Structural and dynamic properties of monoclonal antibodies immobilized on CNTs: a computational study

Due to the widespread application of carbon nanotube (CNT)-based materials in nanomedicine, it is nowadays of paramount importance to unravel at the atomistic level of detail the structural properties of such bioconjugates in order to rationalize and predict the effect exerted by the graphitic framework on the bio-active counterpart. In this paper, we report for the first time all-atom explicit solvent molecular dynamics (MD) simulations investigating the structural and dynamic properties of a noncovalent bioconjugate in which the monoclonal Cetuximab antibody (Ctx) is adsorbed on a CNT surface. Upon selection of the three most representative adsorption modes as obtained by docking studies, force-field MD and DFT simulations unambiguously showed that hydrophobic interactions mainly govern the adsorption of the protein on the graphitic surface. Two main adsorption poses have been predicted: a pose-fab (p-fab) and pose-fc (p-fc) (fab = fragment antigen binding region; fc = fragment crystallizable region), the former being favored with small-diameter tubes (≤40 Å). In all the predicted poses, the secondary structure of Ctx is largely unaffected by the presence of the graphitic surface and, consistently with previous literature studies, our simulations reveal that positively charged amino acidic residues, such as Lys and Arg, predominantly contribute to the stabilization of the CNT⋅Ctx complex acting like surfactants. The predicted structural models are consistent with the experimental data, for which the immobilization of the antibody on CNTs does not disrupt the structural and recognition properties of the Ctx, consequently supporting the reliability of the used bioconjugation strategy for engineering stable and responsive hybrid nanomaterials for therapeutic applications. Moreover, a remarkable structural similarity of Ctx with antibodies of different isotypes suggests that in principle the CNT framework can interact in the same manner with all antibodies currently used in clinical applications.