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Published on: August 18, 2023
Contact density affects protein evolutionary rate from bacteria to animals.
Tong Zhou1, D Allan Drummond, Claus O Wilke
1Center for Computational Biology and Bioinformatics, Section of Integrative Biology, University of Texas at Austin, Austin, TX 78731, USA.
Journal of Molecular Evolution
|April 2, 2008
Summary
Protein contact density positively correlates with evolutionary rate across four species, suggesting denser proteins evolve faster. This relationship holds for both whole proteins and individual domains, independent of gene expression levels.
Area of Science:
- Evolutionary biology
- Structural bioinformatics
- Genomics
Background:
- Protein structure's contact density is hypothesized to influence protein designability and evolutionary rates.
- Previous studies on the link between contact density and evolutionary rate have yielded conflicting results.
- Understanding this relationship is crucial for evolutionary and protein design studies.
Purpose of the Study:
- To investigate the correlation between protein contact density and gene evolutionary rates across diverse species.
- To examine if gene expression levels confound the relationship between contact density and evolutionary rate.
- To assess the impact of contact density on the evolution of protein domains within multidomain proteins.
Main Methods:
- Comparative analysis of protein structures and gene sequences from Escherichia coli, Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens.
- Statistical correlation analysis to determine the relationship between contact density and evolutionary rates.
- Examination of evolutionary rates within individual domains of multidomain proteins.
Main Results:
- A positive correlation was observed between protein contact density and evolutionary rate in all four studied species.
- The correlation between contact density and evolutionary rate was not confounded by gene expression levels.
- Higher contact density within a protein domain was associated with a faster evolutionary rate for that domain.
Conclusions:
- Protein contact density is a significant factor influencing evolutionary rates at both the whole protein and domain levels.
- The findings support the hypothesis that proteins with higher contact density evolve faster.
- Contact density's influence on evolutionary rate is consistent across different biological scales and species.
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