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 结构和功能取决于它们与DNA相互作用的能力，以 形成和调节染色质结构，调节基因表达 [80，81]。然而，对染色体功能的理解 分子水平上的蛋白质由于缺乏 染色体蛋白质-DNA复合体的结构。我们已经开展了 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与DNA的结合方式[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。提供了络合物的分子动力学模拟 显示最有利模式的数据。该模型进一步扩展了 经过分子动力学模拟提炼和广泛分析。 相应的HMG-D-DNA复合体的结构表现出许多 序列特异性核磁共振结构中的特征 HMG结构域-DNA复合体，淋巴增强因子1(LeF-1)[85]和 睾丸决定因素(SRY)[86]。模型显示了不同 从这些已知的结构可以看出染色体蛋白是如何结合的 与许多不同的DNA序列具有类似的亲和力。

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.