Insights into substrate recognition and specificity for IgG by Endoglycosidase S2.
Insights into substrate recognition and specificity for IgG by Endoglycosidase S2.
复制标题
DOI：
10.1371/journal.pcbi.1009103
复制
发表时间：
2021-07
影响因子：
4.3
通讯作者：
MacKerell AD Jr
中科院分区：
文献类型：
--
作者：
Aytenfisu AH;Deredge D;Klontz EH;Du J;Sundberg EJ;MacKerell AD Jr
抗体以高亲和力和特异性结合外来抗原，导致它们被免疫系统中和和/或清除。IgG上的保守N-聚糖对抗体效应子功能具有显著影响，化脓性链球菌的内切糖苷酶使IgG去糖基化以逃避免疫系统，这是由内切糖苷酶EndoS 2催化的过程。研究表明，EndoS 2的四个结构域中的两个，即碳水化合物结合模块（CBM）和糖苷水解酶（GH）结构域对于催化活性至关重要。为了获得对CBM和GH结构域的贡献以及EndoS 2对蛋白质催化活性的整体灵活性的结构见解，通过增强采样分子动力学（MD）模拟和通过配体竞争性饱和（SILCS）对接的位点鉴定，然后重建和多微秒MD模拟来生成EndoS 2-Fc复合物的模型。建模结果预测，EndoS 2最初通过其CBM与IgG相互作用，然后与GH相互作用，产生催化活性状态。这些可能涉及EndoS 2的CBM和GH同时与相同的Fc CH 2/CH 3结构域或单独与两个Fc CH 2/CH 3结构域相互作用，预测EndoS 2在前一种情况下呈现闭合构象，在后一种情况下呈现开放构象。预测Apo EndoS 2对开放和闭合状态都进行采样，这表明在初始IgG-EndoS 2相遇后可以直接形成任一复合物。预测CBM和GH结构域与IgG的相互作用通过其聚糖和蛋白质区域发生。模拟还预测了Fc聚糖直接从CBM转移到GH，促进催化活性复合物的形成，以及CBM上的734至751环如何促进聚糖从Fc CH 2/CH 3结构域提取。预测模型进行了比较和一致的氢/氘交换数据。此外，复杂模型与EndoS 2对IgG上聚糖的高特异性一致，支持预测模型的有效性。病原体化脓性链球菌使用内切糖苷酶S和S2来切割IgG抗体的Fc部分上的聚糖，导致抗体的细胞毒性降低，从而逃避宿主免疫应答。为了鉴定可能导致IgG聚糖催化水解的EndoS 2与IgG的复合物的潜在结构，应用分子建模和分子动力学模拟。所得的结构模型预测，EndoS 2最初通过其碳水化合物结合模块（CBM）与IgG相互作用，随后与催化糖苷水解酶（GH）结构域相互作用，产生稳定的复合物。在模拟的复合物中，CBM和GH同时与相同的Fc CH 2/CH 3结构域或分别与两个单独的Fc CH 2/CH 3结构域相互作用，以产生潜在的催化活性物质。此外，显示载脂蛋白EndoS 2呈现开放和闭合构象，允许其直接形成任一类型的复合物，其中可能发生单糖基化或二糖基化IgG物质的去糖基化。
Antibodies bind foreign antigens with high affinity and specificity leading to their neutralization and/or clearance by the immune system. The conserved N-glycan on IgG has significant impact on antibody effector function, with the endoglycosidases of Streptococcus pyogenes deglycosylating the IgG to evade the immune system, a process catalyzed by the endoglycosidase EndoS2. Studies have shown that two of the four domains of EndoS2, the carbohydrate binding module (CBM) and the glycoside hydrolase (GH) domain are critical for catalytic activity. To yield structural insights into contributions of the CBM and the GH domains as well as the overall flexibility of EndoS2 to the proteins’ catalytic activity, models of EndoS2-Fc complexes were generated through enhanced-sampling molecular-dynamics (MD) simulations and site-identification by ligand competitive saturation (SILCS) docking followed by reconstruction and multi-microsecond MD simulations. Modeling results predict that EndoS2 initially interacts with the IgG through its CBM followed by interactions with the GH yielding catalytically competent states. These may involve the CBM and GH of EndoS2 simultaneously interacting with either the same Fc CH2/CH3 domain or individually with the two Fc CH2/CH3 domains, with EndoS2 predicted to assume closed conformations in the former case and open conformations in the latter. Apo EndoS2 is predicted to sample both the open and closed states, suggesting that either complex can directly form following initial IgG-EndoS2 encounter. Interactions of the CBM and GH domains with the IgG are predicted to occur through both its glycan and protein regions. Simulations also predict that the Fc glycan can directly transfer from the CBM to the GH, facilitating formation of catalytically competent complexes and how the 734 to 751 loop on the CBM can facilitate extraction of the glycan away from the Fc CH2/CH3 domain. The predicted models are compared and consistent with Hydrogen/Deuterium Exchange data. In addition, the complex models are consistent with the high specificity of EndoS2 for the glycans on IgG supporting the validity of the predicted models. The pathogen Streptococcus pyogenes uses the endoglycosidases S and S2 to cleave the glycans on the Fc portion of IgG antibodies, leading to a decreased cytotoxicity of the antibodies, thereby evading the host immune response. To identify potential structures of the complex of EndoS2 with IgG that could lead to the catalytic hydrolysis of the IgG glycan, molecular modeling and molecular dynamics simulations were applied. The resulting structural models predict that EndoS2 initially interacts through its carbohydrate binding module (CBM) with the IgG with subsequent interactions with the catalytic glycoside hydrolase (GH) domain yielding stable complexes. In the modeled complexes the CBM and the GH interact either simultaneously with the same Fc CH2/CH3 domain or with the two individual Fc CH2/CH3 domains separately to yield potentially catalytically competent species. In addition, apo EndoS2 is shown to assume both open and closed conformations allowing it to directly form either type of complex from which deglycosylation of either mono- or diglycosylated IgG species may occur.
登录
查看更多内容
影响因子：
5.5
作者：
Hess, Berk;Kutzner, Carsten;Lindahl, Erik
通讯作者：
Lindahl, Erik
影响因子：
2.9
作者：
HOOVER, WG
通讯作者：
HOOVER, WG
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
3
作者：
Guvench, Olgun;Greene, Shannon N.;Kamath, Ganesh;Brady, John W.;Venable, Richard M.;Pastor, Richard W.;Mackerell, Alexander D., Jr.
通讯作者：
Mackerell, Alexander D., Jr.
影响因子：
15
作者：
Bowden, Thomas A.;Baruah, Kavitha;Coles, Charlotte H.;Harvey, David J.;Yu, Xiaojie;Song, Byeong-Doo;Stuart, David I.;Aricescu, A. Radu;Scanlan, Christopher N.;Jones, E. Yvonne;Crispin, Max
通讯作者：
Crispin, Max