Missense variants in human ACE2 strongly affect binding to SARS-CoV-2 Spike providing a mechanism for ACE2 mediated genetic risk in Covid-19: A case study in affinity predictions of interface variants.
Missense variants in human ACE2 strongly affect binding to SARS-CoV-2 Spike providing a mechanism for ACE2 mediated genetic risk in Covid-19: A case study in affinity predictions of interface variants.
复制标题
DOI：
10.1371/journal.pcbi.1009922
复制
发表时间：
2022-03
影响因子：
4.3
通讯作者：
Barton GJ
中科院分区：
文献类型：
--
作者：
MacGowan SA;Barton MI;Kutuzov M;Dushek O;van der Merwe PA;Barton GJ
SARS-CoV-2Spike(Spike)与人血管紧张素转换酶2(ACE2)结合，这种相互作用的强度可能会影响与毒力相关的参数。为了探讨ACE2的群体变异是否会影响Spike结合从而影响感染，我们根据亲和力预测和在gnomAD中的流行情况选择了10个ACE2变异，并在37℃下通过表面等离子共振(SPR)测量了它们与Spike受体结合域的亲和力和动力学。我们发现了降低和增强结合的变异，包括三个强烈抑制结合(p.Glu37Lys，ΔΔG=-1.33±0.15kcal ol-1和p.Gly352Val，预测ΔΔG=-1.17kcal ol-1)或取消(p.Asp355Asn)结合的ACE2变异。我们还发现了两个具有不同群体分布的变体，它们增强了对Spike的亲和力。ACE2p.Ser19Pro(ΔΔG=0.5 9±0.0 8kcal m ol-1)在非洲人群中占优势(AF=0.003)，而p.Lys2 6Arg(ΔΔG=0.2 6±0.0 9kcal m ol-1)在德系犹太人(AF=0.0 1)和欧洲非芬兰人(AF=0.006)中占优势。我们比较了ACE2变异体与已发表的SARS-CoV-2假型传染性数据的亲和力，证实对Spike亲和力降低的ACE2变异体可以保护细胞免受感染。具有增强的Spike亲和力的变体的影响尚不清楚，但我们提出了一种机制，即这些等位基因可以导致病毒在组织和细胞类型中更大的传播，这与关于受体亲和力和细胞表面丰度之间相互作用的新理解是一致的。最后，我们将MCSM-PPI2SPR G预测与我们的ΔΔ数据进行了比较，以评估预测在该系统中的实用性。我们发现，结合减少的预测与实验有很好的相关性，并且可以通过校准来改进，但令人失望的是，高度增强结合的预测是不可靠的。计算并用重新校准的对所有可能的ACE2错义变体的预测来估计ACE2变体对新冠肺炎的总体负担。SARS-CoV-2病毒入侵人类细胞的第一件事是与一种名为血管紧张素转换酶2(ACE2)的细胞表面受体结合。病毒通过其刺突蛋白附着在这个受体上，来自其他病毒的知识告诉我们，这种相互作用的强度影响着它的传染性和/或毒力。我们假设，在ACE2与Spike结合的部分有不同氨基酸的人，Spike-ACE2的亲和力可能不同，因此可能受到保护-或更有风险-免受病毒感染。为了验证这一想法，我们测量了几个代表在人类中发现的不同版本的ACE2突变体对Spike蛋白的亲和力，我们发现其中一些加强了相互作用，而另一些则削弱了它。这些变异中的大多数都很罕见，但在某些人群中，每1000人中就有两个人存在，因此可能对新冠肺炎的流行病学很重要。然后，我们使用计算方法预测了比我们在实验室中测试的还要多的ACE2突变体的亲和力，并再次发现了许多可能改变这种相互作用的突变体。这些数据可能有助于识别哪些人患新冠肺炎的风险较高或较低。
SARS-CoV-2 Spike (Spike) binds to human angiotensin-converting enzyme 2 (ACE2) and the strength of this interaction could influence parameters relating to virulence. To explore whether population variants in ACE2 influence Spike binding and hence infection, we selected 10 ACE2 variants based on affinity predictions and prevalence in gnomAD and measured their affinities and kinetics for Spike receptor binding domain through surface plasmon resonance (SPR) at 37°C. We discovered variants that reduce and enhance binding, including three ACE2 variants that strongly inhibited (p.Glu37Lys, ΔΔG = –1.33 ± 0.15 kcal mol-1 and p.Gly352Val, predicted ΔΔG = –1.17 kcal mol-1) or abolished (p.Asp355Asn) binding. We also identified two variants with distinct population distributions that enhanced affinity for Spike. ACE2 p.Ser19Pro (ΔΔG = 0.59 ± 0.08 kcal mol-1) is predominant in the gnomAD African cohort (AF = 0.003) whilst p.Lys26Arg (ΔΔG = 0.26 ± 0.09 kcal mol-1) is predominant in the Ashkenazi Jewish (AF = 0.01) and European non-Finnish (AF = 0.006) cohorts. We compared ACE2 variant affinities to published SARS-CoV-2 pseudotype infectivity data and confirmed that ACE2 variants with reduced affinity for Spike can protect cells from infection. The effect of variants with enhanced Spike affinity remains unclear, but we propose a mechanism whereby these alleles could cause greater viral spreading across tissues and cell types, as is consistent with emerging understanding regarding the interplay between receptor affinity and cell-surface abundance. Finally, we compared mCSM-PPI2 ΔΔG predictions against our SPR data to assess the utility of predictions in this system. We found that predictions of decreased binding were well-correlated with experiment and could be improved by calibration, but disappointingly, predictions of highly enhanced binding were unreliable. Recalibrated predictions for all possible ACE2 missense variants at the Spike interface were calculated and used to estimate the overall burden of ACE2 variants on Covid-19. One of the first things the SARS-CoV-2 virus does to invade human cells is bind to a cell surface receptor called angiotensin-converting enzyme 2 (ACE2). The virus attaches to this receptor through its Spike protein and knowledge from other viruses tells us that the strength of this interaction influences how infectious and or virulent it is. We hypothesised that the Spike-ACE2 affinity might vary in people who have different amino acids in the part of ACE2 where Spike binds and consequently might be protected–or more at risk–from the virus. To test this idea, we measured the affinity of several ACE2 mutants, representing different versions found in humans, for the Spike protein and we found that some strengthened the interactions alongside others that weakened it. Most of these variants are rare, but two are present in over 1 in 1,000 individuals in certain populations and so might be important for the epidemiology of COVID-19. We then used computational methods to predict the affinity of even more ACE2 mutants than we could test in the lab and again found many that might alter this interaction. These data may help identify people who are at higher or lower risk from COVID-19.
登录
查看更多内容
影响因子：
5.4
作者：
Heurich, Adeline;Hofmann-Winkler, Heike;Poehlmann, Stefan
通讯作者：
Poehlmann, Stefan
DOI：
10.3390/v13010067
发表时间：
2021-01-06
期刊：
Viruses
影响因子：
--
作者：
Hashizume M;Gonzalez G;Ono C;Takashima A;Iwasaki M
通讯作者：
Iwasaki M
Arpeggio：用于计算和可视化蛋白质结构中原子间相互作用的Web服务器。
影响因子：
5.6
作者：
Jubb HC;Higueruelo AP;Ochoa-Montaño B;Pitt WR;Ascher DB;Blundell TL
通讯作者：
Blundell TL
DOI：
10.1074/jbc.ra120.015303
发表时间：
2020-12-25
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
Lu J;Sun PD
通讯作者：
Sun PD
影响因子：
11.4
作者：
Li, WH;Zhang, CS;Sui, JH;Kuhn, JH;Moore, MJ;Luo, SW;Wong, SK;Huang, IC;Xu, KM;Vasilieva, N;Murakami, A;He, YQ;Marasco, WA;Guan, Y;Choe, HY;Farzan, M
通讯作者：
Farzan, M