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Cluster conservation as a novel tool for studying protein-protein interactions evolution.
Ofer Rahat1, Assif Yitzhaky, Gideon Schreiber
1Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel.
Proteins
|November 1, 2007
Summary
Protein-protein interfaces exhibit conserved modularity across homologous families, suggesting a simplified approach to protein engineering by targeting these evolutionarily stable modules.
Area of Science:
- Structural biology
- Bioinformatics
- Computational biology
Background:
- Protein-protein interactions form complex networks at the atomic level.
- Analyzing these detailed networks can predict structure-function relationships.
- Homologous protein interfaces share folds but differ in sequence.
Purpose of the Study:
- To investigate conserved network properties in homologous protein-protein interfaces.
- To develop a framework for comparing the modularity of homologous protein networks.
- To determine if interface modularity is an evolutionarily conserved trait.
Main Methods:
- Developed a mathematical framework to compare network modularity.
- Applied the framework to structural data of protein-interface families (hemoglobin, growth hormone-receptor, serine protease-inhibitor).
- Analyzed shared and differing network properties among homologous proteins with varying sequences.
Main Results:
- Interface modularity is an evolutionarily conserved property.
- Protein-protein interfaces can be clustered into a few modules.
- Module boundaries are conserved across homologous protein complexes.
Conclusions:
- Protein-protein interface modularity is a conserved characteristic.
- This conserved modularity simplifies protein engineering strategies.
- Targeting individual modules while maintaining overall interface modularity is feasible.
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