Evolution of protein architecture: The protein world

Contemporary protein architectures can be regarded as molecular fossils, historical imprints that mark important milestones in the history of life. A census of protein structure in proteomes and novel bioinformatics methods uncovered patterns and processes linked to the evolution of both proteins and proteomes that are described here. Timelines of discovery of protein architectures revealed episodes of specialization, reductive evolutionary tendencies of architectural repertoires in proteomes and the rise of modularity in the protein world. Some of these tendencies were driven by recruitment of structures and functions. Our observations have important implications for origins of modern biochemistry, modules in the protein world, and diversification of life.