Cisbio eBook - 8

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

Scott C. Soderberg, Michigan Photography

"In cells, most proteins perform their functions by
interacting with other molecules and we tried to
take advantage of the protein-protein interaction
networks to deduce the function of proteins for
which we cannot identify functional homologies."
-Yang Zhang, PhD
and involves structural biology performed on
intact systems," concludes Bruce. 
Systems structural biology offers the opportunity
to visualize protein complex structural features
that can shed new light on disease pathologies,
provide molecular-level insights on potential
therapies, and greatly expand knowledge of
many biological processes.
"We are trying to interpret what each protein
does in the living cells through computational
algorithms," says Yang Zhang, PhD, professor of

8 | GENengnews.com

computational medicine & bioinformatics and
professor of biological chemistry at the University
of Michigan.
Computer-based protein function annotation
has been historically performed by relying on
homology inference. This approach, established
for years, involved an initial search for functional
homology to a query protein, followed by transferring the functions of the known homologies
(as template) to the unknown query protein.
However, homology-based functional annotation
becomes unreliable when the sequence identity

between the query and template proteins is low,
and typically lower than 30%.
"In cells, most proteins perform their functions
by interacting with other molecules and we
tried to take advantage of the protein-protein
interaction networks to deduce the function of
proteins for which we cannot identify functional
homologies," says Zhang. Based on this idea,
Zhang and colleagues developed a new method,
MetaGO, for automated protein function annotations. "MetaGO predicts the gene ontology of
a query protein using protein-protein interaction networks as an important component," says
Zhang. As a hybrid method, MetaGO integrates
three complementary pipelines-built on evolutionary biology, structural biology, and protein
interaction networks-for multi-level function
annotations.
"The idea of using protein-protein interaction
networks to deduce new protein functions is
not new," says Zhang. In previous approaches,



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Cisbio eBook

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Contents
Cisbio eBook - 1
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Cisbio eBook - Contents
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