Molecular dynamics of spermine-DNA interactions: sequence specificity and DNA bending for a simple ligand.
Molecular dynamics of spermine-DNA interactions: sequence specificity and DNA bending for a simple ligand.
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DOI：
10.1093/nar/17.17.6883
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发表时间：
1989-09
影响因子：
14.9
通讯作者：
B. Feuerstein;N. Pattabiraman;L. Marton
中科院分区：
文献类型：
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作者：
B. Feuerstein;N. Pattabiraman;L. Marton
我们用分子动力学模拟生理上重要的多胺精胺和两个B-DNA低聚物，均聚物（dG）10-（dC）10和杂聚物（dGdC）5-（dGdC）5之间的相互作用。模拟中包括水和抗衡离子。精胺-DNA复合物的起始坐标是通过精胺与两种低聚物的分子力学建模获得的结构;在这些模型中，精胺结合在杂聚物中诱导弯曲，但在均聚物中不诱导。在大约40 psec的分子动力学模拟过程中，精胺从大沟底部移开，并与d（G）10-d（C）10非特异性相互作用。相反，在整个模拟过程中，精胺诱导的（dGdC）5-（dGdC）5螺旋弯曲得以维持，并且精胺仍然与大沟紧密相关。这些结果提供了进一步的证据表明，精胺与核酸的结合可以是序列特异性的，并且交替的嘌呤-嘧啶序列的弯曲可能是精胺结合的生理学重要结果。
We used molecular dynamics to model interactions between the physiologically important polyamine spermine and two B-DNA oligomers, the homopolymer (dG)10-(dC)10 and the heteropolymer (dGdC)5-(dGdC)5. Water and counterions were included in the simulation. Starting coordinates for spermine-DNA complexes were structures obtained by molecular mechanics modeling of spermine with the two oligomers; in these models, spermine binding induced a bend in the heteropolymer but not in the homopolymer. During approximately 40 psec of molecular dynamics simulation, spermine moves away from the floor of the major groove and interacts nospecifically with d(G)10-d(C)10. In contrast, a spermine-induced bend in the helix of (dGdC)5-(dGdC)5 is maintained throughout the simulation and spermine remains closely associated with the major groove. These results provide further evidence that the binding of spermine to nucleic acids can be sequence specific and that bending of alternating purine-pyrimidine sequences may be a physiologically important result of spermine binding.