Quantitative Description of Surface Complementarity of Antibody-Antigen Interfaces

Lorenzo Di Rienzo; Edoardo Milanetti; Giancarlo Ruocco; Rosalba Lepore

doi:10.3389/fmolb.2021.749784

Quantitative Description of Surface Complementarity of Antibody-Antigen Interfaces

Front Mol Biosci. 2021 Sep 30:8:749784. doi: 10.3389/fmolb.2021.749784. eCollection 2021.

Authors

Lorenzo Di Rienzo¹, Edoardo Milanetti^{1

2}, Giancarlo Ruocco^{1

2}, Rosalba Lepore³

Affiliations

¹ Center for Life Nano and Neuro-Science, Istituto Italiano di Tecnologia, Rome, Italy.
² Department of Physics, Sapienza University, Rome, Italy.
³ Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland.

Abstract

Antibodies have the remarkable ability to recognise their cognate antigens with extraordinary affinity and specificity. Discerning the rules that define antibody-antigen recognition is a fundamental step in the rational design and engineering of functional antibodies with desired properties. In this study we apply the 3D Zernike formalism to the analysis of the surface properties of the antibody complementary determining regions (CDRs). Our results show that shape and electrostatic 3DZD descriptors of the surface of the CDRs are predictive of antigen specificity, with classification accuracy of 81% and area under the receiver operating characteristic curve (AUC) of 0.85. Additionally, while in terms of surface size, solvent accessibility and amino acid composition, antibody epitopes are typically not distinguishable from non-epitope, solvent-exposed regions of the antigen, the 3DZD descriptors detect significantly higher surface complementarity to the paratope, and are able to predict correct paratope-epitope interaction with an AUC = 0.75.

Keywords: antibody complementarity determining regions; antibody—antigen complex; antigen recognition; surface complementarity; zernike polynomials.