Systems Analysis of Arrestin Pathway Functions - Progress in Molecular Biology and Translational Science - page 434

one of the most important breakthroughs for phosphoproteomics and
GPCR cellular signaling analysis. The coherent combination of this tech-
nique with quantitative tools has significantly assisted the global understand-
ing of phosphoproteomic signaling patterns. 123,124
It is likely that without significant development of new, radically
advanced, analytical MS-based approaches, the systematic investigation of
multiple GPCR-mediated parallel protein PTM networks remains a distant
target. For the present time, such investigations will be hampered by slow
workflow rates and a lack of direct comparison or association of various
PTM signaling patterns with either G protein or b -arrestin-mediated signal-
ing. However, potential solutions to this issue may yet present themselves via
the application of advanced bioinformatic approaches that will be discussed
in subsequent sections.
3.4. Physical interactomic investigation
While assessments of the PTM status of proteins add an extra level of func-
tional information concerning protein function, this level of investigation
may still be physically removed from the true functional crux of the specific
protein. It is likely that the true physiological ramifications of GPCR-
mediated changes in protein activity may only be fully appreciated by the
combined measurement of expression, PTM, and the eventual subcellular
appreciation of the protein-protein-binding interactions of those proteins.
While the expression profile of proteins forms a global proteome, the direct
functional actions of proteins are probably mediated by the formation of
small complexes of functionally related proteins possessing a specific PTM
state, in a particular subcellular microdomain. 125,70 The physical
protein-protein interaction constellation of any specific protein can be
referred to as its physical interactome. The interactome of a given protein will
depend on the presence in its primary amino acid sequence of classical
protein-protein-binding modules, PTM sites, and biophysical interaction
domains. Specific protein interactomes may vary from 10 to 100 proteins;
however, accurate numerical estimates of the interactome size for most pro-
teins have yet to be effectively determined. Mirroring the flexibility and
variety of GPCR stable isoforms, there are likely to be, for each protein's
interactome, a wide diversity of interactome compositions. As with GPCR
receptorsomes , the direct functional interactome composition of any specific
protein may therefore be a function of the cellular type as well as the tem-
poral and pathophysiological status of the cell or tissue.