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Description
Title: | The early history and emergence of molecular functions and modular scale-free network behavior |
Author(s): | Aziz, Muhammad Fayez |
Advisor(s): | Caetano-Anollés, Gustavo |
Contributor(s): | Rodriguez-Zas, Sandra Luisa; Bhalerao, Kaustubh; Ma, Jian |
Department / Program: | Crop Sciences |
Discipline: | Bioinformatics |
Degree Granting Institution: | University of Illinois at Urbana-Champaign |
Degree: | M.S. |
Genre: | Thesis |
Subject(s): | Protein domains
Elementary loop sequences Bipartite network Network projections Evolutionary timeline Molecular functions Scale-free dynamics Modularity |
Abstract: | 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 (EFL) sequences and domain structures defined at the fold superfamily (FSF) level of Structural Classification of Proteins (SCOP). The resulting ‘elementary functionome’ network and its EFL and FSF graph projections unfold evolutionary ‘waterfalls’ describing emergence of primordial functions. Waterfalls reveal how ancient EFLs are shared by FSF 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 EFLs to emerging FSFs. Remarkably, we find that the emergence of molecular functions induces hierarchical modularity and power law behavior in network evolution as the networks of motifs and structures expand metabolic pathways and translation. |
Issue Date: | 2015-12-03 |
Type: | Text |
URI: | http://hdl.handle.net/2142/89192 |
Rights Information: | Copyright 2015 Muhammad Fayez Aziz. Materials in this document (all chapters, including the abstract) are reprinted, with permission, from Aziz MF, Caetano-Anollés K and Caetano-Anollés G, 2015, “The early history and emergence of molecular functions and modular scale-free network behavior,” manuscript submitted |
Date Available in IDEALS: | 2016-03-02 2018-03-03 |
Date Deposited: | 2015-12 |
This item appears in the following Collection(s)
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Dissertations and Theses - Crop Sciences
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Graduate Dissertations and Theses at Illinois
Graduate Theses and Dissertations at Illinois