Loonen Stefan, van Steenis Lina, Bauer Marianne, Šoštarić Nikolina
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, HZ, the Netherlands.
Proteins. 2025 Oct;93(10):1701-1716. doi: 10.1002/prot.26842. Epub 2025 May 15.
The SARS-CoV-2 nucleocapsid protein, or N-protein, is a structural protein that plays an important role in the SARS-CoV-2 life cycle. The N-protein takes part in the regulation of viral RNA replication and drives highly specific packaging of full-length genomic RNA prior to virion formation. One regulatory mechanism that is proposed to drive the switch between these two operating modes is the phosphorylation state of the N-protein. Here, we assess the dynamic behavior of non-phosphorylated and phosphorylated versions of the N-protein homodimer through atomistic molecular dynamics simulations. We show that the introduction of phosphorylation yields a more dynamic protein structure and decreases the binding affinity between the N-protein and RNA. Furthermore, we find that secondary structure is essential for the preferential binding of particular RNA elements from the 5' UTR of the viral genome to the N-terminal domain of the N-protein. Altogether, we provide detailed molecular insights into N-protein dynamics, N-protein:RNA interactions, and phosphorylation. Our results corroborate the hypothesis that phosphorylation of the N-protein serves as a regulatory mechanism that determines N-protein function.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）核衣壳蛋白，即N蛋白，是一种结构蛋白，在SARS-CoV-2的生命周期中发挥着重要作用。N蛋白参与病毒RNA复制的调控，并在病毒粒子形成之前驱动全长基因组RNA的高度特异性包装。一种被认为驱动这两种运作模式之间转换的调控机制是N蛋白的磷酸化状态。在此，我们通过原子分子动力学模拟评估了N蛋白同二聚体的非磷酸化和磷酸化形式的动态行为。我们表明，磷酸化的引入产生了更具动态性的蛋白质结构，并降低了N蛋白与RNA之间的结合亲和力。此外，我们发现二级结构对于病毒基因组5'非翻译区（UTR）的特定RNA元件与N蛋白N端结构域的优先结合至关重要。总之，我们提供了关于N蛋白动力学、N蛋白与RNA相互作用以及磷酸化的详细分子见解。我们的结果证实了N蛋白磷酸化作为一种决定N蛋白功能的调控机制的假说。
