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https://www.readbyqxmd.com/read/28529698/seven-perspectives-on-gpcr-h-d-exchange-proteomics-methods
#1
Xi Zhang
Recent research shows surging interest to visualize human G protein-coupled receptor (GPCR) dynamic structures using the bottom-up H/D-exchange (HDX) proteomics technology. This opinion article clarifies critical technical nuances and logical thinking behind the GPCR HDX proteomics method, to help scientists overcome cross-discipline pitfalls, and understand and reproduce the protocol at high quality. The 2010 89% HDX structural coverage of GPCR was achieved with both structural and analytical rigor. This article emphasizes systematically considering membrane protein structure stability and compatibility with chromatography and mass spectrometry (MS) throughout the pipeline, including the effects of metal ions, zero-detergent shock, and freeze-thaws on HDX result rigor...
2017: F1000Research
https://www.readbyqxmd.com/read/28520987/proteosign-an-end-user-online-differential-proteomics-statistical-analysis-platform
#2
Georgios Efstathiou, Andreas N Antonakis, Georgios A Pavlopoulos, Theodosios Theodosiou, Peter Divanach, David C Trudgian, Benjamin Thomas, Nikolas Papanikolaou, Michalis Aivaliotis, Oreste Acuto, Ioannis Iliopoulos
Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28501997/using-laser-capture-microdissection-to-isolate-cortical-laminae-in-nonhuman-primate-brain
#3
Brian A Corgiat, Claudius Mueller
Laser capture microdissection (LCM) is a technique that allows procurement of an enriched cell population from a heterogeneous tissue sample under direct microscopic visualization. Fundamentally, laser capture microdissection consists of three main steps: (1) visualizing the desired cell population by microscopy, (2) melting a thermolabile polymer onto the desired cell populations using infrared laser energy to form a polymer-cell composite (capture method) or photovolatizing a region of tissue using ultraviolet laser energy (cutting method), and (3) removing the desired cell population from the heterogeneous tissue...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28500349/quantitative-succinyl-proteome-profiling-of-camellia-sinensis-cv-anji-baicha-during-periodic-albinism
#4
Yan-Xia Xu, Chen-Jia Shen, Jian-Qiang Ma, Wei Chen, Juan Mao, Yan-Yan Zhou, Liang Chen
Lysine succinylation is a novel dynamic and evolutionarily conserved post-translational modification (PTM) that regulates various biological processes. 'Anji Baicha' is an albino tea variety that exhibits temperature-based variability of leaf colour and amino acid concentrations. However, the mechanism underlying albinism in 'Anji Baicha' has not been investigated at the level of succinylation. Here, we identify 3530 lysine succinylation sites mapped to 2132 proteins in 'Anji Baicha', representing the first extensive data on the lysine succinylome in the tea plant...
May 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28497124/parv4-prevalence-phylogeny-immunology-and-coinfection-with-hiv-hbv-and-hcv-in-a-multicentre-african-cohort
#5
Colin P Sharp, William F Gregory, Louise Hattingh, Amna Malik, Emily Adland, Samantha Daniels, Anriette van Zyl, Jonathan M Carlson, Susan Wareing, Anthony Ogwu, Roger Shapiro, Lynn Riddell, Fabian Chen, Thumbi Ndung'u, Philip J R Goulder, Paul Klenerman, Peter Simmonds, Pieter Jooste, Philippa C Matthews
Background: The seroprevalence of human parvovirus-4 (PARV4) varies considerably by region. In sub-Saharan Africa, seroprevalence is high in the general population, but little is known about the transmission routes or the prevalence of coinfection with blood-borne viruses, HBV, HCV and HIV.  Methods: To further explore the characteristics of PARV4 in this setting, with a particular focus on the prevalence and significance of coinfection, we screened a cohort of 695 individuals recruited from Durban and Kimberley (South Africa) and Gaborone (Botswana) for PARV4 IgG and DNA, as well as documenting HIV, HBV and HCV status...
April 7, 2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28494929/investigation-of-corneal-autoantibodies-in-horses-with-immune-mediated-keratitis-immk
#6
B K Braus, I Miller, S Kummer, K J H Kleinwort, S Hirmer, S M Hauck, R J McMullen, M Kerschbaumer, C A Deeg
Immune mediated keratitis (IMMK) is primarily a non-ulcerative keratitis in horses causing intermittent ocular pain, eventually resulting in visual impairment. Affected horses typically respond to immunomodulatory treatment. However, the underlying cause of the disease remains enigmatic. The current study was undertaken to investigate the presence of autoantibodies in horses with immune mediated keratitis. Using 28 horses with IMMK and 27 healthy controls screening for serum autoantibodies against the corneal proteome using indirect immunofluorescence, one-dimensional (1DE) and two-dimensional electrophoresis (2DE) with subsequent western blot analysis was performed followed by mass spectrometric identification of bands or spots of interest...
May 2017: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/28493612/identification-of-extracellular-matrix-protein-1-as-a-potential-plasma-biomarker-of-escc-by-proteomic-analysis-using-itraq-and-2d-lc-ms-ms
#7
Xianghu Wang, Yuan Peng, Ming Xie, Zhikui Gao, Lihong Yin, Yuepu Pu, Ran Liu
PURPOSE: This study was aimed to conduct a proteomics profiling analysis on plasma obtained from ESCC patients with the goal of identifying appropriate plasma protein biomarkers in the progression of ESCC. EXPERIMENTAL DESIGN: Plasma from 28 ESCC patients and 28 Healthy controls (HC) were analyzed by iTRAQ combined with 2D-LC-MS/MS. ProteinPilot software was used to identify the differentially expressed plasma proteins in ESCC compared to HC. Western blot was performed to verify the expression of selected proteins in 37 independent ESCC patients and 37 HC...
May 11, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28481733/tissue-proteome-analysis-of-different-grades-of-human-gliomas-provides-major-cues-for-glioma-pathogenesis
#8
Kishore Gollapalli, Saicharan Ghantasala, Apurva Atak, Srikanth Rapole, Aliasgar Moiyadi, Sridhar Epari, Sanjeeva Srivastava
Gliomas are heterogeneous and most commonly occurring brain tumors. Blood-brain barrier restricts the entry of brain tumor proteins into blood stream thus limiting the usage of serum or plasma for proteomic analysis. Our study aimed at understanding the molecular basis of aggressiveness of various grades of brain tumors using isobaric tagging for relative and absolute quantification (iTRAQ) based mass spectrometry. Tissue proteomic analysis of various grades of gliomas was performed using four-plex iTRAQ. We labeled five sets (each set consists of control, grade-II, III, and IV tumor samples) of individual glioma patients using iTRAQ reagents...
May 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28479398/isolation-and-characterization-of-conohyal-p1-a-hyaluronidase-from-the-injected-venom-of-conus-purpurascens
#9
Carolina Mӧller, Evan Clark, Helena Safavi-Hemani, Anthony DeCaprio, Frank Marí
Hyaluronidases are ubiquitous enzymes commonly found in venom and their main function is to degrade hyaluran, which is the major glycosaminoglycan of the extracellular matrix in animal tissues. Here we describe the purification and characterization of a 60kDa hyaluronidase found in the injected venom from Conus purpurascens, Conohyal-P1. Using a combined strategy based on transcriptomic and proteomic analysis, we determined the Conohyal-P1 sequence. Conohyal-P1 has conserved consensus catalytic and positioning domain residues characteristic of hyaluronidases and a C-terminus EGF-like domain...
May 4, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28472330/dynomics-dynamics-of-structural-proteome-and-beyond
#10
Hongchun Li, Yuan-Yu Chang, Ji Young Lee, Ivet Bahar, Lee-Wei Yang
DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core of the portal is a newly developed server, ENM 1.0, which permits users to efficiently generate information on the collective dynamics of any structure in PDB format, user-uploaded or database-retrieved...
May 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28471460/using-hyperlopit-to-perform-high-resolution-mapping-of-the-spatial-proteome
#11
Claire M Mulvey, Lisa M Breckels, Aikaterini Geladaki, Nina Kočevar Britovšek, Daniel J H Nightingale, Andy Christoforou, Mohamed Elzek, Michael J Deery, Laurent Gatto, Kathryn S Lilley
The organization of eukaryotic cells into distinct subcompartments is vital for all functional processes, and aberrant protein localization is a hallmark of many diseases. Microscopy methods, although powerful, are usually low-throughput and dependent on the availability of fluorescent fusion proteins or highly specific and sensitive antibodies. One method that provides a global picture of the cell is localization of organelle proteins by isotope tagging (LOPIT), which combines biochemical cell fractionation using density gradient ultracentrifugation with multiplexed quantitative proteomics mass spectrometry, allowing simultaneous determination of the steady-state distribution of hundreds of proteins within organelles...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28456751/methods-tools-and-current-perspectives-in-proteogenomics
#12
Kelly V Ruggles, Karsten Krug, Xiaojing Wang, Karl R Clauser, Jing Wang, Samuel H Payne, David Fenyö, Bing Zhang, D R Mani
With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics, i.e., the integrative analysis of proteomic and genomic data, has emerged as a new research field. Early efforts in the field were focused on improving protein identification using sample-specific genomic and transcriptomic sequencing data. More recently, integrative analysis of quantitative measurements from genomic and proteomic studies have identified novel insights into gene expression regulation, cell signaling, and disease...
April 29, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28440506/association-between-high-mobility-group-box%C3%A2-1-protein-expression-and-cell-death-in-acute-pancreatitis
#13
Enjun Gao, Yanfeng Jiang, Zhituo Li, Dongbo Xue, Weihui Zhang
The present study used caerulein stimulation of AR42J rat pancreatic cells as an in vitro acute pancreatitis (AP) model to investigate proteins differentially expressed in apoptosis and necrosis. AR42J cells were stimulated with 10‑8mol/l caerulein and incubated for 24 h. Apoptosis and necrosis were detected using flow cytometry. The sorted Annexin V‑positive cells (apoptotic) and the Annexin V/propidium iodide double‑positive cells (necrotic) were analysed using proteomics. Results showed that numerous proteins were differentially expressed in these 2 groups...
June 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28438675/integrating-cell-biology-and-proteomic-approaches-in-plants
#14
Tomáš Takáč, Olga Šamajová, Jozef Šamaj
Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science...
April 21, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28391044/experimental-design-and-data-analysis-in-label-free-quantitative-lc-ms-proteomics-a-tutorial-with-msqrob
#15
Ludger J E Goeminne, Kris Gevaert, Lieven Clement
Label-free shotgun proteomics is routinely used to assess proteomes. However, extracting relevant information from the massive amounts of generated data remains difficult. This tutorial provides a strong foundation on analysis of quantitative proteomics data. We provide key statistical concepts that help researchers to design proteomics experiments and we showcase how to analyze quantitative proteomics data using our recent free and open-source R package MSqRob, which was developed to implement the peptide-level robust ridge regression method for relative protein quantification described by Goeminne et al...
April 5, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28386060/single-molecule-translation-imaging-visualizes-the-dynamics-of-local-%C3%AE-actin-synthesis-in-retinal-axons
#16
Florian Ströhl, Julie Qiaojin Lin, Romain F Laine, Hovy Ho-Wai Wong, Vasja Urbančič, Roberta Cagnetta, Christine E Holt, Clemens F Kaminski
Local mRNA translation occurs in growing axons enabling precise control of the proteome in response to signals. To measure quantitatively the spatiotemporal dynamics of protein synthesis in growth cones, we further developed a technique for single molecule translation imaging (SMTI). We report that Netrin-1 triggers a burst of β-actin synthesis at multiple non-repetitive sites, particularly in the periphery. The response is remarkably rapid starting within 20 seconds of cue application.
April 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28379287/viptree-the-viral-proteomic-tree-server
#17
Yosuke Nishimura, Takashi Yoshida, Megumi Kuronishi, Hideya Uehara, Hiroyuki Ogata, Susumu Goto
Summary: ViPTree is a web server provided through GenomeNet to generate viral proteomic trees for classification of viruses based on genome-wide similarities. Users can upload viral genomes sequenced either by genomics or metagenomics. ViPTree generates proteomic trees for the uploaded genomes together with flexibly selected reference viral genomes. ViPTree also serves as a platform to visually investigate genomic alignments and automatically annotated gene functions for the uploaded viral genomes, thus providing virus researchers the first choice for classifying and understanding newly sequenced viral genomes...
March 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28374590/binding-site-characterization-of-am1336-a-novel-covalent-inverse-agonist-at-human-cannabinoid-2-receptor-using-mass-spectrometric-analysis
#18
Srikrishnan Mallipeddi, Simion Kreimer, Nikolai Zvonok, V Kiran Vemuri, Barry L Karger, Alexander R Ivanov, Alexandros Makriyannis
Cannabinoid 2 receptor (CB2R), a Class A G-protein coupled receptor (GPCR), is a promising drug target in a wide array of pathological conditions. Rational drug design has been hindered due to our poor understanding of the structural features involved in ligand binding. Binding of a high-affinity biarylpyrazole inverse agonist AM1336 to a library of the human CB2 receptor (hCB2R) cysteine-substituted mutants provided indirect evidence that two cysteines in transmembrane helix-7 (H7) were critical for the covalent attachment...
April 4, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28370546/cancer-associated-stimuli-driven-turn-on-theranostics-for-multimodality-imaging-and-therapy
#19
REVIEW
Xingshu Li, Jihoon Kim, Juyoung Yoon, Xiaoyuan Chen
Advances in bioinformatics, genomics, proteomics, and metabolomics have facilitated the development of novel anticancer agents that have decreased side effects and increased safety. Theranostics, systems that have combined therapeutic effects and diagnostic capabilities, have garnered increasing attention recently because of their potential use in personalized medicine, including cancer-targeting treatments for patients. One interesting approach to achieving this potential involves the development of cancer-associated, stimuli-driven, turn on theranostics...
March 29, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28368001/genetic-and-proteomic-characterization-of-bile-salt-export-pump-bsep-in-snake-liver
#20
Xinle Tan, Fei Gao, Hexiu Su, Yajun Gong, Jie Zhang, Mitchell A Sullivan, Jiachun Chen
Snake gallbladder, a traditional Chinese medicine, has been believed in various Asian countries to improve visual acuity and alleviate rheumatism. Bile acids, a major component of the gallbladder, are toxic to the liver and kidney in humans and animals due to its detergent effects, while also exhibiting therapeutic effects due to an increase in the gallbladder contractions of muscle strips in patients with cholesterol gallstones. Secretion of bile acids in human and mammals depends on the bile salt export pump (BSEP), a liver-specific adenosine triphosphate (ATP)-binding cassette transporter encoded by ABCB11...
April 3, 2017: Scientific Reports
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