Comparative <i>in silico</i> study of the differences in the structure and ligand interaction properties of three alpha-expansin proteins from <i>Fragaria chiloensis</i> fruit
收藏资源简介：
Expansins are cell wall proteins associated with several processes, including changes in the cell wall during ripening of fruit, which matches softening of the fruit. We have previously reported an increase in expression of specific expansins transcripts during softening of <i>Fragaria chiloensis</i> fruit. Here, we characterized three <i>α-expansins</i>. Their full-length sequences were obtained, and through qRT-PCR (real-time PCR) analyses, their transcript accumulation during softening of <i>F. chiloensis</i> fruit was confirmed. Interestingly, differential but overlapping expression patterns were observed. With the aim of elucidating their roles, 3D protein models were built using comparative modeling methodology. The models obtained were similar and displayed cellulose binding module(CBM ) with a β-sandwich structure, and a catalytic domain comparable to the catalytic core of protein of the family 45 glycosyl hydrolase. An open groove located at the central part of each expansin was described; however, the shape and size are different. Their protein–ligand interactions were evaluated, showing favorable binding affinity energies with xyloglucan, homogalacturonan, and cellulose, cellulose being the best ligand. However, small differences were observed between the protein–ligand conformations. Molecular mechanics-generalized Born-surface area (MM-GBSA) analyses indicate the major contribution of van der Waals forces and non-polar interactions. The data provide a dynamic view of interaction between expansins and cellulose as putative cell wall ligands at the molecular scale. Communicated by Ramaswamy H. Sarma
扩张蛋白（expansins）是一类参与多种生理过程的细胞壁蛋白，其功能涵盖果实成熟阶段的细胞壁重塑，该过程与果实软化密切相关。本课题组此前已报道，智利草莓（Fragaria chiloensis）果实软化过程中，特定扩张蛋白的转录本表达量显著上调。本研究对三种α-扩张蛋白（α-expansins）开展了系统表征：成功获取了三者的全长序列，并通过qRT-PCR（实时PCR，即real-time PCR）分析验证了智利草莓（F. chiloensis）果实软化进程中其转录本的积累模式。值得注意的是，三者的表达模式既存在特异性差异，又存在部分重叠区域。为阐明这三种α-扩张蛋白的生物学功能，本研究采用比较建模法构建了其三维蛋白质结构模型。所获得的结构模型整体相似，均包含具有β-三明治结构的纤维素结合结构域（CBM），以及与糖苷水解酶45家族蛋白催化核心结构高度同源的催化结构域。每个扩张蛋白的中心区域均存在一个开放凹槽，但三者的凹槽形状与尺寸存在显著差异。研究评估了三者与不同配体的相互作用，结果显示其与木葡聚糖、同型半乳糖醛酸聚糖及纤维素均具有良好的结合亲和能，其中与纤维素的结合效果最优。不过不同扩张蛋白与配体结合的构象存在细微差异。分子力学-广义玻恩-表面积法（MM-GBSA）分析结果表明，范德华力与非极性相互作用是结合自由能的主要贡献来源。本研究数据从分子尺度揭示了扩张蛋白与作为推定细胞壁配体的纤维素之间的动态相互作用模式。本文由Ramaswamy H. Sarma转交。
