, no. 26 (2020): 14613–20. http://dx.doi.org/10.1039/d0cp00450b.

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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 an

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Tsukakoshi, Kaori, Rikako Kubo та Kazunori Ikebukuro. "Development of Alkaline Phosphatase-Fused Mouse Prion Protein and Its Application in Toxic Aβ Oligomer Detection". International Journal of Molecular Sciences 23, № 23 (2022): 14588. http://dx.doi.org/10.3390/ijms232314588.

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Amyloid β (Aβ) oligomers play a key role in the progression of Alzheimer’s disease (AD). Multiple forms of Aβ assemblies have been identified by in vitro and in vivo analyses; however, it is uncertain which oligomer is highly neurotoxic. Thus, understanding the pathogenesis of AD by detecting toxic Aβ oligomers is crucial. In this study, we report a fusion protein of cellular prion protein (PrPc) and alkaline phosphatase (ALP) from Escherichia coli as a sensing element for toxic Aβ oligomers. Since the N-terminus domain of PrPc (residue 23–111) derived from mice is known to bind to toxic Aβ ol

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Gaber, Aljaž, and Miha Pavšič. "Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches." International Journal of Molecular Sciences 22, no. 16 (2021): 9081. http://dx.doi.org/10.3390/ijms22169081.

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Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches. Here, we first provide a brief overview of the nature of protein homo-oligomerization. Next, we describe how the symmetry of homo-oligomers is addressed b

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Fernández-Silva, Arline, Fernando Lledías, Jonathan Rodríguez-López, et al. "The Common Bean Small Heat Shock Protein Nodulin 22 from Phaseolus vulgaris L. Assembles into Functional High-Molecular-Weight Oligomers." Molecules 27, no. 24 (2022): 8681. http://dx.doi.org/10.3390/molecules27248681.

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Small heat shock proteins (sHsps) are present in all domains of life. These proteins are responsible for binding unfolded proteins to prevent their aggregation. sHsps form dynamic oligomers of different sizes and constitute transient reservoirs for folding competent proteins that are subsequently refolded by ATP-dependent chaperone systems. In plants, the sHsp family is rather diverse and has been associated with the ability of plants to survive diverse environmental stresses. Nodulin 22 (PvNod22) is an sHsp of the common bean (Phaseolus vulgaris L.) located in the endoplasmic reticulum. This

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You, Young Suk, Jae-Hoon Kim, Jong-Soo Lee, and Hyeseong Cho. "The mitochodnrial E3 ligase MARCH5 resolves RIG-I and MAVS aggregates in innate immunity." Journal of Immunology 198, no. 1_Supplement (2017): 222.13. http://dx.doi.org/10.4049/jimmunol.198.supp.222.13.

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Abstract Ubiquitin proteasome system (UPS) on the mitochondrial is one of quality control systems that works as a first line of defense barrier against aggregated or misfolded proteins. In innate immunity formation of the MAVS(Mitochondrial anti-viral signaling protein) oligomers elicits robust type-I interferon induction upon viral infection and however, persistent RIG-I and MAVS complex rather leads to host immunopathology. We recently reported that mitochondria-resident E3 ligase, MARCH5, recognizes the oligomeric form of RIG-I and MAVS complex. MARCH5+/− mice and MARCH5 deficient immune ce

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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 sep

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Trevelyan, Sarah J., Jodi L. Brewster, Abigail E. Burgess, et al. "Structure-based mechanism of preferential complex formation by apoptosis signal–regulating kinases." Science Signaling 13, no. 622 (2020): eaay6318. http://dx.doi.org/10.1126/scisignal.aay6318.

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Apoptosis signal–regulating kinases (ASK1, ASK2, and ASK3) are activators of the p38 and c-Jun N-terminal kinase (JNK) mitogen-activated protein kinase (MAPK) pathways. ASK1–3 form oligomeric complexes known as ASK signalosomes that initiate signaling cascades in response to diverse stress stimuli. Here, we demonstrated that oligomerization of ASK proteins is driven by previously uncharacterized sterile-alpha motif (SAM) domains that reside at the carboxy-terminus of each ASK protein. SAM domains from ASK1–3 exhibited distinct behaviors, with the SAM domain of ASK1 forming unstable oligomers,

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Bokor, Mónika, and Ágnes Tantos. "Protein–Protein Connections—Oligomer, Amyloid and Protein Complex—By Wide Line 1H NMR." Biomolecules 11, no. 5 (2021): 757. http://dx.doi.org/10.3390/biom11050757.

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The amount of bonds between constituting parts of a protein aggregate were determined in wild type (WT) and A53T α-synuclein (αS) oligomers, amyloids and in the complex of thymosin-β4–cytoplasmic domain of stabilin-2 (Tβ4-stabilin CTD). A53T αS aggregates have more extensive βsheet contents reflected by constant regions at low potential barriers in difference (to monomers) melting diagrams (MDs). Energies of the intermolecular interactions and of secondary structures bonds, formed during polymerization, fall into the 5.41 kJ mol−1 ≤ Ea ≤ 5.77 kJ mol−1 range for αS aggregates. Monomers lose mor

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Avery, Ross A., and William J. Bettger. "The oligomeric state of spectrin in the rat erythrocyte membrane skeleton." Biochemistry and Cell Biology 68, no. 6 (1990): 936–43. http://dx.doi.org/10.1139/o90-138.

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The oligomeric state of spectrin in the erythrocyte membrane skeleton of the rat was investigated following extraction in a low ionic strength buffer for 24 and 96 h. All analyses were quantitively compared with preparations from human erythrocyte membranes. After nondenaturing agarose–polyacrylamide gel electrophoresis, the human samples revealed their characteristic spectrin oligomer pattern; there were high molecular weight complexes near the origin of the gel, followed by several high order oligomers, tetramers, and dimers. The pattern in the rat membrane skeleton also included tetramers a

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Carugo, Oliviero. "A structural proteomics filter: prediction of the quaternary structural type of hetero-oligomeric proteins on the basis of their sequences." Journal of Applied Crystallography 40, no. 6 (2007): 986–89. http://dx.doi.org/10.1107/s0021889807041076.

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A protein chain can correspond to a monomeric protein or it can form, together with other chains, oligomeric assemblies, which can be either homo-oligomers or hetero-oligomers. In the latter case, the three-dimensional structure of the single protein chain is unlikely to be determined, since it will probably be difficult to express and crystallize. A computational method is presented here that allows one to predict if a chain participates in hetero-oligomeric assemblies, on the basis of its amino acid composition, with accuracy close to 80%. Such a technique should improve the success rate of

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Gurevich, Vsevolod V., and Eugenia V. Gurevich. "Solo vs Chorus: Monomers and Oligomers of Arrestin Proteins." International Journal of Molecular Sciences 23, no. 13 (2022): 7253. http://dx.doi.org/10.3390/ijms23137253.

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Three out of four subtypes of arrestin proteins expressed in mammals self-associate, each forming oligomers of a distinct kind. Monomers and oligomers have different subcellular localization and distinct biological functions. Here we summarize existing evidence regarding arrestin oligomerization and discuss specific functions of monomeric and oligomeric forms, although too few of the latter are known. The data on arrestins highlight biological importance of oligomerization of signaling proteins. Distinct modes of oligomerization might be an important contributing factor to the functional diffe

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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

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Poon, G. M. K. "Enhancement of oligomeric stability by covalent linkage and its application to the human p53tet domain: thermodynamics and biological implications." Biochemical Society Transactions 35, no. 6 (2007): 1574–78. http://dx.doi.org/10.1042/bst0351574.

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The formation of oligomeric proteins proceeds at a major cost of reducing the translational and rotational entropy for their subunits in order to form the stabilizing interactions found in the oligomeric state. Unlike site-directed mutations, covalent linkage of subunits represents a generically applicable strategy for enhancing oligomeric stability by reducing the entropic driving force for dissociation. Although this can be realized by introducing de novo disulfide cross-links between subunits, issues with irreversible aggregation limit the utility of this approach. In contrast, tandem linka

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Uguzzoni, Guido, Shalini John Lovis, Francesco Oteri, Alexander Schug, Hendrik Szurmant, and Martin Weigt. "Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis." Proceedings of the National Academy of Sciences 114, no. 13 (2017): E2662—E2671. http://dx.doi.org/10.1073/pnas.1615068114.

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Proteins have evolved to perform diverse cellular functions, from serving as reaction catalysts to coordinating cellular propagation and development. Frequently, proteins do not exert their full potential as monomers but rather undergo concerted interactions as either homo-oligomers or with other proteins as hetero-oligomers. The experimental study of such protein complexes and interactions has been arduous. Theoretical structure prediction methods are an attractive alternative. Here, we investigate homo-oligomeric interfaces by tracing residue coevolution via the global statistical direct cou

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Busija, Anna R., Hemal H. Patel, and Paul A. Insel. "Caveolins and cavins in the trafficking, maturation, and degradation of caveolae: implications for cell physiology." American Journal of Physiology-Cell Physiology 312, no. 4 (2017): C459—C477. http://dx.doi.org/10.1152/ajpcell.00355.2016.

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Caveolins (Cavs) are ~20 kDa scaffolding proteins that assemble as oligomeric complexes in lipid raft domains to form caveolae, flask-shaped plasma membrane (PM) invaginations. Caveolae (“little caves”) require lipid-lipid, protein-lipid, and protein-protein interactions that can modulate the localization, conformational stability, ligand affinity, effector specificity, and other functions of proteins that are partners of Cavs. Cavs are assembled into small oligomers in the endoplasmic reticulum (ER), transported to the Golgi for assembly with cholesterol and other oligomers, and then exported

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Gwyther, Rebecca E. A., D. Dafydd Jones, and Harley L. Worthy. "Better together: building protein oligomers naturally and by design." Biochemical Society Transactions 47, no. 6 (2019): 1773–80. http://dx.doi.org/10.1042/bst20190283.

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Protein oligomers are more common in nature than monomers, with dimers being the most prevalent final structural state observed in known structures. From a biological perspective, this makes sense as it conserves vital molecular resources that may be wasted simply by generating larger single polypeptide units, and allows new features such as cooperativity to emerge. Taking inspiration from nature, protein designers and engineers are now building artificial oligomeric complexes using a variety of approaches to generate new and useful supramolecular protein structures. Oligomerisation is thus of

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Dabney-Smith, Carole, and Kenneth Cline. "Clustering of C-Terminal Stromal Domains of Tha4 Homo-oligomers during Translocation by the Tat Protein Transport System." Molecular Biology of the Cell 20, no. 7 (2009): 2060–69. http://dx.doi.org/10.1091/mbc.e08-12-1189.

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The chloroplast Twin arginine translocation (Tat) pathway uses three membrane proteins and the proton gradient to transport folded proteins across sealed membranes. Precursor proteins bind to the cpTatC-Hcf106 receptor complex, triggering Tha4 assembly and protein translocation. Tha4 is required only for the translocation step and is thought to be the protein-conducting component. The organization of Tha4 oligomers was examined by substituting pairs of cysteine residues into Tha4 and inducing disulfide cross-links under varying stages of protein translocation. Tha4 formed tetramers via its tra

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Sangwan, Smriti, Anni Zhao, Katrina L. Adams, et al. "Atomic structure of a toxic, oligomeric segment of SOD1 linked to amyotrophic lateral sclerosis (ALS)." Proceedings of the National Academy of Sciences 114, no. 33 (2017): 8770–75. http://dx.doi.org/10.1073/pnas.1705091114.

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Fibrils and oligomers are the aggregated protein agents of neuronal dysfunction in ALS diseases. Whereas we now know much about fibril architecture, atomic structures of disease-related oligomers have eluded determination. Here, we determine the corkscrew-like structure of a cytotoxic segment of superoxide dismutase 1 (SOD1) in its oligomeric state. Mutations that prevent formation of this structure eliminate cytotoxicity of the segment in isolation as well as cytotoxicity of the ALS-linked mutants of SOD1 in primary motor neurons and in a Danio rerio (zebrafish) model of ALS. Cytotoxicity ass

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Zhu, Lixin, Yuechueng Liu, and John G. Forte. "Ezrin oligomers are the membrane-bound dormant form in gastric parietal cells." American Journal of Physiology-Cell Physiology 288, no. 6 (2005): C1242—C1254. http://dx.doi.org/10.1152/ajpcell.00521.2004.

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Ezrin is a member of ezrin, radixin, moesin (ERM) protein family that links F-actin to membranes. The NH2- and COOH-terminal association domains of ERM proteins, known respectively as N-ERMAD and C-ERMAD, participate in interactions with membrane proteins and F-actin, and intramolecular and intermolecular interactions within and among ERM proteins. In gastric parietal cells, ezrin is heavily represented on the apical membrane and is associated with cell activation. Ezrin-ezrin interactions are presumably involved in functional regulation of ezrin and thus became a subject of our study. Fluores

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Birchenall-Roberts, M. C., C. Ferrer, D. Ferris, et al. "Inhibition of murine monocyte proliferation by a colony-stimulating factor-1 antisense oligodeoxynucleotide. Evidence for autocrine regulation." Journal of Immunology 145, no. 10 (1990): 3290–96. http://dx.doi.org/10.4049/jimmunol.145.10.3290.

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Abstract Using a combination of v-myc and v-ras oncogenes, we have established a growth factor-independent monocyte cell line from murine fetal liver (FL-ras/myc). Biologic and molecular characterization demonstrated that the gene for the macrophage growth factor CSF-1 and the c-fms proto-oncogene (CSF-1 receptor) are expressed in this cell line, thus suggesting autocrine regulation as a possible mechanism for the unregulated growth of these cells. To study this possibility, we used 1) mAb, to neutralize the CSF-1 protein produced by the cell line, and 2) antisense oligomers, to inhibit CSF-1

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Dulle, Jennifer E., Rachel E. Bouttenot, Lisa A. Underwood, and Heather L. True. "Soluble oligomers are sufficient for transmission of a yeast prion but do not confer phenotype." Journal of Cell Biology 203, no. 2 (2013): 197–204. http://dx.doi.org/10.1083/jcb.201307040.

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Amyloidogenic proteins aggregate through a self-templating mechanism that likely involves oligomeric or prefibrillar intermediates. For disease-associated amyloidogenic proteins, such intermediates have been suggested to be the primary cause of cellular toxicity. However, isolation and characterization of these oligomeric intermediates has proven difficult, sparking controversy over their biological relevance in disease pathology. Here, we describe an oligomeric species of a yeast prion protein in cells that is sufficient for prion transmission and infectivity. These oligomers differ from the

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Walsh, D. M., I. Klyubin, G. M. Shankar та ін. "The role of cell-derived oligomers of Aβ in Alzheimer's disease and avenues for therapeutic intervention". Biochemical Society Transactions 33, № 5 (2005): 1087–90. http://dx.doi.org/10.1042/bst0331087.

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Burgeoning evidence suggests that soluble oligomers of Aβ (amyloid β-protein) are the earliest effectors of synaptic compromise in Alzheimer's disease. Whereas most other investigators have employed synthetic Aβ peptides, we have taken advantage of a β-amyloid precursor protein-overexpressing cell line (referred to as 7PA2) that secretes sub-nanomolar levels of low-n oligomers of Aβ. These are composed of heterogeneous Aβ peptides that migrate on SDS/PAGE as dimers, trimers and tetramers. When injected into the lateral ventricle of rats in vivo, these soluble oligomers inhibit hippocampal long

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Byrne, Patrick O., Kalina Hristova, and Daniel J. Leahy. "EGFR forms ligand-independent oligomers that are distinct from the active state." Journal of Biological Chemistry 295, no. 38 (2020): 13353–62. http://dx.doi.org/10.1074/jbc.ra120.012852.

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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 d

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Roh, Soung-Hun, Corey F. Hryc, Hyun-Hwan Jeong, et al. "Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM." Proceedings of the National Academy of Sciences 114, no. 31 (2017): 8259–64. http://dx.doi.org/10.1073/pnas.1704725114.

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Single-particle electron cryo-microscopy (cryo-EM) is an emerging tool for resolving structures of conformationally heterogeneous particles; however, each structure is derived from an average of many particles with presumed identical conformations. We used a 3.5-Å cryo-EM reconstruction with imposed D7 symmetry to further analyze structural heterogeneity among chemically identical subunits in each GroEL oligomer. Focused classification of the 14 subunits in each oligomer revealed three dominant classes of subunit conformations. Each class resembled a distinct GroEL crystal structure in the Pro

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Marchenkova, Margarita A., Petr V. Konarev, Yuliya V. Kordonskaya, et al. "The Role of Cations and Anions in the Formation of Crystallization Oligomers in Protein Solutions as Revealed by Combination of Small-Angle X-ray Scattering and Molecular Dynamics." Crystals 12, no. 6 (2022): 751. http://dx.doi.org/10.3390/cryst12060751.

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As is known from molecular dynamics simulation, lysozyme oligomers in crystallization solutions are most stable when taking into account as many precipitant ions as possible embedded in the corresponding crystal structure. Therefore, the number of precipitant ions associated with crystallographic oligomer models can play a role during the modeling of small-angle X-ray scattering (SAXS) data. This hypothesis has been tested in the present work. As a result, it turned out that the best fit quality to the experimental SAXS data is reached when using oligomers without precipitant ions at all or wi

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