Abstract Trichoderma spp. are plant beneficial fungi that colonize roots, but unlike plant pathogens, impart defence. Recently, however, some small secreted cysteine-rich proteins have been identified in Trichoderma secretome, deletion of which improves induced defence. The mechanism of such “unusual” behaviour of a plant-beneficial fungus is not understood. In the present study, through in silico analysis, we attempted to explore if such proteins indeed suppress defence by interacting with plant proteins, much like pathogens, taking Alt a 1 protein of T. virens and maize PR5, a thaumatin-like defence protein as predicted interacting partners (with cue from some plant-pathogen interactions). Using computational analysis, we test the hypothesis that Trichoderma Alt a 1 inactivates maize PR5 to suppress plant defence in order to be able to colonize roots. The tertiary structures of both Alt a 1 and PR5 were modelled through homology as well as de novo modelling, followed by model validation through different quality check tools. Prior to protein-protein docking, MD (molecular dynamics) optimisation and refinement of computational models were carried-out. Docking results indicated that Alt a 1 exhibits strong binding affinity with PR5 suggesting that Alt a 1 and PR5 might interact much like in a plant-pathogen interactions resulting in suppression of plant defence to facilitate colonization.

中文翻译：

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Trichoderma virens Alt a 1 蛋白可能靶向玉米 PR5/thaumatin 样蛋白以抑制植物防御：计算机分析

摘要木霉属。是定植于根部的植物有益真菌，但与植物病原体不同，它们具有防御作用。然而，最近在木霉分泌组中发现了一些小的分泌型富含半胱氨酸的蛋白质，删除这些蛋白质可提高诱导防御。对植物有益的真菌的这种“不寻常”行为的机制尚不清楚。在本研究中，通过计算机分析，我们试图探索这些蛋白质是否确实通过与植物蛋白相互作用来抑制防御，就像病原体一样，将 T. virens 和玉米 PR5 的 Alt a 1 蛋白（一种类奇异果甜蛋白）作为预测的相互作用伙伴（来自一些植物病原体相互作用的线索）。使用计算分析，我们检验了 Trichoderma Alt a 1 使玉米 PR5 失活以抑制植物防御以便能够定植根部的假设。Alt a 1 和 PR5 的三级结构通过同源性和从头建模进行建模，然后通过不同的质量检查工具进行模型验证。在蛋白质-蛋白质对接之前，进行了 MD（分子动力学）优化和计算模型的细化。对接结果表明Alt a 1 表现出与PR5 的强结合亲和力，这表明Alt a 1 和PR5 可能很像植物-病原体相互作用中的相互作用，从而抑制植物防御以促进定植。然后通过不同的质量检查工具进行模型验证。在蛋白质-蛋白质对接之前，进行了 MD（分子动力学）优化和计算模型的细化。对接结果表明Alt a 1 表现出与PR5 的强结合亲和力，表明Alt a 1 和PR5 可能很像植物-病原体相互作用中的相互作用，从而抑制植物防御以促进定植。然后通过不同的质量检查工具进行模型验证。在蛋白质-蛋白质对接之前，进行了 MD（分子动力学）优化和计算模型的细化。对接结果表明Alt a 1 表现出与PR5 的强结合亲和力，表明Alt a 1 和PR5 可能很像植物-病原体相互作用中的相互作用，从而抑制植物防御以促进定植。