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Protein footprinting

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https://www.readbyqxmd.com/read/28715365/analysis-of-the-c-kit-ligand-promoter-using-chromatin-immunoprecipitation
#1
Pingyu Zhang, Andres Rojas, Boris Blechacz
Multiple cellular processes, including DNA replication and repair, DNA recombination, and gene expression, require interactions between proteins and DNA. Therefore, DNA-protein interactions regulate multiple physiological, pathophysiological, and biological functions, such as cell differentiation, cell proliferation, cell cycle control, chromosome stability, epigenetic gene regulation, and cell transformation. In eukaryotic cells, the DNA interacts with histone and nonhistone proteins and is condensed into chromatin...
June 27, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28708998/profiling-ssb-nascent-chain-interactions-reveals-principles-of-hsp70-assisted-folding
#2
Kristina Döring, Nabeel Ahmed, Trine Riemer, Harsha Garadi Suresh, Yevhen Vainshtein, Markus Habich, Jan Riemer, Matthias P Mayer, Edward P O'Brien, Günter Kramer, Bernd Bukau
The yeast Hsp70 chaperone Ssb interacts with ribosomes and nascent polypeptides to assist protein folding. To reveal its working principle, we determined the nascent chain-binding pattern of Ssb at near-residue resolution by in vivo selective ribosome profiling. Ssb associates broadly with cytosolic, nuclear, and hitherto unknown substrate classes of mitochondrial and endoplasmic reticulum (ER) nascent proteins, supporting its general chaperone function. Ssb engages most substrates by multiple binding-release cycles to a degenerate sequence enriched in positively charged and aromatic amino acids...
July 13, 2017: Cell
https://www.readbyqxmd.com/read/28708131/a-clinicopathological-approach-to-the-diagnosis-of-dementia
#3
REVIEW
Fanny M Elahi, Bruce L Miller
The most definitive classification systems for dementia are based on the underlying pathology which, in turn, is categorized largely according to the observed accumulation of abnormal protein aggregates in neurons and glia. These aggregates perturb molecular processes, cellular functions and, ultimately, cell survival, with ensuing disruption of large-scale neural networks subserving cognitive, behavioural and sensorimotor functions. The functional domains affected and the evolution of deficits in these domains over time serve as footprints that the clinician can trace back with various levels of certainty to the underlying neuropathology...
July 14, 2017: Nature Reviews. Neurology
https://www.readbyqxmd.com/read/28674401/quantitative-protein-topography-measurements-by-high-resolution-hydroxyl-radical-protein-footprinting-enable-accurate-molecular-model-selection
#4
Boer Xie, Amika Sood, Robert J Woods, Joshua S Sharp
We report an integrated workflow that allows mass spectrometry-based high-resolution hydroxyl radical protein footprinting (HR-HRPF) measurements to accurately measure the absolute average solvent accessible surface area (<SASA>) of amino acid side chains. This approach is based on application of multi-point HR-HRPF, electron-transfer dissociation (ETD) tandem MS (MS/MS) acquisition, measurement of effective radical doses by radical dosimetry, and proper normalization of the inherent reactivity of the amino acids...
July 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28671673/ews-fli1-perturbs-mrtfb-yap-1-tead-target-gene-regulation-inhibiting-cytoskeletal-autoregulatory-feedback-in-ewing-sarcoma
#5
A M Katschnig, M O Kauer, R Schwentner, E M Tomazou, C N Mutz, M Linder, M Sibilia, J Alonso, D N T Aryee, H Kovar
Ewing sarcoma (EWS) is a paediatric bone cancer with high metastatic potential. Cellular plasticity resulting from dynamic cytoskeletal reorganization, typically regulated via the Rho pathway, is a prerequisite for metastasis initiation. Here, we interrogated the role of the Ewing sarcoma driver oncogene EWS-FLI1 in cytoskeletal reprogramming. We report that EWS-FLI1 strongly represses the activity of the Rho-F-actin signal pathway transcriptional effector MRTFB, affecting the expression of a large number of EWS-FLI1-anticorrelated genes including structural and regulatory cytoskeletal genes...
July 3, 2017: Oncogene
https://www.readbyqxmd.com/read/28667374/human-umbilical-cord-mesenchymal-stem-cells-protect-against-sca3-by-modulating-the-level-of-70-kd-heat-shock-protein
#6
Tan Li, Yi Liu, Linjie Yu, Jiamin Lao, Meijuan Zhang, Jiali Jin, Zhengjuan Lu, Zhuo Liu, Yun Xu
Spinocerebellar ataxia 3 (SCA3), which is a progressive neurodegenerative disease, is currently incurable. Emerging studies have reported that human umbilical cord mesenchymal stem cells (HUC-MSCs) transplantation could be a promising therapeutic strategy for cerebellar ataxias. However, few studies have evaluated the effects of HUC-MSCs on SCA3 transgenic mouse. Thus, we investigated the effects of HUC-MSCs on SCA3 mice and the underlying mechanisms in this study. SCA3 transgenic mice received systematic administration of 2 × 10(6) HUC-MSCs once per week for 12 continuous weeks...
June 30, 2017: Cellular and Molecular Neurobiology
https://www.readbyqxmd.com/read/28663783/questions-on-unusual-mimivirus-like-structures-observed-in-human-cells
#7
Elena Angela Lusi, Dan Maloney, Federico Caicci, Paolo Guarascio
Background: Mimiviruses or giant viruses that infect amoebas have the ability to retain the Gram stain, which is usually used to colour bacteria. There is some evidence suggesting that Mimiviruses can also infect human cells. Guided by these premises, we performed a routine Gram stain on a variety of human specimens to see if we could detect the same Gram positive blue granules that identify Mimiviruses in the amoebas.  Methods: We analysed 24 different human specimens (liver, brain, kidney, lymph node and ovary) using Gram stain histochemistry, electron microscopy immunogold, high resolution mass spectrometry and protein identification...
2017: F1000Research
https://www.readbyqxmd.com/read/28662383/tracking-the-missing-footprints-of-idle-ribosomes
#8
Nicholas T Ingolia
Once inactive ribosomes are accounted for, ribosome footprint profiling data and pulse-labeled proteomics provide similar, accurate measurements of protein synthesis.
June 28, 2017: Cell Systems
https://www.readbyqxmd.com/read/28637753/structural-mimicry-of-the-dengue-virus-envelope-glycoprotein-revealed-by-the-crystallographic-study-of-an-idiotype-anti-idiotype-fab-complex
#9
Yee Hwa Wong, Boon Chong Goh, She Yah Lim, En Wei Teo, Angeline P C Lim, Pete C Dedon, Brendon J Hanson, Paul A MacAry, Julien Lescar
A detailed understanding of the fine specificity of serotype-specific human antibodies is vital for the development and evaluation of new vaccines for pathogenic Flaviviruses such as Dengue virus (DENV) and Zika virus. In this study, we thoroughly characterize the structural footprint of an anti-idiotype antibody (E1) specific for a potent, fully human DENV serotype 1-specific antibody termed HM14c10, derived from a recovered patient. The crystal structure at a resolution of 2.5 Å of a complex between the Fab fragments of E1 and HM14c10 provides the first detailed molecular comparison of an anti-idiotype paratope specific for a human antibody with its analogous epitope- a discontinuous quaternary structure located at the surface of the viral particle that spans adjacent envelope (E) proteins...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28631757/resolving-mixed-mechanisms-of-protein-subdiffusion-at-the-t-cell-plasma-membrane
#10
Yonatan Golan, Eilon Sherman
The plasma membrane is a complex medium where transmembrane proteins diffuse and interact to facilitate cell function. Membrane protein mobility is affected by multiple mechanisms, including crowding, trapping, medium elasticity and structure, thus limiting our ability to distinguish them in intact cells. Here we characterize the mobility and organization of a short transmembrane protein at the plasma membrane of live T cells, using single particle tracking and photoactivated-localization microscopy. Protein mobility is highly heterogeneous, subdiffusive and ergodic-like...
June 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28631230/sequence-analysis-of-chromosome-1-revealed-different-selection-patterns-between-chinese-wild-mice-and-laboratory-strains
#11
Fuyi Xu, Shixian Hu, Tianzhu Chao, Maochun Wang, Kai Li, Yuxun Zhou, Hongyan Xu, Junhua Xiao
Both natural and artificial selection play a critical role in animals' adaptation to the environment. Detection of the signature of selection in genomic regions can provide insights for understanding the function of specific phenotypes. It is generally assumed that laboratory mice may experience intense artificial selection while wild mice more natural selection. However, the differences of selection signature in the mouse genome and underlying genes between wild and laboratory mice remain unclear. In this study, we used two mouse populations: chromosome 1 (Chr 1) substitution lines (C1SLs) derived from Chinese wild mice and mouse genome project (MGP) sequenced inbred strains and two selection detection statistics: Fst and Tajima's D to identify the signature of selection footprint on Chr 1...
June 19, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28624520/dissecting-the-chloroplast-proteome-of-chickpea-cicer-arietinum-l-provides-new-insights-into-classical-and-non-classical-functions
#12
Nilesh Vikram Lande, Pratigya Subba, Pragya Barua, Dipak Gayen, T S Keshava Prasad, Subhra Chakraborty, Niranjan Chakraborty
Chloroplast, the energy organelle unique to plant cells, is a dynamic entity which integrates an array of metabolic pathways and serves as first level for energy conversion for the entire ecological hierarchy. Increasing amount of sequence data and evolution of mass spectrometric approaches has opened up new avenues for opportune exploration of the global proteome of this organelle. In our study, we aimed at generation of a comprehensive catalogue of chloroplast proteins in a grain legume, chickpea and provided a reference proteome map...
June 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28621526/orthogonal-mass-spectrometry-based-footprinting-for-epitope-mapping-and-structural-characterization-the-il-6-receptor-upon-binding-of-protein-therapeutics
#13
Ke Sherry Li, Guodong Chen, Jingjie Mo, Richard Y-C Huang, Ekaterina G Deyanova, Brett R Beno, Steve R O'Neil, Adrienne A Tymiak, Michael L Gross
Higher-order structure (HOS) is a crucial determinant for the biological functions and quality attributes of protein therapeutics. Mass spectrometry (MS)-based protein footprinting approaches play an important role in elucidating the relationship between protein biophysical properties and structure. Here, we describe the use of a combined method including hydrogen-deuterium exchange (HDX), fast photochemical oxidation of proteins (FPOP), and site-specific carboxyl group footprinting to investigate the HOS of protein and protein complexes...
July 6, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28615380/leucine-differentially-regulates-gene-specific-translation-in-mouse-skeletal-muscle
#14
Micah J Drummond, Paul T Reidy, Lisa M Baird, Brian K Dalley, Michael T Howard
Background: Amino acids, especially leucine, are particularly effective in promoting protein synthesis. Leucine is known to increase the rate of protein synthesis in skeletal muscle through the mechanistic target of rapamycin complex 1-dependent, as well as -independent, signaling pathways. However, the overall translation program is poorly defined, and it is unknown how the activation of these pathways differentially controls the translation of specific mRNAs.Objective: Ribosome profiling and RNA sequencing were used to precisely define the translational program activated by an acute oral dose of leucine...
June 14, 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/28615373/yogurt-consumption-as-a-signature-of-a-healthy-diet-and-lifestyle
#15
REVIEW
Angelo Tremblay, Shirin Panahi
Yogurt is considered to be a nutrient-dense food that significantly contributes to the intake of several nutrients, including calcium and protein. As described in this paper, yogurt consumers have a higher nutrient intake than do nonconsumers. Yogurt consumers are also characterized by healthier dietary habits than nonconsumers, which partly explains their reduced incidence of overweight and obesity. Recent studies also suggest that yogurt consumers exhibit healthier nonnutritional behaviors, such as reduced smoking and greater participation in physical activity, than do nonconsumers...
July 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/28606577/effect-of-footprint-preparation-on-tendon-to-bone-healing-a-histologic-and-biomechanical-study-in-a-rat-rotator-cuff-repair-model
#16
Haruhiko Nakagawa, Toru Morihara, Hiroyoshi Fujiwara, Yukichi Kabuto, Tsuyoshi Sukenari, Yoshikazu Kida, Ryuhei Furukawa, Yuji Arai, Ken-Ichi Matsuda, Mitsuhiro Kawata, Masaki Tanaka, Toshikazu Kubo
PURPOSE: To compare the histologic and biomechanical effects of 3 different footprint preparations for repair of tendon-to-bone insertions and to assess the behavior of bone marrow-derived cells in each method of insertion repair. METHODS: We randomized 81 male Sprague-Dawley rats and green fluorescent protein-bone marrow chimeric rats into 3 groups. In group A, we performed rotator cuff repair after separating the supraspinatus tendon from the greater tuberosity and removing the residual tendon tissue...
June 9, 2017: Arthroscopy: the Journal of Arthroscopic & related Surgery
https://www.readbyqxmd.com/read/28595938/bifidobacteria-derived-lipoproteins-inhibit-infection-with-coxsackievirus-b4-in-vitro
#17
Khalil Antoine El Kfoury, Marie-Bénédicte Romond, Angelo Scuotto, Enagnon Kazali Alidjinou, Fouad Dabboussi, Monzer Hamze, Ilka Engelmann, Famara Sane, Didier Hober
The aim of the present study was to investigate the potential of bifidobacteria in protecting cells from coxsackievirus B4 (CV-B4) infection. Bifidobacterial screening identified two of five strains that protected human epithelial type 2 (HEp-2) cell viability when bifidobacteria were incubated with viral particles prior to inoculation. In contrast, no effect was shown by incubating HEp-2 cells with bifidobacteria prior to CV-B4 inoculation. Cell wall lipoprotein aggregates (LpAs) secreted by the selected strains were assayed for their antiviral activity...
June 5, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/28582469/dynamic-metabolic-modeling-of-heterotrophic-and-mixotrophic-microalgal-growth-on-fermentative-wastes
#18
Caroline Baroukh, Violette Turon, Olivier Bernard
Microalgae are promising microorganisms for the production of numerous molecules of interest, such as pigments, proteins or triglycerides that can be turned into biofuels. Heterotrophic or mixotrophic growth on fermentative wastes represents an interesting approach to achieving higher biomass concentrations, while reducing cost and improving the environmental footprint. Fermentative wastes generally consist of a blend of diverse molecules and it is thus crucial to understand microalgal metabolism in such conditions, where switching between substrates might occur...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28578850/time-resolved-proteomics-extends-ribosome-profiling-based-measurements-of-protein-synthesis-dynamics
#19
Tzu-Yu Liu, Hector H Huang, Diamond Wheeler, Yichen Xu, James A Wells, Yun S Song, Arun P Wiita
Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics. We focus on multiple myeloma cells exposed to bortezomib, a first-line chemotherapy and proteasome inhibitor. In the absence of drug effects, we found that direct measurement of protein synthesis by pSILAC correlated well with indirect measurement of synthesis from ribosome footprint density...
June 28, 2017: Cell Systems
https://www.readbyqxmd.com/read/28558972/structure-based-identification-of-inhibitors-targeting-obstruction-of-the-hivgp41-n-heptad-repeat-trimer
#20
T Dwight McGee, Hyun Ah Yi, William J Allen, Amy Jacobs, Robert C Rizzo
The viral protein HIVgp41 is an attractive and validated drug target that proceeds through a sequence of conformational changes crucial for membrane fusion, which facilitates viral entry. Prior work has identified inhibitors that interfere with the formation of a required six-helix bundle, composed of trimeric C-heptad (CHR) and N-heptad (NHR) repeat elements, through blocking association of an outer CHR helix or obstructing formation of the inner NHR trimer itself. In this work, we employed similarity-based scoring to identify and experimentally characterize 113 compounds, related to 2 small-molecule inhibitors recently reported by Allen et al...
July 15, 2017: Bioorganic & Medicinal Chemistry Letters
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