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Proteome Science

Chunyu Hou, Yuan Li, Huiqin Liu, Mengjiao Dang, Guoxuan Qin, Ning Zhang, Ruibing Chen
Background: Protein kinase C ζ (PKCζ), an isoform of the atypical protein kinase C, is a pivotal regulator in cancer. However, the molecular and cellular mechanisms whereby PKCζ regulates tumorigenesis and metastasis are still not fully understood. In this study, proteomics and bioinformatics analyses were performed to establish a protein-protein interaction (PPI) network associated with PKCζ, laying a stepping stone to further understand the diverse biological roles of PKCζ. Methods: Protein complexes associated with PKCζ were purified by co-immunoprecipitation from breast cancer cell MDA-MB-231 and identified by LC-MS/MS...
2018: Proteome Science
Christos Spanos, Elaina M Maldonado, Ciarán P Fisher, Petchpailin Leenutaphong, Ernesto Oviedo-Orta, David Windridge, Francisco J Salguero, Alexandra Bermúdez-Fajardo, Mark E Weeks, Caroline Evans, Bernard M Corfe, Naila Rabbani, Paul J Thornalley, Michael H Miller, Huan Wang, John F Dillon, Alberto Quaglia, Anil Dhawan, Emer Fitzpatrick, J Bernadette Moore
Background: Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide. However, its molecular pathogenesis is incompletely characterized and clinical biomarkers remain scarce. The aims of these experiments were to identify and characterize liver protein alterations in an animal model of early, diet-related, liver injury and to assess novel candidate biomarkers in NAFLD patients. Methods: Liver membrane and cytosolic protein fractions from high fat fed apolipoprotein E knockout (ApoE-/- ) animals were analyzed by quantitative proteomics, utilizing isobaric tags for relative and absolute quantitation (iTRAQ) combined with nano-liquid chromatography and tandem mass spectrometry (nLC-MS/MS)...
2018: Proteome Science
Alfredo Toledo-Leyva, Julio César Villegas-Pineda, Sergio Encarnación-Guevara, Dolores Gallardo-Rincón, Patricia Talamás-Rohana
Background: Epithelial ovarian cancer is the second most lethal gynecological cancer worldwide. Ascites can be found in all clinical stages, however in advanced disease stages IIIC and IV it is more frequent and could be massive, associated with worse prognosis. Due to the above, it was our interest to understanding how the ascites of ovarian cancer patients induces the mechanisms by which the cells present in it acquire a more aggressive phenotype and to know new proteins associated to this process...
2018: Proteome Science
Pureun-Haneul Lee, Byeong-Gon Kim, Sun-Hye Lee, George D Leikauf, An-Soo Jang
Background: Acrolein (allyl Aldehyde) as one of smoke irritant exacerbates chronic airway diseases and increased in sputum of patients with asthma and chronic obstructive lung disease. But underlying mechanism remains unresolved. The aim of study was to identify protein expression in human lung microvascular endothelial cells (HMVEC-L) exposed to acrolein. Methods: A proteomic approach was used to determine the different expression of proteins at 8 h and 24 h after treatment of acrolein 30 nM and 300 nM to HMVEC-L...
2018: Proteome Science
Ho Jeong Kwon, Peter Karuso
No abstract text is available yet for this article.
2018: Proteome Science
Yeonyee Oh, Suzanne L Robertson, Jennifer Parker, David C Muddiman, Ralph A Dean
Background: Fungi are constantly exposed to nitrogen limiting environments, and thus the efficient regulation of nitrogen metabolism is essential for their survival, growth, development and pathogenicity. To understand how the rice blast pathogen Magnaporthe oryzae copes with limited nitrogen availability, a global proteome analysis under nitrogen supplemented and nitrogen starved conditions was completed. Methods: M. oryzae strain 70-15 was cultivated in liquid minimal media and transferred to media with nitrate or without a nitrogen source...
2017: Proteome Science
Junbo Xiong, Yan Sun, Qingchuan Yang, Hong Tian, Heshan Zhang, Yang Liu, Mingxin Chen
Background: Alfalfa (Medicago sativa) is the most extensively cultivated forage legume in the world, and salinity stress is the most problematic environmental factors limiting alfalfa production. To evaluate alfalfa tissue variations in response to salt stress, comparative physiological and proteomic analyses were made of salt responses in the roots and shoots of the alfalfa. Method: A two-dimensional gel electrophoresis (2-DE)-based proteomic technique was employed to identify the differentially abundant proteins (DAPs) from salt-treated alfalfa roots and shoots of the salt tolerance cultivars Zhongmu No 1 cultivar, which was subjected to a range of salt stress concentrations for 9 days...
2017: Proteome Science
Carmine Mancone, Alessio Grimaldi, Giulia Refolo, Isabella Abbate, Gabriella Rozera, Dario Benelli, Gian Maria Fimia, Vincenzo Barnaba, Marco Tripodi, Mauro Piacentini, Fabiola Ciccosanti
BACKGROUND: Changes in iron metabolism frequently accompany HIV-1 infection. However, while many clinical and in vitro studies report iron overload exacerbates the development of infection, many others have found no correlation. Therefore, the multi-faceted role of iron in HIV-1 infection remains enigmatic. METHODS: RT-qPCR targeting the LTR region, gag, Tat and Rev were performed to measure the levels of viral RNAs in response to iron overload. Spike-in SILAC proteomics comparing i) iron-treated, ii) HIV-1-infected and iii) HIV-1-infected/iron treated T lymphocytes was performed to define modifications in the host cell proteome...
2017: Proteome Science
Margaret L Wong, Jason Murphy, Edmund Harrington, Carrie M Gower, Rishi K Jain, Markus Schirle, Jason R Thomas
BACKGROUND: Identifying selective kinase inhibitors remains a major challenge. The design of bivalent inhibitors provides a rational strategy for accessing potent and selective inhibitors. While bivalent kinase inhibitors have been successfully designed, no comprehensive assessment of affinity and selectivity for a series of bivalent inhibitors has been performed. Here, we present an evaluation of the structure activity relationship for bivalent kinase inhibitors targeting ABL1. METHODS: Various SNAPtag constructs bearing different specificity ligands were expressed in vitro...
2016: Proteome Science
Michael P Gotsbacher, Sungmin Cho, Ho Jeong Kwon, Peter Karuso
BACKGROUND: Daptomycin is a recently introduced, last-resort antibiotic that displays a unique mode of action against Gram-positive bacteria that is not fully understood. Several bacterial targets have been proposed but no human binding partner is known. METHODS: In the present study we tested daptomycin in cell viability and proliferation assays against six human cell lines, describe the synthesis of biotinylated and fluorescently labeled analogues of daptomycin...
2016: Proteome Science
Kyungtae Kang, Jongmin Park, Eunha Kim
Determining small molecule-target protein interaction is essential for the chemical proteomics. One of the most important keys to explore biological system in chemical proteomics field is finding first-class molecular tools. Chemical probes can provide great spatiotemporal control to elucidate biological functions of proteins as well as for interrogating biological pathways. The invention of bioorthogonal chemistry has revolutionized the field of chemical biology by providing superior chemical tools and has been widely used for investigating the dynamics and function of biomolecules in live condition...
2016: Proteome Science
Dhiraj P Murale, Seong Cheol Hong, Md Mamunul Haque, Jun-Seok Lee
Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific proteins, including affinity chromatography, activity-based probes, affinity-based probes and photo-affinity labeling (PAL). PAL has become one of the most powerful strategies to study PPIs. Traditional photocrosslinkers are used in PAL, including benzophenone, aryl azide, and diazirine. Upon photoirradiation, these photocrosslinkers (Pls) generate highly reactive species that react with adjacent molecules, resulting in a direct covalent modification...
2016: Proteome Science
André Mateus, Tomi A Määttä, Mikhail M Savitski
In recent years, phenotypic-based screens have become increasingly popular in drug discovery. A major challenge of this approach is that it does not provide information about the mechanism of action of the hits. This has led to the development of multiple strategies for target deconvolution. Thermal proteome profiling (TPP) allows for an unbiased search of drug targets and can be applied in living cells without requiring compound labeling. TPP is based on the principle that proteins become more resistant to heat-induced unfolding when complexed with a ligand, e...
2016: Proteome Science
Lucas T Vu, Sophia M Orbach, W Keith Ray, Margaret E Cassin, Padmavathy Rajagopalan, Richard F Helm
BACKGROUND: Liver models that closely mimic the in vivo microenvironment are useful for understanding liver functions, capabilities, and intercellular communication processes. Three-dimensional (3D) liver models assembled using hepatocytes and liver sinusoidal endothelial cells (LSECs) separated by a polyelectrolyte multilayer (PEM) provide a functional system while also permitting isolation of individual cell types for proteomic analyses. METHODS: To better understand the mechanisms and processes that underlie liver model function, hepatocytes were maintained as monolayers and 3D PEM-based formats in the presence or absence of primary LSECs...
2016: Proteome Science
Saul Chemonges, Rajesh Gupta, Paul C Mills, Steven R Kopp, Pawel Sadowski
BACKGROUND: Unlike humans, there is currently no publicly available reference mass spectrometry-based circulating acellular proteome data for sheep, limiting the analysis and interpretation of a range of physiological changes and disease states. The objective of this study was to develop a robust and comprehensive method to characterise the circulating acellular proteome in ovine serum. METHODS: Serum samples from healthy sheep were subjected to shotgun proteomic analysis using nano liquid chromatography nano electrospray ionisation tandem mass spectrometry (nanoLC-nanoESI-MS/MS) on a quadrupole time-of-flight instrument (TripleTOF® 5600+, SCIEX)...
2016: Proteome Science
Emily L O'Reilly, Richard J Burchmore, Nicholas H Sparks, P David Eckersall
BACKGROUND: In poultry production intestinal health and function is paramount to achieving efficient feed utilisation and growth. Uncovering the localised molecular mechanisms that occur during the early and important periods of growth that allow birds to grow optimally is important for this species. The exposure of young chicks to used litter from older flocks, containing mixed microbial populations, is a widely utilised model in poultry research. It rarely causes mortality but effects an immunogenic stimulation sufficient enough to cause reduced and uneven growth that is reflective of a challenging growing environment...
2016: Proteome Science
Zepeng Yin, Jing Ren, Lijuan Zhou, Lina Sun, Jiewan Wang, Yulong Liu, Xingshun Song
BACKGROUND: Drought (Water deficit, WD) poses a serious threat to extensively economic losses of trees throughout the world. Chinese dwarf cherry (Cerasus humilis) is a good perennial plant for studying the physiological and sophisticated molecular network under WD. The aim of this study is to identify the effect of WD on C. humilis through physiological and global proteomics analysis and improve understanding of the WD resistance of plants. METHODS: Currently, physiological parameters were applied to investigate C...
2016: Proteome Science
Jonatan Eriksson, Simone Andersson, Roger Appelqvist, Elisabet Wieslander, Mikael Truedsson, May Bugge, Johan Malm, Magnus Dahlbäck, Bo Andersson, Thomas E Fehniger, György Marko-Varga
BACKGROUND: Data from biological samples and medical evaluations plays an essential part in clinical decision making. This data is equally important in clinical studies and it is critical to have an infrastructure that ensures that its quality is preserved throughout its entire lifetime. We are running a 5-year longitudinal clinical study, KOL-Örestad, with the objective to identify new COPD (Chronic Obstructive Pulmonary Disease) biomarkers in blood. In the study, clinical data and blood samples are collected from both private and public health-care institutions and stored at our research center in databases and biobanks, respectively...
2016: Proteome Science
Seyma Katrinli, Kamil Ozdil, Abdurrahman Sahin, Oguzhan Ozturk, Gozde Kir, Ahmet Tarik Baykal, Emel Akgun, Omer Sinan Sarac, Mehmet Sokmen, H Levent Doğanay, Gizem Dinler Doğanay
BACKGROUND: Hepatitis B virus (HBV) is a global health problem, and infected patients if left untreated may develop cirrhosis and eventually hepatocellular carcinoma. This study aims to enlighten pathways associated with HBV related liver fibrosis for delineation of potential new therapeutic targets and biomarkers. METHODS: Tissue samples from 47 HBV infected patients with different fibrotic stages (F1 to F6) were enrolled for 2D-DIGE proteomic screening. Differentially expressed proteins were identified by mass spectrometry and verified by western blotting...
2016: Proteome Science
Kazuko Morino, Mayumi Kimizu, Masayuki Fujiwara
BACKGROUND: Reactive oxygen species (ROS) production is an early event in the immune response of plants. ROS production affects the redox-based modification of cysteine residues in redox proteins, which contribute to protein functions such as enzymatic activity, protein-protein interactions, oligomerization, and intracellular localization. Thus, the sensitivity of cysteine residues to changes in the cellular redox status is critical to the immune response of plants. METHODS: We used disulfide proteomics to identify immune response-related redox proteins...
2016: Proteome Science
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