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  1 / 6528 MEDLINE  
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[PMID]:29378185
[Au] Autor:Cook A; Hari-Gupta Y; Toseland CP
[Ad] Endereço:School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
[Ti] Título:Application of the SSB biosensor to study in vitro transcription.
[So] Source:Biochem Biophys Res Commun;496(3):820-825, 2018 02 12.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Gene expression, catalysed by RNA polymerases (RNAP), is one of the most fundamental processes in living cells. The majority of methods to quantify mRNA are based upon purification of the nucleic acid which leads to experimental inaccuracies and loss of product, or use of high cost dyes and sensitive spectrophotometers. Here, we describe the use of a fluorescent biosensor based upon the single stranded binding (SSB) protein. In this study, the SSB biosensor showed similar binding properties to mRNA, to that of its native substrate, single-stranded DNA (ssDNA). We found the biosensor to be reproducible with no associated loss of product through purification, or the requirement for expensive dyes. Therefore, we propose that the SSB biosensor is a useful tool for comparative measurement of mRNA yield following in vitro transcription.
[Mh] Termos MeSH primário: Técnicas Biossensoriais/métodos
Proteínas de Ligação a DNA/metabolismo
Corantes Fluorescentes/metabolismo
Técnicas de Sonda Molecular
RNA Mensageiro/metabolismo
Espectrometria de Fluorescência/métodos
Transcrição Genética/fisiologia
[Mh] Termos MeSH secundário: Escherichia coli/metabolismo
Sondas Moleculares/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA-Binding Proteins); 0 (Fluorescent Dyes); 0 (Molecular Probes); 0 (RNA, Messenger)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180222
[Lr] Data última revisão:
180222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180130
[St] Status:MEDLINE


  2 / 6528 MEDLINE  
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[PMID]:29366791
[Au] Autor:Ganareal TACS; Balbin MM; Monserate JJ; Salazar JR; Mingala CN
[Ad] Endereço:Department of Chemistry, College of Arts and Sciences, Central Luzon State University, Science City of Muñoz 3120, Nueva Ecija, Philippines.
[Ti] Título:Gold nanoparticle-based probes for the colorimetric detection of Mycobacterium avium subspecies paratuberculosis DNA.
[So] Source:Biochem Biophys Res Commun;496(3):988-997, 2018 02 12.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Gold nanoparticle (AuNP) is considered to be the most stable metal nanoparticle having the ability to be functionalized with biomolecules. Recently, AuNP-based DNA detection methods captured the interest of researchers worldwide. Paratuberculosis or Johne's disease, a chronic gastroenteritis in ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP), was found to have negative effect in the livestock industry. In this study, AuNP-based probes were evaluated for the specific and sensitive detection of MAP DNA. AuNP-based probe was produced by functionalization of AuNPs with thiol-modified oligonucleotide and was confirmed by Fourier-Transform Infrared (FTIR) spectroscopy. UV-Vis spectroscopy and Scanning Electron Microscopy (SEM) were used to characterize AuNPs. DNA detection was done by hybridization of 10 µL of DNA with 5 µL of probe at 63 °C for 10 min and addition of 3 µL salt solution. The method was specific to MAP with detection limit of 103 ng. UV-Vis and SEM showed dispersion and aggregation of the AuNPs for the positive and negative results, respectively, with no observed particle growth. This study therefore reports an AuNP-based probes which can be used for the specific and sensitive detection of MAP DNA.
[Mh] Termos MeSH primário: Colorimetria/métodos
DNA/genética
DNA/isolamento & purificação
Ouro/química
Nanopartículas Metálicas/química
Mycobacterium avium/genética
Mycobacterium avium/isolamento & purificação
[Mh] Termos MeSH secundário: Técnicas Biossensoriais/métodos
Hibridização In Situ/métodos
Técnicas de Sonda Molecular
Sondas Moleculares/química
Reprodutibilidade dos Testes
Sensibilidade e Especificidade
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Molecular Probes); 7440-57-5 (Gold); 9007-49-2 (DNA)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180222
[Lr] Data última revisão:
180222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180126
[St] Status:MEDLINE


  3 / 6528 MEDLINE  
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[PMID]:29364904
[Au] Autor:Garland M; Schulze CJ; Foe IT; van der Linden WA; Child MA; Bogyo M
[Ad] Endereço:Cancer Biology Program, Stanford University School of Medicine, Stanford, California, United States of America.
[Ti] Título:Development of an activity-based probe for acyl-protein thioesterases.
[So] Source:PLoS One;13(1):e0190255, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Protein palmitoylation is a dynamic post-translational modification (PTM) important for cellular functions such as protein stability, trafficking, localization, and protein-protein interactions. S-palmitoylation occurs via the addition of palmitate to cysteine residues via a thioester linkage, catalyzed by palmitoyl acyl transferases (PATs), with removal of the palmitate catalyzed by acyl protein thioesterases (APTs) and palmitoyl-protein thioesterases (PPTs). Tools that target the regulators of palmitoylation-PATs, APTs and PPTs-will improve understanding of this essential PTM. Here, we describe the synthesis and application of a cell-permeable activity-based probe (ABP) that targets APTs in intact mammalian cells and the parasite Toxoplasma gondii. Using a focused library of substituted chloroisocoumarins, we identified a probe scaffold with nanomolar affinity for human APTs (HsAPT1 and HsAPT2) and synthesized a fluorescent ABP, JCP174-BODIPY TMR (JCP174-BT). We use JCP174-BT to profile HsAPT activity in situ in mammalian cells, to detect an APT in T. gondii (TgPPT1). We show discordance between HsAPT activity levels and total protein concentration in some cell lines, indicating that total protein levels may not be representative of APT activity in complex systems, highlighting the utility of this probe.
[Mh] Termos MeSH primário: Sondas Moleculares/metabolismo
[Mh] Termos MeSH secundário: Animais
Mamíferos
Processamento de Proteína Pós-Traducional
Tioléster Hidrolases
Toxoplasma/enzimologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (Molecular Probes); EC 3.1.2.- (Thiolester Hydrolases); EC 3.1.2.22 (palmitoyl-protein thioesterase)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180221
[Lr] Data última revisão:
180221
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180125
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190255


  4 / 6528 MEDLINE  
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[PMID]:29305261
[Au] Autor:Magni C; Sessa F; Capraro J; Duranti M; Maffioli E; Scarafoni A
[Ad] Endereço:Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via G. Celoria, 2, 20133, Milan, Italy.
[Ti] Título:Structural and functional insights into the basic globulin 7S of soybean seeds by using trypsin as a molecular probe.
[So] Source:Biochem Biophys Res Commun;496(1):89-94, 2018 01 29.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The basic 7S globulin (Bg7S) is one of the major globulins of soybean seeds. Despite its dual subunit composition and oligomeric assembly, Bg7S has a compact 3D structure (PDB: 3AUP) which is stabilized by a network of inter- and intra-chain disulphide bridges. Bg7S shares several structural elements with a number of homologous proteins from other seeds, whose function is still uncertain. In this work, Bg7S native conformation was probed by using the proteolytic enzyme trypsin. In spite of the presence of many arginine and lysine residues, the protein resulted extremely recalcitrant to in vitro enzymatic cleavage. Indeed, only two scissile bonds located near the C- and N-termini of the large and small subunits, respectively, were cleaved. The partially cleaved products were stable even at prolonged incubation times. Although the generated small peptide fragments were not covalently bound to the remnant of the main chains, they were held in place, as assessed by denaturing and non-denaturing chromatographic approaches. Moreover, both the already observed pH-dependent association/dissociation behaviour of the protein and its insulin binding capacity were preserved both at neutral and acidic pH values. These results are in line with the growing view that the degradation of seed proteins, either storage and non-storage, may be a controlled process related to specific functionalities.
[Mh] Termos MeSH primário: Globulinas/química
Técnicas de Sonda Molecular
Sementes/química
Proteínas de Soja/química
Feijão de Soja/química
Tripsina/química
[Mh] Termos MeSH secundário: Sítios de Ligação
Modelos Químicos
Modelos Moleculares
Sondas Moleculares/química
Ligação Proteica
Conformação Proteica
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Globulins); 0 (Molecular Probes); 0 (Soybean Proteins); EC 3.4.21.4 (Trypsin)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180215
[Lr] Data última revisão:
180215
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180107
[St] Status:MEDLINE


  5 / 6528 MEDLINE  
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[PMID]:27778291
[Au] Autor:Soriano GP; Overkleeft HS; Florea BI
[Ad] Endereço:Bio-organic Synthesis Group, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
[Ti] Título:Two-Step Activity-Based Protein Profiling with the Proteasome System as Model of Study.
[So] Source:Methods Mol Biol;1491:205-215, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Activity-based protein profiling (ABPP) is a method to highlight enzymatic activities in a biological sample, which uses chemical probes that react covalently with the catalytic nucleophile of the enzyme. To circumvent disadvantages associated with the presence of reporter tags on chemical probes, the probe is equipped with a ligation handle to which the reporter can be reacted at the desired time and place in the ABPP workflow. This chapter demonstrates the power of a triple bioorthogonal ligation strategy which addresses the three activities of the proteasome: the ß5-subunit selective norbornene-tagged probe is reacted with fluorescent tetrazine, the ß1-selective azide-functionalized probe was addressed with a biotinylated phosphine, followed by an alkyne-substituted pan-reactive probe to label the remaining ß2 activity to which an azide-coupled fluorophore was ligated. The result of the triple ligation was similar to each reaction performed separately demonstrating the value of the triple ligation strategy for a single experiment.
[Mh] Termos MeSH primário: Modelos Químicos
Complexo de Endopeptidases do Proteassoma/química
Proteínas/química
[Mh] Termos MeSH secundário: Azidas/química
Química Click
Células HEK293
Seres Humanos
Sondas Moleculares/química
Complexo de Endopeptidases do Proteassoma/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Azides); 0 (Molecular Probes); 0 (Proteins); EC 3.4.25.1 (Proteasome Endopeptidase Complex)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180116
[Lr] Data última revisão:
180116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161026
[St] Status:MEDLINE


  6 / 6528 MEDLINE  
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[PMID]:27778290
[Au] Autor:Yang Y; Fonovic M; Verhelst SH
[Ad] Endereço:Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
[Ti] Título:Cleavable Linkers in Chemical Proteomics Applications.
[So] Source:Methods Mol Biol;1491:185-203, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The discovery of the protein targets of small molecule probes is a crucial aspect of activity-based protein profiling and chemical biology. Mass spectrometry is the primary method for target identification, and in the last decade, cleavable linkers have become a popular strategy to facilitate protein enrichment and identification. In this chapter, we provide an overview of cleavable linkers used in chemical proteomics approaches, discuss their different chemistries, and describe how they aid in protein identification.
[Mh] Termos MeSH primário: Proteínas/química
Proteômica
[Mh] Termos MeSH secundário: Sondas Moleculares
Fotoquímica
Proteólise
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Molecular Probes); 0 (Proteins)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180116
[Lr] Data última revisão:
180116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161026
[St] Status:MEDLINE


  7 / 6528 MEDLINE  
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[PMID]:27778289
[Au] Autor:Claessen JH; Witte MD
[Ad] Endereço:MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
[Ti] Título:A Protocol for Protein Profiling Using Chemoselective Cleavable Linker Probes in Semi-permeabilized Cells.
[So] Source:Methods Mol Biol;1491:173-184, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Activity-based protein profiling using activity-based probes (ABPs) resulted in the identification of various enzymes that are involved in the onset and progress of diseases. Detection of such proteins, often expressed at low abundance, is greatly enhanced by incorporating chemically cleavable linkers in the ABP of choice. Initial affinity purification, followed by tailored chemical cleavage of the linker, allows for specific release of the captured enzymes and their interaction partners. When the ABPs are delivered directly to semi-permeabilized cells, in contrast to a crude cell lysate, the sensitivity and efficacy of cell impermeable probes can be enhanced even further.
[Mh] Termos MeSH primário: Permeabilidade da Membrana Celular
Proteínas/química
[Mh] Termos MeSH secundário: Cromatografia de Afinidade
Eletroforese em Gel de Poliacrilamida
Células HEK293
Células HeLa
Seres Humanos
Sondas Moleculares/química
Proteínas/isolamento & purificação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Molecular Probes); 0 (Proteins)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180116
[Lr] Data última revisão:
180116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161026
[St] Status:MEDLINE


  8 / 6528 MEDLINE  
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[PMID]:27778280
[Au] Autor:Chandrasekar B; Hong TN; van der Hoorn RA
[Ad] Endereço:The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829, Cologne, Germany.
[Ti] Título:Inhibitor Discovery by Convolution ABPP.
[So] Source:Methods Mol Biol;1491:47-56, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Activity-based protein profiling (ABPP) has emerged as a powerful proteomic approach to study the active proteins in their native environment by using chemical probes that label active site residues in proteins. Traditionally, ABPP is classified as either comparative or competitive ABPP. In this protocol, we describe a simple method called convolution ABPP, which takes benefit from both the competitive and comparative ABPP. Convolution ABPP allows one to detect if a reduced signal observed during comparative ABPP could be due to the presence of inhibitors. In convolution ABPP, the proteomes are analyzed by comparing labeling intensities in two mixed proteomes that were labeled either before or after mixing. A reduction of labeling in the mix-and-label sample when compared to the label-and-mix sample indicates the presence of an inhibitor excess in one of the proteomes. This method is broadly applicable to detect inhibitors in proteomes against any proteome containing protein activities of interest. As a proof of concept, we applied convolution ABPP to analyze secreted proteomes from Pseudomonas syringae-infected Nicotiana benthamiana leaves to display the presence of a beta-galactosidase inhibitor.
[Mh] Termos MeSH primário: Inibidores Enzimáticos/química
Proteômica/métodos
[Mh] Termos MeSH secundário: Inibidores Enzimáticos/farmacologia
Sondas Moleculares/química
Proteínas/química
Pseudomonas syringae/isolamento & purificação
Tabaco/química
beta-Galactosidase/antagonistas & inibidores
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Enzyme Inhibitors); 0 (Molecular Probes); 0 (Proteins); EC 3.2.1.23 (beta-Galactosidase)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180116
[Lr] Data última revisão:
180116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161026
[St] Status:MEDLINE


  9 / 6528 MEDLINE  
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[PMID]:27778279
[Au] Autor:Zweerink S; Pollmann T; Ninck S; Kaschani F; Kaiser M
[Ad] Endereço:ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.
[Ti] Título:Activity-Based Protein Profiling with Natural Product-Derived Chemical Probes in Human Cell Lysates.
[So] Source:Methods Mol Biol;1491:23-46, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Bioreactive natural products represent versatile starting points for the development of structurally unique activity-based probes. In the present protocol, we describe the workflow for an activity-based protein profiling (ABPP) experiment with an alkyne-tagged natural product derivative. Our protocol includes experimental procedures for in vivo labeling, sample preparation and 2-step (click chemistry) visualization and sample preparation for mass spectrometry-based target identification.
[Mh] Termos MeSH primário: Produtos Biológicos/química
Sondas Moleculares/química
Proteínas/química
[Mh] Termos MeSH secundário: Química Click
Células Hep G2
Seres Humanos
Proteoma
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Biological Products); 0 (Molecular Probes); 0 (Proteins); 0 (Proteome)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180116
[Lr] Data última revisão:
180116
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161026
[St] Status:MEDLINE


  10 / 6528 MEDLINE  
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[PMID]:29220150
[Au] Autor:Jia J; Zhang Y; Zheng M; Shan C; Yan H; Wu W; Gao X; Cheng B; Liu W; Tang Y
[Ad] Endereço:State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, and ‡Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, La
[Ti] Título:Functionalized Eu(III)-Based Nanoscale Metal-Organic Framework To Achieve Near-IR-Triggered and -Targeted Two-Photon Absorption Photodynamic Therapy.
[So] Source:Inorg Chem;57(1):300-310, 2018 Jan 02.
[Is] ISSN:1520-510X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The postsynthetic-modified nanoscale metal-organic framework (NMOF) probes selected as potential drug delivery platforms and photodynamic therapy agents to fulfill the effective and safe treatment of neoplastic diseases have attracted increasing attention recently. Herein, a Eu(III)-based NMOF probe elaborately postsynthetically modified with a ß-diketonate two-photon-absorbing (TPA) ligand is rationally designed and further functionalized by assembling the photosensitizer molecule (methylene blue, MB) in the pores and a cyclic peptide targeting motif on the surface of the NMOF, which could achieve highly efficient near-infrared (NIR)-triggered and -targeted photodynamic therapy (PDT). On the basis of the luminescence resonance energy transfer process between the NMOF donor and the photosensitizer MB acceptor, the probe can achieve a high tissue-penetrable TPA-PDT effect. Thus, the NMOFs in this study play the role of not only the nanocontainer for the photosensitizer but also the energy-transfer donor. Studies in vitro show enhanced cellular uptake and satisfactory PDT effectiveness toward cancer cells compared to the free photosensitizer MB. It is highly expected that this study contributes to the development of smart luminescent diagnostic and therapeutic probes.
[Mh] Termos MeSH primário: Antineoplásicos/farmacologia
Európio/farmacologia
Sondas Moleculares/farmacologia
Compostos Organometálicos/farmacologia
Fotoquimioterapia
Fótons
Fármacos Fotossensibilizantes/farmacologia
[Mh] Termos MeSH secundário: Antineoplásicos/síntese química
Antineoplásicos/química
Morte Celular/efeitos dos fármacos
Proliferação Celular/efeitos dos fármacos
Ensaios de Seleção de Medicamentos Antitumorais
Európio/química
Seres Humanos
Raios Infravermelhos
Sondas Moleculares/síntese química
Sondas Moleculares/química
Nanopartículas/química
Compostos Organometálicos/síntese química
Compostos Organometálicos/química
Tamanho da Partícula
Fármacos Fotossensibilizantes/síntese química
Fármacos Fotossensibilizantes/química
Propriedades de Superfície
Células Tumorais Cultivadas
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antineoplastic Agents); 0 (Molecular Probes); 0 (Organometallic Compounds); 0 (Photosensitizing Agents); 444W947O8O (Europium)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180109
[Lr] Data última revisão:
180109
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171209
[St] Status:MEDLINE
[do] DOI:10.1021/acs.inorgchem.7b02475



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