Molecular Dynamics Simulations of Wild-Type and Variant Ternary TBR1 DBD–SSL DNA–FOXP2 FHD Complexes

This dataset comprises molecular dynamics (MD) simulation trajectories and associated files for three ternary protein–DNA complexes involving the TBR1 DNA-binding domain (DBD), SSL DNA, and the FOXP2 forkhead domain (FHD). The systems include the wild-type (WT) TBR1 DBD and two neurodevelopmental disorder-associated variants, N374H and N374Y. All structures were generated using AlphaFold3-based modelling and subsequently refined and simulated using the Desmond MD engine within the Schrödinger Maestro 13.0 suite. Each system was solvated in an explicit TIP3P water model with physiological ionic strength (0.15 M NaCl) and simulated under NPT conditions (300 K, 1.013 bar) for 500 ns per system, with trajectory frames recorded every 100 ps. The dataset includes system configuration files, trajectories, energy profiles, and representative structural snapshots for each complex. These simulations were designed to evaluate structural stability, conformational dynamics, and interaction persistence, with a particular focus on how the N374H and N374Y variants alter protein–DNA and protein–protein interfaces relative to the wild-type complex.本数据集包含三类三元蛋白质-DNA复合物的分子动力学（molecular dynamics, MD）模拟轨迹及相关文件，所涉复合物涵盖TBR1 DNA结合结构域（DNA-binding domain, DBD）、SSL DNA以及FOXP2叉头结构域（forkhead domain, FHD）。三类系统分别包含野生型（wild-type, WT）TBR1 DBD，以及两种与神经发育障碍相关的突变体N374H与N374Y。 所有结构均基于AlphaFold3建模生成，随后通过Schrödinger Maestro 13.0套件中的Desmond MD引擎完成结构优化与动力学模拟。每个系统均采用显式TIP3P水模型进行溶剂化，并设置生理离子强度（0.15 M NaCl），随后在NPT条件（300 K、1.013 bar）下进行单系统时长500 ns的模拟，每100 ps采集一帧轨迹数据。 本数据集包含各复合物的系统配置文件、模拟轨迹、能量分布曲线以及代表性结构快照。本系列模拟旨在评估复合物的结构稳定性、构象动力学与相互作用持久性，重点聚焦N374H与N374Y突变体相较于野生型复合物，如何改变蛋白质-DNA及蛋白质-蛋白质相互作用界面。