Discrimination between biological interfaces and crystal-packing contacts

Yuko Tsuchiya¹, Haruki Nakamura², Kengo Kinoshita^1,3

¹Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan; ²Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan; ³Bioinformatics Research and Development, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan

Abstract: A discrimination method between biologically relevant interfaces and artificial crystal-packing contacts in crystal structures was constructed. The method evaluates protein-protein interfaces in terms of complementarities for hydrophobicity, electrostatic potential and shape on the protein surfaces, and chooses the most probable biological interfaces among all possible contacts in the crystal. The method uses a discriminator named as “COMP”, which is a linear combination of the complementarities for the above three surface features and does not correlate with the contact area. The discrimination of homo-dimer interfaces from symmetry-related crystal-packing contacts based on the COMP value achieved the modest success rate. Subsequent detailed review of the discrimination results raised the success rate to about 88.8%. In addition, our discrimination method yielded some clues for understanding the interaction patterns in several examples in the PDB. Thus, the COMP discriminator can also be used as an indicator of the “biological-ness” of protein-protein interfaces.

Keywords: protein-protein interaction, complementarity analysis, homo-dimer interface, crystal-packing contact, biological interfaces