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Finding evolutionary relations beyond superfamilies: fold-based superfamilies
Keiko Matsuda1, Takaaki Nishioka, Kengo Kinoshita
1Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, 630-0101, Japan.
Protein Science : a Publication of the Protein Society
|September 23, 2003
Summary
Protein superfamilies can be defined by global fold and function. Analysis revealed over 20 independent ATP-binding protein superfamilies, originating from conserved evolutionary diffusion of protein folds and functions.
Area of Science:
- Structural biology
- Bioinformatics
- Molecular evolution
Background:
- Protein superfamily classification traditionally relies on sequence, fold, or function similarity.
- Defining superfamilies based on global fold-function relationships offers a novel perspective.
Purpose of the Study:
- To investigate the possibility of defining protein superfamilies based solely on the global fold-function relationship.
- To classify protein domains by beta-sheet topology and analyze evolutionary kinship.
Main Methods:
- Classified protein domains based on beta-sheet topology.
- Introduced kinship relations based on beta-strand addition/deletion events in molecular evolution.
- Constructed a protein domain network representing evolutionary events.
- Mapped ATP-binding domains onto the network to identify clusters.
Main Results:
- Identified over 20 distinct, disjointed clusters of protein domains on the network.
- Each cluster represents a fold-based superfamily.
- Demonstrated that over 20 ATP-binding protein superfamilies evolved independently.
Conclusions:
- Protein superfamilies can be defined by their global fold and function.
- The independent invention of over 20 ATP-binding superfamilies highlights conserved evolutionary diffusion.
- Global fold and function conservation drives relationships between protein superfamilies.