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Molecular Dynamics Calculation and X-ray Crystallographic Study of Interaction mode between Plyamine and Z-DNA

聚胺与Z-DNA相互作用模式的分子动力学计算和X射线晶体学研究

基本信息

批准号：
12672097
负责人：
OHISHI Hirofumi
金额：
$ 1.66万
依托单位：
Osaka University of Pharmaceutical Sciences
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
2000
资助国家：
日本
起止时间：
2000 至 2002
项目状态：
已结题

项目摘要

As for the transcription from DNA to t-RNA, it knows that it depends on a state of relaxation of the vector very much. About the transdiption of the vector, it knows that it doesn't happen under the state of super coil. Though a super coil is made to relax, Z-DNA plays a big part. The structure of Z-DNA depends on the kind of the surrounding metal ion concentration, polyamine concentration. We made seven kinds of the complex crystals about polyarnines and d(CG)_3 and succeeded in all the crystallization, and we could get data very expensive resolution up to 1.0Å completely. As a result of x-ray crystallographic analysis of polyamine, N1-{2-[(2-Amino-ethylamino) -ethylamino] -ethyl} -ethane-1,2-diamine and Z-DNA complex crystal, two polyamines went into the minor groove of the Z-DNA completely, and Z-DNA was stabilized.It is the first time to clear the matter that two polyamines combined with the minor groove of Z-DNA at the room temperature by the X-ray crystal structure analysis. We m … More ade the complex crystal of polyamine of thermine N1-[3-(3-Amino-propylamino) -propyl] -propane-1,3-diamine which exists in the living body and d(CG)_3,and as a result of X-ray crystal analysis with a high resolution up to 10 Å, this polyamine connected to the minorgroove of Z-DNA too. It was cleared that two thermine molecules were combined for the minor groove of the d(CG)_3 molecule completely. It is the first time that X-ray crystallographic structural analysis cleared the matter that the natural polyamines combined with Z-DNA at the room temperature. It succeeded in the crystallization of Z-DNA of the long chain d(CG)_6 which nobody succeeded into the crystallization and we did data measurement by SPring-8, and we could collect data up to 1.7 Å resolution. It is the first time that the X-ray crystal structure analysis of the longest Z-DNA could be done. It may introduce the mechanism of relaxation of super coil by Z-DNA. So, we are trying to dear the condition of the B-Z transition by the X-ray crystallographic structure analysis. Therefore using d(CGCGCGAATTCGCGCG) with polyamines which we found stabilize the Z-DNA, we crystallize d(CGCGCGAATTCGCGCG) complexed with these polyamines, and made the combination crystal of Z-DNA and B-DNA. According to these molecules we succeeded in the molecular dynamics calculation. If we can clear the structure by x-ray crystallographic study, we can make the suggestion of B-Z transition mechanism. Less

至于从DNA到t-RNA的转录，它知道它非常依赖于载体的松弛状态。关于矢量的变换，它知道在超螺旋状态下不发生。虽然超级线圈是为了放松，但Z-DNA起着重要作用。Z-DNA的结构取决于周围金属离子的种类浓度、多胺的浓度。制备了七种聚苯胺与d（CG）_3的配合物晶体，并全部结晶成功，获得了高达1.0 μ m的数据分辨率。作为多胺的X射线晶体学分析的结果，N1-{2-[（2-氨基-乙氨基）-乙氨基] -乙基} -乙烷-1，2-二胺与Z-DNA复合物晶体，两种多胺完全进入Z-DNA的小沟，首次用X-射线荧光光谱法明确了两种多胺在室温下与Z-DNA小沟结合的情况，X射线晶体结构分析我们 ...更多信息本文报道了生物体内存在的热胺N_1-[3-（3-氨基-丙氨基）-丙基] -丙-1，3-二胺与d（CG）_3的多胺配合物晶体，经X射线晶体分析，其分辨率高达10 μ m，表明该多胺也与Z-DNA的小沟相连。结果表明，d（CG）_3分子的小沟完全由两个热胺分子结合而成。X射线晶体结构分析首次明确了天然多胺在室温下与Z-DNA结合的问题。用SPring-8进行了数据测量，数据分辨率可达1.7 μ m。这是第一次可以对最长的Z-DNA进行X射线晶体结构分析。这可能是Z-DNA对超螺旋松弛的机制。因此，我们试图通过X射线晶体结构分析来明确B-Z转变的条件。因此，我们将d（CGCGCGAATTCGCGCG）与我们发现的稳定Z-DNA的多胺一起结晶，使d（CGCGCGAATTCGCGCG）与这些多胺形成复合物，并制成Z-DNA和B-DNA的结合晶体。根据这些分子，我们成功地进行了分子动力学计算。如果能通过X射线晶体学研究明确其结构，就能提出B-Z转变机制的建议。少