Effect of the size of gold nanoparticles on conformational changes of all-α proteins

Proteins, as biological macromolecules, are considered to be one of the most significant components of living systems, consisting of amino acids with a high degree of structural diversity. As an important nanomaterial, gold nanoparticles have a wide range of applications in the fields of drug delivery, biosensing and cancer therapy. The use of molecular dynamics to simulate the interaction system between gold nanoparticles and proteins is conducive to revealing the structural changes and stability of proteins under the influence of gold nanoparticles, as well as their interaction mechanisms in biological processes. In this paper, the molecular dynamics simulation method is utilized to employ GROMACS software in the study of the effect of the size of gold nanoparticles and the nature of amino acid side chains on the gold nanoparticle-protein composite system. It is concluded that as the size of gold nanoparticles increases, the proteins are more affected by the gold nanoparticles and the degree of deconvolution of the α-helix structure increases. Furthermore, analysis of the secondary structure of the protein chain revealed that a protein chain constructed from the hydrophobic amino acid Ala was able to maintain a stable α-helix structure in comparison to a hydrophilic amino acid Ser. In addition, the formation of the disulfide bond of Cys, due to the presence of the -SH group, resulted in the most stable structure of the proteins constituted by Cys.