Assessment by molecular dynamics simulations of the structural determinants of DNA-binding specificity for transcription factor Sp1
Assessment by molecular dynamics simulations of the structural determinants of DNA-binding specificity for transcription factor Sp1
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DOI：
10.1016/s0022-2836(03)00243-2
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发表时间：
2003-04-18
影响因子：
5.6
通讯作者：
Gago, F
中科院分区：
文献类型：
--
作者：
Marco, E;García-Nieto, R;Gago, F
普遍存在的转录因子Sp1的DNA结合结构域（DBD）由三个连续的锌指组成，其识别许多核苷酸序列，这些核苷酸序列与结构上更好表征的早期生长反应蛋白1（EGR 1，也称为Zif 268，Krox-24和NGFI-A）识别的核苷酸序列不同，但相关，有时重叠。公认的Sp1的共有结合序列通常由不对称六核苷酸核心GGGCGG定义，但该序列不包括构成Sp1与wt 1启动子结合的高亲和力位点的GAG（= CTC）重复序列等。由于没有3D结构的整个DBD的Sp1是可用的，无论是单独的或与DNA的复合物，一个基于同源性的模型建立和它的相互作用与两个DNA 14聚体的研究使用纳秒分子动力学模拟在显式水分子的存在下。这些寡核苷酸代表存在于mdr 1和wt 1基因启动子中的Sp1靶位点。为了比较目的和验证方案，在相同条件下模拟EGR 1的DBD与其近端mdr 1启动子内的DNA靶位点之间的复合物。一些水分子被认为在蛋白质-DNA复合物的识别和稳定中起重要作用。我们的研究结果，这是支持现有的实验证据表明，在推定的Sp1结合位点的预测的准确性，可以提高通过解释一组规则，这是一个混合的严格性和宽容性，为并列的三重亚位点，每个锌指结合。我们的方法可以外推到WT 1和其他相关的天然或人工含锌指的DNA结合蛋白，并可能有助于指定特定的DNA片段作为允许或不允许的结合位点。(C)2003爱思唯尔科技有限公司版权所有
The DNA-binding domain (DBD) of the ubiquituous transcription factor Sp1 consists of three consecutive zinc fingers that recognize a number of nucleotide sequences different from, but related to and sometimes overlapping, those recognized by the structurally better characterized early growth response protein 1 (EGR1, also known as Zif268, Krox-24, and NGFI-A). The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG ( = CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter. Since no 3D structure of the whole DBD of Sp1 is available, either alone or in complex with DNA, a homology-based model was built and its interaction with two DNA 14-mers was studied using nanosecond molecular dynamics simulations in the presence of explicit water molecules. These oligonucleotides represent Sp1 target sites that are present in the promoters of the mdr1 and wt1 genes. For comparative purposes and validation of the protocol, the complex between the DBD of EGR1 and its DNA target site within the proximal mdr1 promoter was simulated under the same conditions. Some water molecules were seen to play an important role in recognition and stabilization of the protein-DNA complexes. Our results, which are supported by the available experimental evidence, suggest that the accuracy in the prediction of putative Sp1-binding sites can be improved by interpreting a set of rules, which are a blend of both stringency and tolerance, for the juxtaposed triplet subsites to which each zinc finger binds. Our approach can be extrapolated to WT1 and other related natural or artificial zinc-finger-containing DNA-binding proteins and may aid in the assignment of particular DNA stretches as allowed or disallowed-binding sites. (C) 2003 Elsevier Science Ltd. All rights reserved