ABSTRACT
Interactions between domains occur in multidomain proteins, in stable complexes and in transient interactions between proteins that also exist independently. This chapter introduces two types of large-scale experimental approaches: yeast-two-hybrid screening and routine purification of complexes followed by mass spectrometry. Both approaches have been applied to the Saccharomyces cerevisiae proteome on a genome wide scale in efforts towards determining the complete network of protein interactions in this organism. The chapter discusses methods for prediction of protein interactions based on gene structure or gene order. An approach for predicting protein interactions is to look for cases across a set of genomes where two or more orthologs are part of the same gene in one genome, presumably as a result of gene fusion. In prokaryotes, genes are organized into operons of co-regulated and co-expressed groups of genes. Thus conservation of gene order across different, distantly related genomes has been used as a method for predicting protein interactions.
