Direct observation of the external force mediated conformational dynamics of an IHF bound Holliday junction
Direct observation of the external force mediated conformational dynamics of an IHF bound Holliday junction
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DOI：
10.1039/c7fd00184c
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发表时间：
2018-04-01
影响因子：
3.4
通讯作者：
Mishra，Padmaja P.
中科院分区：
文献类型：
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作者：
Bera，Subhas C.;Paul，Tapas;Mishra，Padmaja P.
利用单分子FRET方法研究了整合宿主因子（IHF，DNA结合蛋白）与4路霍利迪连接（4 WHJs）在外力作用下的异构化动力学和可能的能量分布.在外力的影响下，已经观察到蛋白质结合的4 WHJ的异构化过程的向前和向后速率的减慢，这表明对构象转换的限制。这也反映在刚性的增加上，如从单分子FRET（smFRET）-各向异性值（0.270 ± 0.012至0.360 ± 0.008）的增加所观察到的。外力的应用有助于构象转变共享非堆叠的开放结构中间体，具有不同的限速步骤和能量景观中的巨大诱导变化。此外，4 WHJ的相关景观是可视化的很少相互转换的状态嵌入到两个异构体通过使用非线性动力学分析，这表明该系统的混沌性增加在中间力（0.4至1.6 pN）。研究中对混沌的识别为全面解释系统复杂行为的起源提供了有用的信息，有效地帮助我们感知了IHF束缚4 WHJ在外力影响下的动力学行为，也证明了非线性动力学分析在生物学领域的适用性。
We have investigated the isomerization dynamics and plausible energy landscape of 4-way Holliday junctions (4WHJs) bound to integration host factor (IHF, a DNA binding protein), considering the effect of applied external force, by single-molecule FRET methods. A slowing down of the forward as well as the backward rates of the isomerization process of the protein bound 4WHJ has been observed under the influence of an external force, which indicates an imposed restriction on the conformational switching. This has also been reflected by an increase in rigidity, as observed from the increase in the single-molecule FRET (smFRET)-anisotropy values (0.270 ± 0.012 to 0.360 ± 0.008). The application of an external force has assisted the conformational transitions to share the unstacked open structure intermediate, with different rate-limiting steps and a huge induced variation in the energy landscape. Furthermore, the associated landscape of the 4WHJ is visualized in terms of rarely interconverting states embedded into the two isoforms by using nonlinear dynamics analysis, which shows that the chaoticity of the system increases at intermediate force (0.4 to 1.6 pN). The identification of chaos in our investigation provides useful information for a comprehensive explanation of the origin of the complex behavior of the system, which effectively helps us to perceive the dynamics of IHF bound 4WHJs under the influence of external force, and also demonstrates the applicability of nonlinear dynamics analysis in the field of biology.