The early history and emergence of molecular functions and modular scale-free network behavior

M. Fayez Aziz, Kelsey Caetano-Anollés, Gustavo Caetano-Anollés

Research output: Contribution to journalArticlepeer-review


The formation of protein structural domains requires that biochemical functions, defined by conserved amino acid sequence motifs, be embedded into a structural scaffold. Here we trace domain history onto a bipartite network of elementary functional loop sequences and domain structures defined at the fold superfamily level of SCOP classification. The resulting elementary functionome network and its loop motif and structural domain graph projections create evolutionary waterfalls describing the emergence of primordial functions. Waterfalls reveal how ancient loops are shared by domain structures in two initial waves of functional innovation that involve founder p-loop and winged helix domain structures. They also uncover a dynamics of modular motif embedding in domain structures that is ongoing, which transfers preferential cooption properties of ancient loops to emerging domains. Remarkably, we find that the emergence of molecular functions induces hierarchical modularity and power law behavior in network evolution as the network of motifs and structures expand metabolic pathways and translation.

Original languageEnglish (US)
Article number25058
JournalScientific reports
StatePublished - Apr 28 2016

ASJC Scopus subject areas

  • General


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