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Pattern in the Scribble

Representations of protein-protein interactions can look like a scribble drawn by a toddler. But as Jeffrey Marlow points out at The Extremo Files, researchers have been developing approaches to better separate the signal from the noise in the interactome.

The Max Planck Institute of Biochemistry's Matthias Mann and his colleagues recently described an approach in Cell "to not only capture these interactions, but also to quantify their occurrence and characterize their strength," Marlow says.

Mann and his colleagues developed an approach they dubbed QUBIC, for quantitative BAC-GFP interactomics, that combines two approaches they previously developed. In their paper, they describe creating a library of HeLa cell lines that expressed 1,125 GFP-tagged proteins from BAC transgenes. Using this, they conducted 3,990 LC-MS runs to find some 28,500 interactions among nearly 5,500 proteins.

As Marlow notes, these interacting pairs included protein complexes needed for bone development and cell division. But, "[p]erhaps most striking was how common PPIs are," he says.

Many of these interactions are temporary and thus thought to be not that importance, Marlow says. However, he adds that some new studies are beginning to indicate that these transient interactions may "regulate broader processes or signal a change in the environment. "