MD Simulation Data for the AlphaFold2-predicted Amyloidogenic Light Chains and Their Correlation with VL Domain Mutations and Aggregation Propensity

This dataset contains: 1. Alphafold predicted structures for 181 full-length, patient-derived LC sequences from four common amyloidogenic germlines (λ6, λ1, λ3, κ1) 2. The input and output files from MD simulations performed on a representative set of LC dimers from four antibody germlines: λ1, λ3, λ6, and κ1. For λ1, λ3, and λ6 germlines, two open and two closed dimeric conformations were randomly selected, while for the κ1 germline, three closed dimers were chosen. For each selected conformation, two independent replicates (R1, R2) were simulated using the GROMACS software package. Each system folder includes: topol.top – Topology parameters Alphafold-predicted structure – Initial protein model used for simulation MD.tpr – Run input file for each replica MD_dt1ns.xtc – Trajectory file with coordinates saved every 1 ns for each replica