Yadav Kavita, Sardana Deepika, Shweta Him, Clovis Ndege Simisi, Sen Sobhan
Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
J Phys Chem B. 2022 Mar 3;126(8):1668-1681. doi: 10.1021/acs.jpcb.1c09349. Epub 2022 Feb 16.
Understanding molecular interactions and dynamics of proteins and DNA in a cell-like crowded environment is crucial for predicting their functions within the cell. Noncanonical G-quadruplex DNA (GqDNA) structures adopt various topologies that were shown to be strongly affected by molecular crowding. However, it is unknown how such crowding affects the solvation dynamics in GqDNA. Here, we study the effect of cosolvent (acetonitrile) crowding on ligand (DAPI) solvation dynamics within human telomeric antiparallel GqDNA through direct comparison of time-resolved fluorescence Stokes shift (TRFSS) experiments and molecular dynamics (MD) simulations results. We show that ligand binding affinity to GqDNA is drastically affected by acetonitrile (ACN). Solvation dynamics probed by DAPI in GqDNA groove show dispersed dynamics from ∼100 fs to 10 ns in the absence and presence of 20% and 40% (v/v) ACN. The nature of dynamics remain similar in buffer and 20% ACN, although in 40% ACN, distinct dynamics is observed in <100 ps. MD simulations performed on GqDNA/DAPI complex reveal preferential solvation of ligand by ACN, particularly in 40% ACN. Simulated solvation time-correlation functions calculated from MD trajectories compare very well to the overall solvation dynamics of DAPI in GqDNA, observed in experiments. Linear response decomposition of simulated solvation correlation functions unfolds the origin of dispersed dynamics, showing that the slower dynamics is dominated by DNA-motion in the presence of ACN (and also by the ACN dynamics at higher concentration). However, water-DNA coupled motion controls the slow dynamics in the absence of ACN. Our data, thus, unravel a detailed molecular picture showing that though ACN crowding affect ligand binding affinity to GqDNA significantly, the overall dispersed solvation dynamics in GqDNA remain similar in the absence and the presence of 20% ACN, albeit with a small effect on the dynamics in the presence of 40% ACN due to preferential solvation of ligand by ACN.
了解细胞样拥挤环境中蛋白质和DNA的分子相互作用及动力学对于预测它们在细胞内的功能至关重要。非经典G-四链体DNA（GqDNA）结构具有多种拓扑结构，已表明这些拓扑结构会受到分子拥挤的强烈影响。然而，尚不清楚这种拥挤如何影响GqDNA中的溶剂化动力学。在此，我们通过直接比较时间分辨荧光斯托克斯位移（TRFSS）实验和分子动力学（MD）模拟结果，研究了助溶剂（乙腈）拥挤对人端粒反平行GqDNA内配体（DAPI）溶剂化动力学的影响。我们表明，乙腈（ACN）会极大地影响配体与GqDNA的结合亲和力。在不存在ACN以及存在20%和40%（v/v）ACN的情况下，DAPI在GqDNA沟槽中探测到的溶剂化动力学显示出从约100飞秒到10纳秒的分散动力学。在缓冲液和20% ACN中，动力学性质保持相似，尽管在40% ACN中，在<100皮秒时观察到了不同的动力学。对GqDNA/DAPI复合物进行的MD模拟揭示了ACN对配体的优先溶剂化作用，特别是在40% ACN中。从MD轨迹计算得到的模拟溶剂化时间相关函数与实验中观察到的DAPI在GqDNA中的整体溶剂化动力学非常吻合。对模拟溶剂化相关函数的线性响应分解揭示了分散动力学的起源，表明在存在ACN的情况下（以及在较高浓度时由ACN动力学主导），较慢的动力学主要由DNA运动控制。然而，在不存在ACN的情况下，水-DNA耦合运动控制着缓慢的动力学。因此，我们的数据揭示了一个详细的分子图景，表明尽管ACN拥挤会显著影响配体与GqDNA的结合亲和力，但在不存在ACN和存在20% ACN的情况下，GqDNA中的整体分散溶剂化动力学仍然相似，尽管由于ACN对配体的优先溶剂化作用，在存在40% ACN时对动力学有较小影响。
