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

Abstract

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.