ABSTRACT
With expanding interest in proteomics, we are faced with the daunting task of literally connecting all the “dots.” Even the protein maps of relatively simple organisms such as
Drosophila melanogaster
reveal tens of thousands of potential interactions, which
are represented in most proteomics maps by tiny dots interconnected by lines (fig. 14.1) [1]. But, of course, proteins are not dots and, more importantly, the connections between them are not simply lines. Proteins are dynamic, and their relationships are complex. They interact with themselves, other proteins, nucleic
acids, substrates, cofactors, membranes, and other biomolecules. It is the dynamics of protein interactions that define their activity but, unfortunately, dynamics is the one thing that is often missing from protein interaction maps. If we intend to put proteome maps to use, we will need to supplement these static representations of pathways with kinetic information that reveals the time scale of binding events.
