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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
Divergent evolution of a structural proteome: phenomenological models.
C Brian Roland1, Eugene I Shakhnovich
1Chemical Physics Program, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
Biophysical Journal
|October 31, 2006
Summary
We modeled the evolution of protein structural domains in prokaryotic genomes. Our evolving-graph model explains the nonrandom organization of the Protein Domain Universe Graph (oPDUG), revealing two distinct domain innovation dynamics.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Genomes evolve through changes in protein structural domains.
- The arrangement of these domains forms complex networks, such as the organismal Protein Domain Universe Graph (oPDUG).
- Existing oPDUGs exhibit nonrandom structures, including degree distributions resembling Pareto laws.
Purpose of the Study:
- To model the divergent evolution of genomes focusing on protein structural domains.
- To explain the nonrandom organization observed in oPDUGs using an evolving-graph model.
- To identify patterns reflecting evolutionary mechanisms in domain arrangement.
Main Methods:
- Developed an evolving-graph model incorporating only divergent domain discovery mechanisms.
- Analyzed the arrangement of protein structural domains across various prokaryote species.
- Modeled the organismal Protein Domain Universe Graph (oPDUG) as a network of structural similarities.
Main Results:
- The model successfully reproduces Pareto-law-like degree distributions and characteristic clustering coefficients of oPDUGs.
- Analytical computation in the infinite-graph limit determined the exponent and phase diagram.
- Identified two distinct regimes governing domain innovation dynamics.
Conclusions:
- Divergent evolutionary dynamics quantitatively explain the nonrandom organization of oPDUGs.
- The proposed model provides a framework for understanding long-timescale evolutionary dynamics of protein domain organization.
- The findings offer insights into genome evolution mechanisms driven by domain discovery.
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