Bioinformatic analysis of adhesion proteins

Proteins that mediate cell-cell and cell-extracellular matrix (ECM) adhesion have been fundamental in the evolution of multicellular animals. Fibrillar collagens, proteoglycans, integrins, and cadherins are present in all animals from sponges to mammals, and many other adhesion proteins have arisen during animal evolution. In general, adhesion proteins are large multidomain molecules and are encoded in larger gene families in vertebrates than in invertebrates. With the increasing availability of completely sequenced genomes representing different points on the animal tree of life, bioinformatics is proving to be a very valuable approach for the analysis of the domain organization and relationships of adhesion proteins, which can direct or enhance experimental tests. Here we describe, with examples from the literature, the major methods for identifying sequence homologies; analyzing domain organization and potential for oligomerization; analyzing sequence relationships by multiple sequence alignments and phylogenetic trees, and assessing adhesion proteins as components of functional pathways and tissue systems through comparative genomics.