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Journal of Proteome Research

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https://www.readbyqxmd.com/read/29350038/efficient-mass-spectral-analysis-of-active-transporters-overexpressed-in-escherichia-coli
#1
Mamiyo Kawakami, Narinobu Juge, Yuri Kato, Hiroshi Omote, Yoshinori Moriyama, Takaaki Miyaji
Structural analysis of purified active membrane proteins can be performed by mass spectrometry (MS). However, no large-scale expression systems for active eukaryotic membrane proteins are available. Moreover, because membrane proteins cannot easily be digested by trypsin and ionized, they are difficult to analyze by MS. Here, we developed a method for mass spectral analysis of eukaryotic membrane proteins combined to an overexpression system in Escherichia coli. Vesicular glutamate transporter 2 (VGLUT2/SLC17A6) with a soluble α-helical protein and histidine tag on the N- and C-terminus, respectively, was overexpressed in E...
January 19, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29343059/top-down-characterization-of-heavily-modified-histones-using-193-nm-ultraviolet-photodissociation-uvpd-mass-spectrometry
#2
Sylvester M Greer, Jennifer S Brodbelt
The characterization of protein post-translational modifications (PTMs) remains a significant challenge for traditional bottom-up proteomics methods owing to the lability of PTMs and the difficulty of mapping combinatorial patterns of PTMs based on analysis of small peptides. These shortcomings have accelerated interest in top-down MS/MS methods which focus on analysis of intact proteins. Mapping all protein PTMs simultaneously requires the ability to obtain extensive sequence coverage to allow confident localization of the modifications...
January 18, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29338241/characterization-of-macrophage-endogenous-s-nitrosoproteome-using-a-cysteine-specific-phosphonate-adaptable-tag-in-combination-with-tio2-chromatography
#3
Maria Ibañez-Vea, Honggang Huang, Xabier Martinez de Morentin, Estela Perez, Maria Gato, Miren Zuazo, Hugo Arasanz, Joaquin Fernandez-Irigoyen, Enrique Santamaría, Gonzalo Fernandez-Hinojal, Martin R Larsen, David Escors, Grazyna Kochan
Protein S-nitrosylation is a cysteine post-translational modification mediated by nitric oxide. An increasing number of studies highlight S-nitrosylation as an important regulator of signaling involved in numerous cellular processes. Despite of the significant progress in the development of redox proteomic methods, identification and quantification of endogeneous S-nitrosylation using high-throughput mass spectrometry-based methods is a technical challenge as this modification is highly labile. To overcome this drawback most methods induce S-nitrosylation chemically in proteins using nitrosylating compounds before analysis, with the risk of introducing non-physiological S-nitrosylation...
January 17, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29336158/chromosome-gene-orientations-inversion-networks-goins-of-plasmodium-proteome
#4
Viviana F Quevedo-Tumailli, Bernabe Ortega-Tenezaca, Humbert Gonzalez-Diaz
The spatial distribution of genes in chromosomes seems not to be random. For instance, only 10% of genes are transcribed from bidirectional promoters in humans and many more are organised in larger clusters. This raises intriguing questions asked by different authors before. We would like to add a few more questions in this context, related to gene orientation inversions. Does gene orientation (inversion) follow a random pattern? Is it relevant to biological activity somehow? In this paper, we define a new kind of network coined as the Gene Orientation Inversion Network (GOIN)...
January 16, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29332401/proteomic-profiling-of-leishmania-donovani-promastigote-subcellular-organelles
#5
Armando Jardim, Darryl B Hardie, Jan Boitz, Christoph H Borchers
To facilitate a greater understanding of the biological processes in the medically important Leishmania donovani parasite, a combination of differential and density-gradient ultracentrifugation techniques were used to achieve a comprehensive subcellular fractionation of the promastigote stage. An in-depth label-free proteomic LC-MS/MS analysis of the density gradients resulted in the identification of ~50% of the Leishmania proteome (3883 proteins detected), which included ~645 integral membrane proteins and 1737 uncharacterized proteins...
January 15, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29332387/proteome-wide-characterization-of-phosphorylation-induced-conformational-changes-in-breast-cancer
#6
He Meng, Michael C Fitzgerald
Because of the close link between protein function and protein folding stability, knowledge about phosphorylation-induced protein folding stability changes can lead to a better understanding of the functional effects of protein phosphorylation. Here, the Stability of Proteins from Rates of OXidation (SPROX) and Limited Proteolysis (LiP) techniques are used to compare the conformational properties of proteins in two MCF-7 cell lysates, including one that was and one that was not dephosphorylated with alkaline phosphatase...
January 15, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29322779/mining-the-secretome-of-c2c12-muscle-cells-data-dependent-experimental-approach-to-analyze-protein-secretion-using-label-free-quantification-and-peptide-based-analysis
#7
Leonie Grube, Rafael Dellen, Fabian Kruse, Holger Schwender, Kai Stuehler, Gereon Poschmann
Secretome analysis faces several challenges, including detection of low abundant proteins and the discrimination of bona fide secreted proteins from false-positive identifications stemming from cell leakage or serum. Here, we developed a two-step secretomics approach and applied it to the analysis of secreted proteins of C2C12 skeletal muscle cells since the skeletal muscle has been identified as an important endocrine organ secreting myokines as signaling molecules. First, we compared culture supernatants with corresponding cell lysates by mass spectrometry-based proteomics and label-free quantification...
January 11, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29302971/metabonomics-approach-to-comparing-the-anti-stress-effects-of-four-panax-ginseng-components-in-rats
#8
Jingcheng Wang, Yuanlong Hou, Zhiying Jia, Xie Xie, Jiajian Liu, Yani Kang, Xin Wang, Xiaoyan Wang, Wei Jia
Different components of P. ginseng have different properties and medicinal effects. Metabonomics was a perspective approach to analyze global endogenous metabolites response to physiological and pathological processe. In this study, untargeted -metabonomics method using GC/TOFMS combined with multivariate statistical techniques was applied to compare entire metabolite differences and the anti-stress variations among four components of P. ginseng, total ginsenosides (TG), panaxadiol (PD), panaxatriol (PT) and ginseng polysaccharide (PS), in Sprague Dawley rats...
January 5, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29301397/haloferax-volcanii-proteome-response-to-deletion-of-a-rhomboid-protease-gene
#9
Mariana I Costa, Micaela Cerletti, Roberto A Paggi, Christian Trötschel, Rosana De Castro, Ansgar Poetsch, Maria I Gimenez
Rhomboids are conserved intramembrane serine proteases involved in cell signaling processes. Their role in prokaryotes is scarcely known and remains to be investigated in Archaea. We previously constructed a rhomboid homolog deletion mutant (ΔrhoII) in Haloferax volcanii, which showed reduced motility, increased novobiocin sensitivity and an N- glycosylation defect. To address the impact of rhoII deletion on H. volcanii physiology, the proteomes of mutant and parental strains were compared by shotgun proteomics...
January 5, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29300489/itraq-based-proteomic-analysis-reveals-recovery-of-impaired-mitochondrial-function-in-ischemic-myocardium-by-shenmai-formula
#10
Yi Wang, Yu Zhao, Wei Jiang, Xiaoping Zhao, Guanwei Fan, Han Zhang, Peiqiang Shen, Jiangmin He, Xiaohui Fan
Shenmai formula (SM) is a traditional medicinal remedy for treating cardiovascular diseases in China since 800 years ago, however its mechanism of action remains unclear. To explore the mechanism underlying cardioprotective effects of SM, iTRAQ-based proteomic approach was applied to analyze protein of myocardium in rats with myocardial ischemic injury. Upon treatment with SM and its two major components Red ginseng (RG) and Radix Ophiopogonis (OP), 101 differentially expressed proteins were filtered from a total of 711 detected and annotated proteins...
January 4, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29299929/proteome-of-bovine-mitochondria-and-rod-outer-segment-disks-commonalities-and-differences
#11
Maurizio Bruschi, Andrea Petretto, Federico Caicci, Martina Bartolucci, Daniela Calzia, Laura Santucci, Lucia Manni, Luca A Ramenghi, Gian Marco Ghiggeri, Carlo E Traverso, Giovanni Candiano, Isabella Panfoli
The retinal rod outer segment (OS) is a stack of disks surrounded by the plasma membrane, housing proteins related to phototransduction, as well as mitochondrial proteins involved in oxidative phosphorylation (OxPhos). This prompted us to compare the proteome of bovine OS disks and mitochondria, to assess the significant top gene signatures of each sample. The two proteomes, obtained by LTQ-Orbitrap Velos mass spectrometry, were compared by statistical analyses. 4139 proteins were identified, 2045 of which overlapping in the two sets...
January 4, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29285938/novel-kunitz-like-peptides-discovered-in-the-zoanthid-palythoa-caribaeorum-through-transcriptome-sequencing
#12
Qiwen Liao, Shengnan Li, Shirley Weng In Siu, Binrui Yang, Chen Huang, Judy Yuet-Wa Chan, Jean-Étienne Morlighem, Clarence Tsun Ting Wong, Gandhi Radis-Baptista, Simon Ming-Yuen Lee
Palythoa caribaeorum (class Anthozoa) is a zoanthid that together jellyfishes, hydra, and sea anemones, which are venomous and predatory, belongs to the Phyllum Cnidaria. The distinguished feature in these marine animals is the cnidocytes in the body tissues, responsible for toxin production and injection that are used majorly for prey capture and defense. With exception for other anthozoans, the toxin cocktails of zoanthids have been scarcely studied and are poorly known. Here, based on the analysis of P. caribaeorum transcriptome, numerous predicted venom-featured polypeptides were identified, including allergens, neurotoxins, membrane-active and Kunitz-like peptides (PcKuz)...
December 29, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29251506/scanning-quadrupole-data-independent-acquisition-part-b-application-to-the-analysis-of-the-calcineurin-interacting-proteins-during-treatment-of-aspergillus-fumigatus-with-azole-and-echinocandin-antifungal-drugs
#13
Praveen R Juvvadi, M Arthur Moseley, Christopher J Hughes, Erik J Soderblom, Sarah Lennon, Simon R Perkins, J Will Thompson, Scott J Geromanos, Jason Wildgoose, Keith Richardson, James I Langridge, Johannes P C Vissers, William J Steinbach
Calcineurin is a critical cell-signaling protein that orchestrates growth, stress response, virulence, and antifungal drug resistance in several fungal pathogens. Blocking calcineurin signaling increases the efficacy of several currently available antifungals and suppresses drug resistance. We demonstrate the application of a novel scanning quadrupole DIA method for the analysis of changes in the proteins coimmunoprecipitated with calcineurin during therapeutic antifungal drug treatments of the deadly human fungal pathogen Aspergillus fumigatus...
December 29, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29249144/biosite-a-method-for-direct-detection-and-quantitation-of-site-specific-biotinylation
#14
Dae In Kim, Jevon A Cutler, Chan Hyun Na, Sina Reckel, Santosh Renuse, Anil K Madugundu, Raiha Tahir, Hana L Goldschmidt, Karen L Reddy, Richard L Huganir, Xinyan Wu, Natasha E Zachara, Oliver Hantschel, Akhilesh Pandey
Biotin-based labeling strategies are widely employed to study protein-protein interactions, subcellular proteomes and post-translational modifications, as well as, used in drug discovery. While the high affinity of streptavidin for biotin greatly facilitates the capture of biotinylated proteins, it still presents a challenge, as currently employed, for the recovery of biotinylated peptides. Here we describe a strategy designated Biotinylation Site Identification Technology (BioSITe) for the capture of biotinylated peptides for LC-MS/MS analyses...
December 28, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29281288/reverse-and-random-decoy-methods-for-false-discovery-rate-estimation-in-high-mass-accuracy-peptide-spectral-library-searches
#15
Zheng Zhang, Meghan Burke, Yuri A Mirokhin, Dmitrii V Tchekhovskoi, Sanford P Markey, Wen Yu, Raghothama Chaerkady, Sonja Hess, Stephen E Stein
Spectral library searching (SLS) is an attractive alternative to sequence database searching (SDS) for peptide identification due to its speed, sensitivity, and ability to include any selected mass spectra. While decoy methods for SLS have been developed for low mass accuracy peptide spectral libraries, it is not clear that they are optimal or directly applicable to high mass accuracy spectra. Therefore, in this paper we report the development and validation of methods for high mass accuracy decoy libraries...
December 27, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29261316/omics-based-platform-for-studying-chemical-toxicity-using-stem-cells
#16
Yan Han, Jinghua Zhao, Ruili Huang, Menghang Xia, Daojing Wang
The new strategy for chemical toxicity testing and modeling is to use in vitro human cell-based assays in conjunction with quantitative high-throughput screening (qHTS) technology, to identify molecular mechanisms and predict in vivo responses. Stem cells are more physiologically relevant than immortalized cell lines because of their unique proliferation and differentiation potentials. We established a robust two stem cells-two lineages assay system, encompassing human mesenchymal stem cells (hMSCs) along osteogenesis and human induced pluripotent stem cells (hiPSCs) along hepatogenesis...
December 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29260567/stoichiometry-absolute-abundance-and-localization-of-proteins-in-the-bacillus-cereus-spore-coat-insoluble-fraction-determined-using-a-qconcat-approach
#17
Sacha K Stelder, Celia Benito de Moya, Huub C J Hoefsloot, Leo J de Koning, Stanley Brul, Chris G de Koster
Spores of Bacillus cereus pose a threat to food safety due to their high resistance to the heat or acid treatments commonly used to make food microbiologically safe. As spores may survive these treatments and later resume growth either on foodstuffs or, after ingestion, upon entering the gut they are capable of producing toxins which cause either vomiting or diarrhoea. The outer layers of the spore consist primarily of proteins which may serve as potential biomarkers for detection. The major morphogenetic protein CotE is important for correct assembly and attachment of the outermost layer, the exosporium and by extension retention of many proteins...
December 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29250956/an-integrated-analysis-of-protein-abundance-transcript-level-and-tissue-diversity-to-reveal-developmental-regulation-of-maize
#18
Haitao Jia, Wei Sun, Manfei Li, Zuxin Zhang
The differentiation and subsequent development of plant tissues or organs are tightly regulated at multiple levels, including the transcriptional, posttranscriptional, translational, and posttranslational levels. Transcriptomes define many of the tissue-specific gene expression patterns in maize, and some key genes and their regulatory networks have been established at the transcriptional level. In this study, the sequential window acquisition of all theoretical spectra-mass spectrometry technique was employed as a quantitative proteome assay of four representative maize tissues, and a set of high confidence proteins were identified...
December 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29249155/exploring-ecd-on-a-benchtop-q-exactive-orbitrap-mass-spectrometer
#19
Kyle L Fort, Christian N Cramer, Valery G Voinov, Yury V Vasilev, Nathan I Lopez, Joseph S Beckman, Albert J R Heck
As the application of mass spectrometry intensifies in scope and diversity, the need for advanced instrumentation addressing a wide variety of analytical needs also increases. To this end, many modern, top-end mass spectrometers are designed or modified to include a wider range of fragmentation technologies, e.g. ECD, ETD, EThcD, and UVPD. Still, the majority of instrument platforms are limited to more conventional methods, such as CID and HCD. While these latter methods have performed well, the less conventional fragmentation methods have been shown to lead to increased information in many applications including middle-down proteomics, top-down proteomics, glycoproteomics and disulfide bond mapping...
December 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29235871/increased-levels-of-circulating-fatty-acids-are-associated-with-protective-effects-against-future-cardiovascular-events-in-non-diabetics
#20
Muhammad Anas Kamleh, Olga McLeod, Antonio Checa, Damiano Baldassarre, Fabrizio Veglia, Karl Gertow, Steve E Humphries, Rainer Rauramaa, Ulf deFaire, Andries J Smit, Philippe Giral, Sudhir Kurl, Elmo Mannarino, Elena Tremoli, Angela Silveira, John Orvik, Anders Hamsten, Craig E Wheelock
Cardiovascular disease (CVD) is a major cause of morbidity and mortality worldwide, particularly in individuals with diabetes. The current study objective was to determine the circulating metabolite profiles associated with the risk of future cardiovascular events, with emphasis on diabetes status. Non-targeted metabolomics analysis was performed by LC-HRMS in combination with targeted quantification of eicosanoids and endocannabinoids. Plasma from 375 individuals from the IMPROVE pan-European cohort were included in a case-control study design...
December 13, 2017: Journal of Proteome Research
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