Mubassir M H M, Naser M Abu, Abdul-Wahab Mohd Firdaus, Jawad Tanvir, Alvy Raghib Ishraq, Hamdan Salehhuddin
Department of Mathematics and Natural Sciences, BRAC University 66 Mohakhali Dhaka-1212 Bangladesh
Faculty Bioscience and Medical Engineering, Universiti Teknologi Malaysia 81310 Johor Bahru Johor Malaysia
RSC Adv. 2020 Apr 21;10(27):15800-15814. doi: 10.1039/d0ra01396j.
The first layer of defense that plants deploy to ward off a microbial invasion comes in the form of pattern-triggered immunity (PTI), which is initiated when the pattern-recognition receptors (PRRs) bind with the pathogen-associated molecular patterns (PAMPs) and co-receptor proteins, and transmit a defense signal. Although several plant PRRs have been discovered, very few of them have been fully characterized, and their functional parameters assessed. In this study, the 3D-model prediction of an entire plant PRR protein, Xa21, was done by implementing multiple modeling techniques. Subsequently, the PAMP RaxX21-sY (sulphated RaxX21) and leucine-rich repeat (LRR) domain of the co-receptor OsSERK2 were docked with the LRR domain of Xa21. The docked complex of these three proteins formed a heterodimer that closely resembles the other crystallographic PTI complexes available. Molecular dynamics simulations and MM/PBSA calculations were applied for an in-depth analysis of the interactions between Xa21 LRR, RaxX21-sY, and OsSERK2 LRR. Arg230 and Arg185 from Xa21 LRR, Val2 and Lys15 from RaxX21-sY and Lys164 from OsSERK2 LRR were found to be the prominent residues which might contribute significantly in the formation of a heterodimer during the PTI process mediated by Xa21. Additionally, RaxX21-sY interacted much more favorably with Xa21 LRR in the presence of OsSERK2 LRR in the complex, which substantiates the necessity of the co-receptor in Xa21 mediated PTI to recognize the PAMP RaxX21-sY. However, the free energy binding calculation reveals the favorability of a heterodimer formation of PRR Xa21 and co-receptor OsSERK2 without the presence of PAMP RaxX21-sY, which validate the previous lab result.
植物抵御微生物入侵所部署的第一道防线是以模式触发免疫（PTI）的形式出现的，当模式识别受体（PRR）与病原体相关分子模式（PAMP）和共受体蛋白结合并传递防御信号时，PTI就会启动。尽管已经发现了几种植物PRR，但其中很少有被完全表征的，也没有对它们的功能参数进行评估。在本研究中，通过实施多种建模技术对整个植物PRR蛋白Xa21进行了三维模型预测。随后，将PAMP RaxX21-sY（硫酸化RaxX21）和共受体OsSERK2的富含亮氨酸重复序列（LRR）结构域与Xa21的LRR结构域进行对接。这三种蛋白质的对接复合物形成了一个异二聚体，与其他可用的晶体学PTI复合物非常相似。应用分子动力学模拟和MM/PBSA计算对Xa21 LRR、RaxX21-sY和OsSERK2 LRR之间的相互作用进行深入分析。发现来自Xa21 LRR的Arg230和Arg185、来自RaxX21-sY的Val2和Lys15以及来自OsSERK2 LRR的Lys164是突出的残基，它们可能在由Xa21介导的PTI过程中对异二聚体的形成有显著贡献。此外，在复合物中存在OsSERK2 LRR的情况下，RaxX21-sY与Xa21 LRR的相互作用更有利，这证实了共受体在Xa21介导的PTI中识别PAMP RaxX21-sY的必要性。然而，自由能结合计算揭示了在没有PAMP RaxX21-sY存在的情况下PRR Xa21和共受体OsSERK2形成异二聚体的有利性，这验证了之前的实验室结果。
