Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait.
Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Kuwait.
Life Sci. 2020 Oct 15;259:118219. doi: 10.1016/j.lfs.2020.118219. Epub 2020 Aug 5.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel member of the betacoronaviruses family affecting the lower respiratory tract mainly through binding to angiotensin converting enzyme 2 (ACE2) via its S-protein. Genetic analysis of (ACE2) gene revealed several variants that have been suggested to regulate the interaction with S protein. This study investigates the N720D variant, positioned in the collectrin-like domain (CLD) at proximity to type II transmembrane serine protease (TMPRSS2) cleavage site.
The effect of N720D variant on ACE2 structure and thermodynamic stability was studied by DynaMut. HDOCK was utilised to model TMPRSS2 protease binding to ACE2 WT and D720 variant cleavage site. PRODIGY was used to calculate binding affinities and MD simulation tools calculated the at 100 ns for ACE2 apo structure and the ACE2-TMPRSS2 complex.
The N720D variant is a more dynamic structure with a free energy change (ΔΔG): -0.470 kcal/mol. As such, introducing a tighter binding affinity of K = 3.2 × 10 M between TMPRSS2 and N720D variant. RMSD, RMSF calculations showed the N720D variant is less stable, however, RMSF values of the D720-TMPRSS2 complex reflected a slower dynamic motion.
The hotspot N720D variant in the CLD of ACE2 affected the stability and flexibility of ACE2 by increasing the level of motion in the loop region, resulting in a more favourable site for TMPRSS2 binding and cleavage. Consequently, this would facilitate S-protein binding and can potentially increase viral entry highlighting the importance of variants affecting the ACE2-TMPRSS2 complex.
严重急性呼吸系统综合征冠状病毒 2（SARS-CoV-2）是一种新型的β冠状病毒家族成员，主要通过其 S 蛋白与血管紧张素转换酶 2（ACE2）结合而影响下呼吸道。（ACE2）基因的遗传分析显示，有几个变体被认为可以调节与 S 蛋白的相互作用。本研究调查了位于靠近 II 型跨膜丝氨酸蛋白酶（TMPRSS2）切割位点的集胞藻样结构域（CLD）中的 N720D 变体。
通过 DynaMut 研究 N720D 变体对 ACE2 结构和热力学稳定性的影响。利用 HDOCK 对 TMPRSS2 蛋白酶与 ACE2 WT 和 D720 变体切割位点的结合进行建模。利用 PRODIGY 计算结合亲和力，使用 MD 模拟工具计算 ACE2 apo 结构和 ACE2-TMPRSS2 复合物的 100ns。
N720D 变体是一种更具动态性的结构，自由能变化（ΔΔG）为-0.470 kcal/mol。因此，TMPRSS2 和 N720D 变体之间的结合亲和力增加到 K=3.2×10^M。RMSD、RMSF 计算表明 N720D 变体不太稳定，然而，D720-TMPRSS2 复合物的 RMSF 值反映了较慢的动态运动。
ACE2 的 CLD 中的热点 N720D 变体通过增加环区的运动水平，影响 ACE2 的稳定性和灵活性，从而为 TMPRSS2 结合和切割提供更有利的位点。因此，这将促进 S 蛋白的结合，并可能增加病毒进入，突出了影响 ACE2-TMPRSS2 复合物的变体的重要性。
