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Trends in Protein-Protein Interactions Research | Protein-Protein Interactions: Lessons from the Past and Current Directions

PDGF receptor by its use of a transmembrane
interaction. "That started the idea to create
artificial transmembrane proteins, and we
wonder if there are similar proteins in cells
that people never looked for," says DiMaio.
Some of these proteins are small and could
easily be missed or ignored during genomic or
biochemical searches, but may have biological
value. "There may be a whole universe of
proteins out there that has not been studied
very much, and this conceivably could represent a whole new class of therapeutics,"
concludes DiMaio.
 "We got engaged in the idea of chemical crosslinking to look at protein-protein interactions
early on, but we identified some major stumbling
blocks," says James E. Bruce, PhD, professor of
genome sciences at the University of Washington.
Crosslinking has been successfully used for
decades, and made it relatively easy to identify
binding partners from small protein databases or
for few interacting proteins. Comparatively, using
conventional crosslinking for large-scale applications has been challenging. "With conventional
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crosslinking the identification of each crosslinked
peptide has been a real bottleneck," says Bruce,
"and the task rapidly can become intractable for
most approaches."

Identifying Crosslinked Peptides
In a recent study, Bruce and colleagues developed a protein interaction reporter-based
crosslinking approach combined with mass
spectrometry, and used it to identify crosslinked
peptides generated from the mitochondrial
interactome. This strategy provided unprecedented insights into the structure
of many mitochondrial proteins,
including the ones involved
in oxidative phosphorylation.
Some of the peptide pairs that
were identified supported the
existence of the respirasome.
"The underpinning of this whole
approach is to learn about what
proteins are interacting and what
conformational features of proteins exist
in the system when we do the crosslinking,"
explains Bruce.

This technique promises to unveil details of
the interactions between drugs and proteins in
complex systems. In a recent research effort that
quantitatively examined cancer cells targeted
with HSP-90 inhibitors, Bruce and colleagues
identified conformational changes and protein-
protein interaction, specifically in the HSP-90
network in a drug concentration-dependent
and a drug mechanism of action-specific
manner. "A new area that we are proposing, as
to where this technology can go, is what we call
'systems structural biology,'


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