Phosphoprotein profiling by PA-GeLC-MS/MS.
A significant consequence of protein phosphorylation is to alter protein-protein interactions, leading to dynamic regulation of the components of protein complexes that direct many core biological processes. Recent proteomic studies have populated databases with extensive compilations of cellular phosphoproteins and phosphorylation sites and a similarly deep coverage of the subunit compositions and interactions in multiprotein complexes. However, considerably less data are available on the dynamics of phosphorylation, composition of multiprotein complexes or that define their interdependence. We describe a method to identify candidate phosphoprotein complexes by combining phosphoprotein affinity chromatography, separation by size, denaturing gel electrophoresis, protein identification by tandem mass spectrometry, and informatics analysis. Toward developing phosphoproteome profiling, we have isolated native phosphoproteins using a phosphoprotein affinity matrix, Pro-Q Diamond resin (Molecular Probes-Invitrogen). This resin quantitatively retains phosphoproteins and associated proteins from cell extracts. Pro-Q Diamond purification of a yeast whole cell extract followed by 1-D PAGE separation, proteolysis and ESI LC-MS/MS, a method we term PA-GeLC-MS/MS, yielded 108 proteins, a majority of which were known phosphoproteins. To identify proteins that were purified as parts of phosphoprotein complexes, the Pro-Q eluate was separated into two fractions by size, <100 kDa and >100 kDa, before analysis by PAGE and ESI LC-MS/MS and the component proteins queried against databases to identify protein-protein interactions. The <100 kDa fraction was enriched in phosphoproteins indicating the presence of monomeric phosphoproteins. The >100 kDa fraction contained 171 proteins of 20-80 kDa, nearly all of which participate in known protein-protein interactions. Of these 171, few are known phosphoproteins, consistent with their purification by participation in protein complexes. By comparing the results of our phosphoprotein profiling with the informational databases on phosphoproteomics, protein-protein interactions and protein complexes, we have developed an approach to examining the correlation between protein interactions and protein phosphorylation.
Department of Molecular Genetics and Cell Biology, and Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois 60637, USA.
Kolbrun
K
Kristjansdottir
Donald
D
Wolfgeher
Nick
N
Lucius
David Sigfredo
DS
Angulo
Stephen J
SJ
Kron
D002853:Chromatography, Liquid; D016208:Databases, Factual; D005656:Fungal Proteins / Q000096:biosynthesis; D006801:Humans; D020014:K562 Cells; D046912:Multiprotein Complexes / Q000032:analysis; D010750:Phosphoproteins / Q000032:analysis* / Q000302:isolation & purification / Q000378:metabolism; D010744:Phosphoric Monoester Hydrolases / Q000037:antagonists & inhibitors; D010766:Phosphorylation; D010769:Phosphothreonine / Q000032:analysis; D019000:Phosphotyrosine / Q000032:analysis; D020543:Proteome / Q000032:analysis*; D053719:Tandem Mass Spectrometry; D015003:Yeasts / Q000378:metabolism
D005656:Fungal Proteins; D046912:Multiprotein Complexes; D010750:Phosphoproteins; D020543:Proteome; D010769:Phosphothreonine; D019000:Phosphotyrosine; D010744:Phosphoric Monoester Hydrolases