Protein interactions control the life and death of cells, yet we are only beginning to appreciate the nature and complexity of these networks. Two problems will be discussed. The first is how to synthesize information from fully sequenced genomes and microarray studies into knowledge about the network of interacting proteins in cells. Clustered genome-wide interaction maps will be explained and applied to Micobacterium
tuberculosis and other organisms. The outcome is increased understanding of the network of interacting proteins, and enhanced knowledge of the contextual function of proteins. These inferred interactions can be compared to directly measured protein interactions, collected in the
Database of Interacting Proteins [http://dip.doe-mbi.ucla.edu].
The second problem is the nature of the amyloid state, in which normally soluble proteins undergo a transition to linear, insoluble fibers. Evidence will be presented that short peptide segments are sufficient to form amyloid, and a model for amyloids of whole proteins will be presented, based on this and other evidence.