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1.
J Proteome Res ; 21(9): 2146-2159, 2022 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-35939567

RESUMO

High-grade serous ovarian cancer (HGSOC) represents the major histological type of ovarian cancer, and the lack of effective screening tools and early detection methods significantly contributes to the poor prognosis of HGSOC. Currently, there are no reliable diagnostic biomarkers for HGSOC. In this study, we performed liquid chromatography data-independent acquisition tandem mass spectrometry (MS) on depleted serum samples from 26 HGSOC cases and 24 healthy controls (HCs) to discover potential HGSOC diagnostic biomarkers. A total of 1,847 proteins were identified across all samples, among which 116 proteins showed differential expressions between HGSOC patients and HCs. Network modeling showed activations of coagulation and complement cascades, platelet activation and aggregation, neutrophil extracellular trap formation, toll-like receptor 4, insulin-like growth factor, and transforming growth factor ß signaling, as well as suppression of lipoprotein assembly and Fc gamma receptor activation in HGSOC. Based on the network model, we prioritized 28 biomarker candidates and validated 18 of them using targeted MS assays in an independent cohort. Predictive modeling showed a sensitivity of 1 and a specificity of 0.91 in the validation cohort. Finally, in vitro functional assays on four potential biomarkers (FGA, VWF, ARHGDIB, and SERPINF2) suggested that they may play an important role in cancer cell proliferation and migration in HGSOC. All raw data were deposited in PRIDE (PXD033169).


Assuntos
Cistadenocarcinoma Seroso , Neoplasias Ovarianas , Biomarcadores Tumorais , Estudos de Coortes , Cistadenocarcinoma Seroso/diagnóstico , Cistadenocarcinoma Seroso/patologia , Feminino , Humanos , Espectrometria de Massas , Neoplasias Ovarianas/diagnóstico , Neoplasias Ovarianas/patologia , Inibidor beta de Dissociação do Nucleotídeo Guanina rho
3.
Nat Methods ; 11(2): 149-55, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24317253

RESUMO

Multiple reaction monitoring (MRM) mass spectrometry has been successfully applied to monitor targeted proteins in biological specimens, raising the possibility that assays could be configured to measure all human proteins. We report the results of a pilot study designed to test the feasibility of a large-scale, international effort for MRM assay generation. We have configured, validated across three laboratories and made publicly available as a resource to the community 645 novel MRM assays representing 319 proteins expressed in human breast cancer. Assays were multiplexed in groups of >150 peptides and deployed to quantify endogenous analytes in a panel of breast cancer-related cell lines. The median assay precision was 5.4%, with high interlaboratory correlation (R(2) > 0.96). Peptide measurements in breast cancer cell lines were able to discriminate among molecular subtypes and identify genome-driven changes in the cancer proteome. These results establish the feasibility of a large-scale effort to develop an MRM assay resource.


Assuntos
Bioensaio/normas , Biomarcadores Tumorais/metabolismo , Neoplasias da Mama/metabolismo , Proteoma/análise , Proteômica , Espectrometria de Massas em Tandem/métodos , Biomarcadores Tumorais/genética , Neoplasias da Mama/classificação , Neoplasias da Mama/mortalidade , Cromatografia Líquida de Alta Pressão , Eletroforese em Gel Bidimensional , Estudos de Viabilidade , Feminino , Humanos , Projetos Piloto , Taxa de Sobrevida , Células Tumorais Cultivadas
4.
Mol Cell Proteomics ; 13(2): 407-19, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-24319058

RESUMO

Apolipoprotein E (ApoE) polymorphism has been appreciated as a valuable predictor of Alzheimer disease (AD), and the associated ε4 allele has been recognized as an indicator of susceptibility to this disease. However, serum ApoE levels have been a controversial issue in AD, due to the great variability regarding the different target detection methods, ethnicity, and the geographic variations of cohorts. The aim of this study was to validate serum ApoE levels in relation to AD, particularly using two distinct detection methods, liquid chromatography-selected reaction monitoring (SRM) mass spectrometry and microsphere-based fluorescence-activated cell sorting (FACS) analysis, to overcome experimental variations. Also, comparison of serum ApoE levels was performed between the level of protein detection by FACS and peptide level by SRM in both control and AD patients. Results from the two detection methods were cross-confirmed and validated. Both methods produced fairly consistent results, showing a significant decrease of serum ApoE levels in AD patients relative to those of a control cohort (43 control versus 45 AD, p < 0.0001). Significant correlation has been revealed between results from FACS and SRM (p < 0.0001) even though lower serum ApoE concentration values were measured in protein by FACS analysis than in peptide-level detections by SRM. Correlation study suggested that a decrease of the serum ApoE level in AD is related to the mini-mental state exam score in both results from different experimental methods, but it failed to show consistent correlation with age, gender, or clinical dementia rating.


Assuntos
Doença de Alzheimer/sangue , Apolipoproteínas E/sangue , Análise Química do Sangue/métodos , Citometria de Fluxo/métodos , Espectrometria de Massas/métodos , Idoso , Idoso de 80 Anos ou mais , Sequência de Aminoácidos , Estudos de Casos e Controles , Regulação para Baixo , Feminino , Humanos , Masculino , Microesferas , Pessoa de Meia-Idade , Dados de Sequência Molecular , Reprodutibilidade dos Testes
5.
EMBO J ; 30(5): 859-72, 2011 Mar 02.
Artigo em Inglês | MEDLINE | ID: mdl-21183953

RESUMO

Gcn4p is a well-characterized bZIP transcription factor that activates more than 500 genes encoding amino acids and purine biosynthesis enzymes, and many stress-response genes under various stress conditions. Under these stresses, it had been shown that transcriptions of ribosomal protein (RP) genes were decreased. However, the detailed mechanism of this downregulation has not been elucidated. In this study, we present a novel mechanistic model for a repressive role of Gcn4p on RP transcription, especially under amino-acid starvation. It was found that Gcn4p bound directly to Rap1p, which in turn inhibited Esa1p-Rap1p binding. The inhibition of Esa1p recruitment to RP promoters ultimately reduced the level of histone H4 acetylation and RP transcription. These data revealed that Gcn4p has simultaneous dual roles as a repressor for RP genes as well as an activator for amino-acid biosynthesis genes. Moreover, our results showed evidence of a novel link between general control of amino-acid biosynthesis and ribosome biogenesis mediated by Gcn4p at an early stage of adaptation to amino-acid starvation.


Assuntos
Aminoácidos/deficiência , Fatores de Transcrição de Zíper de Leucina Básica/metabolismo , Regulação Fúngica da Expressão Gênica , Proteínas Repressoras/metabolismo , Proteínas Ribossômicas/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Transcrição Gênica , Fatores de Transcrição de Zíper de Leucina Básica/genética , Northern Blotting , Western Blotting , Histona Acetiltransferases/genética , Histona Acetiltransferases/metabolismo , Imunoprecipitação , Regiões Promotoras Genéticas , RNA Mensageiro/genética , Proteínas Repressoras/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Proteínas Ribossômicas/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/crescimento & desenvolvimento , Proteínas de Saccharomyces cerevisiae/genética , Complexo Shelterina , Proteínas de Ligação a Telômeros/genética , Proteínas de Ligação a Telômeros/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
6.
J Bacteriol ; 195(2): 180-92, 2013 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23123905

RESUMO

2-Nitrobenzoate 2-nitroreductase (NbaA) of Pseudomonas fluorescens strain KU-7 is a unique enzyme, transforming 2-nitrobenzoic acid (2-NBA) and 2,4-dinitrobenzoic acid (2,4-DNBA) to the 2-hydroxylamine compounds. Sequence comparison reveals that NbaA contains a conserved cysteine residue at position 141 and two variable regions at amino acids 65 to 74 and 193 to 216. The truncated mutant Δ65-74 exhibited markedly reduced activity toward 2,4-DNBA, but its 2-NBA reduction activity was unaffected; however, both activities were abolished in the Δ193-216 mutant, suggesting that these regions are necessary for the catalysis and specificity of NbaA. NbaA showed different lag times for the reduction of 2-NBA and 2,4-DNBA with NADPH, and the reduction of 2,4-DNBA, but not 2-NBA, failed in the presence of 1 mM dithiothreitol or under anaerobic conditions, indicating oxidative modification of the enzyme for 2,4-DNBA. The enzyme was irreversibly inhibited by 5,5'-dithio-bis-(2-nitrobenzoic acid) and ZnCl(2), which bind to reactive thiol/thiolate groups, and was eventually inactivated during the formation of higher-order oligomers at high pH, high temperature, or in the presence of H(2)O(2). SDS-PAGE and mass spectrometry revealed the formation of intermolecular disulfide bonds by involvement of the two cysteines at positions 141 and 194. Site-directed mutagenesis indicated that the cysteines at positions 39, 103, 141, and 194 played a role in changing the enzyme activity and specificity toward 2-NBA and 2,4-DNBA. This study suggests that oxidative modifications of NbaA are responsible for the differential specificity for the two substrates and further enzyme inactivation through the formation of disulfide bonds under oxidizing conditions.


Assuntos
Nitrobenzoatos/metabolismo , Nitrorredutases/metabolismo , Pseudomonas fluorescens/enzimologia , Sequência de Aminoácidos , Dissulfetos/metabolismo , Eletroforese em Gel de Poliacrilamida , Peróxido de Hidrogênio , Concentração de Íons de Hidrogênio , Espectrometria de Massas , Dados de Sequência Molecular , Mutagênese Sítio-Dirigida , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , NADP/metabolismo , Nitrorredutases/genética , Oxirredução , Deleção de Sequência , Homologia de Sequência de Aminoácidos , Especificidade por Substrato , Temperatura
7.
J Proteome Res ; 12(6): 2582-96, 2013 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-23586733

RESUMO

Lung cancer-related transcription factors (TFs) were identified by integrating previously reported genomic, transcriptomic, and proteomic data and were quantified by multiple reaction monitoring (MRM) in various cell lines. All experiments were performed without affinity depletion or subfractionation of cell lysates. Since the target proteins were expected to be present in low abundance, we experimentally optimized MRM transition parameters with chemically synthesized peptides. Quantitation was based on stable isotope-labeled standard peptides (SIS peptides). Out of 288 MRM measurements (36 peptides representing 28 TFs × 8 cell lines), 241 were successfully obtained within a quantitation limit of 15 amol, 221 measurements (91.7%) showed coefficients of variation (CVs) of ≤ 20%, and 149 (61.8%) showed CVs of ≤ 10%, quantifying as low as 19.4 amol/µg protein for STAT2 with a CV of 6.3% in an A549 cell. Comparisons between MRM measurements and levels of the corresponding mRNAs revealed linear, nonlinear, or no relationship between protein and mRNA levels, indicating the need for an MRM assay. An integrative analysis of MRM and gene expression profiles from doxorubicin-resistant H69AR and sensitive H69 cells further showed that 14 differentially expressed TFs, such as STAT1 and SMAD4, regulated genes associated with drug resistance and cell differentiation-related processes. Thus, the analytical performance of MRM for the quantitation of low abundance TFs suggests its usefulness for biological application.


Assuntos
Carcinoma/química , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Neoplasias Pulmonares/química , Proteínas de Neoplasias/genética , RNA Mensageiro/genética , Fator de Transcrição STAT1/genética , Proteína Smad4/genética , Antibióticos Antineoplásicos/farmacologia , Carcinoma/genética , Carcinoma/metabolismo , Extratos Celulares/química , Linhagem Celular Tumoral , Doxorrubicina/farmacologia , Resistencia a Medicamentos Antineoplásicos , Humanos , Marcação por Isótopo , Limite de Detecção , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Proteínas de Neoplasias/metabolismo , Peptídeos/isolamento & purificação , Proteômica , RNA Mensageiro/metabolismo , Fator de Transcrição STAT1/metabolismo , Proteína Smad4/metabolismo
8.
Mol Cell Proteomics ; 10(10): M111.011023, 2011 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-21799047

RESUMO

Prediction of the responses to neoadjuvant chemotherapy (NACT) can improve the treatment of patients with advanced breast cancer. Genes and proteins predictive of chemoresistance have been extensively studied in breast cancer tissues. However, noninvasive serum biomarkers capable of such prediction have been rarely exploited. Here, we performed profiling of N-glycosylated proteins in serum from fifteen advanced breast cancer patients (ten patients sensitive to and five patients resistant to NACT) to discover serum biomarkers of chemoresistance using a label-free liquid chromatography-tandem MS method. By performing a series of statistical analyses of the proteomic data, we selected thirteen biomarker candidates and tested their differential serum levels by Western blotting in 13 independent samples (eight patients sensitive to and five patients resistant to NACT). Among the candidates, we then selected the final set of six potential serum biomarkers (AHSG, APOB, C3, C9, CP, and ORM1) whose differential expression was confirmed in the independent samples. Finally, we demonstrated that a multivariate classification model using the six proteins could predict responses to NACT and further predict relapse-free survival of patients. In summary, global N-glycoproteome profile in serum revealed a protein pattern predictive of the responses to NACT, which can be further validated in large clinical studies.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Biomarcadores Farmacológicos/sangue , Proteínas Sanguíneas/análise , Neoplasias da Mama/tratamento farmacológico , Glicoproteínas/análise , Terapia Neoadjuvante , Proteômica , Adulto , Proteínas Sanguíneas/genética , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Resistencia a Medicamentos Antineoplásicos , Feminino , Glicoproteínas/sangue , Humanos , Pessoa de Meia-Idade , Estadiamento de Neoplasias , Coloração e Rotulagem
9.
J Proteome Res ; 11(6): 3219-30, 2012 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-22564194

RESUMO

The effects of redox-sensitive proteins on Escherichia coli were investigated by overexpressing Pseudomonas 2-nitrobenzoate nitroreductase (NbaA) and its mutants. Overexpression of wild-type and mutant NbaA proteins significantly altered the sensitivity of E. coli to antibiotics and reactive oxygen species regardless of the enzyme activity for reduction of 2-nitrobenzoic acid. The overexpressed proteins rendered cells 100-10000-fold more sensitive to superoxide anion (O2(•-))-generating paraquat and 10-100-fold more resistant to H2O2. A significant increase in intracellular levels of O2(•-), but not H2O2, was observed during expression of wild-type and truncated (Δ65-74, Δ193-216, and Δ65-74Δ193-216) NbaA. From two-dimensional nonreducing/reducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometry analyses, 29 abundant proteins in the cytoplasm were identified to form interchain disulfide bonds, when cells were exposed to polymyxin B. Of them, down-regulation and modifications of SodB, KatE, and KatG were strongly associated with elevated cellular O2(•-) levels. Western blotting showed up-regulation of cell death signal sensor, CpxA, and down-regulation of cytoplasmic superoxide dismutase, SodB, with ∼2-fold up-regulation of heterodimeric integration host factor, Ihf. Activity gel assays revealed significant reduction of glyceraldehyde-3-phosphate dehydrogenase with constant levels of 6-phosphogluconate dehydrogenase. These changes would support a high level of NADPH to reduce H2O2-induced disulfide bonds by forced expression of thioredoxin A via thioredoxin reductase. Thus, overexpression of wild-type and truncated NbaA partially compensates for the lack of KatE and KatG to degrade H2O2, thereby enhancing disulfide bond formation in the cytoplasm, and modifies a regulatory network of disulfide-bonded proteins to increase intracellular O2(•-) levels.


Assuntos
Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Nitrorredutases/genética , Espécies Reativas de Oxigênio/farmacologia , Substituição de Aminoácidos , Antibacterianos/farmacologia , Cistina/metabolismo , Regulação para Baixo , Escherichia coli/efeitos dos fármacos , Escherichia coli/crescimento & desenvolvimento , Expressão Gênica , Cinética , Redes e Vias Metabólicas , Testes de Sensibilidade Microbiana , Nitrorredutases/biossíntese , Nitrorredutases/química , Oxirredução , Estresse Oxidativo , Mapas de Interação de Proteínas , Pseudomonas/enzimologia , Espécies Reativas de Oxigênio/metabolismo , Proteínas Recombinantes/biossíntese , Proteínas Recombinantes/genética , Regulação para Cima
10.
J Proteome Res ; 11(2): 1078-88, 2012 Feb 03.
Artigo em Inglês | MEDLINE | ID: mdl-22074005

RESUMO

Although doxorubicin (Doxo) and docetaxel (Docet) in combination are widely used in treatment regimens for a broad spectrum of breast cancer patients, a major obstacle has emerged in that some patients are intrinsically resistant to these chemotherapeutics. Our study aimed to discover potential prediction markers of drug resistance in needle-biopsied tissues of breast cancer patients prior to neoadjuvant chemotherapy. Tissues collected before chemotherapy were analyzed by mass spectrometry. A total of 2,331 proteins were identified and comparatively quantified between drug sensitive (DS) and drug resistant (DR) patient groups by spectral count. Of them, 298 proteins were differentially expressed by more than 1.5-fold. Some of the differentially expressed proteins (DEPs) were further confirmed by Western blotting. Bioinformatic analysis revealed that the DEPs were largely associated with drug metabolism, acute phase response signaling, and fatty acid elongation in mitochondria. Clinical validation of two selected proteins by immunohistochemistry found that FKBP4 and S100A9 might be putative prediction markers in discriminating the DR group from the DS group of breast cancer patients. The results demonstrate that a quantitative proteomics/bioinformatics approach is useful for discovering prediction markers of drug resistance, and possibly for the development of a new therapeutic strategy.


Assuntos
Biomarcadores Tumorais/análise , Neoplasias da Mama/tratamento farmacológico , Neoplasias da Mama/metabolismo , Calgranulina B/análise , Proteoma/análise , Proteínas de Ligação a Tacrolimo/análise , Sequência de Aminoácidos , Biomarcadores Tumorais/metabolismo , Western Blotting , Calgranulina B/metabolismo , Quimioterapia Adjuvante , Análise por Conglomerados , Resistencia a Medicamentos Antineoplásicos , Feminino , Humanos , Imuno-Histoquímica , Dados de Sequência Molecular , Terapia Neoadjuvante , Proteoma/metabolismo , Proteômica , Reprodutibilidade dos Testes , Estatísticas não Paramétricas , Proteínas de Ligação a Tacrolimo/metabolismo , Espectrometria de Massas em Tandem , Resultado do Tratamento
11.
Acta Crystallogr D Biol Crystallogr ; 68(Pt 5): 531-40, 2012 May.
Artigo em Inglês | MEDLINE | ID: mdl-22525751

RESUMO

When the Z-type variant of human α(1)-antitrypsin was overexpressed in Saccharomyces cerevisiae, proteomics analysis identified YLR301w as one of the up-regulated proteins. YLR301w is a 27.5 kDa protein with no sequence homology to any known protein and has been reported to interact with Sec72 and Hrr25. The crystal structure of S. cerevisiae YLR301w has been determined at 2.3 Å resolution, revealing a novel ß-structure. It consists of an N-terminal ten-stranded ß-barrel with two short α-helices connected by a 23-residue linker to a seven-stranded half-barrel with two short helices at the C-terminus. The N-terminal barrel has a highly conserved hydrophobic channel that can bind hydrophobic molecules such as PEG. It forms a homodimer both in the crystal and in solution. YLR301w binds Sec72 with a K(d) of 6.2 µM, but the biological significance of this binding requires further investigation.


Assuntos
Proteínas de Transporte/química , Proteínas de Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/química , Sequência de Aminoácidos , Proteínas de Transporte/metabolismo , Cristalografia por Raios X , Modelos Moleculares , Dados de Sequência Molecular , Polietilenoglicóis/metabolismo , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Estrutura Secundária de Proteína , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Alinhamento de Sequência
12.
PLoS Comput Biol ; 7(6): e1002093, 2011 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-21738461

RESUMO

The mitochondrial protein repertoire varies depending on the cellular state. Protein component modifications caused by mitochondrial DNA (mtDNA) depletion are related to a wide range of human diseases; however, little is known about how nuclear-encoded mitochondrial proteins (mt proteome) changes under such dysfunctional states. In this study, we investigated the systemic alterations of mtDNA-depleted (ρ(0)) mitochondria by using network analysis of gene expression data. By modularizing the quantified proteomics data into protein functional networks, systemic properties of mitochondrial dysfunction were analyzed. We discovered that up-regulated and down-regulated proteins were organized into two predominant subnetworks that exhibited distinct biological processes. The down-regulated network modules are involved in typical mitochondrial functions, while up-regulated proteins are responsible for mtDNA repair and regulation of mt protein expression and transport. Furthermore, comparisons of proteome and transcriptome data revealed that ρ(0) cells attempted to compensate for mtDNA depletion by modulating the coordinated expression/transport of mt proteins. Our results demonstrate that mt protein composition changed to remodel the functional organization of mitochondrial protein networks in response to dysfunctional cellular states. Human mt protein functional networks provide a framework for understanding how cells respond to mitochondrial dysfunctions.


Assuntos
Mitocôndrias/fisiologia , Proteínas Mitocondriais/biossíntese , Proteínas Mitocondriais/genética , Linhagem Celular Tumoral , Análise por Conglomerados , Biologia Computacional/métodos , DNA Mitocondrial/genética , DNA Mitocondrial/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Redes Reguladoras de Genes , Humanos , Microscopia de Fluorescência , Mitocôndrias/metabolismo , Proteínas Mitocondriais/metabolismo , Proteoma , RNA Mensageiro/biossíntese , RNA Mensageiro/genética , Reprodutibilidade dos Testes
13.
Mol Cell Proteomics ; 8(5): 1072-81, 2009 May.
Artigo em Inglês | MEDLINE | ID: mdl-19136720

RESUMO

The native state of alpha(1)-antitrypsin (alpha(1)AT), a member of the serine protease inhibitor (serpin) family, is considered a kinetically trapped folding intermediate that converts to a more stable form upon complex formation with a target protease. Although previous structural and mutational studies of alpha(1)AT revealed the structural basis of the native strain and the kinetic trap, the mechanism of how the native molecule overcomes the kinetic barrier to reach the final stable conformation during complex formation remains unknown. We hypothesized that during complex formation, a substantial portion of the molecule undergoes unfolding, which we dubbed functional unfolding. Hydrogen-deuterium exchange coupled with ESI-MS was used to analyze this serpin in three forms: native, complexing, and complexed with bovine beta-trypsin. Comparing the deuterium content at the corresponding regions of these three samples, we probed the unfolding of alpha(1)AT during complex formation. A substantial portion of the alpha(1)AT molecule unfolded transiently during complex formation, including not only the regions expected from previous structural studies, such as the reactive site loop, helix F, and the following loop, but also regions not predicted previously, such as helix A, strand 6 of beta-sheet B, and the N terminus. Such unfolding of the native interactions may elevate the free energy level of the kinetically trapped native serpin sufficiently to cross the transition state during complex formation. In the current study, we provide evidence that protein unfolding has to accompany functional execution of the protein molecule.


Assuntos
Deutério/química , Espectrometria de Massas , Dobramento de Proteína , alfa 1-Antitripsina/química , alfa 1-Antitripsina/metabolismo , Sequência de Aminoácidos , Animais , Bovinos , Dados de Sequência Molecular , Peptídeos/química , Estrutura Secundária de Proteína , Termodinâmica , Tripsina/metabolismo
14.
Anal Chem ; 82(20): 8510-8, 2010 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-20863060

RESUMO

Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, "integrated post-experiment monoisotopic mass refinement" (iPE-MMR), integrates steps (1) generation of refined MS/MS data by DeconMSn; (2) additional refinement of the resultant MS/MS data by a modified version of PE-MMR; and (3) elimination of systematic errors of precursor masses using DtaRefinery. iPE-MMR is the first method that utilizes all MS information from multiple MS scans of a precursor ion including multiple charge states, in an MS scan, to determine precursor mass. With the combination of these methods, iPE-MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data.


Assuntos
Espectrometria de Massas em Tandem/métodos , Peptídeos/análise , Proteoma/análise , Proteômica , Saccharomyces cerevisiae/química
15.
Electrophoresis ; 31(20): 3428-36, 2010 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-20872419

RESUMO

Autoantibodies obtained from cancer patients have been identified as useful tools for cancer diagnostics, prognostics, and as potential targets for immunotherapy. Serological proteome analysis in combination with 2-DE is a classic strategy for identification of tumor-associated antigens in the serum of cancer patients. However, serological proteome analysis cannot always indicate the true antigen out of a complex proteome identified from a single protein spot because the most abundant protein is not always the most antigenic. To address this problem, we utilized multiple parallel separation (MPS) for proteome separation. The common identities present in the fractions obtained using different separation methods were regarded as the true antigens. The merit of our MPS technique was validated using anti-ARPC2 and anti-PTEN antibodies. Next, we applied the MPS technique for the identification of glycyl-tRNA synthetase as the cognate antigen for an autoantibody that was overexpressed in the plasma of breast cancer patients. These results reveal that MPS can unambiguously identify an antibody cognate antigen by reducing false-positives. Therefore, MPS could be used for the characterization of diagnostic antibodies raised in laboratory animals as well as autoantibodies isolated from diseased patients.


Assuntos
Antígenos de Neoplasias/sangue , Biomarcadores Tumorais/sangue , Neoplasias da Mama/imunologia , Eletroforese em Gel Bidimensional/métodos , Proteômica/métodos , Idoso , Antígenos de Neoplasias/isolamento & purificação , Autoanticorpos/sangue , Autoanticorpos/isolamento & purificação , Biomarcadores Tumorais/imunologia , Biomarcadores Tumorais/isolamento & purificação , Neoplasias da Mama/sangue , Estudos de Casos e Controles , Linhagem Celular Tumoral , Feminino , Humanos , Immunoblotting , Pessoa de Meia-Idade , Reprodutibilidade dos Testes
16.
Arch Biochem Biophys ; 494(2): 159-65, 2010 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-19944668

RESUMO

We studied the decolorization of malachite green (MG) by the fungus Cunninghamella elegans. The mitochondrial activity for MG reduction was increased with a simultaneous increase of a 9-kDa protein, called CeCyt. The presence of cytochrome c in CeCyt protein was determined by optical absorbance spectroscopy with an extinction coefficient (E(550-535)) of 19.7+/-6.3 mM(-1) cm(-1) and reduction potential of + 261 mV. When purified CeCyt was added into the mitochondria, the specific activity of CeCyt reached 440 +/- 122 micromol min(-1) mg(-1) protein. The inhibition of MG reduction by stigmatellin, but not by antimycin A, indicated a possible linkage of CeCyt activity to the Qo site of the bc1 complex. The RT-PCR results showed tight regulation of the cecyt gene expression by reactive oxygen species. We suggest that CeCyt acts as a protein reductant for MG under oxidative stress in a stationary or secondary growth stage of this fungus.


Assuntos
Cor , Cunninghamella/citologia , Citocromos c/metabolismo , Mitocôndrias/metabolismo , Corantes de Rosanilina/metabolismo , Sequência de Aminoácidos , Biocatálise , Cunninghamella/efeitos dos fármacos , Cunninghamella/crescimento & desenvolvimento , Cunninghamella/metabolismo , Citocromos c/química , Citocromos c/genética , Citocromos c/isolamento & purificação , Citocromos c1/genética , Citocromos c1/metabolismo , Transporte de Elétrons/efeitos dos fármacos , Regulação Fúngica da Expressão Gênica/efeitos dos fármacos , Mitocôndrias/efeitos dos fármacos , Mitocôndrias/enzimologia , Dados de Sequência Molecular , NAD/metabolismo , Estresse Oxidativo/efeitos dos fármacos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Corantes de Rosanilina/toxicidade
17.
BMC Cancer ; 10: 114, 2010 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-20346108

RESUMO

BACKGROUND: Breast cancer is one of the leading causes of women's death worldwide. It is important to discover a reliable biomarker for the detection of breast cancer. Plasma is the most ideal source for cancer biomarker discovery since many cells cross-communicate through the secretion of soluble proteins into blood. METHODS: Plasma proteomes obtained from 6 breast cancer patients and 6 normal healthy women were analyzed by using the isotope-coded affinity tag (ICAT) labeling approach and tandem mass spectrometry. All the plasma samples used were depleted of highly abundant 6 plasma proteins by immune-affinity column chromatography before ICAT labeling. Several proteins showing differential abundance level were selected based on literature searches and their specificity to the commercially available antibodies, and then verified by immunoblot assays. RESULTS: A total of 155 proteins were identified and quantified by ICAT method. Among them, 33 proteins showed abundance changes by more than 1.5-fold between the plasmas of breast cancer patients and healthy women. We chose 5 proteins for the follow-up confirmation in the individual plasma samples using immunoblot assay. Four proteins, alpha1-acid glycoprotein 2, monocyte differentiation antigen CD14, biotinidase (BTD), and glutathione peroxidase 3, showed similar abundance ratio to ICAT result. Using a blind set of plasmas obtained from 21 breast cancer patients and 21 normal healthy controls, we confirmed that BTD was significantly down-regulated in breast cancer plasma (Wilcoxon rank-sum test, p = 0.002). BTD levels were lowered in all cancer grades (I-IV) except cancer grade zero. The area under the receiver operating characteristic curve of BTD was 0.78. Estrogen receptor status (p = 0.940) and progesterone receptor status (p = 0.440) were not associated with the plasma BTD levels. CONCLUSIONS: Our study suggests that BTD is a potential serological biomarker for the detection of breast cancer.


Assuntos
Biomarcadores Tumorais/sangue , Biotinidase/sangue , Neoplasias da Mama/enzimologia , Proteoma/metabolismo , Adulto , Biomarcadores Tumorais/biossíntese , Biomarcadores Tumorais/genética , Biotinidase/biossíntese , Biotinidase/genética , Western Blotting , Neoplasias da Mama/sangue , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Cromatografia Líquida , Feminino , Humanos , Marcação por Isótopo/métodos , Pessoa de Meia-Idade , Espectrometria de Massas em Tandem
18.
Mol Cell Proteomics ; 7(6): 1124-34, 2008 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-18303012

RESUMO

Methods for treating MS/MS data to achieve accurate peptide identification are currently the subject of much research activity. In this study we describe a new method for filtering MS/MS data and refining precursor masses that provides highly accurate analyses of massive sets of proteomics data. This method, coined "postexperiment monoisotopic mass filtering and refinement" (PE-MMR), consists of several data processing steps: 1) generation of lists of all monoisotopic masses observed in a whole LC/MS experiment, 2) clusterization of monoisotopic masses of a peptide into unique mass classes (UMCs) based on their masses and LC elution times, 3) matching the precursor masses of the MS/MS data to a representative mass of a UMC, and 4) filtration of the MS/MS data based on the presence of corresponding monoisotopic masses and refinement of the precursor ion masses by the UMC mass. PE-MMR increases the throughput of proteomics data analysis, by efficiently removing "garbage" MS/MS data prior to database searching, and improves the mass measurement accuracies (i.e. 0.05 +/- 1.49 ppm for yeast data (from 4.46 +/- 2.81 ppm) and 0.03 +/- 3.41 ppm for glycopeptide data (from 4.8 +/- 7.4 ppm)) for an increased number of identified peptides. In proteomics analyses of glycopeptide-enriched samples, PE-MMR processing greatly reduces the degree of false glycopeptide identification by correctly assigning the monoisotopic masses for the precursor ions prior to database searching. By applying this technique to analyses of proteome samples of varying complexities, we demonstrate herein that PE-MMR is an effective and accurate method for treating massive sets of proteomics data.


Assuntos
Cromatografia Líquida/métodos , Proteômica/métodos , Espectrometria de Massas em Tandem/métodos , Automação , Proteínas Sanguíneas/análise , Feminino , Glicopeptídeos/química , Glicosilação , Humanos , Modelos Estatísticos , Mapeamento de Peptídeos/métodos , Peptídeos/química , Reprodutibilidade dos Testes , Saccharomyces cerevisiae/genética , Software
19.
Cancer Epidemiol Biomarkers Prev ; 18(5): 1357-64, 2009 May.
Artigo em Inglês | MEDLINE | ID: mdl-19423516

RESUMO

We sought to identify a new serum biomarker for breast cancer screening and diagnosis using stepwise proteomic analysis of sera from breast cancer patients to detect the presence of autoantibodies that react with urinary protein. Two-dimensional immunoblotting was done for screening autoimmunogenic tumor antigens in the urine of breast cancer patients. Reactive spots were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Among urinary proteins separated by two-dimensional electrophoresis, 13 spots showed strong reactivity with pooled sera from breast cancer patients or control sera. By mass spectrometry, we identified alpha 2-HS glycoprotein (AHSG) as a tumor antigen. Peripheral blood was obtained from 81 women diagnosed with breast cancer before surgery and 73 female donors without evidence of any malignancy for the individual analysis. In one-dimensional Western blot analysis, AHSG autoantibody was detected in 64 of 81 breast cancer patients (79.1%) and in 7 of 73 controls (9.6%). The sensitivity of this test in breast cancer patients was 79.0%. Our results suggest that AHSG and anti-AHSG autoantibody may be useful serum biomarkers for breast cancer screening and diagnosis.


Assuntos
Antígenos de Neoplasias/sangue , Biomarcadores Tumorais/sangue , Proteínas Sanguíneas/metabolismo , Neoplasias da Mama/diagnóstico , Adulto , Antígenos de Neoplasias/urina , Biomarcadores Tumorais/urina , Proteínas Sanguíneas/urina , Western Blotting , Neoplasias da Mama/sangue , Neoplasias da Mama/urina , Detecção Precoce de Câncer , Eletroforese em Gel Bidimensional , Feminino , Humanos , Técnicas Imunoenzimáticas , Pessoa de Meia-Idade , Curva ROC , Sensibilidade e Especificidade , alfa-2-Glicoproteína-HS
20.
Nat Struct Mol Biol ; 11(12): 1179-85, 2004 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-15543158

RESUMO

The Escherichia coli OxyR transcription factor is activated by cellular hydrogen peroxide through the oxidation of reactive cysteines. Although there is substantial evidence for specific disulfide bond formation in the oxidative activation of OxyR, the presence of the disulfide bond has remained controversial. By mass spectrometry analyses and in vivo labeling assays we found that oxidation of OxyR in the formation of a specific disulfide bond between Cys199 and Cys208 in the wild-type protein. In addition, using time-resolved kinetic analyses, we determined that OxyR activation occurs at a rate of 9.7 s(-1). The disulfide bond-mediated conformation switch results in a metastable form that is locally strained by approximately 3 kcal mol(-1). On the basis of these observations we conclude that OxyR activation requires specific disulfide bond formation and that the rapid kinetic reaction path and conformation strain, respectively, drive the oxidation and reduction of OxyR.


Assuntos
Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Dissulfetos/metabolismo , Proteínas Repressoras/química , Proteínas Repressoras/metabolismo , Fatores de Transcrição/química , Fatores de Transcrição/metabolismo , Proteínas de Ligação a DNA/genética , Dissulfetos/química , Escherichia coli/química , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli , Cinética , Modelos Moleculares , Oxidantes/farmacologia , Oxirredução/efeitos dos fármacos , Desnaturação Proteica/efeitos dos fármacos , Dobramento de Proteína , Estrutura Terciária de Proteína , Proteínas Repressoras/genética , Espectrometria de Fluorescência , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Termodinâmica , Fatores de Transcrição/genética , Triptofano/metabolismo , Ureia/farmacologia
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