Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.
Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.
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纳米抗体SARS-CoV-2刺突蛋白复合物的结合亲和力与构象熵之间的相关性。
DOI：
10.1073/pnas.2205412119
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发表时间：
2022-08-02
影响因子：
11.1
通讯作者：
中科院分区：
文献类型：
--
作者：
理解决定纳米抗体与严重急性呼吸综合征冠状病毒2的刺突蛋白的结合亲和力的结构原理一直很困难。我们分析了纳米抗体-刺突复合物的电子显微镜图，并量化了结合的构象熵。这为设计与刺突蛋白结合改善的工程纳米抗体提供了信息。这一结果为针对刺突的纳米抗体的合理成熟提供了指导原则。高结合效力的纳米抗体已被证明在动物模型中有效;因此，这项技术可能在未来的大流行中得到应用。骆驼科单域抗体，也称为纳米抗体，可以很容易地从针对特定靶点的原始库中分离出来，但通常与靶点的结合太弱，无法立即使用。基于化学的基因工程方法，以提高其亲和力，称为成熟，可以提供有用的试剂，为不同领域的生物学和潜在的医学。使用严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）刺突蛋白的受体结合结构域（RBD）和原始文库，我们产生了具有微摩尔至纳摩尔结合亲和力的密切相关的纳米抗体。通过使用X射线晶体学、冷冻电子显微镜和生物物理学方法分析结构-活性关系，我们观察到在刺突蛋白-纳米抗体复合物形成中较高的构象熵损失与更紧密的结合相关。为了研究这一点，我们产生了不同的复合物的电子显微镜图和相关的构象波动与结合亲和力的结构合奏。这一见解指导了对刺突蛋白具有改善的亲和力的纳米抗体的工程化。
Understanding the structural principles that determine the binding affinity of nanobodies to the spike protein of severe acute respiratory syndrome coronavirus 2 has been difficult. We analyzed electron microscopy maps of nanobody-spike complexes and quantified the conformational entropy of binding. This informed the design of an engineered nanobody with improved binding to the spike protein. This result offers a guiding principle for the rational maturation of nanobodies directed against the spike. High-binding potency nanobodies have been shown to be effective in animal models; thus, this technology could have application in future pandemics. Camelid single-domain antibodies, also known as nanobodies, can be readily isolated from naïve libraries for specific targets but often bind too weakly to their targets to be immediately useful. Laboratory-based genetic engineering methods to enhance their affinity, termed maturation, can deliver useful reagents for different areas of biology and potentially medicine. Using the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and a naïve library, we generated closely related nanobodies with micromolar to nanomolar binding affinities. By analyzing the structure–activity relationship using X-ray crystallography, cryoelectron microscopy, and biophysical methods, we observed that higher conformational entropy losses in the formation of the spike protein–nanobody complex are associated with tighter binding. To investigate this, we generated structural ensembles of the different complexes from electron microscopy maps and correlated the conformational fluctuations with binding affinity. This insight guided the engineering of a nanobody with improved affinity for the spike protein.
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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/s0907444904019158
发表时间：
2004-12-01
影响因子：
2.2
作者：
Emsley, P;Cowtan, K
通讯作者：
Cowtan, K
影响因子：
4.4
作者：
Andricioaei, I;Karplus, M
通讯作者：
Karplus, M
影响因子：
9.8
作者：
Heffron AS;McIlwain SJ;Amjadi MF;Baker DA;Khullar S;Armbrust T;Halfmann PJ;Kawaoka Y;Sethi AK;Palmenberg AC;Shelef MA;O'Connor DH;Ong IM
通讯作者：
Ong IM
DOI：
10.1074/mcp.o115.052209
发表时间：
2015-10
期刊：
Molecular & cellular proteomics : MCP
影响因子：
--
作者：
Hornsby M;Paduch M;Miersch S;Sääf A;Matsuguchi T;Lee B;Wypisniak K;Doak A;King D;Usatyuk S;Perry K;Lu V;Thomas W;Luke J;Goodman J;Hoey RJ;Lai D;Griffin C;Li Z;Vizeacoumar FJ;Dong D;Campbell E;Anderson S;Zhong N;Gräslund S;Koide S;Moffat J;Sidhu S;Kossiakoff A;Wells J
通讯作者：
Wells J