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枯草芽孢杆菌伸展蛋白EXLX1的分子动力学:与底物的相互作用及突变体活性缺失的结构基础

Molecular dynamics of the Bacillus subtilis expansin EXLX1: interaction with substrates and structural basis of the lack of activity of mutants.

作者信息

Silveira Rodrigo L, Skaf Munir S

机构信息

Institute of Chemistry, University of Campinas, Campinas, Cx. P. 6154, 13084-862, SP, Brazil.

出版信息

Phys Chem Chem Phys. 2016 Feb 7;18(5):3510-21. doi: 10.1039/c5cp06674c.

Abstract

Expansins are disruptive proteins that loosen growing plant cell walls and can enhance the enzymatic hydrolysis of cellulose. The canonical expansin structure consists of one domain responsible for substrate binding (D2) and another domain (D1) of unknown function, but essential for activity. Although the effects of expansins on cell walls and cellulose fibrils are known, the molecular mechanism underlying their biophysical function is poorly understood. Here, we use molecular dynamics simulations to gain insights into the mechanism of action of the Bacillus subtilis expansin BsEXLX1. We show that BsEXLX1 can slide on the hydrophobic surface of crystalline cellulose via the flat aromatic surface of its binding domain D2, comprised mainly of residues Trp125 and Trp126. Also, we observe that BsEXLX1 can hydrogen bond a free glucan chain in a twisted conformation and that the twisting is chiefly induced by means of residue Asp82 located on D1, which has been shown to be essential for expansin activity. These results suggest that BsEXLX1 could move on the surface of cellulose and disrupt hydrogen bonds by twisting glucan chains. Simulations of the inactive BsEXLX1 mutants Asp82Asn and Tyr73Ala indicate structural alterations around the twisting center in the domain D1, which suggest a molecular basis for the lack of activity of these mutants and corroborate the idea that BsEXLX1 works by inducing twists on glucan chains. Moreover, simulations of the double mutant Asp82Asn/Tyr73Leu predict the recovery of the lost activity of BsEXLX1-Asp82Asn. Our results provide a dynamical view of the expansin-substrate interactions at the molecular scale and help shed light on the expansin mechanism.

摘要

扩展蛋白是一种能破坏植物细胞壁结构的蛋白质,可使生长中的植物细胞壁松弛,并能增强纤维素的酶促水解作用。典型的扩展蛋白结构由一个负责底物结合的结构域(D2)和另一个功能未知但对活性至关重要的结构域(D1)组成。尽管扩展蛋白对细胞壁和纤维素微纤丝的作用已为人所知,但其生物物理功能的分子机制仍知之甚少。在此,我们通过分子动力学模拟来深入了解枯草芽孢杆菌扩展蛋白BsEXLX1的作用机制。我们发现,BsEXLX1可以通过其主要由色氨酸125和色氨酸126残基组成的结合结构域D2的平面芳香表面,在结晶纤维素的疏水表面上滑动。此外,我们观察到BsEXLX1可以与呈扭曲构象的游离葡聚糖链形成氢键,且这种扭曲主要是由位于D1上的天冬氨酸82残基引起的,该残基已被证明对扩展蛋白活性至关重要。这些结果表明,BsEXLX1可以在纤维素表面移动,并通过扭曲葡聚糖链来破坏氢键。对无活性的BsEXLX1突变体天冬氨酸82→天冬酰胺和酪氨酸73→丙氨酸的模拟表明,D1结构域中扭曲中心周围存在结构改变,这为这些突变体缺乏活性提供了分子基础,并证实了BsEXLX1通过诱导葡聚糖链扭曲发挥作用的观点。此外,对双突变体天冬氨酸82→天冬酰胺/酪氨酸73→亮氨酸的模拟预测,BsEXLX1-天冬氨酸82→天冬酰胺丧失的活性将会恢复。我们的结果在分子尺度上提供了扩展蛋白-底物相互作用的动态视图,并有助于阐明扩展蛋白的作用机制。

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