The rapidly evolving field of protein science has now come to
realize the ubiquity and importance of protein-protein
interactions. It had been known for some time that proteins may
interact with each other to form functional complexes, but it was
thought to be the property of only a handful of key proteins.
However, with the advent of high throughput proteomics to monitor
protein-protein interactions at an organism level, we can now
safely state that protein-protein interactions are the norm and not
the exception. Thus, protein function must be understood in the
larger context of the various binding complexes that each protein
may form with interacting partners at a given time in the life
cycle of a cell. Proteins are now seen as forming sophisticated
interaction networks subject to remarkable regulation. The study of
these interaction networks and regulatory mechanism, which I would
like to term "systems proteomics," is one of the thriving fields of
proteomics.
The bird-eye view that systems proteomics offers should not
however mask the fact that proteins are each characterized by a
unique set of physical and chemical properties. In other words, no
protein looks and behaves like another. This complicates enormously
the design of high-throughput proteomics methods. Unlike genes,
which, by and large, display similar physico-chemical behaviors and
thus can be easily used in a high throughput mode, proteins are not
easily amenable to the same treatment. It is thus important to
remind researchers active in the proteomics field the fundamental
basis of protein chemistry. This book attempts to bridge the two
extreme ends of protein science: on one end, systems proteomics,
whichdescribes, at a system level, the intricate connection network
that proteins form in a cell, and on the other end, protein
chemistry and biophysics, which describe the molecular properties
of individual proteins and the structural and thermodynamic basis
of their interactions within the network.
Bridging the two ends of the spectrum is bioinformatics and
computational chemistry. Large data sets created by systems
proteomics need to be mined for meaningful information, methods
need to be designed and implemented to improve experimental
designs, extract signal over noise, and reject artifacts, and
predictive methods need to be worked out and put to the test.
Computational chemistry faces similar challenges. The prediction of
binding thermodynamics of protein-protein interaction is still in
its infancy. Proteins are large objects, and simplifying
assumptions and shortcuts still need to be applied to make
simulations manageable, and this despite exponential progress in
computer technology.
Finally, the study of proteins impacts directly on human health.
It is an obvious statement to say that, for decades, enzymes,
receptors, and key regulator proteins have been targeted for drug
discovery. However, a recent and exciting development is the
exploitation of our knowledge of protein-protein interaction for
the design of new pharmaceuticals. This presents particular
challenges because protein-protein interfaces are generally shallow
and interactions are weak. However, progress is clearly being made
and the book seeks to provide examples of successes in this
area.
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