Prediction of Protein–protein Interactions from Evolutionary Information Evolutionary Features Related with Structure and Function Afvvtdncikckytdcvevcpvdcfyegpnflvihpdecidcalcepecp Pyvvtencikckyqdcvevcpvdcfyegenflvinpdecidcgvcnpecp Phvicqpcigvkdqscvevcpveciydggdqfyihpeecidcgacvpacp Pfvitspeigekaadc

INTRODUCTION The more we know about the molecular biology of the cell, the more we see genes and proteins as part of networks or pathways instead of as isolated entities and understand their function as a variable of the cellular context. To fulfill this new paradigm, genomic sequences offer a catalog of building blocks, and protein interactions provide the first information for the challenging task of understanding the functions of these genes and proteins within their situation in networks and pathways. To further refine the information on the context and timing in which these observed biological functions take place, additional insight from genetic regulatory mechanisms and genetic specificity (cell-type specificity, individual differences, etc.) will become increasingly important. The study of protein interactions can be divided into two complementary aspects, the determination of the residues or regions implicated in the interactions and the deciphering of the identity of the interaction partners (which proteins interact with which ones). These two problems have been typically addressed by biophysical and biochemical techniques, such as binding studies (chromatographic isolation of complexes, coimmunoprecipitation, protection , cross-linking studies, etc.) and indirect genetic methods (gene suppression studies, systematic mutagenesis, and interspecies exchanges). The development of genomic and postgenomic technologies has changed the panorama considerably, with the possibility of obtaining systematically massive amounts of data about protein interactions. Progress has been done in the automation of experimental approaches such as yeast-two-hybrid based methods and mass spectrometry determination of components of macromolecular complexes. At the same time, a number of new bioinformatics techniques have been developed based on the considerable amount of sequence and genomic information that is being accumulated in databases. In the following, we review the status of these bioinformatics approaches to the study of protein interactions, including the prediction of interaction partners and protein–protein binding regions. Multiple sequence alignments (MSA) represent the main source of evolutionary information available. The relation between equivalent positions of homologous proteins compiles the result of the changes allowed by the evolution of the corresponding proteins at different positions. The interplay of structural and functional requirements contributing to the stabilization of natural variants creates complex patterns of mutational behavior of the positions that have been exploited by a number of computational methods in the search for structural and/or functional constraints (Figure 26.1). Conserved Positions. The information most widely extracted from multiple sequence alignments is related with conserved positions (Zuckerkandl and Pauling, 1965). These …