Proteome-Wide Characterization of Phosphorylation-Induced Conformational Changes in Breast Cancer

Because of the close link between protein function and protein folding stability, knowledge about phosphorylation-induced protein folding stability changes can lead to a better understanding of the functional effects of protein phosphorylation. Here, the stability of proteins from rates of oxidation (SPROX) and limited proteolysis (LiP) techniques are used to compare the conformational properties of proteins in two MCF-7 cell lysates including one that was and one that was not dephosphorylated with alkaline phosphatase. A total of 168 and 251 protein hits were identified with dephosphorylation-induced stability changes using the SPROX and LiP techniques, respectively. Many protein hits are previously known to be differentially phosphorylated or differentially stabilized in different human breast cancer subtypes, suggesting that the phosphorylation-induced stability changes detected in this work are disease related. The SPROX hits were enriched in proteins with aminoacyl-tRNA ligase activity. These enriched protein hits included many aminoacyl-tRNA synthetases (aaRSs), which are known from previous studies to have their catalytic activity modulated by phosphorylation. The SPROX results revealed that the magnitudes of the destabilizing effects of dephoshporylation on the different aaRSs were directly correlated with their previously reported aminoacylation activity change upon dephosphorylation. This substantiates the close link between protein folding and function.