Biology Reference
In-Depth Information
Chapter 8
Protein-Protein Interaction Networks:
Assembly and Analysis
Christian von Mering
1. Introduction
Protein-protein interactions are essential for all cellular life.
1
Only very
few proteins, if any, can function entirely on their own — presumably
only in self-contained processes such as constitutive transport or trivial
enzymatic reactions. Indeed, the vast majority of proteins are bound by
specific protein partners at one point or another during their functional
life cycle, either because they need to be controlled and regulated in their
activity or because they can only function as part of a larger molecular
complex.
Specific and functionally relevant interactions between proteins are
often conceptualized in the form of “interaction networks”. In interac-
tion networks, the proteins are defined as nodes, and the interactions as
edges; the latter can be further subclassified depending on the type and
strength of interaction. By convention, interaction networks do not
include nonspecific, generic interactions between proteins, such as the
interaction between a nascent protein chain and the ribosome, between
a freshly produced protein and downstream processing enzymes (chaper-
ones), or between a damaged protein and the protein degradation
machinery. Thus, protein-protein interaction networks aim to focus on
the set of specific and functionally relevant protein interaction interfaces
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