Improving All-Atom Force Field to Accurately Describe DNA G‑Quadruplex Loops

The DNA G-quadruplex (GQ) displays structural polymorphisms, and interactions between its loops and flanking sequences critically determine which of the diverse GQ conformers is adopted. All-atom molecular dynamics (MD) simulations of GQs are computationally challenging due to slow folding times and force field (ff) artifacts. In an earlier study, a direct folding simulation of the simplest DNA GQ (TBA15) was first reported using a modified version of the AMBER bsc1 ff (bsc1_vdW ff). Despite this successful folding simulation, it was later found that the bsc1_vdW ff is somewhat limited in terms of describing loop structures of GQs, which is problematic because GQ loop regions play key roles in ligand binding to modulate GQ activities. In this study, we further modified the bsc1_vdW ff to enhance the GQ loop prediction by fine-tuning a limited number of van der Waals (vdW) parameters of the standard AMBER bsc1 ff to improve the GQ loop distribution of a target GQ system (three-layered antiparallel GQ; mHtel21). Test simulations of this newly generated ff (bsc1_vdWL ff) on DNA GQs with diverse topologies (hybrid1, hybrid2, and parallel propeller) revealed that loop structures were predicted more accurately than by the bsc1_vdW ff. We consider that enhanced sampling MD simulation methods in combination with bsc1_vdWL provide useful simulation protocols for resolving outstanding issues of DNA GQ folding and GQ/ligand binding at the all-atom level.DNA G-四链体（G-quadruplex，GQ）存在结构多态性，其环区与侧翼序列之间的相互作用，关键决定了该GQ会采取何种多样的构象。全原子分子动力学（molecular dynamics，MD）模拟GQ体系具有较高计算难度，原因在于折叠过程缓慢以及力场（force field，ff）存在人工伪影。在一项早期研究中，研究人员首次利用经过修改的AMBER bsc1力场（bsc1_vdW力场），实现了最简DNA G-四链体（TBA15）的直接折叠模拟。尽管该折叠模拟取得成功，但后续研究发现bsc1_vdW力场在描述GQ环区结构方面存在一定局限，而这一问题不容忽视——因为GQ环区在配体结合以调控GQ活性的过程中发挥着关键作用。本研究中，我们对bsc1_vdW力场进行了进一步优化：通过微调标准AMBER bsc1力场中有限数量的范德华（van der Waals，vdW）参数，以提升目标GQ体系（三层反平行GQ；mHtel21）的GQ环区分布预测精度。针对该新构建的力场（bsc1_vdWL力场），我们在具有不同拓扑结构的DNA G-四链体（hybrid1、hybrid2与平行推进式GQ）上开展了测试模拟，结果显示其对环区结构的预测精度优于bsc1_vdW力场。我们认为，将增强采样分子动力学模拟方法与bsc1_vdWL力场相结合，可为在全原子层面解析DNA G-四链体折叠以及GQ/配体结合等未决难题提供切实可行的模拟方案。