Investigation of Protein-Protein Interactions by Blue Native-PAGE & Mass Spectrometry

Challenges in Structural Investigation of Transient Protein-Protein Interactions

“…Analysis of PPIs in signaling pathways starts with the Immunoprecipitation (IP) of the receptors followed by identification of their protein interaction partners. In the next step, additional interacting partners may be identified [1][2][3][4][5][6][7][8][9]. A very common method for studying PPIs is co-Immunoprecipitation (co-IP) [10,11].…”

“…Mass spectrometry (MS) is one of the most powerful tools for identifying proteins [2,[19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34] and PPIs [1,3,4,10,14,35,36], simply because it can be easily combined with IP, SDS-PAGE, chromatography, native PAGE, BN-PAGE CN-PAGE, and allows one to identify many potential interacting partners of a protein by analyzing the proteins or protein complexes (isolated and/or purified by one of the previously described methods) by Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) or by liquid chromatographytandem mass spectrometry (LC-MS/MS), in an approach referred to as proteomics [3][4][5]14,29,30,[36][37][38][39][40][41][42]. As such, most PPIs are indirectly identified through digestion of the protein complexes purified through one of the previously described methods (i.e.…”

Post-Translational Modification (PTM) Proteomics: Challenges and Perspectives

“…Proteins are the gene products and thus their effectors [1][2][3][4][5][6]. Proteins can be part of two or more different biological processes due to two main intrinsic properties: protein-protein interactions (PPIs) and PTMs of proteins [1,2,[7][8][9][10]. Being part of a protein complex with inhibitory properties (towards a particular biological process, e.g.…”

“…Proteomics is the study of proteins, protein PTMs, PPIs of the cells, tissues, organs or organisms (or bodily fluids) at a particular stage or time-point (physiological or pathological, or during development) [1,2,7,17,[34][35][36]. Proteomics is performed at both qualitative (protein and protein PTMs identification and characterization) and quantitative (protein and protein PTMs quantitation) [1,2,7,17,[34][35][36].…”

Tumor Differentiation Factor (TDF) and its Receptor (TDF-R): Is TDF-R an Inducible Complex with Multiple Docking Sites?

“…Virtually, all expressed proteins in a given cell are arranged into multi-protein complexes [1][2][3][4][5][6][7][8][9]. Identification of individual components of those complexes is extremely important for their functional characterization [5,8,[10][11][12][13][14][15][16][17][18][19][20]. One of the most powerful methods in identifying proteins is mass spectrometry, in particular, Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) [5,8,[15][16][17][18][19].…”