共查询到20条相似文献,搜索用时 62 毫秒
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Elena M. Pugacheva Samuel Rivero-Hinojosa Celso A. Espinoza Claudia Fabiola Méndez-Catalá Sungyun Kang Teruhiko Suzuki Natsuki Kosaka-Suzuki Susan Robinson Vijayaraj Nagarajan Zhen Ye Abdelhalim Boukaba John E. J. Rasko Alexander V. Strunnikov Dmitri Loukinov Bing Ren Victor V. Lobanenkov 《Genome biology》2015,16(1)
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Binding of the estrogen receptor to DNA. The role of waters. 总被引:2,自引:0,他引:2
Molecular dynamics simulations are carried out to investigate the binding of the estrogen receptor, a member of the nuclear hormone receptor family, to specific and non-specific DNA. Two systems have been simulated, each based on the crystallographic structure of a complex of a dimer of the estrogen receptor DNA binding domain with DNA. One structure includes the dimer and a consensus segment of DNA, ds(CCAGGTCACAGTGACCTGG); the other structure includes the dimer and a nonconsensus segment of DNA, ds(CCAGAACACAGTGACCTGG). The simulations involve an atomic model of the protein-DNA complex, counterions, and a sphere of explicit water with a radius of 45 A. The molecular dynamics package NAMD was used to obtain 100 ps of dynamics for each system with complete long-range electrostatic interactions. Analysis of the simulations revealed differences in the protein-DNA interactions for consensus and nonconsensus sequences, a bending and unwinding of the DNA, a slight rearrangement of several amino acid side chains, and inclusion of water molecules at the protein-DNA interface region. Our results indicate that binding specificity and stability is conferred by a network of direct and water mediated protein-DNA hydrogen bonds. For the consensus sequence, the network involves three water molecules, residues Glu-25, Lys-28, Lys-32, Arg-33, and bases of the DNA. The binding differs for the nonconsensus DNA sequence in which case the fluctuating network of hydrogen bonds allows water molecules to enter the protein-DNA interface. We conclude that water plays a role in furnishing DNA binding specificity to nuclear hormone receptors. 相似文献
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