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吸附驱动的 SARS-CoV-2 变体 RBD 蛋白在生物和非生物表面的变形和足迹。

Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces.

机构信息

Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.

Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia.

出版信息

J Chem Inf Model. 2024 Aug 12;64(15):5977-5990. doi: 10.1021/acs.jcim.4c00460. Epub 2024 Jul 31.

Abstract

Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of the receptor-binding domain (RBD) of the spike protein mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native biological interfaces, specifically the angiotensin-converting enzyme 2. Notably, we identify a 2-fold increase in structural deformations for the protein's receptor binding motif (RBM) onto inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of adsorbed amino acids (landing footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface, with roughly half of the adsorbed amino acids arranged in opposite sites. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, where the wild-type RBD adsorbs more strongly than the Delta or Omicron RBDs. In contrast, the adsorption of Delta and Omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces show the embedded high-deformation capacity of the RBD without losing its secondary structure, which could lead to current experimental strategies in the design of virucidal surfaces.

摘要

呼吸道病毒通过空气传播的微飞沫传播,经常附着在表面上,包括塑料和金属。然而,我们对病毒与材料之间相互作用的理解仍然有限,特别是在涉及可极化表面的情况下。在这里,我们使用分子模拟研究了刺突蛋白突变的受体结合域 (RBD) 在疏水和亲水表面上吸附 SARS-CoV-2 的作用。为了使我们的发现具有背景意义,我们将无生命表面上的相互作用与天然生物界面(特别是血管紧张素转换酶 2)上的相互作用进行了对比。值得注意的是,我们发现蛋白质的受体结合基序 (RBM) 在无生命表面上的结构变形增加了两倍,表明增强了减震机制。此外,无生命表面上吸附氨基酸(着陆足迹)的分布相对于生物界面表现出明显的区域不对称性,大约一半的吸附氨基酸排列在相反的位置。尽管在亲水基底上形成了氢键,但模拟始终显示与疏水表面的接触和界面面积更多,其中野生型 RBD 的吸附比 Delta 或奥密克戎 RBD 更强。相比之下,Delta 和奥密克戎在亲水表面上的吸附以独特的跳跃模式为特征。在无生命表面上病毒吸附中识别出的新型减震机制表明 RBD 具有嵌入式的高变形能力,而不会失去其二级结构,这可能会导致目前在杀病毒表面设计方面的实验策略。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5fcc/11323246/4c8958f25969/ci4c00460_0001.jpg

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