Fonseca Emily C M, da Costa Kauê S, Lameira Jerônimo, Alves Cláudio Nahum, Lima Anderson H
Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará Rua Augusto Corrêa 01. Guamá. 66075-110 Belém Pará Brazil
Instituto de Biodiversidade, Universidade Federal do Oeste do Pará 68035-110, Rua Vera Paz, s/n Salé Santarém Pará Brazil 68040-255
RSC Adv. 2020 Dec 16;10(72):44352-44360. doi: 10.1039/d0ra09061a. eCollection 2020 Dec 9.
The shikimate pathway enzyme 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS) catalyzes the reaction involved in the production of amino acids essential for plant growth and survival. Thus, EPSPS is the main target of various herbicides, including glyphosate, a broad-spectrum herbicide that acts as a competitive inhibitor of phosphoenolpyruvate (PEP), which is the natural substrate of EPSPS. However, punctual mutations in the EPSPS gene have led to glyphosate resistance in some plants. Here, we investigated the mechanism of EPSPS resistance to glyphosate in mutants of two weed species, (mutant, P106T) and (mutant, T102I/P106S), both of which have an economic impact on industrial crops. Molecular dynamics (MD) simulations and binding free energy calculations revealed the influence of the mutations on the affinity of glyphosate in the PEP-binding site. The amino acid residues of the EPSPS protein in both species involved in glyphosate resistance were elucidated as well as other residues that could be useful for protein engineering. In addition, during MD simulations, we identified conformational changes in glyphosate when complexed with resistant EPSPS, related to loss of herbicide activity and binding affinity. Our computational findings are consistent with previous experimental results and clarify the inhibitory activity of glyphosate as well as the structural target-site resistance of EPSPS against glyphosate.
莽草酸途径中的酶5-烯醇丙酮酰莽草酸-3-磷酸合酶（EPSPS）催化参与植物生长和存活所必需氨基酸生产的反应。因此，EPSPS是包括草甘膦在内的各种除草剂的主要靶标，草甘膦是一种广谱除草剂，作为磷酸烯醇丙酮酸（PEP）的竞争性抑制剂起作用，而PEP是EPSPS的天然底物。然而，EPSPS基因中的点突变已导致一些植物对草甘膦产生抗性。在这里，我们研究了两种杂草物种（突变体P106T）和（突变体T102I/P106S）的突变体中EPSPS对草甘膦的抗性机制，这两种杂草对经济作物都有经济影响。分子动力学（MD）模拟和结合自由能计算揭示了突变对草甘膦在PEP结合位点亲和力的影响。阐明了这两种物种中EPSPS蛋白参与草甘膦抗性的氨基酸残基以及可能对蛋白质工程有用的其他残基。此外，在MD模拟过程中，我们确定了与抗性EPSPS复合时草甘膦的构象变化，这与除草剂活性和结合亲和力的丧失有关。我们的计算结果与先前的实验结果一致，并阐明了草甘膦的抑制活性以及EPSPS对草甘膦的结构靶标位点抗性。
