Structure of the Anti-C60 Fullerene Antibody Fab Fragment: Structural Determinants of Fullerene Binding

58 | ACTA NATURAE | VOL. 11 No 1 (40) 2019RESEARCH ARTICLES INTRODUCTION The problem of immune recognition is one of the main challenges of modern biochemistry, important both for understanding biological processes and for designing new drugs and vaccines. A considerable body of the-oretical and experimental data accumulated in recent years provides deeper understanding of the structural and functional patterns of immune interactions [1–5]. X-ray crystallography is among the most powerful methods used to study the three-dimensional struc-tures of specific antibody–antigen complexes and gather detailed insights into the interactions of anti-bodies with various high-molecular-weight antigens (proteins, polysaccharides, lipids, etc.) and water-solu-ble low-molecular-weight haptens [6–9].In recent years, there has been a significant ex-pansion of the range of potential targets for immune recognition, in particular due to particles with a struc-turally degenerate surface. This class includes engi-neered nanoparticles (ENPs) that are characterized by a growing production and applications in various fields of science and technology [10]. The opportu-nity to manipulate the physicochemical parameters of nanoparticles opens new prospects for the synthesis of nanoparticles with desired properties for application in targeted drug delivery, disease diagnosis, imaging of organs and tissues, etc. [11–13]. The use of ENPs in medicine and biotechnology raises the question of their immunogenic properties.Antigens that do not fit into the standard patterns of the immune reaction include fullerenes: nanoparticles consisting exclusively of carbon atoms and character-ized by a unique geometry and properties [14]. A num-ber of studies provide evidence of the possible forma-tion of fullerene-specific antibodies [15–18].The structure of the fullerene-binding site of an-tibodies was considered in the only study [15]. Using X-ray crystallography and computer simulation, the specific fullerene-binding site was shown to be a spher-ical cavity 7 Å in diameter that is formed by a cluster of hydrophobic amino acids. However, in the structural model of the fullerene-Fab complex [15], hydrophobic Structure of the Anti-C60 Fullerene Antibody Fab Fragment: Structural Determinants of Fullerene BindingЕ. M. Osipov1, О. D. Hendrickson1, Т. V. Tikhonova1, A. V. Zherdev1, O. N. Solopova2, P. G. Sveshnikov2, B. B. Dzantiev1, V. О. Popov1*1Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia2Russian Research Center of Molecular Diagnostics and Therapy, Simpheropolsky Blvd. 8, 113149, Moscow, Russia*E-mail: vpopov@inbi.ras.ruReceived October 11, 2018; in final form February 12, 2019Copyright © 2019 National Research University Higher School of Economics. This is an open access article distributed under the Creative Commons Attribution License,which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT The structure of the anti-C60 fullerene antibody Fab fragment (FabC60) was solved by X-ray crystal-lography. The computer-aided docking of C60 into the antigen-binding pocket of FabC60 showed that binding of C60 to FabC60 is governed by the enthalpy and entropy; namely, by π-π stacking interactions with aromatic residues of the antigen-binding site and reduction of the solvent-accessible area of the hydrophobic surface of C60. A fragment of the mobile CDR H3 loop located on the surface of FabC60 interferes with C60 binding in the antigen-binding site, thereby resulting in low antibody affinity for C60. The structure of apo-FabC60 has been deposited with pdbid 6H3H.