Recognition of Weak Homology of Proteins Using Information from 3D-structures

Yo Matsuo
Ken Nishikawa

Protein Engineering Research Institute


The structure of protein can be predicted if the homology to a protein of known structure is detected. However, as the similarity of two sequences gets weaker, it becomes harder to judge whether they are truly homologous or not. Here, a method is presented which discriminates between true homology and noise, using the fact that the hydrophobic nature of buried residues of homologous proteins is well conserved even if their overall sequence similarity is low. We defined, for a given protein of unknown structure, buried and exposed residues according to the sequence alignment with a protein of known structure, and then measured total hydrophobicities for the buried and exposed residues, respectively. Large hydrophobicity is expected for buried residues, and large hydrophilicity for exposed residues. In this way, the homology between two sequences is recognized.