The Role of Water H-Bond Imbalances in B-DNA Substate Transitions and Peptide Recognition Revealed by Time-Resolved FTIR Spectroscopy
The Role of Water H-Bond Imbalances in B-DNA Substate Transitions and Peptide Recognition Revealed by Time-Resolved FTIR Spectroscopy
复制标题
DOI：
10.1021/ja108863v
复制
发表时间：
2011-04-20
影响因子：
15
通讯作者：
Fahmy, Karim
中科院分区：
文献类型：
--
作者：
Khesbak, Hassan;Saychuk, Olesya;Fahmy, Karim
B-DNA 中磷酸二酯骨架的构象亚态 B-I 和 B-II 被认为有助于 DNA 灵活性和蛋白质识别。我们通过快速扫描 FTIR 光谱研究了其固有时间尺度上的等温 B-I-B-II 转变。 DNA 水合壳可逆增量增长后数秒内发生的红外吸收变化的相关分析识别出水群体 w(1)（PO2-结合）和 w(2)（非 PO2-结合）分别表现出比大量水中的氢键更弱和更强的氢键。 B-II 子状态由 w(2) 稳定。 3-4 kJ mol(-1) 的水氢键不平衡在形成 v(OH) 带宽减小的连续水网络（每个 DNA 磷酸盐有 12-14 个 H2O 分子）时以很小的焓成本平衡。在这种状态下，水合水通过额外的 w(2)-水接触取代 w(2)-DNA 相互作用，而不是结合到 B-I 特异性水合位点，从而协同稳定 B-I 构象异构体。这种水重排有助于吲哚西丁 (indolicidin) 识别 DNA，吲哚西丁是一种来自牛中性粒细胞的抗菌 13 聚体肽，尽管其内在结构很少，但在水介导的诱导配合中优先与 B-I 构象异构体结合。 FTIR 光谱解析了从 PO2 溶剂化到亚态转变并最终导致复合物中碱基堆积变化的连续步骤。结合圆二色光谱滴定，数据表明，在没有大量水相的情况下，如在分子拥挤的环境中，DNA水合壳内的水重新定位允许熵的贡献类似于溶液中DNA配体识别时分配给水的熵贡献。
The conformational substates B-I and B-II of the phosphodiester backbone in B-DNA are thought to contribute to DNA flexibility and protein recognition. We have studied by rapid scan FTIR spectroscopy the isothermal B-I-B-II transition on its intrinsic time scale. Correlation analysis of IR absorption changes occurring within seconds after a reversible incremental growth of the DNA hydration shell identifies water populations w(1) (PO2--bound) and w(2) (non-PO2--bound) exhibiting weaker and stronger H-bonds, respectively, than those dominating in bulk water. The B-II substate is stabilized by w(2). The water H-bond imbalance of 3-4 kJ mol(-1) is equalized at little enthalpic cost upon formation of a contiguous water network (at 12-14 H2O molecules per DNA phosphate) of reduced v(OH) bandwidth. In this state, hydration water cooperatively stabilizes the B-I conformer via the entropically favored replacement of w(2)-DNA interactions by additional w(2)-water contacts, rather than binding to B-I-specific hydration sites. Such water rearrangements contribute to the recognition of DNA by indolicidin, an antimicrobial 13-mer peptide from bovine neutrophils which, despite little intrinsic structure, preferentially binds to the B-I conformer in a water-mediated induced fit. The FTIR spectra resolve sequential steps leading from PO2--solvation to substate transition and eventually to base stacking changes in the complex. In combination with CD-spectral titrations, the data indicate that, in the absence of a bulk aqueous phase, as in molecular crowded environments, water relocation within the DNA hydration shell allows for entropic contributions similar to those assigned to water upon DNA ligand recognition in solution.