Many, if not all, essential biological processes require selective
interactions between proteins. Complex signaling systems require
sequential, ordered protein-protein interactions at essentially all
levels of the signaling cascade. For example, peptide hormones interact
with selective membrane receptor proteins, and autophosphorylation of
the receptor then recruits other key regulatory proteins that initiate
kinase cascades in which each phosphorylation event requires selective
recognition of the protein substrate. The ultimate signaling effect, in
many cases, is the regulation of RNA polymerase II-directed transcr-
tion in the nucleus, a process that involves numerous, multiprotein
complexes important for transcription initiation, elongation,
termination, and reinitiation. Defining, characterizing, and
understanding the relevance of these protein- protein interactions is an
arduous task, but substantial inroads have been made over the past 20
years. The development of more recent methodologies, such as mammalian
expression systems, immunopurification schemes, expression cloning
strategies, surface plasmon resonance (BiaCore), and nanosequencing
technologies, has contributed a wealth of new insights into these
complex multiprotein mechanisms and clearly accelerated the discovery
process. Arguably, the yeast two-hybrid system has been one of the
predominant and most powerful tools in this discovery process.
