Enzyme structures and functions
- Analysis and developing prediction methods of specificity of protein-protein, protein-compound interactions
1. Analysis of enzyme detailed functions
- We showed the subsequences determined by only the literature information and ligand-enzyme complex structures had sufficient information to detect functional subclasses.
- Nagao C, Nagano N, Mizuguchi K. Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies. Proteins 2010;78(10):2369-2384.
Nozomi Nagano (CBRC)
2. Analysis of specificity determining residues in protein-protein interactions
- We defined a “structure-based specificity determining position (sbSDP)” as a set of equivalent residues in a protein family showing a large variation in their interaction energy with different partners. The importance of many sbSDP for determining specificity had been verified experimentally.
- Nagao C, Izako N, Soga S, Khan SH, Kawabata S, Shirai H, Mizuguchi K. Computational design, construction and characterization of a set of specificity determining residues in protein-protein interactions., Proteins, 2012, PubMed