Initial models and trajectories for the molecular dynamics simulations of FAP53's involvement in microtubule doublets formation

These models and trajectories are from molecular dynamics simulation designed to assess the effect of FAP53 on B01 attachment during microtubule doublet assembly. Three initial models are provided: the system without FAP53 (no_fap53.gro), the system with FAP53 bound at the α-tubulin at the minus end of the B01 heterodimer (fap53_bottom.gro), and the system with FAP53 bound at the β-tubulin at the plus end (fap53_top.gro). Molecular models of GTP-tubulin dimer docking onto the A10-A11 protofilament patch was based on 6U42 PDB structures (Ma et al., Cell, 2019). The structures of TBB-4 and TBA-5 tubulin binding to Mg2+-GTP predicted by AlphaFold 3 (www.alphafoldserver.com) were used as alpha- and beta-tubulin. The tubulins were then aligned to the outer junction of 6U42 model. Protonation state of ionizable amino acid residues were predicted by PDBFixer. To simplify the model, the ligands on A10-A11 protofilament were removed. The modeling of FAP53 residues 2-40 involved structural alignment with B01 tubulin dimer termini (plus/minus end), guided by their 6U42 conformation. The trajectory files (*.xtc) are extracted from 1 microsecond simulations, with frames written every 1 nanosecond in the output trajectories.