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. 2023 Mar 17;26(3):106110.
doi: 10.1016/j.isci.2023.106110. Epub 2023 Feb 4.

Probing the affinity of noble metal nanoparticles to the segments of the SARS-CoV-2 spike protein

Qiuyang Lu  1 , Baiyang Zhang  2 , Mingzi Sun  1 , Lu Lu  1 , Baian Chen  1 , Hon Ho Wong  1 , Cheuk Hei Chan  1 , Tong Wu  1 , Bolong Huang  1   3
Affiliations

Probing the affinity of noble metal nanoparticles to the segments of the SARS-CoV-2 spike protein

Qiuyang Lu et al. iScience. .

Abstract

Currently, scientists have devoted great efforts to finding effective treatments to combat COVID-19 infections. Although noble metal nanoparticles are able to realize protein modifications, their interactions with the protein are still unclear from the atomic perspective. To supply a general understanding, in this work, we have carried out theoretical calculations to investigate the interaction between protein segments (RBD1, RBD2, RBD3) of SARS-Cov-2 spike protein and a series of noble metal (Au, Ag, Cu, Pd, Pt) surfaces regarding the binding strength, protein orientations, and electronic modulations. In particular, the Au surface has shown the strongest binding preferences for the protein segments, which induces electron transfer between the Au and receptor-binding domain (RBD) segments. This further leads to the polarization of segments for virus denaturation. This work has offered a direct visualization of protein interactions with noble metal surfaces from the atomic level, which will benefit anti-virus material developments in the future.

Keywords: analytical method in materials science; chemical property; simulation in materials science.

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Conflict of interest statement

The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
Schematic diagram of the proposed noble metal designed for anti-virus applications such as masks and filters
Figure 2
Figure 2
Adsorption behaviors of RBD segments (A–D) Adsorption energy comparison of different RBD segments on different metal surfaces. N-term and C-term represent the binding configurations. Adsorption energy comparison of (B) RBD1, (C) RBD2, and (D) RBD3 segments on Au (111) surfaces with different binding configurations.
Figure 3
Figure 3
Electronic modulations of interactions between Au surface and RBD segments (A–C) PDOS of Temp2 binding configuration for RBD1 on Au surface. PDOS of (B) C-terminated and (C) N-terminated binding configurations for RBD1 on Au surface. (D–F) PDOS of Temp2 binding configuration for RBD2 on Au surface. PDOS of (E) C-terminated and (F) N-terminated binding configurations for RBD2 on Au surface. (G) Site-dependent PDOS of Au-5d in different binding configurations. (H) Site-dependent PDOS of RBD1-s,p orbitals in different binding configurations. (I) Site-dependent PDOS of RBD2-s,p orbitals in different binding configurations.
Figure 4
Figure 4
Visualizations of orbital coupling between Au surface and RBD segments (A and B) 3D contour plots of the electronic distributions in (A) RBD1-Temp3 and (B) RBD2-Temp1 on the Au surface. The green isosurface represents the anti-bonding orbitals and the blue isosurface represents the bonding orbitals. The purple isosurface represents the orbital couplings of Au and RBD segments. Gold balls = Au, Grey balls = C, Blue balls = N, Red balls = O, and White balls = H.
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