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Oligomerization

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https://www.readbyqxmd.com/read/28531329/alternative-stable-conformation-capable-of-protein-misinteraction-links-trna-synthetase-to-peripheral-neuropathy
#1
David Blocquel, Sheng Li, Na Wei, Herwin Daub, Mathew Sajish, Maria-Luise Erfurth, Grace Kooi, Jiadong Zhou, Ge Bai, Paul Schimmel, Albena Jordanova, Xiang-Lei Yang
While having multiple aminoacyl-tRNA synthetases implicated in Charcot-Marie-Tooth (CMT) disease suggests a common mechanism, a defect in enzymatic activity is not shared among the CMT-causing mutants. Protein misfolding is a common hypothesis underlying the development of many neurological diseases. Its process usually involves an initial reduction in protein stability and then the subsequent oligomerization and aggregation. Here, we study the structural effect of three CMT-causing mutations in tyrosyl-tRNA synthetase (TyrRS or YARS)...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28530838/an-innovative-high-throughput-screening-approach-for-discovery-of-small-molecules-that-inhibit-tnf-receptors
#2
Chih Hung Lo, Nagamani Vunnam, Andrew K Lewis, Ting-Lan Chiu, Benjamin E Brummel, Tory M Schaaf, Benjamin D Grant, Prachi Bawaskar, David D Thomas, Jonathan N Sachs
Tumor necrosis factor receptor 1 (TNFR1) is a transmembrane receptor that binds tumor necrosis factor or lymphotoxin-alpha and plays a critical role in regulating the inflammatory response. Upregulation of these ligands is associated with inflammatory and autoimmune diseases. Current treatments reduce symptoms by sequestering free ligands, but this can cause adverse side effects by unintentionally inhibiting ligand binding to off-target receptors. Hence, there is a need for new small molecules that specifically target the receptors, rather than the ligands...
May 1, 2017: SLAS Discovery
https://www.readbyqxmd.com/read/28530804/characterization-of-growth-patterns-of-nanoscale-organic-films-on-carbon-electrodes-by-surface-enhanced-raman-spectroscopy
#3
Mustafa Supur, Scott R Smith, Richard L McCreery
Electrochemical deposition of aromatic organic molecules by reduction of diazonium reagents enables formation of molecular layers with sufficient integrity for use in molecular electronic junctions of interest to microelectronics. Characterization of organic films with thicknesses in the 1-10 nm range is difficult with Raman spectroscopy, since most molecular structures of electronic interest have Raman cross sections which are too small to observe as either thin films on solid electrodes or within intact molecular junctions...
May 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28529565/prodelphinidins-isolated-from-chinese-bayberry-leaves-induces-apoptosis-via-the-p53-dependent-signaling-pathways-in-ovcar-3-human-ovarian-cancer-cells
#4
Yu Fu, Xingqian Ye, Malcolm Lee, Gary Rankin, Yi Charlie Chen
Chinese bayberry leaves are rich in prodelphinidins. Since the isolation and purification of prodelphinidins is difficult, the association between the degree of prodelphinidin polymerization and their anti-carcinogenic activity remains ambiguous. The cytotoxic and apoptotic activities of prodelphinidin Chinese bayberry leaf extracts (PCBLs), oligomeric proanthocyanidins (OPAs) and polymeric proanthocyanidins (PPAs), isolated by normal-phase preparative high-performance liquid chromatography were investigated in OVCAR-3 human ovarian cancer cells...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28528958/investigation-of-calcium-dependent-activity-and-conformational-dynamics-of-zebra-fish-12-lipoxygenase
#5
Monica Mittal, Mahmudul Hasan, Navisraj Balagunaseelan, Alexander Fauland, Craig Wheelock, Olof Rådmark, Jesper Z Haeggström, Agnes Rinaldo-Matthis
BACKGROUND: A 12-lipoxygenase in zebra fish (zf12-LOX) was found to be required for normal embryonic development and LOXs are of great interest for targeted drug designing. In this study, we investigate the structural-functional aspects of zf12-LOX in response to calcium. METHODS: A soluble version of zf12-LOX was created by mutagenesis. Based on multiple sequence alignment, we mutated the putative calcium-responsive amino acids in N-PLAT domain of soluble zf12-LOX...
May 18, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28528776/structural-basis-of-tpr-mediated-oligomerization-and-activation-of-oncogenic-fusion-kinases
#6
Kuntal Pal, Abhishek Bandyopadhyay, X Edward Zhou, Qingping Xu, David P Marciano, Joseph S Brunzelle, Smitha Yerrum, Patrick R Griffin, George Vande Woude, Karsten Melcher, H Eric Xu
The nuclear pore complex subunit TPR is found in at least five different oncogenic fusion kinases, including TPR-MET, yet how TPR fusions promote activation of kinases and their oncogenic activities remains poorly understood. Here we report the crystal structure of TPR(2-142), the MET fusion partner of oncogenic TPR-MET. TPR(2-142) contains a continuous 124-residue α helix that forms an antiparallel tetramer from two leucine zipper-containing parallel coiled coils. Remarkably, single mutations cause strikingly different conformations of the coiled coil, indicating its highly dynamic nature...
May 18, 2017: Structure
https://www.readbyqxmd.com/read/28527888/tetrameric-structure-of-the-flagellar-cap-protein-flid-from-serratia-marcescens
#7
So Yeon Cho, Wan Seok Song, Ho Jeong Hong, Geun-Shik Lee, Seung Goo Kang, Hyun-Jeong Ko, Pyeung-Hyeun Kim, Sung-Il Yoon
Bacterial motility is provided by the flagellum. FliD is located at the distal end of the flagellum and plays a key role in the insertion of each flagellin protein at the growing tip of the flagellar filament. Because FliD functions as an oligomer, the determination of the oligomeric state of FliD is critical to understanding the molecular mechanism of FliD-mediated flagellar growth. FliD has been shown to adopt a pentameric or a hexameric structure depending on the bacterial species. Here, we report another distinct oligomeric form of FliD based on structural and biochemical studies...
May 17, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28527208/neuronal-expression-of-truncated-tau-efficiently-promotes-neurodegeneration-in-animal-models-pitfalls-of-toxic-oligomer-analysis
#8
Rostislav Skrabana, Branislav Kovacech, Peter Filipcik, Norbert Zilka, Santosh Jadhav, Tomas Smolek, Eva Kontsekova, Michal Novak
Animal models of neurodegeneration induced by neuronal expression of truncated tau protein emerge as an important tool for understanding the pathogenesis of human tauopathies and for therapy development. Here we highlight common features of truncated tau models and make a critical assessment of possible pitfalls in their analysis. Particularly, the amount of soluble tau oligomers, which are suspected to be neurotoxic agents participating on the spreading of pathology inside the brain, may be overestimated due to a post-lysis oxidative tau oligomerization...
May 17, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28527044/endocytic-vesicle-rupture-is-a-conserved-mechanism-of-cellular-invasion-by-amyloid-proteins
#9
William P Flavin, Luc Bousset, Zachary C Green, Yaping Chu, Stratos Skarpathiotis, Michael J Chaney, Jeffrey H Kordower, Ronald Melki, Edward M Campbell
Numerous pathological amyloid proteins spread from cell to cell during neurodegenerative disease, facilitating the propagation of cellular pathology and disease progression. Understanding the mechanism by which disease-associated amyloid protein assemblies enter target cells and induce cellular dysfunction is, therefore, key to understanding the progressive nature of such neurodegenerative diseases. In this study, we utilized an imaging-based assay to monitor the ability of disease-associated amyloid assemblies to rupture intracellular vesicles following endocytosis...
May 19, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28526409/expression-and-purification-of-functional-pdgf-receptor-beta
#10
Qingbin Shang, Liang Zhao, Xiaojing Wang, Meimei Wang, Sen-Fang Sui, Li-Zhi Mi
Platelet Derived Growth Factor receptors (PDGFRs), members of receptor tyrosine kinase superfamily, play essential roles in early hematopoiesis, angiogenesis and organ development. Dysregulation of PDGF receptor signaling under pathological conditions associates with cancers, vascular diseases, and fibrotic diseases. Therefore, they are attractive targets in drug development. Like any other membrane proteins with a single-pass transmembrane domain, the high-resolution structural information of the full-length PDGF receptors is still not resolved...
May 16, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28525957/determining-dominant-driving-forces-affecting-controlled-protein-release-from-polymeric-nanoparticles
#11
Josh Smith, Kayla G Sprenger, Rick Liao, Andrea Joseph, Elizabeth Nance, Jim Pfaendtner
Enzymes play a critical role in many applications in biology and medicine as potential therapeutics. One specific area of interest is enzyme encapsulation in polymer nanostructures, which have applications in drug delivery and catalysis. A detailed understanding of the mechanisms governing protein/polymer interactions is crucial for optimizing the performance of these complex systems for different applications. Using a combined computational and experimental approach, this study aims to quantify the relative importance of molecular and mesoscale driving forces to protein release from polymeric nanoparticles...
May 19, 2017: Biointerphases
https://www.readbyqxmd.com/read/28525282/crowding-controlled-cluster-size-in-concentrated-aqueous-protein-solutions-structure-self-and-collective-diffusion
#12
Michal Katharina Braun, Marco Grimaldo, Felix Roosen-Runge, Ingo Hoffmann, Orsolya Czakkel, Michael Sztucki, Fajun Zhang, Frank Schreiber, Tilo Seydel
We investigate the concentration-controlled formation of clusters in β-lactoglobulin (BLG) protein solutions combining structural and dynamical scattering techniques. The static structure factor from small-angle X-ray scattering as well as de-Gennes narrowing in the nanosecond diffusion function D(q) from neutron spin echo spectroscopy support a picture of cluster formation. Using neutron backscattering spectroscopy, a monotonous increase of the average hydrodynamic cluster radius is monitored over a broad protein concentration range, corresponding to oligomeric structures of BLG ranging from the native dimers up to roughly four dimers...
May 19, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28524105/structural-analysis-of-polymer-composites-using-spectral-domain-optical-coherence-tomography
#13
Muhammad Faizan Shirazi, Mansik Jeon, Jeehyun Kim
The structural analysis of nylon/graphene oxide (NY/GO) and polyetherblockamide/ trisilinolphenyl-polyhederal oligomeric silsesquioxane (PEBA/t-POSS) composites were performed using high-resolution spectral domain optical coherence tomography (SD-OCT). This optical technology revealed both cross-sectional, as well as sub-layer depth information of sample. The non-destructive real-time imaging demonstrated the nature of defects in the composites. The thickness and location of each defect point in the composites were measured using A-scan analysis on the SD-OCT images...
May 18, 2017: Sensors
https://www.readbyqxmd.com/read/28523739/mechanisms-of-peptide-sex-pheromone-regulation-of-conjugation-in-enterococcus-faecalis
#14
Yuqing Chen, Arpan Bandyopadhyay, Briana K Kozlowicz, Heather A H Haemig, Albert Tai, Wei-Shou Hu, Gary M Dunny
In many gram positive bacteria, horizontal transfer and virulence are regulated by peptide-mediated cell-cell signaling. The heptapeptide cCF10 (C) activates conjugative transfer of the Enterococcus faecalis plasmid pCF10, whereas the iCF10 (I) peptide inhibits transfer. Both peptides bind to the same domain of the master transcription regulator PrgX, a repressor of transcription of the prgQ operon encoding conjugation genes. We show that repression of prgQ by PrgX tetramers requires formation of a pCF10 DNA loop where each of two PrgX DNA-binding sites is occupied by a dimer...
May 19, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28523271/the-protein-chaperone-clpx-targets-native-and-non-native-aggregated-substrates-for-remodeling-disassembly-and-degradation-with-clpp
#15
Christopher J LaBreck, Shannon May, Marissa G Viola, Joseph Conti, Jodi L Camberg
ClpX is a member of the Clp/Hsp100 family of ATP-dependent chaperones and partners with ClpP, a compartmentalized protease, to degrade protein substrates bearing specific recognition signals. ClpX targets specific proteins for degradation directly or with substrate-specific adaptor proteins. Native substrates of ClpXP include proteins that form large oligomeric assemblies, such as MuA, FtsZ, and Dps in Escherichia coli. To remodel large oligomeric substrates, ClpX utilizes multivalent targeting strategies and discriminates between assembled and unassembled substrate conformations...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28522847/a-molecular-basis-for-selective-antagonist-destabilization-of-dopamine-d3-receptor-quaternary-organization
#16
Sara Marsango, Gianluigi Caltabiano, Mireia Jiménez-Rosés, Mark J Millan, John D Pediani, Richard J Ward, Graeme Milligan
The dopamine D3 receptor (D3R) is a molecular target for both first-generation and several recently-developed antipsychotic agents. Following stable expression of this mEGFP-tagged receptor, Spatial Intensity Distribution Analysis indicated that a substantial proportion of the receptor was present within dimeric/oligomeric complexes and that increased expression levels of the receptor favored a greater dimer to monomer ratio. Addition of the antipsychotics, spiperone or haloperidol, resulted in re-organization of D3R quaternary structure to promote monomerization...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28520783/effect-of-n-terminal-region-of-nuclear-drosophila-melanogaster-small-heat-shock-protein-dmhsp27-on-function-and-quaternary-structure
#17
Mohamed Taha Moutaoufik, Geneviève Morrow, Stéphanie Finet, Robert M Tanguay
The importance of the N-terminal region (NTR) in the oligomerization and chaperone-like activity of the Drosophila melanogaster small nuclear heat shock protein DmHsp27 was investigated by mutagenesis using size exclusion chromatography and native gel electrophoresis. Mutation of two sites of phosphorylation in the N-terminal region, S58 and S75, did not affect the oligomerization equilibrium or the intracellular localization of DmHsp27 when transfected into mammalian cells. Deletion or mutation of specific residues within the NTR region delineated a motif (FGFG) important for the oligomeric structure and chaperone-like activity of this sHsp...
2017: PloS One
https://www.readbyqxmd.com/read/28520587/complementary-roles-of-nod2-in-hematopoietic-and-nonhematopoietic-cells-in-preventing-gut-barrier-dysfunction-dependent-on-mlck-activity
#18
Ziad Al Nabhani, Nicolas Montcuquet, Maryline Roy, Monique Dussaillant, Jean-Pierre Hugot, Frédérick Barreau
BACKGROUND: Crohn's disease (CD) pathogenesis is multifactorial involving genetic and environmental factors. Loss of function mutations in the nucleotide oligomerization domain 2 (NOD2) gene are the main genetic risk factor for CD. Like patients with CD, Nod2 mice are characterized by an enhanced Th1 immune response and a defective mucosal barrier function evidenced by increased intestinal permeability. We previously showed that the latter is related to hematopoietic Nod2 deficiency. Our aim was to explore the mechanisms by which Nod2 expressed in the hematopoietic and in the nonhematopoietic compartments interplay to control epithelial paracellular permeability...
May 16, 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28520443/effective-interactions-and-colloidal-stability-of-bovine-%C3%AE-globulin-in-solution
#19
Stefano Da Vela, Felix Roosen-Runge, Maximilian W A Skoda, Robert M J Jacobs, Tilo Seydel, Henrich Frielinghaus, Michael Sztucki, Ralf Schweins, Fajun Zhang, Frank Schreiber
Interactions and phase behavior of γ-globulins are of fundamental interest in biophysical and pharmaceutical research, as these are among the most abundant proteins in blood plasma. In this work, we report the characterization of the oligomeric state of bovine γ-globulin, the effective protein-protein interactions and the colloidal stability in aqueous solution as a function of protein concentration and ionic strength. Classical biochemical techniques, such as size exclusion chromatography (SEC) and gel electrophoresis together with small angle X-ray and neutron scattering (SAXS/SANS) were employed for this study...
May 18, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28516844/clues-for-two-step-virion-infectivity-factor-regulation-by-core-binding-factor-beta
#20
Youwei Ai, Jianzhang Ma, Xiaojun Wang
Lentiviruses threaten human and animal health. Virion infectivity factor (Vif) is essential for the infectivity of most lentiviruses, except for the equine infectious anaemia virus (EIAV). Vif promotes viral infectivity by recruiting a Cullin-based E3 ligase to induce the degradation of a class of host restriction factors, named APOBEC3. Core binding factor beta (CBF-β) is necessary for several primate lentiviral Vif functions, including HIV-1 Vif. Although much progress has been made in understanding the contribution of CBF-β to Vif function, the precise mechanism has not yet been fully elucidated...
May 18, 2017: Journal of General Virology
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