A束的大小沟中的DNA弯曲和“结构”水。蒙特卡罗计算机模拟
DNA bending and "structural" waters in major and minor grooves of A-tracts. Monte Carlo computer simulations
摘要：
为了阐明结构水在稳定弯曲DNA中可能的作用，用Monte Carlo模拟研究了含AT的十聚体（A5 T5）2和A10：T10的各种构象。双链体被限制为在两个温度下再现A束的NMR质子间距离：5 ℃和35 ℃。水壳结构的分析揭示了一方面槽宽与另一方面水合模式的类型及其概率之间的强相关性。根据小沟的宽度，在该沟中观察到以下模式：链间“水合脊柱”，或链间两水桥，或链内糖基“水弦”的双带。水化壳在大沟中的规则性比在小沟中的规则性差，这与晶体学数据相一致。如在先前的研究中，发现具有窄小沟和宽大沟（B '-样DNA）的A束构象具有能量有利的水合作用，已知其与DNA弯曲和曲率相关。此外，我们的计算表明，这种DNA构象的优势是加上腺嘌呤N7水合在大沟中的增加。由于大沟打开更宽，其水化壳通过与属于两个相邻腺嘌呤的三个亲水中心（两个N7原子和一个氨基质子H（N6））键合的能量有利的“三叉水”来富集。基于这些结果，我们认为，在大沟中形成的新的水合模式的因素之一，负责稳定的B '样构象的A-束在低温下在脱水剂的情况下，反过来导致强的固有曲率的DNA含有交替的A-束和“混合”GC丰富的序列。
英文摘要：
To elucidate the possible role of structural waters in stabilizing bent DNA, various conformations of AT-containing decamers, (A5T5)2 and A10:T10, were studied by Monte Carlo simulations. The duplexes were constrained to reproduce the NMR inter-proton distances for the A-tracts at two temperatures: 5 and 35C. Analysis of the water shell structures revealed a strong correlation between the groove widths on the one hand, and the types of hydration patterns and their probabilities on the other hand. Depending on the minor groove width, the following patterns were observed in this groove: either an interstrand "hydration spine", or interstrand two-water bridges, or a double ribbon of intrastrand sugar-base "water strings". Hydration shell in the major groove is less regular than in the minor groove, which agrees with crystallographic data. As in previous studies, energetically advantageous hydration is found for the A-tract conformations with narrow minor groove and wide major groove (B'-like DNA), known to be correlated with DNA bending and curvature. In addition, our calculations indicate that the advantage of such DNA conformations is coupled with the increase in adenine N7 hydration in the major groove. As the major groove is opened wider, its hydration shell is enriched by energetically favorable "trident waters" hydrogen bonded to three hydrophilic centers belonging to two adjacent adenines: two N7 atoms and one amino-proton H(N6). Based on these results, we suggest that formation of the novel hydration pattern in the major groove is one of the factors responsible for stabilization of the B'-like conformations of A-tracts at low temperature in the absense of dehydrating agents, leading in turn to the strong intrinsic curvature of DNA containing alternating A-tracts and "mixed" GC-rich sequences.
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