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Did evolution leap to create the protein universe?
1CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, BB217, New York, NY 10032, USA. rost@columbia.edu
Current Opinion in Structural Biology
|July 20, 2002
Summary
Comparative proteomics reveals surprising similarities and key differences in protein structures across life's kingdoms. Eukaryotes utilize longer proteins and unique structural domains, suggesting discrete protein fold space.
Area of Science:
- Genomics
- Proteomics
- Structural Biology
Background:
- Over 60 genomes from all three kingdoms of life are now sequenced.
- Protein inventories show surprising similarities across kingdoms.
- Eukaryotes exhibit distinct protein characteristics compared to other kingdoms.
Purpose of the Study:
- To compare protein inventories and structural features across different kingdoms of life.
- To investigate the implications of observed protein diversity for protein fold space.
- To highlight challenges and future directions in comparative proteomics.
Main Methods:
- Genome sequencing and analysis of over 60 organisms.
- Comparative analysis of protein inventories and structural features.
- Identification of protein domains, coiled-coil helices, and secondary structures.
Main Results:
- Eukaryotes possess longer proteins and more coiled-coil helices and regular secondary structures.
- Specific structural domains are prevalent in certain pathways, often occurring uniquely.
- A significant number of proteins lack close homologs across species (orphan proteins).
Conclusions:
- Protein fold space may be discrete, with potential for species-specific folds.
- Alternatively, protein structure evolution might involve fragment aggregation in a continuous space.
- Advanced comparative proteomics methods are crucial for understanding proteome diversity.