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Bridging Themes: Short Protein Segments Found in Different Architectures
Rachel Kolodny1, Sergey Nepomnyachiy1, Dan S Tawfik2
1Department of Computer Science, University of Haifa, Haifa, Israel.
Molecular Biology and Evolution
|January 27, 2021
Summary
Protein evolution benefits from reusing building blocks. Researchers found short, shared protein segments ("bridging themes") between independently evolved domains, suggesting a common origin for these essential protein structures.
Area of Science:
- Molecular Biology
- Evolutionary Biology
- Structural Biology
Background:
- Most random protein sequences do not fold or function.
- Protein evolution likely utilizes existing building blocks (themes) over de novo creation.
- Sequence similarity often indicates common ancestry for protein sequences.
Purpose of the Study:
- To investigate short protein sequence fragments (themes) shared between independently evolved domains.
- To understand the role of these short themes in the emergence and evolution of protein domains.
- To identify potential mechanisms for domain innovation and diversification.
Main Methods:
- Identification and analysis of 525 representative short themes (20-80 residues).
- Comparison of themes across domains with presumed independent evolutionary origins.
- Focus on themes shared between ancient and fundamental protein domains.
Main Results:
- Discovery of 525 short themes unexpectedly shared between independently evolved domains.
- Identification of "bridging themes" connecting ancient domains like Rossmann, P-loop NTPase, TIM-barrel, flavodoxin, and ferredoxin-like.
- Several bridging themes were found to mediate ligand binding.
Conclusions:
- Short themes shared across diverse domains suggest a deeper level of evolutionary connection than previously recognized.
- Ligand binding mediated by bridging themes may have enhanced stability and facilitated their integration into new or existing domains.
- These findings provide insights into the modular nature of protein evolution and domain emergence.
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