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J Integr Plant Biol, 2003, 45 (11): 1297-1306, Research Article
Modeling Rice rgMT as a Plant Metallothionein-Like Protein by the Distance Geometry and Homology Methods
LÜ Tun, LIU Jin-Yuan*, ZHANG Ri-Qing, ZHAO Nan-Ming

Rice metallothionein-like protein (rgMT) shows characteristics of a three-section pattern composed of two highly conserved cysteine rich (CR) domains in the terminals and a spacer without cysteine (cys) residues in the center of the molecule. In this paper, the two CR domains and the spacer region were modeled by the distance geometry and homology methods separately. For the CR domains, twenty random models were generated for each cys combination based on the constraint conditions of CXC (C represents cys, X represents any amino acid other than cys), and CXXC motifs and a metal-sulfur chelating cluster. Four models for the N-terminal and two for C-terminal CR domain containing metal chelating structures formed by different combinations of cys were selected from 900 possible conformations. The GOR method was used to predict the secondary structure of the spacer region and its model was built by the homology method. After three parts of the protein were modeled, they were connected to form a three-dimensional structure model of rgMT. The whole conformation showed that rgMT could form two independent metal-sulfur chelating structures connected by a spacer peptide, without a structural or energy barrier for them to form two independent metal-chelating clusters just as mammalian metallothionein (MT) proteins. As all plant metallothionein-like (MT-L) proteins have the same primary structural characteristic, two CR domains connected by a spacer region, and many have the same cys arrangement pattern as rgMT, the three-dimensional structure model of rgMT will provide an important reference for the structural study of other plant MT-L proteins.

用距离几何算法和同源建模法对水稻类金属硫蛋白(r g M T )的三维结构建模
吕 暾 刘进元  张日清 赵南明
( 清华大学生命科学与工程研究院,生物科学与技术系,蛋白质科学教育部重点实验室,北京 100084)

摘要: 水稻类金属硫蛋白(rgMT)的两端是高度保守的半胱氨酸富含区的结构域(CR 区),中间是不含半胱氨酸的间隔区,呈典型的三段式结构。本研究分别采用距离几何算法和同源建模相结合的方法对水稻类金属硫蛋白进行三级结构建模。在排列出CR区的所有可能的半胱氨酸金属硫络合的组合方式,并对每一种组合方式给出一定的限制条件后各生成20 个随机构象。根据生成的随机构象是否能形成金属硫络合结构,从900 个随机构象中最终选出6 个构象(N 端4 种,C 端2 种组合)作为可能的结构模型。另一方面,采用GOR 方法对间隔区进行了二级结构预测,随后用同源建模法对其建模。 将上述建成的三部分模型连接起来后形成rgMT 的整体三维构象。结果表明rgMT 能像哺乳动物MT 蛋白一样,可形成两个独立的、在结构和能量上均没有障碍的金属- 硫络合结构。介于所有植物类金属硫蛋白都具有典型的三段式结构,其中的一部分还具有与rgMT 相同的半胱氨酸排列方式,所以rgMT 三维结构模型的建立对于其他植物类金属硫蛋白的结构研究具有重要的参考价值。
关键词: 距离几何算法; 同源建模法;水稻类金属硫蛋白;结构模型

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