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

Aziz, Muhammad Fayez

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https://hdl.handle.net/2142/89192 Copy

Description

Title

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

Author(s)

Aziz, Muhammad Fayez

Issue Date

2015-12-03

Director of Research (if dissertation) or Advisor (if thesis)

Caetano-Anollés, Gustavo

Committee Member(s)

• Rodriguez-Zas, Sandra Luisa
• Bhalerao, Kaustubh
• Ma, Jian

Department of Study

Crop Sciences

Discipline

Bioinformatics

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

M.S.

Degree Level

Thesis

Keyword(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.

Graduation Semester

2015-12

Type of Resource

text

Permalink

http://hdl.handle.net/2142/89192

Copyright and License 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

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