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Oligomerization

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https://www.readbyqxmd.com/read/29234103/an-exhaustive-search-algorithm-to-aid-nmr-based-structure-determination-of-rotationally-symmetric-transmembrane-oligomers
#1
Jing Yang, Alessandro Piai, Hong-Bin Shen, James J Chou
Nuclear magnetic resonance (NMR) has been an important source of structural restraints for solving structures of oligomeric transmembrane domains (TMDs) of cell surface receptors and viral membrane proteins. In NMR studies, oligomers are assembled using inter-protomer distance restraints. But, for oligomers that are higher than dimer, these distance restraints all have two-fold directional ambiguity, and resolving such ambiguity often requires time-consuming trial-and-error calculations using restrained molecular dynamics (MD) with simulated annealing (SA)...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29233889/transcriptionally-inducible-pleckstrin-homology-like-domain-family-a-member-1-attenuates-erbb-receptor-activity-by-inhibiting-receptor-oligomerization
#2
Shigeyuki Magi, Kazunari Iwamoto, Noriko Yumoto, Michio Hiroshima, Takeshi Nagashima, Rieko Ohki, Amaya Garcia-Munoz, Natalia Volinsky, Alexander von Kriegsheim, Yasushi Sako, Koichi Takahashi, Shuhei Kimura, Boris N Kholodenko, Mariko Okada-Hatakeyama
Feedback control is a key mechanism in signal transduction, intimately involved in regulating the outcome of the cellular response. Here we report a novel mechanism by which PHLDA1, Pleckstrin homology-like domain, family A, member 1, negatively regulates ErbB receptor signaling by inhibition of receptor oligomerization. We have found that the ErbB3 ligand, heregulin, induces PHILDA1 expression in MCF-7 cells. Transcriptionally-induced PHLDA1 protein directly binds to ErbB3, while knockdown of PHLDA1 increases complex formation between ErbB3 and ErbB2...
December 12, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29233859/intraring-allostery-controls-the-function-and-assembly-of-a-hetero-oligomeric-class-ii-chaperonin
#3
Deborah K Shoemark, Richard B Sessions, Andrea Brancaccio, Maria Giulia Bigotti
Class II chaperonins are essential multisubunit complexes that aid the folding of nonnative proteins in the cytosol of archaea and eukarya. They use energy derived from ATP to drive a series of structural rearrangements that enable polypeptides to fold within their central cavity. These events are regulated by an elaborate allosteric mechanism in need of elucidation. We employed mutagenesis and experimental analysis in concert with in silico molecular dynamics simulations and interface-binding energy calculations to investigate the class II chaperonin from Thermoplasma acidophilum Here we describe the effects on the asymmetric allosteric mechanism and on hetero-oligomeric complex formation in a panel of mutants in the ATP-binding pocket of the α and β subunits...
December 12, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29233715/catalytic-activation-of-bacillus-laccase-after-temperature-treatment-structural-biochemical-characterization
#4
Nasrin Mollania, Marjan Heidari, Khosro Khajeh
Laccases belong to a family of multicopper oxidases that have strong oxidation ability towards phenolic compounds. Here, more detailed investigations were carried out on a Bacillus laccase with remarkable behavior of activation after thermal treatment. The kcat of the enzyme was increased 2.5 fold after 50min incubation at 70°C. Copper content determination revealed a molar copper to protein ratio of 3.2 in the both sample. The present paper concerns the differences which are induced in enzyme structure after thermal treatment using common biochemical methods Intrinsic fluorescence of the enzyme was increased after incubation at 70°C indicating higher compactness of the structure in comparison to untreated molecules...
December 9, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29233218/secondary-nucleation-of-monomers-on-fibril-surface-dominates-%C3%AE-synuclein-aggregation-and-provides-autocatalytic-amyloid-amplification
#5
Ricardo Gaspar, Georg Meisl, Alexander K Buell, Laurence Young, Clemens F Kaminski, Tuomas P J Knowles, Emma Sparr, Sara Linse
Parkinson's disease (PD) is characterized by proteinaceous aggregates named Lewy Bodies and Lewy Neurites containing α-synuclein fibrils. The underlying aggregation mechanism of this protein is dominated by a secondary process at mildly acidic pH, as in endosomes and other organelles. This effect manifests as a strong acceleration of the aggregation in the presence of seeds and a weak dependence of the aggregation rate on monomer concentration. The molecular mechanism underlying this process could be nucleation of monomers on fibril surfaces or fibril fragmentation...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29232996/structural-elucidation-of-fucosylated-chondroitin-sulfates-from-sea-cucumber-using-fticr-ms-ms
#6
Isaac Agyekum, Lauren Pepi, Yanlei Yu, Junhui Li, Lufeng Yan, Robert J Linhardt, Shiguo Chen, I Jonathan Amster
Fucosylated chondroitin sulfates are complex polysaccharides extracted from sea cucumber. They have been extensively studied for their anticoagulant properties and have been implicated in other biological activities. While nuclear magnetic resonance spectroscopy has been used to extensively characterize fucosylated chondroitin sulfate oligomers, we herein report the first detailed mass characterization of fucosylated chondroitin sulfate using high-resolution Fourier transform ion cyclotron resonance mass spectrometry...
January 1, 2017: European Journal of Mass Spectrometry
https://www.readbyqxmd.com/read/29232949/anti-oxidative-flavan-3-ol-dimers-from-the-leaves-of-camellia-fangchengensis
#7
Xiu-Hua Meng, Chang Liu, Rong Fan, Li-Fang Zhu, Shi-Xiong Yang, Hong-Tao Zhu, Dong Wang, Chong-Ren Yang, Ying-Jun Zhang
Camellia fangchengensis Liang et Zhong, belonging to the genus Camellia sect. Thea (Theaceae), is an endemic tea species to the south and southwest areas of Guangxi province, P. R. China. Known as a wild tea plant, the leaves have been used for producing green tea or black tea by the local people of its growing area. HPLC and LC-MS analysis showed the leaves contain oligomeric catechins as major phenolic components. Further detailed phytochemical study led to the identification of five flavan-3-ol dimers (1 ¬¬- 5) including two new ones, fangchengbisflavans A (1) and B (2) from the leaves of C...
December 12, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29230394/acetylome-of-acinetobacter-baumannii-sk17-reveals-a-highly-conserved-modification-of-histone-like-protein-hu
#8
Jiahn-Haur Liao, Cheng-Han Tsai, Sanjay G Patel, Jhih-Tian Yang, I-Fan Tu, Matteo Lo Cicero, Magdalena Lipka-Lloyd, Wan-Ling Wu, Wen-Jie Shen, Meng-Ru Ho, Chi-Chi Chou, Garima R Sharma, Hiroki Okanishi, Louis Y P Luk, Yu-Hsuan Tsai, Shih-Hsiung Wu
Lysine acetylation is a prevalent post-translational modification in both eukaryotes and prokaryotes. Whereas this modification is known to play pivotal roles in eukaryotes, the function and extent of this modification in prokaryotic cells remain largely unexplored. Here we report the acetylome of a pair of antibiotic-sensitive and -resistant nosocomial pathogen Acinetobacter baumannii SK17-S and SK17-R. A total of 145 lysine acetylation sites on 125 proteins was identified, and there are 23 acetylated proteins found in both strains, including histone-like protein HU which was found to be acetylated at Lys13...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/29229420/ros-mediated-oligomerization-of-vdac2-is-associated-with-quinocetone-induced-apoptotic-cell-death
#9
Xiayun Yang, Shusheng Tang, Daowen Li, Bin Li, Xilong Xiao
Quinocetone (QCT) has been approved and widely used as an animal feed additive in China since 2003. However, investigations indicate that QCT shows potential toxicity both in vitro and in vivo. Although voltage dependent anion channel 1 (VDAC1) involved in regulating QCT-induced apoptotic cell death has been established, the role of voltage dependent anion channel 2 (VDAC2) in QCT-induced toxicity remains unclear. In this study, we showed that QCT-induced cell death was coupled to VDAC2 oligomerization. Moreover, VDAC inhibitor 4, 4'-diisothiocyano stilbene-2, 2'-disulfonic acid (DIDS) alleviated QCT-induced cell death and VDAC2 oligomerization...
December 8, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
https://www.readbyqxmd.com/read/29228971/alpha-synuclein-oligomer-selective-antibodies-reduce-intracellular-accumulation-and-mitochondrial-impairment-in-alpha-synuclein-exposed-astrocytes
#10
Gabriel Gustafsson, Veronica Lindström, Jinar Rostami, Eva Nordström, Lars Lannfelt, Joakim Bergström, Martin Ingelsson, Anna Erlandsson
BACKGROUND: Due to its neurotoxic properties, oligomeric alpha-synuclein (α-syn) has been suggested as an attractive target for passive immunization against Parkinson's disease (PD). In mouse models of PD, antibody treatment has been shown to lower the levels of pathogenic α-syn species, including oligomers, although the mechanisms of action remain unknown. We have previously shown that astrocytes rapidly engulf α-syn oligomers that are intracellularly stored, rather than degraded, resulting in impaired mitochondria...
December 11, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/29228690/cartilage-oligomeric-matrix-protein-promotes-prostate-cancer-progression-by-enhancing-invasion-and-disrupting-intracellular-calcium-homeostasis
#11
Emelie Englund, Giacomo Canesin, Konstantinos S Papadakos, Neelanjan Vishnu, Emma Persson, Bart Reitsma, Aseem Anand, Laila Jacobsson, Leszek Helczynski, Hindrik Mulder, Anders Bjartell, Anna M Blom
Cartilage oligomeric matrix protein (COMP) was recently implicated in the progression of breast cancer. Immunostaining of 342 prostate cancer specimens in tissue microarrays showed that COMP expression is not breast cancer-specific but also occurs in prostate cancer. The expression of COMP in prostate cancer cells correlated with a more aggressive disease with faster recurrence. Subcutaneous xenografts in immunodeficient mice showed that the prostate cancer cell line DU145 overexpressing COMP formed larger tumors in vivo as compared to mock-transfected cells...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29226012/hydride-transfer-versus-deprotonation-kinetics-in-the-isobutane-propene-alkylation-reaction-a-computational-study
#12
Chong Liu, Rutger A van Santen, Ali Poursaeidesfahani, Thijs J H Vlugt, Evgeny A Pidko, Emiel J M Hensen
The alkylation of isobutane with light alkenes plays an essential role in modern petrochemical processes for the production of high-octane gasoline. In this study we have employed periodic DFT calculations combined with microkinetic simulations to investigate the complex reaction mechanism of isobutane-propene alkylation catalyzed by zeolitic solid acids. Particular emphasis was given to addressing the selectivity of the alkylate formation versus alkene formation, which requires a high rate of hydride transfer in comparison to the competitive oligomerization and deprotonation reactions resulting in catalyst deactivation...
December 1, 2017: ACS Catalysis
https://www.readbyqxmd.com/read/29223533/atomic-structure-and-enzymatic-insights-into-the-vancomycin-resistant-enterococcus-faecalis-v583-alkylhydroperoxide-reductase-subunit-c
#13
Ankita Pan, Asha Manikkoth Balakrishna, Wilson Nartey, Andreas Kohlmeier, Phat Vinh Dip, Shashi Bhushan, Gerhard Grüber
The Enterococcus faecalis alkyl hydroperoxide reductase complex (AhpR) with its subunits AhpC (EfAhpC) and AhpF (EfAhpF) are of paramount importance to restore redox homeostasis. Recently, the novel phenomenon of swapping of the catalytic domains of EfAhpF was uncovered. Here, we visualized its counterpart EfAhpC (187 residues) from the vancomycin-resistant E. faecalis (V583) bacterium by electron microscopy and demonstrate, that in contrast to other bacterial AhpCs, EfAhpC forms a stable decamer-ring irrespective of the redox state...
December 6, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29223157/self-organization-of-recombinant-membrane-porin-ompf-from-yersinia-pseudotuberculosis-in-aqueous-environments
#14
E V Sidorin, V A Khomenko, N Yu Kim, P S Dmitrenok, A M Stenkova, O D Novikova, T F Solov'eva
Recombinant porin OmpF (an integral protein of bacterial outer membrane) from Yersinia pseudotuberculosis was synthesized in Escherichia coli cells as inclusion bodies. By combining the methods of anion-exchange and gel filtration chromatographies, recombinant OmpF (rOmpF) was isolated as an individual protein in its denatured state, and its characteristic properties (molecular mass, N-terminal amino acid sequence, and hydrodynamic radius of the protein in 8 M urea solution) were determined. According to the data of gel filtration, dynamic light scattering, optical spectroscopy, and binding of the hydrophobic fluorescent probe 8-anilino-1-naphthalenesulfonic acid, the rOmpF is fully unfolded in 8 M urea and exists in random coil conformation...
November 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29223151/the-power-and-limitations-of-influenza-virus-hemagglutinin-assays
#15
REVIEW
N B Ustinov, E G Zavyalova, I G Smirnova, A M Kopylov
Influenza virus hemagglutinins (HAs) are surface proteins that bind to sialic acid residues at the host cell surface and ensure further virus internalization. Development of methods for the inhibition of these processes drives progress in the design of new antiviral drugs. The state of the isolated HA (i.e. combining tertiary structure and extent of oligomerization) is defined by multiple factors, like the HA source and purification method, posttranslational modifications, pH, etc. The HA state affects HA functional activity and significantly impacts the results of numerous HA assays...
November 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29223072/alteration-of-autophagy-related-proteins-in-peripheral-blood-mononuclear-cells-of-patients-with-parkinson-s-disease
#16
Yasuo Miki, Shuji Shimoyama, Tomoya Kon, Tatsuya Ueno, Ryo Hayakari, Kunikazu Tanji, Tomoh Matsumiya, Eiki Tsushima, Fumiaki Mori, Koichi Wakabayashi, Masahiko Tomiyama
Previous postmortem studies demonstrated dysregulation of autophagy in patients with Parkinson's disease (PD). To clarify whether this alteration reflects a fundamental aspect of PD or represents the final stage of autophagy dysregulation resulting from a long neurodegenerative process, we focused on basal autophagy in peripheral blood mononuclear cells (PBMCs) of PD patients (n = 35) and controls (n = 23). The whole-transcriptome assay revealed downregulation of mRNAs for 6 core regulators of autophagy (UNC-51-like kinase [ULK] 3, autophagy-related [Atg] 2A, Atg4B, Atg5, Atg16L1, and histone deacetylase 6)...
November 21, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/29222414/structural-dynamics-of-the-mscl-c-terminal-domain
#17
Navid Bavi, Adam D Martinac, D Marien Cortes, Omid Bavi, Pietro Ridone, Takeshi Nomura, Adam P Hill, Boris Martinac, Eduardo Perozo
The large conductance mechanosensitive channel (MscL), acts as an osmoprotective emergency valve in bacteria by opening a large, water-filled pore in response to changes in membrane tension. In its closed configuration, the last 36 residues at the C-terminus form a bundle of five α-helices co-linear with the five-fold axis of symmetry. Here, we examined the structural dynamics of the C-terminus of EcMscL using site-directed spin labelling electron paramagnetic resonance (SDSL EPR) spectroscopy. These experiments were complemented with computational modelling including molecular dynamics (MD) simulations and finite element (FE) modelling...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222017/increasing-susceptibility-to-oxidative-stress-by-cataract-causing-crystallin-mutations
#18
Wei-Jie Zhao, Yong-Bin Yan
Cataract, a crystallin protein aggregation disease, is the leading cause of human blindness worldwide. Congenital cataract may be induced by many factors and genetic disorders accounts for about half of the cases. Inherited mutations can promote cataract formation by affecting crystallin structure, solubility, stability, protein interactions and aggregatory propensity. In this research, we investigated the potential role of oxidative damage in congenital cataracts caused by six mutations in γC- and γD-crystallins, the predominant structural proteins in the lens...
December 5, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29221925/detecting-protein-aggregation-and-interactions-in-live-cells-a-guide-to-number-and-brightness
#19
REVIEW
Rory Nolan, Maro Iliopoulou, Luis Alvarez, Sergi Padilla-Parra
The possibility to detect and quantify protein-protein interactions with good spatial and temporal resolutions in live cells is crucial in biology. Number and Brightness is a powerful approach to detect both protein aggregation/desegregation dynamics and stoichiometry in live cells. Importantly, this technique can be applied in commercial set ups: both camera based and laser scanning microscopes. It provides pixel-by-pixel information on protein oligomeric states. If performed with two colours, the technique can retrieve the stoichiometry of the reaction under study...
December 5, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29220865/silver-nano-particles-ameliorate-learning-and-spatial-memory-of-male-wistar-rats-by-prevention-of-amyloid-fibril-induced-neurotoxicity
#20
H Ramshini, A-S Moghaddasi, L-S Aldaghi, N Mollania, A Ebrahim-Habibi
Alzheimer's disease (AD) is a chronic degenerative disease characterized by the presence of amyloid plaques and neurofibrillary tangles (NFTs), which results into memory and learning impairments. In the present study, we showed that the aggregates formed by a protein that has no link with Alzheimer's disease, namely the hen egg white lysozyme (HEWL), were cytotoxic and decreased spatial learning and memory in rats. The effect of Ag-nano particles (Ag-NPs) was investigated on disruption of amyloid aggregation and preservation of cognitive behavior of rats...
December 8, 2017: Archives Italiennes de Biologie
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