Khavani Mohammad, Mehranfar Aliyeh, Mofrad Mohammad R K
Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California 94720, United States.
J Chem Inf Model. 2023 Feb 27;63(4):1276-1292. doi: 10.1021/acs.jcim.2c01378. Epub 2023 Feb 3.
The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is considered in many research studies. In this research article, we employ full atomistic molecular dynamics (MD) models to study the interactions between the receptor binding domain (RBD) and spike protein of the coronavirus and different metals such as gold (Au), platinum (Pt), and silver (Ag) to analyze their sensitivity against this virus. The comparison between the RBD interactions with ACE2 (angiotensin-converting enzyme 2) and different metals indicates that metals have remarkable effects on the structural features and dynamical properties of the RBD. The binding site of the RBD has more affinity to the surfaces of gold, platinum, and silver than to the other parts of the protein. Moreover, the initial configuration of the RBD relative to the metal surface plays an important role in the stability of metal complexes with the RBD. The binding face of the protein to the metal surface has been changed in the presence of different metals. In other words, the residues of the RBD that participate in RBD interactions with the metals are different irrespective of the initial configurations in which the [Asn, Thr, Tyr], [Ser, Thr, Tyr], and [Asn, Asp, Tyr] residues of the protein have a greater affinity to Ag, Au, and Pt, respectively. The corresponding metals have a considerable affinity to the RBD, which due to strong interactions with the protein can change the secondary structure and structural features. Based on the obtained results during the complexation process between the protein and metals, the helical structure of the protein changes to the bend and antiparallel β-sheets. The calculated binding energies for the RBD complexes with silver, gold, and platinum are -95.03, -138.03, and -133.96 kcal·mol, respectively. The adsorption process of the spike protein on the surfaces of different metals represents similar results and indicates that the entire spike protein of the coronavirus forms a more stable complex with the gold surface compared with other metals. Moreover, the RBD of the spike protein has more interactions with the surfaces than with the other parts of the protein. Therefore, it is possible to predict the properties of the coronavirus on the metal surface based on the dynamical behavior of the RBD. Overall, our computational results confirm that the gold surface can be considered as an outstanding substrate for developing new sensors with the highest sensitivity against SARS-CoV-2.
新型冠状病毒疾病及其并发症促使人们设计具有最高灵敏度的新型传感器，许多研究都考虑了对严重急性呼吸综合征冠状病毒 2（SARS-CoV-2）病毒检测的亲和力。在这篇研究文章中，我们采用全原子分子动力学（MD）模型来研究冠状病毒的受体结合域（RBD）与刺突蛋白以及不同金属（如金（Au）、铂（Pt）和银（Ag））之间的相互作用，以分析它们对这种病毒的敏感性。RBD 与血管紧张素转换酶 2（ACE2）以及不同金属之间相互作用的比较表明，金属对 RBD 的结构特征和动力学性质有显著影响。RBD 的结合位点与金、铂和银的表面的亲和力比对蛋白质的其他部分更高。此外，RBD 相对于金属表面的初始构型在其与金属的复合物稳定性中起着重要作用。在不同金属存在的情况下，蛋白质与金属表面的结合面发生了变化。换句话说，参与 RBD 与金属相互作用的 RBD 残基是不同的，无论蛋白质的初始构型如何，其中的[天冬酰胺、苏氨酸、酪氨酸]、[丝氨酸、苏氨酸、酪氨酸]和[天冬酰胺、天冬氨酸、酪氨酸]残基分别对银、金和铂具有更高的亲和力。相应的金属对 RBD 具有相当大的亲和力，由于与蛋白质的强相互作用，会改变蛋白质的二级结构和结构特征。基于蛋白质与金属络合过程中获得的结果，蛋白质的螺旋结构转变为弯曲和反平行的β折叠。RBD 与银、金和铂的复合物的计算结合能分别为-95.03、-138.03 和-133.96 kcal·mol。冠状病毒刺突蛋白在不同金属表面的吸附过程呈现出类似的结果，表明与其他金属相比，冠状病毒的整个刺突蛋白与金表面形成更稳定的复合物。此外，刺突蛋白的 RBD 与表面的相互作用比与蛋白质的其他部分更多。因此，基于 RBD 的动力学行为可以预测冠状病毒在金属表面的性质。总体而言，我们的计算结果证实，金表面可被视为开发对 SARS-CoV-2 具有最高灵敏度的新型传感器的优异底物。
