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Protein footprinting

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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
#1
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
#2
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
#3
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
#4
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
#5
Ke Sherry Li, Guodong Chen, Jingjie Mo, Richard Y-C Huang, Ekaterina G Deyanova, Brett R Beno, Steve 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...
June 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28615380/leucine-differentially-regulates-gene-specific-translation-in-mouse-skeletal-muscle
#6
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
#7
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...
June 14, 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
#8
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
#9
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
#10
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
#11
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...
May 26, 2017: Cell Systems
https://www.readbyqxmd.com/read/28558972/structure-based-identification-of-inhibitors-targeting-obstruction-of-the-hivgp41-n-heptad-repeat-trimer
#12
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
https://www.readbyqxmd.com/read/28527796/genetic-parameters-of-mid-infrared-methane-predictions-and-their-relationships-with-milk-production-traits-in-holstein-cattle
#13
P B Kandel, M-L Vanrobays, A Vanlierde, F Dehareng, E Froidmont, N Gengler, H Soyeurt
Many countries have pledged to reduce greenhouse gases. In this context, the dairy sector is one of the identified sectors to adapt production circumstances to address socio-environmental constraints due to its large carbon footprint related to CH4 emission. This study aimed mainly to estimate (1) the genetic parameters of 2 milk mid-infrared-based CH4 proxies [predicted daily CH4 emission (PME, g/d), and log-transformed predicted CH4 intensity (LMI)] and (2) their genetic correlations with milk production traits [milk (MY), fat (FY), and protein (PY) yields] from first- and second-parity Holstein cows...
July 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28526559/a-single-nucleotide-polymorphism-of-cyclin-dependent-kinase-inhibitor-1b-p27-kip1-associated-with-human-vein-graft-failure-affects-growth-of-human-venous-adventitial-cells-but-not-smooth-muscle-cells
#14
Richard D Kenagy, Shinsuke Kikuchi, Lihua Chen, Errol S Wijelath, Andrew B Stergachis, John Stamatoyannopoulos, Gale L Tang, Alexander W Clowes, Michael Sobel
BACKGROUND: Cyclin-dependent kinase inhibitor 1B (p27(Kip1)) is a cell-cycle inhibitor whose -838C>A single nucleotide polymorphism (rs36228499; hereafter called p27 SNP) has been associated with the clinical failure of peripheral vein grafts, but the functional effects of this SNP have not been demonstrated. METHODS: Human saphenous vein adventitial cells and intimal/medial smooth muscle cells (SMCs) were derived from explants obtained at the time of lower extremity bypass operations...
May 16, 2017: Journal of Vascular Surgery
https://www.readbyqxmd.com/read/28525600/a-novel-double-kink-turn-module-in-euryarchaeal-rnase-p-rnas
#15
Lien B Lai, Akiko Tanimoto, Stella M Lai, Wen-Yi Chen, Ila A Marathe, Eric Westhof, Vicki H Wysocki, Venkat Gopalan
RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn (K-turn), an RNA structural element that causes axial bending. However, the number and location of K-turns in archaeal RNase P RNAs (RPRs) are unclear. As part of an integrated approach, we used native mass spectrometry to assess the number of L7Ae copies that bound the RPR and site-specific hydroxyl radical-mediated footprinting to localize the K-turns...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28525347/sustainable-farming-of-the-mealworm-tenebrio-molitor-for-the-production-of-food-and-feed
#16
Thorben Grau, Andreas Vilcinskas, Gerrit Joop
The farming of edible insects is an alternative strategy for the production of protein-rich food and feed with a low ecological footprint. The industrial production of insect-derived protein is more cost-effective and energy-efficient than livestock farming or aquaculture. The mealworm Tenebrio molitor is economically among the most important species used for the large-scale conversion of plant biomass into protein. Here, we review the mass rearing of this species and its conversion into food and feed, focusing on challenges such as the contamination of food/feed products with bacteria from the insect gut and the risk of rapidly spreading pathogens and parasites...
May 17, 2017: Zeitschrift Für Naturforschung. C, A Journal of Biosciences
https://www.readbyqxmd.com/read/28516119/affinity-pulldown-of-biotinylated-rna-for-detection-of-protein-rna-complexes
#17
Amaresh C Panda, Jennifer L Martindale, Myriam Gorospe
RNA-binding proteins (RBPs) have recently emerged as crucial players in the regulation of gene expression. The interactions of RBPs with target mRNAs control the levels of gene products by altering different regulatory steps, including pre-mRNA splicing and maturation, nuclear mRNA export, and mRNA stability and translation (Glisovic et al., 2008). There are several methodologies available today to identify RNAs bound to specific RBPs; some detect only recombinant molecules in vitro, others detect recombinant and endogenous molecules, while others detect only endogenous molecules...
December 20, 2016: Bio-protocol
https://www.readbyqxmd.com/read/28514447/global-translational-reprogramming-is-a-fundamental-layer-of-immune-regulation-in-plants
#18
Guoyong Xu, George H Greene, Heejin Yoo, Lijing Liu, Jorge Marqués, Jonathan Motley, Xinnian Dong
In the absence of specialized immune cells, the need for plants to reprogram transcription to transition from growth-related activities to defence is well understood. However, little is known about translational changes that occur during immune induction. Using ribosome footprinting, here we perform global translatome profiling on Arabidopsis exposed to the microbe-associated molecular pattern elf18. We find that during this pattern-triggered immunity, translation is tightly regulated and poorly correlated with transcription...
May 25, 2017: Nature
https://www.readbyqxmd.com/read/28512867/the-structural-basis-for-inhibition-of-the-classical-and-lectin-complement-pathways-by-s-aureus-extracellular-adherence-protein
#19
Jordan L Woehl, Kasra X Ramyar, Benjamin B Katz, John K Walker, Brian V Geisbrecht
The extracellular adherence protein (Eap) plays a crucial role in pathogenesis and survival of Staphylococcus aureus by inhibiting the classical and lectin pathways of complement. We have previously shown that Eap binds with nanomolar affinity to complement C4b and disrupts the initial interaction between C4b and C2, thereby inhibiting formation of the classical and lectin pathway C3 pro-convertase. Although an underlying mechanism has been identified, the structural basis for Eap binding to C4b is poorly understood...
May 16, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28512450/host-plant-compatibility-shapes-the-proteogenome-of-frankia-coriariae
#20
Amir Ktari, Abdellatif Gueddou, Imen Nouioui, Guylaine Miotello, Indrani Sarkar, Faten Ghodhbane-Gtari, Arnab Sen, Jean Armengaud, Maher Gtari
Molecular signaling networks in the actinorhizal rhizosphere select host-compatible Frankia strains, trigger the infection process and eventually the genesis of nitrogen-fixing nodules. The molecular triggers involved remain difficult to ascertain. Root exudates (RE) are highly dynamic substrates that play key roles in establishing the rhizosphere microbiome. RE are known to induce the secretion by rhizobia of Nod factors, polysaccharides, and other proteins in the case of legume symbiosis. Next-generation proteomic approach was here used to decipher the key bacterial signals matching the first-step recognition of host plant stimuli upon treatment of Frankia coriariae strain BMG5...
2017: Frontiers in Microbiology
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