In silico study of substrate chemistry effect on the tethering of engineered antibodies for SARS-CoV-2 detection: Amorphous silica vs gold

Abstract

The influence of the properties of different solid substrates on the tethering of two antibodies, IgG1-CR3022 and IgG1-S309, which were specifically engineered for the detection of SARS-CoV-2, has been examined at the molecular level using conventional and accelerated Molecular Dynamics (cMD and aMD, respectively). Two surfaces with very different properties and widely used in immunosensors for diagnosis, amorphous silica and the most stable facet of the face-centered cubic gold structure, have been considered. The effects of such surfaces on the structure and orientation of the immobilized antibodies have been determined by quantifying the tilt and hinge angles that describe the orientation and shape of the antibody, respectively, and the dihedrals that measure the relative position of the antibody arms with respect to the surface. Results show that the interactions with amorphous silica, which are mainly electrostatic due to the charged nature of the surface, help to preserve the orientation and structure of the antibodies, especially of the IgG1-CR3022, indicating that the primary sequence of those antibodies also plays some role. Instead, short-range van der Waals interactions with the inert gold surface cause a higher degree tilting and fraying of the antibodies with respect to amorphous silica. The interactions between the antibodies and the surface also affect the correlation among the different angles and dihedrals, which increases with their strength. Overall, results explain why amorphous silica substrates are frequently used to immobilize antibodies in immunosensors.

Keywords: Amorphous silica; Antibody immobilization; Gold; Molecular Dynamics; SARS-CoV-2 immunosensor.

Graphical abstract

Scheme 1

Parts of the Y-like shape IgG antibodies.

Scheme 2

Linker obtained by modifying the Lys478 residue of IgG1-CR3022 and IgG1-S309, respectively, when immobilized on amorphous silica. The sphere at the bottom part corresponds to a Si atom.

Fig. 1

(a) RMSD, (b) ΔRMSF and (c) R_g for the engineered antibodies. (a) and (c) display the temporal evolution of the RMSD and R_g for IgG1-CR3022 and IgG1-S309 immobilized on silica and gold, whereas (b) shows the difference between the RMSF values obtained for the antibody immobilized on silica and gold.

Scheme 3

Sketch displaying the α (1−2−3), β (2−3−4), γ (2−3−5) and δ (4−3−5) angles. The meaning of 1, 2, 3 and 4 is described in the text.

Fig. 2

(a) Temporal evolution of α along the cMD trajectories. (b) PMF profiles of α as derived from the aMD samplings for IgG1-CR3022 and IgG1-S309 tethered to the silica and gold surface. The dashed lines in the PMF profiles, which display the region with ΔG ≤ 4.0 kcal/mol, indicate the position of the average from cMD.

Fig. 3

(a) Temporal evolution of β along the cMD trajectories. (b) PMF profiles of β as derived from the aMD samplings for IgG1-CR3022 and IgG1-S309 tethered to the silica and gold surface. The dashed lines in the PMF profiles, which display the region with ΔG ≤ 4.0 kcal/mol, indicate the position of the average from cMD.

Fig. 4

β–α (left) γ–α (center) and γ–β (right) PMF maps from aMD samplings for IgG1-CR3022 tethered to silica (top) and gold (down). The positions of the minima are indicated in black.

Fig. 5

β–α (left) γ–α (center) and γ–β (right) PMF maps from aMD samplings for IgG1-S309 tethered to silica (top) and gold (down). The positions of the minima are indicated in black.

Fig. 6

Temporal evolution of (a) θ and (b) φ along the cMD trajectories.

Fig. 7

θ–φ PMF maps from aMD samplings for IgG1-CR3022 (top) and IgG1-S309 (down) tethered to silica (left) and gold (right). The positions of the minima are indicated in black.

Fig. 8

Last snapshot recorded from cMD simulations for the four studied systems. Non-polar, polar, positively charged and negatively charges residues are displayed in grey, green, blue and red, respectively. (For interpretation of the references to colour in this figure, the reader is referred to the web version of this article.)