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1.
Science ; 366(6462): 189-190, 2019 10 11.
Artigo em Inglês | MEDLINE | ID: mdl-31601760
2.
Se Pu ; 37(8): 836-844, 2019 Aug 08.
Artigo em Chinês | MEDLINE | ID: mdl-31642254

RESUMO

Protein persulfidation is an important oxidative translational modification which plays vital roles in many important processes including cellular senescence, endoplasmic reticulum stress, vasorelaxation, and apoptosis. The proteome-wide analysis of persulfidation is of great importance; therefore, this study combines filter-aided sample preparation with an iodoacetic acid functionalized polyamidoamine dendrimer to enrich persulfidated peptides (denoted as filter-aided dendrimer enrichment strategy, FADE). To evaluate the performance of this strategy, the synthetic persulfidated standard peptide was spiked into bovine serum albumin (BSA) digests at a mass ratio of 1:100, and was successfully identified by FADE. Moreover, in combination with stable isotope labelling by amino acids in cell culture technology, the FADE strategy was applied to enrich persulfidated peptides from NaHS-stimulated SHSY5Y cells over a concentration gradient, resulting in the identification of 163 persulfidated peptides. Bioinformatic analysis indicated that persulfidation might play important roles in the central nervous system.


Assuntos
Dendrímeros , Ácido Iodoacético/química , Peptídeos/química , Animais , Bovinos , Proteoma , Soroalbumina Bovina
3.
Se Pu ; 37(8): 853-862, 2019 Aug 08.
Artigo em Chinês | MEDLINE | ID: mdl-31642256

RESUMO

Diabetes is a systemic metabolic disorder syndrome, mainly characterized by hyperglycemia, and is associated with the dysfunction of various organs, such as liver, pancreas, intestine, adipose muscle tissue, kidney and brain. It has become a global epidemic disease that seriously threatens human health. Therefore, mapping the global molecular signatures of diabetes-related disease spectrum can provide more comprehensive data to understand early clinical diagnosis, molecular typing, and pathological processes involved in diabetes mellitus. In this study, we performed a quantitative differential analysis on the endogenous peptidome of the serum samples obtained from healthy, prediabetes and type 2 diabetes groups to explore the peptidomics evolution in the development of diabetes. Partial least squares-discriminant analysis (PLS-DA) was used for pattern recognition. A nonparametric test was examined to find out the significantly changed endogenous peptides. As a result, 690 serum endogenous peptides were identified totally, among which 163 endogenous peptides were statistically different among the three groups. This could be promising quantitative peptidomics data for early screening, diagnosis and molecular typing of type 2 diabetes mellitus.


Assuntos
Diabetes Mellitus Tipo 2/sangue , Peptídeos/sangue , Proteoma/análise , Humanos
4.
Braz Oral Res ; 33: e043, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31508727

RESUMO

Proteomic techniques have become popular in medicine and dentistry because of their widespread use in analyzing bodily fluids such as blood, saliva, urine, and gingival crevicular fluids as well as hard tissues such as enamel, dentine, and cementum. This review is a guide to proteomic techniques in general dentistry, summarizing techniques and their clinical application in understanding and diagnosing diseases and their use in identifying biomarkers of various diseases.


Assuntos
Proteoma , Proteômica/métodos , Saliva/química , Proteínas e Peptídeos Salivares/química , Biomarcadores/química , Eletroforese em Gel de Poliacrilamida/métodos , Humanos , Espectrometria de Massas/métodos , Neoplasias Bucais/diagnóstico , Síndrome de Sjogren/diagnóstico
5.
Yi Chuan ; 41(9): 863-874, 2019 Sep 20.
Artigo em Chinês | MEDLINE | ID: mdl-31549684

RESUMO

Membrane proteins play important functions not only as receptors and transporters, but also in many other important intracellular functions such as photosynthetic and respiratory electron transport. Identification of membrane proteins is a necessary step to understand their functions. Membrane proteins are generally highly hydrophobic and difficult to be resolved by aqueous solutions, and large-scale proteomic identification of membrane proteins has been a great technical challenge. Significant efforts have been invested in the field to improve the solubility of membrane proteins in aqueous solutions that are compatible for mass spectrometry analysis. This review summarizes the main technological achievements in the field of membrane proteomics particularly for the improvement of membrane protein identification, and uses the photosynthetic model cyanobacterium Synechocystis sp. PCC6803 as an example to illustrate how technology advances push forward the field in terms of the increased coverage of membrane proteome identification.


Assuntos
Proteoma , Proteômica/tendências , Synechocystis/genética , Proteínas de Bactérias/genética , Espectrometria de Massas
6.
Isr Med Assoc J ; 21(7): 444-448, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31507118

RESUMO

BACKGROUND: Although cross-reactions between Epstein-Barr virus (EBV) and human systemic lupus erythematosus (SLE) autoantigens occur, a complete analysis of the potential EBV peptide cross-reactome has not been performed. OBJECTIVES: To analyze the whole EBV proteome searching for peptides common to SLE-related proteins and endowed with an immunological potential. METHODS: Fifty-one SLE-related proteins were analyzed for hexapeptide sharing with EBV proteome using publicly available databases. RESULTS: An extremely high number of hexapeptides are shared between 34 human SLE autoantigens and EBV proteins. The peptide sharing mostly occurs with complement components C4 and Interleukin-10 (IL-10). CONCLUSIONS: This study thoroughly describes the EBV vs. SLE autoantigens peptide overlap and powerfully supports cross-reactivity as a major mechanism in EBV-associated SLE etiopathogenesis.


Assuntos
Autoantígenos/imunologia , Infecções por Vírus Epstein-Barr/imunologia , Lúpus Eritematoso Sistêmico/imunologia , Peptídeos/imunologia , Proteoma , Complemento C4/imunologia , Reações Cruzadas/imunologia , Bases de Dados Factuais , Herpesvirus Humano 4/imunologia , Humanos , Interleucina-10/imunologia
8.
Immunogenetics ; 71(8-9): 519-530, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31520135

RESUMO

Human CD4+ T lymphocytes play an important role in inducing potent immune responses. T cells are activated and stimulated by peptides presented in human leucocyte antigen (HLA)-class II molecules. These HLA-class II molecules typically present peptides of between 12 and 20 amino acids in length. The region that interacts with the HLA molecule, designated as the peptide-binding core, is highly conserved in the residues which anchor the peptide to the molecule. In addition, as these peptides are the product of proteolytic cleavages, certain conserved residues may be expected at the N- and C-termini outside the binding core. To study whether similar conserved residues are present in different cell types, potentially harbouring different proteolytic enzymes, the ligandomes of HLA-DRB1*03:01/HLA-DRB > 1 derived from two different cell types (dendritic cells and EBV-transformed B cells) were identified with mass spectrometry and the binding core and N- and C-terminal residues of a total of 16,568 peptides were analysed using the frequencies of the amino acids in the human proteome. Similar binding motifs were found as well as comparable conservations in the N- and C-terminal residues. Furthermore, the terminal conservations of these ligandomes were compared to the N- and C-terminal conservations of the ligandome acquired from dendritic cells homozygous for HLA-DRB1*04:01. Again, comparable conservations were evident with only minor differences. Taken together, these data show that there are conservations in the terminal residues of peptides, presumably the result of the activity of proteases involved in antigen processing.


Assuntos
Linfócitos B/metabolismo , Células Dendríticas/metabolismo , Antígenos HLA-DR/classificação , Antígenos HLA-DR/metabolismo , Fragmentos de Peptídeos/metabolismo , Proteoma/metabolismo , Motivos de Aminoácidos , Linfócitos B/citologia , Células Cultivadas , Células Dendríticas/citologia , Humanos , Ligantes , Ligação Proteica
9.
Sheng Wu Gong Cheng Xue Bao ; 35(9): 1643-1649, 2019 Sep 25.
Artigo em Chinês | MEDLINE | ID: mdl-31559746

RESUMO

Cerebrospinal fluid surrounds and supports the central nervous system, including the ventricles and subarachnoid spaces. Cerebrospinal fluid should be an important source of biomarkers for central nervous system diseases because it is in direct contact with the central nervous system. Many studies are reported on cerebrospinal fluid proteomics, highlighting many recent progresses. Here, we review recent advances in proteomics technology and clinical application of cerebrospinal fluid.


Assuntos
Proteômica , Biomarcadores , Proteínas do Líquido Cefalorraquidiano , Proteoma
10.
Sheng Wu Gong Cheng Xue Bao ; 35(9): 1715-1722, 2019 Sep 25.
Artigo em Chinês | MEDLINE | ID: mdl-31559753

RESUMO

The liver is the metabolic center of mammalian body. Systematic study on liver's proteome expression under different physiological and pathological conditions helps us understand the functional mechanisms of the liver. With the rapid development of liquid chromatography tandem mass spectrometry technique, numerous studies on liver physiology and pathology features produced a large number of proteomics data. In this paper, 834 proteomics experiments of mouse liver were systematically collected and the mouse liver proteome database (Mouse Liver Portal, http://mouseliver.com) was established. The Mouse Liver Portal contains the liver's proteomics data under different physiology and pathology conditions, such as different gender, age, circadian rhythm, cell type and different phase of partial hepatectomy, non-alcoholic fatty liver. This portal provides the changes in proteins' expression in different conditions of the liver, differently expressed proteins and the biological processes which they are involved in, potential signal transduction and regulatory networks. As the most comprehensive mouse liver proteome database, it can provide important resources and clues for liver biology research.


Assuntos
Proteoma , Proteômica , Animais , Cromatografia Líquida , Bases de Dados Factuais , Fígado , Camundongos
11.
Ann Parasitol ; 65(2): 145-149, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31376344

RESUMO

The aim of this paper was to analyse the amino acid sequences of the 18S rRNA gene of Babesia canis strains and the proteomic analysis of the serum of dogs infected with three various genotypes: 18S rRNA B. canis. Material for the research was DNA B. canis obtained from dogs with babesiosis. In total, 60 DNA tested samples were divided into three groups (20 samples each). The groups were formed by DNA samples of the sequences marked as 18S RNA-A (group 1), 18S RNA-B (group 2), and 18S RNA-C (group 3). The basis for the classification of protozoa to a specific group was the location of relevant nucleotides (GA, AG, or TT) in position 150-151 of the tested nucleotide sequence 18S rRNA. Nucleotide sequences were transcribed into amino acid sequences and then analysed using DNASTAR software. From all 60 infected and ten healthy dogs (control group), the serum was taken to make proteomic tests using MALDI-TOF mass spectrometer. It was demonstrated that the mutations found in position 150 and 151 of the nucleotide sequence, result in a change of amino acid sequences. Moreover, it was also demonstrated that the disease course in dogs infected with different strains of protozoa is different. Each of the analysed strains of protozoa induced in the serum of infected animals the appearance of a protein fraction of mass 51 kDa, which may then be treated as a nonspecific disease marker used for the diagnosis of this disease but not to differentiate the protozoa strains.


Assuntos
Babesia , Babesiose , Doenças do Cão , Proteoma , RNA de Protozoário , RNA Ribossômico 18S , Sequência de Aminoácidos , Animais , Babesia/genética , Babesiose/sangue , Babesiose/parasitologia , Doenças do Cão/sangue , Doenças do Cão/parasitologia , Cães , Proteínas de Protozoários/sangue , Proteínas de Protozoários/química , RNA de Protozoário/química , RNA Ribossômico 18S/química , RNA Ribossômico 18S/genética
12.
Mol Biol (Mosk) ; 53(4): 685-691, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31397442

RESUMO

In the past decade, mass spectrometry studies of skeletal muscles have become common. In this tissue, the abundance of several contractile proteins significantly limits the depth of the panoramic proteome analysis. The use of isobaric labels allows improving assessment of the changes in the protein content, while analyzing up to 10 samples in a single run. Here we present the results of a comparative study of various methods for the fractionation of skeletal muscle peptides labeled with an isobaric label iTRAQ. Samples from m. vastus lateralis of eight young males were collected with a needle biopsy. After digestion into peptides and labeling, the preparations were carried out according to three different protocols: (1) peptide purification, HPLC-MS/MS; (2) peptide purification, isoelectric focusing, HPLC-MS/MS; (3) high pH reverse-phase LC fractionation, HPLC-MS/MS. Fractionation of labeled peptides by high pH reverse-phase LC was the optimal strategy for increasing the depth of the proteome analysis. This approach, in addition to contractile and mitochondrial proteins, allowed us to detect a variety of regulatory molecules, including the nucleic acids binding the proteins, chaperones, receptors, and transcription factors.


Assuntos
Métodos Analíticos de Preparação de Amostras/métodos , Músculo Esquelético/química , Músculo Esquelético/metabolismo , Proteoma/análise , Proteômica/métodos , Coloração e Rotulagem/métodos , Humanos , Focalização Isoelétrica , Proteoma/química , Espectrometria de Massas em Tandem
13.
Chimia (Aarau) ; 73(7): 540-548, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31431214

RESUMO

Predicting how a system behaves under changing conditions is an essential component of science and engineering. The ability to make accurate predictions about the system indicates that it is well understood and provides the opportunity to simulate the response to conditions that would be empirically difficult or impossible to test. In the life sciences, the term systems biology was introduced to articulate the notion that the molecular and phenotypic response of a cell or organism to perturbations is the result of interplay of a multitude of molecules. The ability to predict the behavior of such complex molecular systems remains challenging and inevitably requires the involvement of different types of models and data that support them. In this article, we discuss a range of data-driven models that have proven particularly useful for predicting the behavior of biological systems at different levels of complexity and the matching data generation methods that support them. We specifically focus on predictions based on protein or proteome data generated by mass spectrometry. We describe three case studies that represent frequently encountered situations in systems biology.


Assuntos
Proteoma , Biologia de Sistemas , Espectrometria de Massas
14.
Biomed Khim ; 65(4): 294-305, 2019 Jun.
Artigo em Russo | MEDLINE | ID: mdl-31436170

RESUMO

HL-60 promyelocytic cells are a widely used as a model for studying induced granulocytic differentiation. Investigation of proteins of the nuclear fraction, particularly transcription factors, is necessary for a better understanding of molecular mechanisms of cell maturation. Mass spectrometry is a powerful tool for analyzing a proteome due to its high sensitivity, specificity and performance. In this paper, using the selected reaction monitoring (SRM) method, we have assessed the levels of RBPJ, STAT1, CEBPB, CASP3, VAV1, PRKDC, PARP1 and UBC9 nuclear proteins isolated using hypertonic buffer, detergents (sodium dodecyl sulfate (SDS), sodium deoxycholate (DOC) and fissionable detergent ProteaseMAX™) and using centrifugation in a sucrose density gradient. The minimum and maximum protein content was 1.13±0.28 and 14.34±1.63 fmol/mkg of total protein for the transcription factor RBPJ and ubiquitin-protein ligase type I UBC9, respectively. According to the results of shotgun mass spectrometric analysis of nuclear fractions, 2356 proteins were identified, of which 106 proteins were annotated as transcription factors. 37 transcription factors were uniquely identified in the fraction obtained by centrifugation in a sucrose density gradient, while only 9 and 8 transcription factors were uniquely identified in the nuclear fractions obtained using hypertonic buffer and detergents, respectively. The transcription factors identified in the HL-60 cell line represent regulatory molecules; their directed profiling under the influence of differentiation inducers, will shed light on the mechanism of granulocyte maturation.


Assuntos
Proteínas Nucleares/análise , Proteoma/análise , Proteômica , Fatores de Transcrição/análise , Células HL-60 , Humanos , Espectrometria de Massas
15.
Nat Methods ; 16(9): 809-812, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31406385
16.
Sci Total Environ ; 687: 839-848, 2019 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-31412487

RESUMO

The adverse effects of air pollution have been long studied in the lung and respiratory systems, but the molecular changes that this causes at the central nervous system level have yet to be fully investigated and understood. To explore the evolution with time of protein expression levels in the brain of rats exposed to particulate matter of different sizes, we carried out two-dimensional gel electrophoresis followed by determination of dysregulated proteins through Coomassie blue staining-based densities (SameSpots software) and subsequent protein identification using MALDI-based mass spectrometry. Expression differences in dysregulated proteins were found to be statistically significant with p-value <0.05. A systems biology-based approach was utilized to determine critical biochemical pathways involved in the rats' brain response. Our results suggest that rats' brains have a particulate matter size dependent-response, being the mitochondrial activity and the astrocyte function severely affected. Our proteomic study confirms the dysregulation of different biochemical pathways involving energy metabolism, mitochondrial activity, and oxidative pathways as some of the main effects of PM exposure on the rat brain. SIGNIFICANCE: Rat brains exposed to particulate matter with origin in car engines are affected in two main areas: mitochondrial activity, by the dysregulation of many pathways linked to the respiratory chain, and neuronal and astrocytic function, which stimulates brain changes triggering tumorigenesis and neurodegeneration.


Assuntos
Poluentes Atmosféricos/toxicidade , Encéfalo/metabolismo , Material Particulado/toxicidade , Proteoma/metabolismo , Poluição do Ar/estatística & dados numéricos , Animais , Metabolismo Energético/efeitos dos fármacos , Masculino , Estresse Oxidativo/fisiologia , Proteômica , Ratos
17.
Plant Mol Biol ; 101(3): 325-339, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31399934

RESUMO

KEY MESSAGE: Combining genetic engineering of MPK4 activity and quantitative proteomics, we established an in planta system that enables rapid study of MPK4 signaling networks and potential substrate proteins. Mitogen activated protein kinase 4 (MPK4) is a multifunctional kinase that regulates various signaling events in plant defense, growth, light response and cytokinesis. The question of how a single protein modulates many distinct processes has spurred extensive research into the physiological outcomes resulting from genetic perturbation of MPK4. However, the mechanism by which MPK4 functions is still poorly understood due to limited data on the MPK4 networks including substrate proteins and downstream pathways. Here we introduce an experimental system that combines genetic engineering of kinase activity and quantitative proteomics to rapidly study the signaling networks of MPK4. First, we transiently expressed a constitutively active (MPK4CA) and an inactive (MPK4IN) version of a Brassica napus MPK4 (BnMPK4) in Nicotiana benthamiana leaves. Proteomics analysis revealed that BnMPK4 activation affects multiple pathways (e.g., metabolism, redox regulation, jasmonic acid biosynthesis and stress responses). Furthermore, BnMPK4 activation also increased protein phosphorylation in the phosphoproteome, from which putative MPK4 substrates were identified. Using protein kinase assay, we validated that a transcription factor TCP8-like (TCP8) and a PP2A regulatory subunit TAP46-like (TAP46) were indeed phosphorylated by BnMPK4. Taken together, we demonstrated the utility of proteomics and phosphoproteomics in elucidating kinase signaling networks and in identification of downstream substrates.


Assuntos
Regulação da Expressão Gênica de Plantas , Proteínas Quinases Ativadas por Mitógeno/metabolismo , Proteômica , Arabidopsis , Proteínas de Arabidopsis/metabolismo , Brassica napus/enzimologia , Engenharia Genética , Sistema de Sinalização das MAP Quinases , Fosforilação , Imunidade Vegetal , Folhas de Planta/enzimologia , Proteoma , Transdução de Sinais , Tabaco/enzimologia
18.
Clin Exp Rheumatol ; 37 Suppl 118(3): 240-248, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31464680

RESUMO

In the era of personalised medicine new biomarkers are required to early diagnose Sjögren's syndrome (SS), to define different disease subsets and to direct patients' clinical management and therapeutic intervention. In the last few years, several efforts have evaluated saliva proteome to detect and monitor primary SS. Although clinically valuable, these studies presented some limitations that have partially prevented the use of salivary biomarkers in clinical practice. Nowadays, proteomic of extracellular vesicle (EV) represents an emerging and promising field in the discovery of -omic biomarkers for pSS. EV is a relatively new term that includes exosomes, microvesicles and apoptotic body. EVs are packed with proteins, growth factors, cytokines, bioactive lipids, but also nucleic acids and in particular: mRNA, microRNA, long non-coding RNA, tRNA and rRNA. Therefore, they may represent a useful source for diagnostic, prognostic and therapeutic biomarkers in several conditions. In this review we will specifically focus on EV proteomics as a tool for the identification of novel biomarkers for pSS. In the first part we focused on the state of the art of the studies on proteomics in SS existing in the literature. In the second part we provided a definition of EV with an update on biological sample collection and processing for EV proteomic studies. Finally, we summarised the state of the art of EV -omics in SS highlighting the potential advantages of this novel approach compared to the overall traditional concept of analysing the proteome of blood or saliva.


Assuntos
Vesículas Extracelulares , Proteômica/métodos , Síndrome de Sjogren , Biomarcadores/metabolismo , Vesículas Extracelulares/metabolismo , Humanos , Proteoma/metabolismo , Saliva/metabolismo , Síndrome de Sjogren/metabolismo
19.
Nat Methods ; 16(8): 703-706, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31363206

RESUMO

Proteins can be phosphorylated at neighboring sites resulting in different functional states, and studying the regulation of these sites has been challenging. Here we present Thesaurus, a search engine that detects and quantifies phosphopeptide positional isomers from parallel reaction monitoring and data-independent acquisition mass spectrometry experiments. We apply Thesaurus to analyze phosphorylation events in the PI3K/AKT signaling pathway and show neighboring sites with distinct regulation.


Assuntos
Fosfopeptídeos/análise , Fosfoproteínas/análise , Proteoma/análise , Ferramenta de Busca/métodos , Células HeLa , Humanos , Proteínas Substratos do Receptor de Insulina/metabolismo , Isomerismo , Células MCF-7 , Fosfatidilinositol 3-Quinases/metabolismo , Fosforilação , Proteínas Proto-Oncogênicas c-akt/metabolismo , Transdução de Sinais , Espectrometria de Massas em Tandem
20.
Nat Methods ; 16(9): 894-901, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31384043

RESUMO

Mass spectrometry enables global analysis of posttranslationally modified proteoforms from biological samples, yet we still lack methods to systematically predict, or even prioritize, which modification sites may perturb protein function. Here we describe a proteomic method, Hotspot Thermal Profiling, to detect the effects of site-specific protein phosphorylation on the thermal stability of thousands of native proteins in live cells. This massively parallel biophysical assay unveiled shifts in overall protein stability in response to site-specific phosphorylation sites, as well as trends related to protein function and structure. This method can detect intrinsic changes to protein structure as well as extrinsic changes to protein-protein and protein-metabolite interactions resulting from phosphorylation. Finally, we show that functional 'hotspot' protein modification sites can be discovered and prioritized for study in a high-throughput and unbiased fashion. This approach is applicable to diverse organisms, cell types and posttranslational modifications.


Assuntos
Ensaios de Triagem em Larga Escala/métodos , Fosfoproteínas/análise , Fosfoproteínas/química , Processamento de Proteína Pós-Traducional , Proteoma/análise , Temperatura Ambiente , Células HeLa , Humanos , Fosforilação , Domínios e Motivos de Interação entre Proteínas , Estabilidade Proteica
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