Structural Modeling of Human Myo5c

A structural model of the motor domain of human Myo5c (Uniprot–ID: Q9NQX4) was generated with AlphaFold2 version 2.3.1, the fasta file was accessed on 1 November 2023 (Jumper et al., 2021 (link)). Different conformers and tautomers of PBP [2,3,4–tribromo–5–(3,5–dibromo–2–hydroxyphenyl)–1H–pyrrole] were generated with QM Conformer and Tautomer Predictor of Jaguar (Jaguar, Schrödinger, LLC, New York, NY, 2023). PBP was inserted, with Glide, into the model of human Myo5c (Glide, Schrödinger, LLC, New York, NY, 2023.). The glide grid was generated in accordance to the position of PBP in the structure of the motor domain of Dictyostelium discoideum myosin–2 (PDB–ID: 2JHR). The PDB–structure was accessed on 11 October 2023. Analysis of the structural models and visualization of the results was done with Maestro in the Schrödinger Suite 2023–4 (Maestro, Schrödinger, LLC, New York, NY, 2023). The structure was prepared with the Protein Preparation Workflow and the minimization was done with the Minimization tool of Maestro (Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2023) for 200 cycles with 80 steps per cycle in the VSGB solvate model (Li et al., 2011 (link)). ΔG was calculated with the Prime MM–GBSA v3.000 tool for the minimized structure (Prime, Schrödinger, LLC, New York, NY, 2023).