Initial model for molecular dynamics simulation of the doublet-MT formation in full-length or ΔCTT tubulin configurations

These models are used for molecular dynamics simulation to assess the tubulin tail dependency of B01 attachment and the energy state of the B01 tubulin dimer under varying ΔCTT conditions: full-lebgth alpha-/beta-tubulin, alpha-tubulin CTT deletion/full-length beta-tubulin, full-length alpha-tubulin/beta-tubulin CTT deletion, and alpha-/beta-tubulin CTT deletion. 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.