STRUCTURE PREDICTION OF COMPLEX BETWEEN CHROMOSOMAL PROTEIN HMG D & DNA

非组蛋白染色体蛋白是细胞核的重要组成部分， 由于它们与DNA相互作用的能力， 形成和调节染色质结构，并调节基因表达 [80，81]。 然而，对染色体功能的理解 由于缺乏蛋白质，分子水平的蛋白质研究受到阻碍 染色体蛋白质-DNA复合物的结构。 我们所实施的 分子动力学建模研究 * [82]，以提供对 染色体HMG结构域蛋白HMG-D的DNA结合模式[83， 84]。 推导了HMG-D与DNA结合的三种模型 通过将蛋白质对接到已知的两个不同的DNA片段上， 结构 分子动力学模拟的复合物提供 数据表明最有利的模型。 该模型进一步 经过分子动力学模拟和广泛的分析。 相应的HMG-D-DNA复合物的结构表现出许多 在序列特异性的NMR结构中看到的特征 HMG-结构域-DNA复合物，淋巴增强因子1（LEF-1）[85]和 睾丸决定因子（SRY）[86]。 该模型揭示了差异 从这些已知的结构中， 与许多不同的DNA序列有相似的亲和力。

Non-histone chromosomal proteins are an important part of nuclear structure and function due to their ability to interact with DNA, to form and modulate chromatin structure, and to regulate gene expression [80, 81]. However, the understanding of the function of chromosomal proteins at the molecular level has been hampered by the lack of structures of chromosomal protein-DNA complexes. We have carried out a molecular dynamics modeling study* [82] to provide insight into the mode of DNA binding by the chromosomal HMG-domain protein, HMG-D [83, 84]. Three models of a complex of HMG-D bound to DNA were derived through docking the protein to two different DNA fragments of known structure. Molecular dynamics simulations of the complexes provided data indicating the most favorable model. This model was further refined by molecular dynamics simulation and extensively analyzed. The structure of the corresponding HMG-D-DNA complex exhibits many features seen in the NMR structures of the sequence-specific HMG-domain-DNA complexes, lymphoid enhancer factor 1 (LEF-1) [85] and testis determining factor (SRY) [86]. The model reveals differences from these known structures that suggest how chromosomal proteins bind to many different DNA sequences with comparable affinity.