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A simple definition of structural regions in proteins and its use in analyzing interface evolution
1MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. emmanuel.levy@gmail.com
Journal of Molecular Biology
|September 28, 2010
Summary
This study defines protein structure regions like surface, interior, and interface using accessible surface area. A 25% threshold helps categorize amino acids, revealing insights into protein-protein interactions and evolution.
Area of Science:
- Structural Biology
- Computational Biology
- Biochemistry
Background:
- Protein structure analysis often categorizes regions (surface, interior, interface) without a standardized definition.
- Existing categorization methods lack a consensus, hindering consistent biological interpretation.
Purpose of the Study:
- To establish a general, simple, and biologically insightful definition for protein structure regions.
- To refine the core-rim model of protein-protein interfaces by introducing a 'support' region.
Main Methods:
- Analysis of 1174 protein structures from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens.
- Utilized relative accessible surface area thresholds to segregate amino acids into interior and surface regions.
- Extended the core-rim model to include a support region for protein-protein interfaces.
Main Results:
- A 25% relative accessible surface area threshold effectively distinguishes interior and surface amino acids.
- The interface is characterized by core, rim, and support regions, with core residues dominating contact surfaces.
- Amino acid compositions of interface regions are conserved across organisms and interface types.
Conclusions:
- The support and rim regions of interfaces may pre-exist on protein surfaces and interiors.
- Evolving new protein-protein interactions might primarily involve mutations forming the interface core.
- Protein interaction promiscuity can be better understood by analyzing these defined interface regions.
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