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This is seen for many transient interactions [ 9].
Many transient interactions and low-affinity complexes are difficult to study by alanine scanning or crystallography.
With the co-expression information, our ePPID measure can filter out many transient interactions.
Furthermore, many transient interactions are detected between proteins that are not from the same complex, while not all proteins from the same complex may actually interact.
As indicated above the gp120 specific B cells did not make a single long lasting synapse with the gp120 bearing IFC macrophages, but rather many transient interactions during which time the specific B cells serially extracted gp120 from the IFC cells, much like bumble bees gathering nectar.
Similar(55)
However, a protein with many transient interaction partners may transiently interact with its different partners through the same binding interface (though it is possible that the protein may form a transient complex with its partners through multiple distinct binding interfaces), thus the PPID of the protein may not well reflect the proportion of its interface residues [ 22].
Since ePPID is a measure that integrates protein interactions with gene co-expression information, it can filter out many transient protein interactions.
This is more akin to the liquid state of matter, where many transient homotypic interactions, counteracted by thermal motion, lead to a fluid situation without absolute order but still keeping the molecules together.
This result suggests that ePPID has filtered out many transient protein interactions in the "Y2H-union" dataset, which may be the reason of lower percent variance of evolutionary rate explained by PPID.
However, most of these approaches depend on the availability of prior knowledge and many biologically relevant systems remain out of reach, as additional experimental information is sparse (e.g., membrane proteins, transient interactions, and large complexes).
Even transient interactions can have a profound effect.
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