Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity.
Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity.
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DOI：
10.1126/science.abi6226
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发表时间：
2021-08-06
期刊：
影响因子：
--
通讯作者：
Acharya P
中科院分区：
文献类型：
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作者：
Gobeil SM;Janowska K;McDowell S;Mansouri K;Parks R;Stalls V;Kopp MF;Manne K;Li D;Wiehe K;Saunders KO;Edwards RJ;Korber B;Haynes BF;Henderson R;Acharya P
随着遏制COVID-19大流行的战斗继续进行，人们的注意力集中在严重急性呼吸综合征冠状病毒2 （SARS-CoV-2）病毒的新变体上，这些变体被视为令人担忧的变体，因为它们对感染或疫苗接种引起的抗体具有抵抗力，或者它们增加了传染性或疾病严重程度。三篇论文利用功能和结构研究探讨了病毒刺突蛋白的突变如何影响其感染宿主细胞和逃避宿主免疫的能力。Gobeil等人研究了水貂与人类之间传播的一种变异刺突蛋白，以及B1.1.7 （α）、B.1.351 （β）和P1 （γ）刺突变异；Cai等人关注的是alpha和beta变量；和McCallum等人讨论了来自B1.1.427/B.1.429 （epsilon）变体的刺突蛋白的特性。总之，这些论文显示了增强稳定性的突变，增加与人类受体ACE2结合的突变，以及赋予对中和抗体抗性的突变之间的平衡。SARS-CoV-2如何获得增强的传染性并逃避宿主免疫反应。自大流行开始以来，严重急性呼吸综合征冠状病毒2 （SARS-CoV-2）的变体一直在全球传播。其中一些被称为关注变异（VOC），因为有证据表明它们的传播性增加，疾病严重程度提高，对当前疫苗或以前感染引起的中和抗体产生耐药性，治疗效果降低，或诊断检测方法失败。挥发性有机化合物在尖峰(S)糖蛋白中积累突变。在不同地理位置独立产生的VOCs中，部分VOCs表现出相同的变化，暗示了趋同进化和后天变异的选择性优势。在巴西和南非的B.1.1.28和B.1.351谱系中，分别出现了受体结合域（RBD）上的3个氨基酸替换——lys417→Asn （K417N）、Glu484→Lys （E484K）和Asn501→Tyr （N501Y）。从B.1.1.28分支的P.1谱系包含Lys417→Thr （K417T）替换，同时保留了E484K和N501Y的变化。E484K取代物由于位于许多强效中和抗体的表位内而引起了人们的注意。N501Y替换也发生在起源于英国的B.1.1.7变异中，并与受体结合增加和变异的高传递性有关。反过来，B.1.1.7变异具有His69/Val70刺突缺失突变，与涉及人类和水貂之间传播的变异的刺突相同（ΔFVI）。全球测序计划和体外中和和抗体结合测定迅速提供了有关挥发性有机化合物的关键和及时的信息。在这里，通过结合冷冻电子显微镜（cryo-EM）结构测定和结合分析以及对变异尖刺的计算分析，我们试图可视化氨基酸取代对尖刺构象的影响，以了解这些变化如何影响它们的生物学功能。我们测量了血管紧张素转换酶2 （ACE2）受体与19种SARS-CoV-2 S外结构域构建体的抗体结合情况，这些构建体包含循环变体中发现的氨基酸变化。其中包括一种与人类和水貂之间的SARS-CoV-2跨物种传播有关的变体，以及几种挥发性有机化合物，包括B.1.1.7、B.1.1.28/P。1和B.1.351变体。与已发表的中和数据一致，B.1.1.7显示与n端结构域（NTD）定向抗体的结合减少，而P.1和B.1.351显示与NTD和rbd定向抗体的结合减少。所有变异都显示与ACE2的结合增加，这是由RBD中更高的RBD-up状态倾向和亲和力增强突变介导的。我们观察到貂相关变异的尖峰不稳定性，突出显示在冷冻电镜数据集中存在一个原聚体S1亚基缺失密度的群体。SD1和HR1区域之间接触的调节导致B.1.1.7尖峰的rb -up状态增加，通过稳定和不稳定突变的平衡来维持蛋白质的稳定性。RBD E484K突变的局部不稳定效应与B.1.1.28/P的抗性有关。b .1和B.1.351变体对一些有效的rbd定向中和抗体。我们的研究揭示了氨基酸取代如何影响循环SARS-CoV-2 VOCs中的刺突构象的细节。我们定义了调节尖峰变张力的通信网络，并表明S蛋白使用不同的机制来收敛于改变RBD上下定位的类似解决方案。自然发生的氨基酸变化用彩色球体表示。图中显示了貂相关（ΔFV）（左上）、B.1.1.7（右上）、B.1.351（右下）的穗突变，以及带有三个RBD突变的穗突变（左下）。分别显示了RBD上下种群的相对比例。rbd中的三个氨基酸替换- k417n /T， E484K和n501y -在B.1.1.28变体中被发现，并且与P.1和B.1.351谱系共享。具有多个尖峰突变的严重急性呼吸综合征冠状病毒2 （SARS-CoV-2）变体会增加传播和抗体耐药性。我们结合冷冻电子显微镜（cryo-EM）、结合和计算分析来研究变异尖峰，包括水貂和人类之间传播的尖峰，以及其他在人群中起源和传播的尖峰。所有变异均表现出血管紧张素转换酶2 （ACE2）受体结合增加和受体结合结构域（RBD）向上状态增加的倾向。虽然对水貂的适应导致穗不稳定，但B.1.1.7 （UK）穗平衡了稳定突变和不稳定突变。RBD E484K突变的局部不稳定效应与B.1.1.28/P.1的抗性有关（巴西）和B.1.351（南非）变体来中和抗体。我们的研究揭示了突变的变构效应和驱动种间传播或逃避抗体中和的机制差异。
As battles to contain the COVID-19 pandemic continue, attention is focused on emerging variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus that have been deemed variants of concern because they are resistant to antibodies elicited by infection or vaccination or they increase transmissibility or disease severity. Three papers used functional and structural studies to explore how mutations in the viral spike protein affect its ability to infect host cells and to evade host immunity. Gobeil et al. looked at a variant spike protein involved in transmission between minks and humans, as well as the B1.1.7 (alpha), B.1.351 (beta), and P1 (gamma) spike variants; Cai et al. focused on the alpha and beta variants; and McCallum et al. discuss the properties of the spike protein from the B1.1.427/B.1.429 (epsilon) variant. Together, these papers show a balance among mutations that enhance stability, those that increase binding to the human receptor ACE2, and those that confer resistance to neutralizing antibodies. —VV How SARS-CoV-2 variants gain enhanced infectivity and evade host immune responses. Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been circulating worldwide since the beginning of the pandemic. Some are termed Variants of Concern (VOC) because they show evidence for increased transmissibility, higher disease severity, resistance to neutralizing antibodies elicited by current vaccines or from previous infection, reduced efficacy of treatments, or failure of diagnostic detection methods. VOCs accumulate mutations in the spike (S) glycoprotein. Some VOCs that arose independently in different geographical locations show identical changes, implying convergent evolution and selective advantages of the acquired variations. A set of three amino acid substitutions in the receptor-binding domain (RBD)—Lys417 → Asn (K417N), Glu484 → Lys (E484K), and Asn501 → Tyr (N501Y)—occurred in the B.1.1.28 and B.1.351 lineages that originated in Brazil and South Africa, respectively. The P.1 lineage that branched off B.1.1.28 harbored a Lys417 → Thr (K417T) substitution while retaining the E484K and N501Y changes. The E484K substitution has attracted attention as a result of its location within the epitope of many potent neutralizing antibodies. The N501Y substitution also occurred in the B.1.1.7 variant that originated in the UK and was implicated in increased receptor binding and higher transmissibility of the variant. The B.1.1.7 variant, in turn, shares the His69/Val70 spike deletion mutation with spike from a variant that was implicated in transmission between humans and minks (ΔFVI). Global sequencing initiatives and in vitro neutralization and antibody binding assays have rapidly provided critical and timely information on the VOCs. Here, by combining cryo–electron microscopy (cryo-EM) structural determination with binding assays and computational analyses on the variant spikes, we sought to visualize the impact of the amino acid substitutions on spike conformation to understand how these changes affect their biological function. We measured angiotensin-converting enzyme 2 (ACE2) receptor and antibody binding for 19 SARS-CoV-2 S ectodomain constructs harboring amino acid changes found in circulating variants. These included a variant involved in interspecies SARS-CoV-2 transmission between humans and minks, as well as several VOCs including the B.1.1.7, B.1.1.28/P.1, and B.1.351 variants. Consistent with published neutralization data, B.1.1.7 showed decreased binding to N-terminal domain (NTD)–directed antibodies, whereas P.1 and B.1.351 showed reduced binding to both NTD- and RBD-directed antibodies. All variants showed increased binding to ACE2, which was mediated by higher propensity for RBD-up states, and affinity-enhancing mutations in the RBD. We observed spike instability in the mink-associated variant, highlighted by the presence of a population in the cryo-EM dataset with missing density for the S1 subunit of one protomer. Modulation of contacts between the SD1 and HR1 regions led to increased RBD-up states of the B.1.1.7 spike, with the protein stability maintained by a balance of stabilizing and destabilizing mutations. A local destabilizing effect of the RBD E484K mutation was implicated in resistance of the B.1.1.28/P.1 and B.1.351 variants to some potent RBD-directed neutralizing antibodies. Our study revealed details of how amino acid substitutions affect spike conformation in circulating SARS-CoV-2 VOCs. We define communication networks that modulate spike allostery and show that the S protein uses different mechanisms to converge upon similar solutions for altering the RBD up/down positioning. Naturally occurring amino acid variations are represented by colored spheres. Spike mutations from a mink-associated (ΔFV) (top left), B.1.1.7 (top right), B.1.351 (bottom right), and a spike with three RBD mutations (bottom left) are shown. Relative proportions of the RBD down and up populations are indicated for each. The three amino acid substitutions in the RBD—K417N/T, E484K, and N501Y—were found in the B.1.1.28 variant and are shared with the P.1 and B.1.351 lineages. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with multiple spike mutations enable increased transmission and antibody resistance. We combined cryo–electron microscopy (cryo-EM), binding, and computational analyses to study variant spikes, including one that was involved in transmission between minks and humans, and others that originated and spread in human populations. All variants showed increased angiotensin-converting enzyme 2 (ACE2) receptor binding and increased propensity for receptor binding domain (RBD)–up states. While adaptation to mink resulted in spike destabilization, the B.1.1.7 (UK) spike balanced stabilizing and destabilizing mutations. A local destabilizing effect of the RBD E484K mutation was implicated in resistance of the B.1.1.28/P.1 (Brazil) and B.1.351 (South Africa) variants to neutralizing antibodies. Our studies revealed allosteric effects of mutations and mechanistic differences that drive either interspecies transmission or escape from antibody neutralization.
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影响因子：
64.8
作者：
Barnes CO;Jette CA;Abernathy ME;Dam KA;Esswein SR;Gristick HB;Malyutin AG;Sharaf NG;Huey-Tubman KE;Lee YE;Robbiani DF;Nussenzweig MC;West AP Jr;Bjorkman PJ
通讯作者：
Bjorkman PJ
DOI：
10.1107/s2059798318006551
发表时间：
2018-06-01
期刊：
Acta crystallographica. Section D, Structural biology
影响因子：
--
作者：
Afonine PV;Poon BK;Read RJ;Sobolev OV;Terwilliger TC;Urzhumtsev A;Adams PD
通讯作者：
Adams PD
影响因子：
64.8
作者：
通讯作者：
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影响因子：
4.4
作者：
ESSMANN, U;PERERA, L;PEDERSEN, LG
通讯作者：
PEDERSEN, LG
影响因子：
4.4
作者：
Bestle, Dorothea;Heindl, Miriam Ruth;Boettcher-Friebertshaeuser, Eva
通讯作者：
Boettcher-Friebertshaeuser, Eva