Chakraborty Srirupa, Nguyen Kien N, Zhao Mingfei, Gnanakaran S
Department of Chemical Engineering, Northeastern University, Boston, MA 02115.
Cresset, Cambridgeshire, SG80SS, UK.
bioRxiv. 2025 Mar 12:2025.03.11.642723. doi: 10.1101/2025.03.11.642723.
The SARS-CoV-2 Spike glycoprotein is central to viral infectivity and immune evasion, making it a key target for vaccine and therapeutic design. This trimeric peplomer undergoes dynamic conformational changes, particularly in its Receptor Binding Domain (RBD), which transitions between closed (down) and ACE2-accessible (up) states relative to the rest of the protein, to facilitate host cell entry. Structural understanding of such critical inter-domain motions, as well as epitope exposure quantification, is essential for obtaining an effective molecular handle over this protein and, in turn, exploiting it towards improved immunogen development. Focusing on the early circulating D614G form and the later emerging Delta (B.1.617.2) variant with higher virulence, we performed large-scale molecular dynamics simulations of the soluble form of the Spike in both 'down' and 'up' conformations of the RBD. Guided by differences in overall fluctuations, we described reaction coordinates based on domain rotations and tilting to extract features that distinguish D614G versus Delta structural behavior of the N-terminal Domain (NTD) and RBD. Using reaction coordinate analysis and Principal Component Analysis (PCA), we identify allosteric coupling between the N-terminal Domain (NTD) and RBD, where NTD tilting influences RBD gating. While some of these motions are conserved across variants, Delta exhibits an optimized RBD-gating mechanism that enhances ACE2 accessibility. Additionally, glycan remodeling in Delta enhances shielding at the NTD supersite, contributing to reduced sensitivity to neutralizing antibodies. Finally, we uncover the impact of the D950N mutation in the HR1 region, which modulates downstream Spike dynamics and immune evasion. Together, our findings reveal variant-specific and conserved structural determinants of SARS-CoV-2 Spike function, providing a mechanistic basis for allosteric modulation, glycan-mediated immune evasion, and viral adaptation. These insights offer valuable guidance for rational vaccine and therapeutic design against SARS-CoV-2 and emerging variants.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）刺突糖蛋白对于病毒感染性和免疫逃逸至关重要，使其成为疫苗和治疗设计的关键靶点。这种三聚体纤突蛋白会发生动态构象变化，尤其是在其受体结合域（RBD），该区域相对于蛋白质的其余部分会在封闭（向下）状态和可与血管紧张素转换酶2（ACE2）结合的（向上）状态之间转变，以促进宿主细胞进入。对这种关键的结构域间运动以及表位暴露定量的结构理解，对于有效控制该蛋白质并进而利用它来改进免疫原开发至关重要。我们聚焦于早期流行的D614G形式以及后来出现的具有更高毒力的德尔塔（B.1.617.2）变体，对RBD处于“向下”和“向上”构象的刺突蛋白可溶性形式进行了大规模分子动力学模拟。基于整体波动的差异，我们描述了基于结构域旋转和倾斜的反应坐标，以提取区分D614G与德尔塔N端结构域（NTD）和RBD结构行为的特征。通过反应坐标分析和主成分分析（PCA），我们确定了N端结构域（NTD）和RBD之间的变构偶联，其中NTD倾斜会影响RBD的门控。虽然其中一些运动在不同变体中是保守的，但德尔塔表现出一种优化的RBD门控机制，可增强ACE2可及性。此外，德尔塔中的聚糖重塑增强了NTD超位点的屏蔽作用，有助于降低对中和抗体的敏感性。最后，我们揭示了HR1区域中D950N突变的影响，该突变调节了下游刺突蛋白的动力学和免疫逃逸。总之，我们的研究结果揭示了SARS-CoV-2刺突蛋白功能的变体特异性和保守结构决定因素，为变构调节、聚糖介导的免疫逃逸和病毒适应性提供了机制基础。这些见解为针对SARS-CoV-2及新出现变体的合理疫苗和治疗设计提供了有价值的指导。
