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An Evolutionarily Structured Universe of Protein Architecture

¹ Vital NRG, Knoxville, Tennessee 37919, USA ² Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801, USA

Protein structural diversity encompasses a finite set of architectural designs. Embedded in these topologies are evolutionary histories that we here uncover using cladistic principles and measurements of protein-fold usage and sharing. The reconstructed phylogenies are inherently rooted and depict histories of protein and proteome diversification. Proteome phylogenies showed two monophyletic sister-groups delimiting Bacteria and Archaea, and a topology rooted in Eucarya. This suggests three dramatic evolutionary events and a common ancestor with a eukaryotic-like, gene-rich, and relatively modern organization. Conversely, a general phylogeny of protein architectures showed that structural classes of globular proteins appeared early in evolution and in defined order, the / class being the first. Although most ancestral folds shared a common architecture of barrels or interleaved -sheets and -helices, many were clearly derived, such as polyhedral folds in the all- class and -sandwiches, -propellers, and -prisms in all- proteins. We also describe transformation pathways of architectures that are prevalently used in nature. For example, -barrels with increased curl and stagger were favored evolutionary outcomes in the all- class. Interestingly, we found cases where structural change followed the -to- tendency uncovered in the tree of architectures. Lastly, we traced the total number of enzymatic functions associated with folds in the trees and show that there is a general link between structure and enzymatic function.

³ Corresponding author.
E-MAIL gca{at}uiuc.edu; FAX (217)333-8045.

[Supplemental material is available online at www.genome.org.]

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