Substrate-induced changes in dynamics and molecular motions of cuticle-degrading serine protease PL646: a molecular dynamics study
Substrate-induced changes in dynamics and molecular motions of cuticle-degrading serine protease PL646: a molecular dynamics study
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基质诱导的角质层降解丝氨酸蛋白酶 PL646 的动力学和分子运动变化：分子动力学研究
DOI：
10.1039/c7ra07797a
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发表时间：
2017
期刊：
影响因子：
3.9
通讯作者：
Shu-Qun Liu
中科院分区：
文献类型：
--
作者：
Li-Quan Yang;Peng Sang;Ruo-Peng Zhang;Shu-Qun Liu
由食虫真菌分泌的角质层降解丝氨酸蛋白酶在侵染过程中可降解线虫的角质层。PL 646是一种来源于嗜食线虫真菌淡紫拟青霉的碱性角质降解丝氨酸蛋白酶，已显示具有高杀线虫活性。虽然PL 646的晶体结构为研究其结构-功能关系提供了坚实的基础，但涉及底物结合，取向，催化，产物释放以及如何调节这些过程的动力学的详细方面仍然没有研究。进行了具有和不具有肽底物AAPV的PL 646的分子动力学（MD）模拟和代谢动力学模拟，以研究PL 646在底物结合时的结构、分子运动和自由能景观（FEL）的变化。结果表明，在模拟过程中，与底物结合的PL 646采用比无底物形式更稳定和紧凑的构象。然而，位于底物结合口袋对面或连接到催化残基的几个区域在底物结合时显示出增加的柔性。结合基本动力学（艾德）分析表明，在基板结合，显着的位移不仅发生在基板结合口袋/网站，但也在表面暴露的环。由大的协同运动引起的动态口袋被认为与PL 646的底物识别、结合、定向、催化和产物释放有关。构建的FEL显示，无底物的PL 646比蛋白酶与其底物的复合物具有更坚固、更宽的自由能表面和更高的最低自由能水平，表明底物结合降低了构象灵活性，同时增加了PL 646的稳定性。本研究的结果将有助于更好地理解角质层降解丝氨酸蛋白酶PL 646的结构-动力学-功能关系。
Cuticle-degrading serine proteases secreted by nematophagous fungi can degrade the nematode cuticle during the infection processes. PL646, an alkaline cuticle-degrading serine protease derived from the nematophagous fungus Paecilomyces lilacinus, has been shown to have a high nematicidal activity. Although the crystal structure of PL646 provides a solid basis for investigating its structure–function relationship, the detailed aspects of the dynamics involving the substrate binding, orientation, catalysis, product release, and how these processes are regulated, remain unstudied. Molecular dynamics (MD) simulations and metadynamics simulations of PL646 with and without the peptide substrate AAPV were performed to investigate the changes in structure, molecular motions, and free energy landscape (FEL) of PL646 upon substrate binding. The results indicate that during simulations, the substrate-bound PL646 adopts a more stable and compact conformation than the substrate-free form. However, a few regions located opposite the substrate binding pockets or connected to the catalytic residue show increased flexibility upon substrate binding. Combined essential dynamics (ED) analysis reveals that, upon substrate binding, the noticeable displacements occur not only in the substrate binding pockets/sites, but also in the surface-exposed loops. The dynamic pockets caused by the large concerted motions are proposed to be linked to the substrate recognition, binding, orientation, catalysis, and product release of PL646. The constructed FELs reveal that the substrate-free PL646 has a more rugged and wider free energy surface, and a higher minimum free energy level than the proteinase in complex with its substrate, indicating that the substrate binding reduces the conformational flexibility while increasing the stability of PL646. The results presented in this work will facilitate a better understanding of the structure–dynamics–function relationship of the cuticle-degrading serine protease PL646.