A Quantitative Proteomic Approach for the Identification of DNA Guanine Quadruplex-Binding Proteins

2021 ◽  
Author(s):  
Zi Gao ◽  
Preston Williams ◽  
Lin Li ◽  
Yinsheng Wang
Keyword(s):  
Binding Proteins ◽  
Proteomic Approach ◽  
Guanine Quadruplex

scholarly journals Identification and characterization of RNA guanine-quadruplex binding proteins

2014 ◽  
Vol 42 (10) ◽  
pp. 6630-6644 ◽  
Author(s):  
Annekathrin von Hacht ◽  
Oliver Seifert ◽  
Marcus Menger ◽  
Tatjana Schütze ◽  
Amit Arora ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Guanine Quadruplex ◽  
Identification And Characterization

Profiling and comprehensive expression analysis of ABC transporter solute-binding proteins ofBacillus subtilis membrane based on a proteomic approach

2004 ◽  
Vol 25 (1) ◽  
pp. 141-155 ◽  
Author(s):  
Keigo Bunai ◽  
Masanori Ariga ◽  
Taro Inoue ◽  
Manabu Nozaki ◽  
Shinya Ogane ◽  
...  
Keyword(s):  
Abc Transporter ◽  
Expression Analysis ◽  
Binding Proteins ◽  
Ofbacillus Subtilis ◽  
Proteomic Approach

scholarly journals Middle-down proteomics reveals dense sites of methylation and phosphorylation in arginine-rich RNA-binding proteins

2019 ◽  
Author(s):  
Sean R. Kundinger ◽  
Isaac Bishof ◽  
Eric B. Dammer ◽  
Duc M. Duong ◽  
Nicholas T. Seyfried
Keyword(s):  
Binding Proteins ◽  
Electron Transfer Dissociation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Metabolism ◽  
Hek293 Cells ◽  
Motif Analysis ◽  
Proteomic Approach ◽  
Nuclear Extracts ◽  
And Function

AbstractArginine (Arg)-rich RNA-binding proteins play an integral role in RNA metabolism. Post-translational modifications (PTMs) within Arg-rich domains, such as phosphorylation and methylation, regulate multiple steps in RNA metabolism. However, the identification of PTMs within Arg-rich domains with complete trypsin digestion is extremely challenging due to the high density of Arg residues within these proteins. Here, we report a middle-down proteomic approach coupled with electron transfer dissociation (ETD) mass spectrometry to map previously unknown sites of phosphorylation and methylation within the Arg-rich domains of U1-70K and structurally similar RNA-binding proteins from nuclear extracts of HEK293 cells. Remarkably, the Arg-rich domains in RNA-binding proteins are densely modified by methylation and phosphorylation compared with the remainder of the proteome, with di-methylation and phosphorylation favoring RSRS motifs. Although they favor a common motif, analysis of combinatorial PTMs within RSRS motifs indicate that phosphorylation and methylation do not often co-occur, suggesting they may functionally oppose one another. Collectively, these findings suggest that the level of PTMs within Arg-rich domains may be among the highest in the proteome, and a possible unexplored regulator of RNA metabolism. These data also serve as a resource to facilitate future mechanistic studies of the role of PTMs in RNA-binding protein structure and function.BriefsMiddle-down proteomics reveals arginine-rich RNA-binding proteins contain many sites of methylation and phosphorylation.

scholarly journals A proteomic approach to identify metalloproteins and metal-binding proteins in liver from diabetic rats

2017 ◽  
Vol 96 ◽  
pp. 817-832 ◽  
Author(s):  
Camila Pereira Braga ◽  
José Cavalcante Souza Vieira ◽  
Ryan A. Grove ◽  
Cory H.T. Boone ◽  
Aline de Lima Leite ◽  
...  
Keyword(s):  
Metal Binding ◽  
Binding Proteins ◽  
Diabetic Rats ◽  
Proteomic Approach

scholarly journals A proteomic approach to identification of plutonium-binding proteins in mammalian cells

2012 ◽  
Vol 75 (5) ◽  
pp. 1505-1514 ◽  
Author(s):  
Baikuntha P. Aryal ◽  
Tatjana Paunesku ◽  
Gayle E. Woloschak ◽  
Chuan He ◽  
Mark P. Jensen
Keyword(s):  
Mammalian Cells ◽  
Binding Proteins ◽  
Proteomic Approach

A proteomic approach for the identification of bismuth-binding proteins in Helicobacter pylori

2007 ◽  
Vol 12 (6) ◽  
pp. 831-842 ◽  
Author(s):  
Ruiguang Ge ◽  
Xuesong Sun ◽  
Qing Gu ◽  
Rory M. Watt ◽  
Julian A. Tanner ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Binding Proteins ◽  
Proteomic Approach

scholarly journals A proteomic approach to the identification of heterogeneous nuclear ribonucleoproteins as a new family of poly(ADP-ribose)-binding proteins

2003 ◽  
Vol 371 (2) ◽  
pp. 331-340 ◽  
Author(s):  
Jean-Philippe GAGNÉ ◽  
Joanna M. HUNTER ◽  
Benoît LABRECQUE ◽  
Benoît CHABOT ◽  
Guy G. POIRIER
Keyword(s):  
Protein Identification ◽  
Binding Proteins ◽  
Peptide Mass Fingerprinting ◽  
Sequence Motif ◽  
Dot Blot ◽  
New Family ◽  
Peptide Mass ◽  
Proteomic Approach ◽  
Heterogeneous Nuclear Ribonucleoproteins ◽  
Binding Sequence

A new class of poly(ADP-ribose) (pADPr)-binding proteins, heterogeneous nuclear ribonucleoproteins (hnRNPs), has been identified by a proteomic approach using matrix-assisted laser-desorption–ionization time-of-flight ('MALDI-TOF') MS. Liquid-phase isoelectric focusing with a Rotofor® cell (Bio-Rad) allowed pre-fractionation of proteins extracted from HeLa cells. Rotofor® protein fractions were further separated by SDS/PAGE and then transferred to a PVDF membrane. pADPr-binding proteins were analysed by autoradiography of the protein blot after incubation with 32P-labelled automodified pADPr polymerase-1 (PARP-1). Peptide mass fingerprinting of selected bands identified the most abundant pADPr-binding proteins as hnRNPs, a family of proteins that bind pre-mRNA into functional complexes involved in mRNA maturation and transport to the cytoplasm. Sequence homology database searching against a previously reported pADPr-binding sequence motif revealed that the hnRNPs contain a putative pADPr-binding sequence pattern [Pleschke, Kleczkowska, Strohm and Althaus (2000) J. Biol. Chem. 275, 40974–40980]. pADPr-binding assays performed with synthetic peptides by the dot-blot technique and with nitrocellulose-transferred recombinant hnRNPs confirmed the pADPr-binding protein identification and the specificity of the interaction. These results could establish a link between increased levels of pADPr in DNA damaged cells and the modified protein expression pattern resulting from altered mRNA trafficking.

scholarly journals NPM/ALK binds and phosphorylates the RNA/DNA-binding protein PSF in anaplastic large-cell lymphoma

Blood ◽  
2007 ◽  
Vol 110 (7) ◽  
pp. 2600-2609 ◽  
Author(s):  
Annamaria Galietta ◽  
Rosalind H. Gunby ◽  
Sara Redaelli ◽  
Paola Stano ◽  
Cristiana Carniti ◽  
...  
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Binding Proteins ◽  
Binding Protein ◽  
Cellular Transformation ◽  
Large Cell ◽  
Kinase Domain ◽  
Anaplastic Lymphoma ◽  
Proteomic Approach

The oncogenic fusion tyrosine kinase nucleophosmin/anaplastic lymphoma kinase (NPM/ALK) induces cellular transformation in anaplastic large-cell lymphomas (ALCLs) carrying the t(2;5) chromosomal translocation. Protein-protein interactions involving NPM/ALK are important for the activation of downstream signaling pathways. This study was aimed at identifying novel NPM/ALK-binding proteins that might contribute to its oncogenic transformation. Using a proteomic approach, several RNA/DNA-binding proteins were found to coimmunoprecipitate with NPM/ALK, including the multifunctional polypyrimidine tract binding proteinassociated splicing factor (PSF). The interaction between NPM/ALK and PSF was dependent on an active ALK kinase domain and PSF was found to be tyrosine-phosphorylated in NPM/ALK-expressing cell lines and in primary ALK+ ALCL samples. Furthermore, PSF was shown to be a direct substrate of purified ALK kinase domain in vitro, and PSF Tyr293 was identified as the site of phosphorylation. Y293F PSF was not phosphorylated by NPM/ALK and was not delocalized in NPM/ALK+ cells. The expression of ALK fusion proteins induced delocalization of PSF from the nucleus to the cytoplasm and forced overexpression of PSF-inhibited proliferation and induced apoptosis in cells expressing NPM/ALK. PSF phosphorylation also increased its binding to RNA and decreased the PSF-mediated suppression of GAGE6 expression. These results identify PSF as a novel NPM/ALK-binding protein and substrate, and suggest that PSF function may be perturbed in NPM/ALK-transformed cells.

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