Graph theoretical insights into evolution of multidomain proteins
Teresa Przytycka1, George Davis, Nan Song
1National Center for Biotechnology Information, US National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. prytyck@mail.nih.gov
Summary
Proteins often independently combine existing domains, suggesting domain architectures are not always stable over evolutionary time. This study uses graph theory to analyze protein evolution and domain combinations.
Area of Science:
- Computational Biology
- Bioinformatics
- Evolutionary Biology
Background:
- Multidomain proteins are central to cellular function.
- Understanding the evolutionary dynamics of protein domain architectures is crucial.
Purpose of the Study:
- To investigate protein domain acquisition and persistence using graph theory.
- To explore the frequency of independent domain combination events.
- To assess the stability of protein domain architectures over evolutionary time.
Main Methods:
- Graph theoretical analysis of protein domain structures.
- Modeling protein evolution using variants of Dollo parsimony.
- Examination of domain overlap graphs in protein superfamilies.
Main Results:
- Connections established between domain overlap graphs and Dollo parsimony models.
- Independent merges of domain pairs are frequent in large superfamilies.
- Evidence suggests domain architectures may not always persist.
Conclusions:
- Protein domain combinations occur independently more often than previously assumed.
- The evolutionary pathways of protein domain architectures are complex and dynamic.
- Graph theory provides a powerful framework for studying protein evolution.
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A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
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