Interaction of water with the G-quadruplex loop contributes to the binding energy of G-quadruplex to protein
Interaction of water with the G-quadruplex loop contributes to the binding energy of G-quadruplex to protein
复制标题
水与 G-四链体环的相互作用有助于 G-四链体与蛋白质的结合能
DOI：
10.1039/c2mb25234a
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发表时间：
2012
期刊：
影响因子：
--
通讯作者：
S. Nagatoishi and N. Sugimoto
中科院分区：
文献类型：
--
作者：
S. Nakano;H. Hirayama;D. Miyoshi and N. Sugimoto;S. Nagatoishi and N. Sugimoto
与DNA双链体在与蛋白质相互作用时释放水不同，凝血酶结合适配体（TBA）的DNA g -四链体与凝血酶的结合需要水。为了揭示水分吸收的机制，我们设计了四种TBA突变体（ΔT3， ΔT7， ΔT9， ΔT12），其中TBA g -四重体环区删除了胸腺嘧啶残基（T3, T7， T9和T12）。研究了这些突变体与凝血酶相互作用的热力学和渗透效应。突变体ΔT3、ΔT9和ΔT12降低了g -四重体与凝血酶的结合常数。此外，渗透胁迫分析表明，在突变体ΔT3和ΔT9中，与复合物结合的水分子数量减少。结合亲和力的降低与环核苷酸与水分子的结合丧失有关。因此，g -四重体环与水分子之间的相互作用有助于g -四重体对蛋白质的结合能。我们的研究表明，水结合是g -四重体与蛋白质结合的必要条件。
Unlike DNA duplexes that release water upon interaction with protein, the binding of DNA G-quadruplex of the thrombin-binding aptamer (TBA) to thrombin takes up water. Here, to reveal the mechanism of water uptake, we designed four mutants of TBA (ΔT3, ΔT7, ΔT9, ΔT12), in which thymine residues (T3, T7, T9 and T12) were deleted from the loop regions of TBA G-quadruplex. For the mutants the thermodynamics and the osmolyte effects on the interactions with thrombin were investigated. The mutants ΔT3, ΔT9 and ΔT12 decreased the binding constants of the G-quadruplex to thrombin. Furthermore, an osmotic stress analysis indicated that the number of water molecules binding to the complex decreased in the mutants ΔT3 and ΔT9. The decrease in the binding affinity was related to loss of binding of the loop nucleotides to water molecules. Therefore, the interaction between loops of the G-quadruplex and water molecules contributed to the binding energy of G-quadruplex to protein. Our study suggests that water binding is essential for the binding of G-quadruplex to protein.