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Peptide-based Identification of Functional Motifs and their Binding Partners
Published on: June 30, 2013
Discovering structural motifs using a structural alphabet: application to magnesium-binding sites.
1Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan. frater_ia@yahoo.com <frater_ia@yahoo.com>
BMC Bioinformatics
|March 29, 2007
Summary
Researchers developed a novel method to identify structural motifs in magnesium-binding proteins (Mg2+-proteins). This approach helps predict protein function even without sequence similarity, aiding in the discovery of new Mg2+-dependent biological roles.
Area of Science:
- Structural biology
- Biochemistry
- Bioinformatics
Background:
- Sequence motifs for metal-binding sites are often absent or non-specific, particularly for versatile cofactors like Mg2+.
- Despite low sequence homology, Mg2+-proteins may share similar Mg2+-binding site structures, though structural motifs remain unreported.
Purpose of the Study:
- To develop a general method for discovering structural motifs in ligand-binding sites using 3D protein structures.
- To apply this method to Mg2+-proteins with less than 30% sequence identity to identify characteristic Mg2+-binding site structures.
Main Methods:
- Utilized a structural alphabet to encode 3D protein structures into 1D sequences.
- Identified Mg2+-specific structural motifs as recurring patterns within these sequences.
Main Results:
- Discovered preferences of Mg2+-binding sites for loops over helices.
- Identified 4 distinct Mg2+-structural motifs in 21% of binding sites, with one motif linked to hydrolases.
- Two motifs were unique to Mg2+-proteins, distinguishing them from non-metalloproteins and Ca2+-binding proteins.
Conclusions:
- The developed method is general and applicable to any protein set with known 3D structures.
- This approach is valuable for predicting function in proteins of unknown origin from structural genomics.
- Structural motifs can suggest likely active/binding sites and biological functions for proteins lacking sequence homology.
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