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Structural Proteomics

Xiaoying Lü, Heng Zhang, Yan Huang, Yiwen Zhang
The aim of this article is to apply proteomics in the comparison of the molecular mechanisms of PC12 cell adhesion and growth mediated by the adsorbed serum proteins on the surfaces of chitosan and collagen/chitosan films. First, the chitosan and the collagen/chitosan films were prepared by spin coating; and their surface morphologies were characterized by scanning electron microscopy, X-ray energy dispersive spectroscopy, contact angle measurement and Fourier transform infrared spectroscopy. Subsequently, cell proliferation experiments on two materials were performed and the dynamic curves of protein adsorption on their surfaces were measured...
October 2018: Regenerative Biomaterials
Qian Meng, Jing Gao, Hongwen Zhu, Han He, Zhi Lu, Minhua Hong, Hu Zhou
Dermal fibroblast is one of the major constitutive cells of skin and plays a central role in skin senescence. The replicative senescence of fibroblasts may cause skin aging, bad wound healing, skin diseases and even cancer. In this study, a label-free quantitative proteomic approach was employed to analyzing the serial passaged human skin fibroblast (CCD-1079Sk) cells, resulting in 3371 proteins identified. Of which, 280 proteins were significantly changed in early passage (6 passages, P6), middle passage (12 passages, P12) and late passage (21 passages, P21), with a time-dependent decrease or increase tendency...
October 15, 2018: Biochemical and Biophysical Research Communications
Vladimir N Uversky
Articles assembled to this Special Issue use the perspective of protein intrinsic disorder to highlight different aspects of the dark proteome (i.e., a part of protein universe that includes proteins, which are not amenable to experimental structure determination by existing means and inaccessible to homology modeling) and some of its components. They illustrate that IDPs/IDPRs do not only serve as important constituents of the biological dark matter, but clearly act as the dark horse of the protein universe, being almost completely unknown or at least very little known in a recent past, but suddenly emerging to prominence...
October 18, 2018: Proteomics
Lei Yin, Zhi Zhang, Yingze Liu, Yin Gao, Jingkai Gu
Cells are the most basic structural units that play vital roles in the functioning of living organisms. Analysis of the chemical composition and content of a single cell plays a vital role in ensuring precise investigations of cellular metabolism, and is a crucial aspect of lipidomic and proteomic studies. In addition, structural knowledge provides a better understanding of cell behavior as well as the cellular and subcellular mechanisms. However, single-cell analysis can be very challenging due to the very small size of each cell as well as the large variety and extremely low concentrations of substances found in individual cells...
October 18, 2018: Analyst
Valentin Foulon, Sébastien Artigaud, Manon Buscaglia, Benoit Bernay, Caroline Fabioux, Bruno Petton, Philippe Elies, Kada Boukerma, Claire Hellio, Fabienne Guérard, Pierre Boudry
Bioadhesion of marine organisms has been intensively studied over the last decade because of their ability to attach in various wet environmental conditions and the potential this offers for biotechnology applications. Many marine mollusc species are characterized by a two-phase life history: pelagic larvae settle prior to metamorphosis to a benthic stage. The oyster Crassostrea gigas has been extensively studied for its economic and ecological importance. However, the bioadhesive produced by ready to settle larvae of this species has been little studied...
October 17, 2018: Scientific Reports
Lingli Chen, Jingxuan Wang, Pingping Jiang, Fazheng Ren, Xingen Lei, Huiyuan Guo
BACKGROUND: Gestational hypothyroidism (G-HypoT) is one of the most common thyroid diseases in pregnant women. Human milk, which closely links the mother with infant, is an important factor to the infant health. Here, we analyzed the colostrum whey proteome of women with or without G-HypoT. METHODS AND RESULTS: Using high-mass accuracy and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), 1055 proteins were identified. Tandem Mass Tags (TMT) analysis identified differentially expressed proteins between G-HypoT and non-G-HypoT mothers...
2018: PloS One
Revital Schick, Lucy N Mekies, Yuval Shemer, Binyamin Eisen, Tova Hallas, Ronen Ben Jehuda, Meital Ben-Ari, Agnes Szantai, Lubna Willi, Rita Shulman, Michael Gramlich, Luna Simona Pane, Ilaria My, Dov Freimark, Marta Murgia, Gianluca Santamaria, Mihaela Gherghiceanu, Michael Arad, Alessandra Moretti, Ofer Binah
AIMS: Dilated cardiomyopathy (DCM), a myocardial disorder that can result in progressive heart failure and arrhythmias, is defined by ventricular chamber enlargement and dilatation, and systolic dysfunction. Despite extensive research, the pathological mechanisms of DCM are unclear mainly due to numerous mutations in different gene families resulting in the same outcome-decreased ventricular function. Titin (TTN)-a giant protein, expressed in cardiac and skeletal muscles, is an important part of the sarcomere, and thus TTN mutations are the most common cause of adult DCM...
2018: PloS One
Anuj Sharma, Elias S Manolakos
Protein Structure Comparison (PSC) is a well developed field of computational proteomics with active interest from the research community, since it is widely used in structural biology and drug discovery. With new PSC methods continuously emerging and no clear method of choice, Multi-Criteria Protein Structure Comparison (MCPSC) is commonly employed to combine methods and generate consensus structural similarity scores. We present pyMCPSC, a Python based utility we developed to allow users to perform MCPSC efficiently, by exploiting the parallelism afforded by the multi-core CPUs of today's desktop computers...
2018: PloS One
Jianbo Tian, Zhihua Wang, Shufang Mei, Nan Yang, Yang Yang, Juntao Ke, Ying Zhu, Yajie Gong, Danyi Zou, Xiating Peng, Xiaoyang Wang, Hao Wan, Rong Zhong, Jiang Chang, Jing Gong, Leng Han, Xiaoping Miao
Alternative splicing (AS) is a widespread process that increases structural transcript variation and proteome diversity. Aberrant splicing patterns are frequently observed in cancer initiation, progress, prognosis and therapy. Increasing evidence has demonstrated that AS events could undergo modulation by genetic variants. The identification of splicing quantitative trait loci (sQTLs), genetic variants that affect AS events, might represent an important step toward fully understanding the contribution of genetic variants in disease development...
October 17, 2018: Nucleic Acids Research
Peter V Dubovskii, Roman G Efremov
Being important representatives of various proteomes, membrane-active cationic peptides (CPs) are attractive objects as lead compounds in the design of new antibacterial, anticancer, antifungal, and antiviral molecules. Numerous CPs are found in insect and snake venoms, where many of them reveal cytolytic properties. Due to advances in omics technologies, the number of such peptides is growing dramatically. Areas covered: To understand structure-function relationships for CPs in a living cell, detailed analysis of their hydrophobic/hydrophilic properties is indispensable...
October 17, 2018: Expert Review of Proteomics
Dora Sviben, Dubravko Forcic, Beata Halassy, Günter Allmaier, Martina Marchetti-Deschmann, Marija Brgles
BACKGROUND: Measles (MEV) and mumps virus (MUV) are enveloped, non-segmented, negative single stranded RNA viruses of the family Paramyxoviridae, and are the cause of measles and mumps, respectively, both preventable by vaccination. Aside from proteins coded by the viral genome, viruses are considered to contain host cell proteins (HCPs). The presence of extracellular vesicles (ECVs), which are often co-purified with viruses due to their similarity in size, density and composition, also contributes to HCPs detected in virus preparations, and this has often been neglected...
October 16, 2018: Virology Journal
Antonella Tramutola, Giulia Abate, Chiara Lanzillotta, Francesca Triani, Eugenio Barone, Federica Iavarone, Federica Vincenzoni, Massimo Castagnola, Mariagrazia Marziano, Maurizio Memo, Emirena Garrafa, D Allan Butterfield, Marzia Perluigi, Fabio Di Domenico, Daniela Uberti
Alzheimer's disease (AD) is a progressive form of dementia characterized by increased production of amyloid-β plaques and hyperphosphorylated tau protein, mitochondrial dysfunction, elevated oxidative stress, reduced protein clearance, among other. Several studies showed systemic modifications of immune and inflammatory systems due, in part, to decreased levels of CD3+ lymphocytes in peripheral blood in AD. Considering that oxidative stress, both in the brain and in the periphery, can influence the activation and differentiation of T-cells, we investigated the 3-nitrotyrosine (3-NT) proteome of blood T-cells derived from AD patients compared to non-demented (ND) subjects by using a proteomic approach...
October 12, 2018: Free Radical Biology & Medicine
Saisai Cheng, Xin Ma, Shijie Geng, Xuemei Jiang, Yuan Li, Luansha Hu, Jianrong Li, Yizhen Wang, Xinyan Han
Fecal microbiota transplantation (FMT) is one of the most effective ways to regulate the gut microbiota. Here, we investigated the effect of exogenous fecal microbiota on gut function from the perspective of analysis of the mucosal proteomes in a piglet model. A total of 289 differentially expressed proteins were annotated with 4,068 gene ontology (GO) function entries in the intestinal mucosa, and the levels of autophagy-related proteins in the forkhead box O (FoxO) signaling pathway were increased whereas the levels of proteins related to inflammation response were decreased in the recipient...
September 2018: MSystems
Jonathan D Mortison, Monica Schenone, Jacob A Myers, Ziyang Zhang, Linfeng Chen, Christie Ciarlo, Eamon Comer, S Kundhavai Natchiar, Steven A Carr, Bruno P Klaholz, Andrew G Myers
Apart from their antimicrobial properties, tetracyclines demonstrate clinically validated effects in the amelioration of pathological inflammation and human cancer. Delineation of the target(s) and mechanism(s) responsible for these effects, however, has remained elusive. Here, employing quantitative mass spectrometry-based proteomics, we identified human 80S ribosomes as targets of the tetracyclines Col-3 and doxycycline. We then developed in-cell click selective crosslinking with RNA sequence profiling (icCL-seq) to map binding sites for these tetracyclines on key human rRNA substructures at nucleotide resolution...
October 5, 2018: Cell Chemical Biology
Zhuo A Chen, Juri Rappsilber
The dynamics of protein structures and their interactions are responsible for many cellular processes. The rearrangements and interactions of proteins, which are often transient, occur in solution and may require a biological environment that is difficult to maintain in traditional structural biological approaches. Quantitative crosslinking/mass spectrometry (QCLMS) has emerged as an excellent method to fill this gap. Numerous recent applications of the technique have demonstrated that protein dynamics can now be studied in solution at sufficient resolution to gain valuable biological insights, suggesting that extending these investigations to native environments is possible...
October 11, 2018: Trends in Biochemical Sciences
Jessica Moraes Malheiros, Camila Pereira Braga, Ryan Albert Grove, Felipe Azevedo Ribeiro, Chris Richard Calkins, Jiri Adamec, Luis Artur Loyola Chardulo
The objective of this study was to evaluate the association between oxidative damage to proteins (represented by protein carbonylation) and beef tenderness. Three experimental groups were selected by shear force (SF): tender (38.2 ± 2.9 N), intermediate (51.9 ± 6.8 N), and tough meat (74.5 ± 7.8 N). Two-dimensional electrophoresis with hydrazide fluorophore derivatization was used. The structural proteins actin (ACTA1), myosin (MYL1 and MYL3), desmin (DES) and troponin T (TNNT1 and TNNT3), antioxidant proteins (PRDX1, PRDX2 and PARK7) and heat shock proteins (HSPB1, CRYAB and HSPB6) showed an increase in the oxidative damage in tender meat when compared to the intermediate and tough meat (P < ...
August 23, 2018: Meat Science
Julie A Reisz, Travis Nemkov, Monika Dzieciatkowska, Rachel Culp-Hill, Davide Stefanoni, Ryan C Hill, Tatsuro Yoshida, Andrew Dunham, Tamir Kanias, Larry J Dumont, Michael Busch, Elan Z Eisenmesser, James C Zimring, Kirk C Hansen, Angelo D'Alessandro
BACKGROUND: Being devoid of de novo protein synthesis capacity, red blood cells (RBCs) have evolved to recycle oxidatively damaged proteins via mechanisms that involve methylation of dehydrated and deamidated aspartate and asparagine residues. Here we hypothesize that such mechanisms are relevant to routine storage in the blood bank. STUDY DESIGN AND METHODS: Within the framework of the REDS-III RBC-Omics (Recipient Epidemiology Donor Evaluation Study III Red Blood Cell-Omics) study, packed RBC units (n = 599) were stored under blood bank conditions for 10, 23, and 42 days and profiled for oxidative hemolysis and time-dependent metabolic dysregulation of the trans-sulfuration pathway...
October 12, 2018: Transfusion
Esther Rodríguez-Gallego, Laura Tarancón-Diez, Felipe García, Jorge Del Romero, Jose Miguel Benito, Verónica Alba, Pol Herrero, Anna Rull, Beatriz Dominguez-Molina, Onofre Martinez-Madrid, Luisa Martin-Pena, Federico Pulido, Agathe León, Carmen Rodríguez, Norma Rallón, Joaquim Peraire, Consuelo Viladés, Manuel Leal, Francesc Vidal, Ezequiel Ruiz-Mateos
Background: Elite Controllers (EC) spontaneously control plasma HIV-1-RNA without antiretroviral therapy. However, 25% lose virological control over time. The aim of this work was to study the proteomic profile that preceded this loss of virological control to identify potential biomarkers. Methods: Plasma samples from EC who spontaneously lost virological control (Transient Controllers, TC), at two and one year before the loss of control, were compared with a control group of EC who persistently maintained virological control during the same follow-up period (Persistent Controllers, PC)...
October 12, 2018: Journal of Infectious Diseases
Alexis Zukowski, Juliana Phillips, Soyeon Park, Ronghu Wu, Steven P Gygi, Aaron M Johnson
Heterochromatin domains are stably repressed chromatin structures composed of a core assembly of silencing proteins that condense adjacent nucleosomes. The minimal heterochromatin structure can serve as a platform for recruitment of complementary regulatory factors. We find that a reconstituted budding yeast heterochromatin domain can act as a platform to recruit multiple factors that play a role in regulating heterochromatin function. We uncover the direct interaction between the SIR heterochromatin complex and a chromosomal boundary protein that restricts the spread of heterochromatin...
October 12, 2018: Current Genetics
Peitong Wang, Xi Chen, Xuan Xu, Chenni Lu, Wei Zhang, Fang-Jie Zhao
Arsenic (As) is highly toxic to plants and detoxified primarily through complexation with phytochelatins (PCs) and other thiol compounds. To understand the mechanisms of As toxicity and detoxification beyond PCs, we isolated an arsenate-sensitive mutant of Arabidopsis (Arabidopsis thaliana), arsenate induced chlorosis 1 (aic1), in the background of the PC synthase defective mutant cadmium-sensitive 1-3 (cad1-3). Under arsenate stress, aic1 cad1-3 showed larger decreases in chlorophyll content and the number and size of chloroplasts than cad1-3 and a severely distorted chloroplast structure...
October 11, 2018: Plant Physiology
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