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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Evidence for an episodic model of protein sequence evolution
Romain A Studer1, Marc Robinson-Rechavi
1Department of Ecology and Evolution, Biophore, Lausanne University, CH-1015 Lausanne, Switzerland.
Biochemical Society Transactions
|July 21, 2009
Summary
Protein evolution shows periods of slow and rapid change, suggesting episodic functional shifts. Sophisticated models reveal key amino acid changes driven by positive selection across diverse proteins.
Area of Science:
- Evolutionary biology
- Molecular evolution
- Genomics
Background:
- Protein function evolves over time.
- Evolutionary processes can be episodic, with periods of stasis and rapid change.
- Sophisticated models are needed to detect subtle evolutionary patterns.
Purpose of the Study:
- To present methods for detecting functional shifts in protein evolution.
- To investigate evidence for episodic evolution in protein sequences.
- To identify the role of positive selection in driving functional changes.
Main Methods:
- Application of advanced evolutionary models to large sequence datasets.
- Analysis using amino acid substitution models.
- Analysis using codon models.
Main Results:
- Evidence for punctual shifts in amino acid conservation patterns.
- Identification of key amino acid changes fixed by positive selection.
- The episodic evolution model applies broadly across proteins and organisms.
Conclusions:
- Protein evolution is characterized by alternating conservative and rapid change periods.
- Functional shifts are punctual and can be driven by positive selection.
- The episodic model of evolution is widely applicable, though links to gene duplication remain unclear.
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