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Tsuchiya Y, Nakamura H, Kinoshita K. Discrimination between biological interfaces and crystal-packing contacts. Adv Appl Bioinform Chem. 2008;1:99-113doi: 10.2147/aabc.s4255.
Tsuchiya, Y., Nakamura, H., & Kinoshita, K. (2008). Discrimination between biological interfaces and crystal-packing contacts. Advances and applications in bioinformatics and chemistry : AABC, 199-113. https://doi.org/10.2147/aabc.s4255
Tsuchiya, Yuko, et al. "Discrimination between biological interfaces and crystal-packing contacts." Advances and applications in bioinformatics and chemistry : AABC vol. 1 (2008): 99-113. doi: https://doi.org/10.2147/aabc.s4255
Tsuchiya Y, Nakamura H, Kinoshita K. Discrimination between biological interfaces and crystal-packing contacts. Adv Appl Bioinform Chem. 2008;1:99-113. doi: 10.2147/aabc.s4255. Epub 2008 Nov 02. PMID: 21918609; PMCID: PMC3169932.
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Adv Appl Bioinform Chem. 2008;1:99-113. doi: 10.2147/aabc.s4255. Epub 2008 Nov 02.

Discrimination between biological interfaces and crystal-packing contacts.

Advances and applications in bioinformatics and chemistry : AABC

Yuko Tsuchiya, Haruki Nakamura, Kengo Kinoshita

Affiliations

  1. Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minatoku, Tokyo, 108-8639, Japan.

PMID: 21918609 PMCID: PMC3169932 DOI: 10.2147/aabc.s4255

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

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