Experimental and molecular dynamics data for Amyloid-β(1–40) with Vitamin B12

This dataset contains the experimental data and the molecular dynamics simulation data underlying the reported results. The experimental data comprise the raw and processed measurements of Aβ40 aggregation in the absence and presence of Vitamin B12 (cyanocobalamin): [ThT and ANS fluorescence kinetics, intrinsic tyrosine fluorescence, dynamic light scattering (particle-size distributions), circular dichroism and/or FTIR spectra, and TEM/AFM images], together with the numerical data underlying Figs [1–6]. The simulation data cover five systems simulated with Desmond (Schrödinger Release 2024-4) using the S-OPLS (OPLS4) force field and SPC water at 300 K and 1.01325 bar: the Aβ40 monomer (PDB 1BA4, model 1), the 1:1 Aβ40–Vitamin B12 complex started from the Glide XP pose, and three four-peptide systems containing 0 (S0), 2 (S1) and 4 (S2) Vitamin B12 molecules. For each system the dataset provides the Desmond system files (-in.cms and -out.cms, containing the complete force-field parameters), the relaxation/production protocol (.msj) and settings (.cfg), a solute topology (PDB), and the peptide–ligand trajectory for 0–300 ns at 100 ps intervals (3,000 frames, XTC, water and ions removed). The numerical data underlying Figs 7–13 and S1–S2 (CSV and Simulation Interaction Diagram .eaf files), the ligand preparation and SiteMap files, and the Python analysis and plotting scripts (MDTraj, ProLIF) are also included. README.txt describes all files.