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Updated: Mar 21, 2026
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling
Daisuke Kuroda1, Jeffrey J Gray2
1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Analytical and Physical Chemistry, Showa University School of Pharmacy, Tokyo, 142-8555, Japan.
Motivations:
Characterizing protein-protein interfaces and the hydrogen bonds is a first step to better understand proteins' structures and functions toward high-resolution protein design. However, there are few large-scale surveys of hydrogen bonds of interfaces. In addition, previous work of shape complementarity of protein complexes suggested that lower shape complementarity in antibody-antigen interfaces is related to their evolutionary origin.
Results:
Using 6637 non-redundant protein-protein interfaces, we revealed peculiar features of various protein complex types. In contrast to previous findings, the shape complementarity of antibody-antigen interfaces resembles that of the other interface types. These results highlight the importance of hydrogen bonds during evolution of protein interfaces and rectify the prevailing belief that antibodies have lower shape complementarity.
Contact:
jgray@jhu.edu
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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