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首页> 外文期刊>Journal of Biomolecular Structure and Dynamics >Three dimensional structure of the soybean agglutinin Gal/GalNAc complexes by homology modeling.
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Three dimensional structure of the soybean agglutinin Gal/GalNAc complexes by homology modeling.

机译：大豆凝集素Gal / GalNAc复合物的三维结构通过同源性建模。

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Complexes of soybean agglutinin (SBA) with galactose (Gal) and N-acetyl galactosamine (GalNAc) have been modeled based on its homology to erythrina corallodendron (EcorL) lectin. The three dimensional structure of SBA-Gal modeled with homology techniques agrees well with SBA-(beta-LacNAc)2Gal-R complex determined by X-ray crystallographic techniques at the beta-sheet regions and the regions where Ca2+ and Mn2+ ions bind. However, significant deviations have been observed between the modeled and the X-ray structures, particularly at the loop regions where the polypeptide chain could not be unequivocally traced in the X-ray structure. The hydrogen bonding scheme, predicted from the homology model, shows that the invariant residues i.e. Asp, Gly, Asn, and aromatic residues (Phe) found in all other legume lectins, bind Gal, slightly in a different way than reported in X-ray structure of SBA-pentasaccharide complex. The higher binding affinity of GalNAc over Gal to SBA is due to additional hydrophobic interactions with Tyr107 rather than a hydrogen bond between N-acetamide group of the sugar and the side chain of Asp88 as suggested from X-ray crystal structure studies. Our modeling also suggest that the variation in the length of the loop D observed among galactose binding legume lectins may not have any effect on the binding of sugar at the monosaccharide specific site of the lectins. Soybean agglutinin (SBA) is a member of the leguminous family of lectins. They generally possess a single carbohydrate binding site, besides the tightly bound Ca2+ and Mn2+ ions which are required for their carbohydrate binding activity. They possess a high degree of sequence homology and about 50% of the amino acid residues are invariant. Some of these invariant amino acid residues are involved in the binding of sugar moieties and in metal ion coordination. X-ray crystallographic studies showed that their three-dimensional structures are very similar, though they differ in their carbohydrate binding specificity (1-6). Three of the invariant residues Asp, Gly, and Asn, besides an aromatic residue (Phe or Tyr), are involved in carbohydrate binding. Independent of their sugar specificity, these four residues in legume lectins provide the basic frame for the sugar to bind.
机译：基于大豆凝集素（SBA）与半乳糖（Gal）和N-乙酰半乳糖胺（GalNAc）的复合物，基于其与赤藓珊瑚（EcorL）凝集素的同源性进行了建模。用同源技术建模的SBA-Gal的三维结构与通过X射线晶体学技术在β-折叠区域和Ca2 +和Mn2 +离子结合的区域确定的SBA-（β-LacNAc）2Gal-R复合物非常吻合。然而，在建模的和X射线结构之间已经观察到明显的偏差，特别是在不能明确地在X射线结构中追踪多肽链的环区域。根据同源性模型预测的氢键方案显示，在所有其他豆类植物凝集素中发现的不变残基（即Asp，Gly，Asn和芳香族残基（Phe））与Gal结合的方式与X射线报道的略有不同SBA-五糖复合物的结构。 GalNAc对Gal与SBA的较高结合亲和力是由于与Tyr107的额外疏水相互作用，而不是X射线晶体结构研究表明，糖的N-乙酰胺基和Asp88侧链之间存在氢键。我们的模型还表明，在半乳糖结合的豆科植物凝集素之间观察到的环D长度的变化可能对凝集素的单糖特异性位点处的糖结合没有任何影响。大豆凝集素（SBA）是豆科植物凝集素家族的成员。除了它们的碳水化合物结合活性所需的紧密结合的Ca2 +和Mn2 +离子外，它们通常具有单个碳水化合物结合位点。它们具有高度的序列同源性，并且约50％的氨基酸残基是不变的。这些不变的氨基酸残基中的一些与糖部分的结合和金属离子配位有关。 X射线晶体学研究表明，它们的三维结构非常相似，尽管它们的碳水化合物结合特异性不同（1-6）。除芳香族残基（Phe或Tyr）外，三个不变残基Asp，Gly和Asn还参与碳水化合物的结合。不受其糖特异性影响，豆科植物凝集素中的这四个残基为糖结合提供了基本框架。

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