BRCT 结构域的功能演化与功能位点预测
文献类型：学位论文
| 作者 | 盛自章 |
| 学位类别 | 博士 |
| 答辩日期 | 2011-05 |
| 授予单位 | 中国科学院研究生院 |
| 授予地点 | 北京 |
| 导师 | 黄京飞 |
| 关键词 | BRCT DNA 损伤修复 磷酸结合口袋 蛋白结合 磷酸化蛋白motif |
| 其他题名 | Functional Evolution and functional site prediction of BRCT domain |
| 学位专业 | 细胞生物学 |
| 中文摘要 | BRCT(BRCA1 C-terminus)结构域是DNA损伤修复系统重要的信号传导和蛋白靶向结构域。研究显示，BRCT结构域主要以单体或二联体(串联重复)的形式存在。很多BRCT结构域含有磷酸结合口袋，能够结合DNA磷酸末端或磷酸化的蛋白motif，也有一些BRCT结构域以非磷酸化依赖的方式结合蛋白。利用不断增多的BRCT结构域三维结构和功能研究数据，我们探讨了BRCT结构域的功能演化并预测了其新的功能机制。 首先，本研究通过数据库搜索、系统演化分析、磷酸结合口袋的比较对BRCT结构域的功能演化进行了探讨。我们在细菌和真核生物中发现了新的含有BRCT结构域的蛋白，而且每个物种具有的含BRCT结构域的蛋白的数量与其基因组的复杂度成正相关。系统演化分析显示BRCT单体可以分成两类（sGroup I和sGroup II），BRCT二联体也可以分成两类（dGroup I和dGroup II）。这四类BRCT结构域的磷酸结合口袋具有不同的残基组成。在真核生物中，BRCT结构域的演化可以大致分为三个阶段：在第一个阶段，sGroup I蛋白获取了细菌中的含磷酸结合口袋的BRCT结构域，这种BRCT可以结合DNA的磷酸末端；在第二个阶段，sGroup II中的磷酸结合口袋从DNA结合型演化为磷酸化蛋白motif结合型，sGroup II BRCT的串联复制产生了二联体BRCT，而之后演化出两类二联体BRCT；第三个阶段演化出的BRCT单体都丢掉了磷酸结合口袋而演化出各自特异的蛋白结合位点，新演化出的dGroup I BRCT明显比sGroup II多。此外，BRCT结构域还可以以三联体作为演化和功能单位，其含有的磷酸结合口袋可以结合磷酸化的蛋白motif。结果还显示，BRCT结构域在真核生物基因组的扩张和功能分化受DNA损伤修复系统演化的影响。 其次，我们对XRCC1 BRCT1, PTIP BRCT4, ECT2 BRCT1和 TopBP1 BRCT1结合磷酸化的蛋白配体的机制进行了预测。结构保守性和表面静电势分析显示，四个BRCT的磷酸结合口袋周围都存在结构保守并带正电势的沟槽，很可能是其功能位点，并且类似的沟槽在含磷酸结合口袋的BRCT中普遍存在。沟槽两侧由带正电荷和极性氨基酸残基构成，底部为疏水和极性氨基酸残基，说明沟槽与配体的结合以静电和疏水相互作用为主。沟槽主要位于单个BRCT而且四个BRCT的沟槽在形状和电荷分布上都不同，说明识别特异性主要由一个BRCT决定。与dGroup I只结合磷酸丝氨酸C-端的三个残基不同，四个BRCT的磷酸结合口袋位于沟槽中心说明沟槽可能同时结合含磷酸基的氨基酸残基N-端和C-端的残基。 |
| 英文摘要 | BRCT domain (BRCA1 C-terminal domain) is an important signaling and protein targeting motif in DNA damage response system. BRCT domain, which mainly occur as singleton (single BRCT) or tandem pair (double BRCT), contains a phosphate binding pocket that can bind the phosphate from either DNA end or phosphorylated protein motif. There are also BRCT domains that can bind proteins in phospho-independent manner. By using increasing amount of information on crystal structure and function, we analyzed the functional evolution of BRCT domain and predicted its new functional mechanism. Firstly, we performed database search, phylogeny reconstruction, and phosphate binding pocket comparison to analyze the functional evolution of BRCT domain. We identified new BRCT domain-containing proteins in bacteria and eukaryotes, and found that the number of BRCT containing proteins per genome is correlated with genome complexity. The phylogeny analyses revealed that there are two groups of single BRCT domain (sGroup I and sGroup II) and double BRCT domain (dGroup I and dGroup II). These four BRCT groups showed differences in the phosphate binding pocket. In eukaryotes, the evolution of BRCT domain can be divided into three phases. In the first phase, sGroup I proteins derived the bacteria BRCT fold with the phosphate binding pocket that can bind the phosphate of nicked DNA. In the second phase, the phosphate binding pocket changed from DNA binding type to phosphorylated protein motif binding type in sGroup II. The tandem duplication of sGroup II BRCT domain gave birth to double BRCT domain, from which two structurally and functionally distinct groups were evolved. Both sGroup I and sGroup II BRCT domains originated in third phase lost the phosphate binding pocket and many evolved protein binding sites. Many dGroup I members were evolved in this phase but few dGroup II members were observed. In addition, BRCT domain can evolve and function with three BRCT domains (triple BRCT) as a unit, and the phosphate binding pocket in triple BRCT can bind phosphorylated protein motif. The results further suggested that the BRCT domain expansion and functional change in eukaryote may be driven by the evolution of the DNA damage response system. Secondly, we predicted the phosphorylated protein binding mechanism of XRCC1 BRCT1, PTIP BRCT4, ECT2 BRCT1 and TopBP1 BRCT1. The structural conservation and electrostatic surface calculation showed that conserved grooves with positive potential, which are common among phosphate binding pocket-containing BRCT domains, may be the functional sites of these four BRCT domains. The two sides of grooves are composed of positively charged or hydrophilic residues while the bottoms are composed of hydrophobic residues, suggesting that these grooves may bind to proteins mainly through electrostatic and hydrophobic interactions. The grooves in the four BRCT domains, each of which mainly locates in one BRCT domain, are different in shape and charge distribution indicating that the binding specificity is mainly determined by one BRCT domain. The groove is centered at the phosphate binding pocket implying that the groove can bind both the N-terminal and C-terminal residues of the phosphate containing residue. |
| 语种 | 中文 |
| 公开日期 | 2011-09-20 |
| 源URL | [http://159.226.149.42:8088/handle/353002/6799]  |
| 专题 | 昆明动物研究所_结构生物信息学 |
| 推荐引用方式 GB/T 7714 | 盛自章. BRCT 结构域的功能演化与功能位点预测[D]. 北京. 中国科学院研究生院. 2011. |
入库方式： OAI收割
来源：昆明动物研究所
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