Models from Roland et al., 2019 JBC PMID: 30530492
Protein homology modeling
All structural images were generated using PyMOL. The Dnf1 homology model was previously published (23). Dnf2 and ATP10D homology models used for sculpting were generated using the intensive Phyre2 modeling (65). The Phyre2 intensive modeling process represents an unbiased approach. First, homologous templates are surveyed, and crude backbone models are generated and ranked by coverage and confidence; then loop fragments are modeled in 2–15–residue chunks. A protein folding simulator uses a heuristic process to synthesize multiple templates and leverages ab initiostrategies for regions without predictions. Finally, side chains are placed using a rotamer library, optimized to avoid steric clashes. Unlike the threaded modeling approach, the intensive modeling process facilitates subsequent model manipulation. The Dnf2 model was generated from the synthesis of PDB entries 1MHS (66), 4WIT(67), 3B9B (68), 3IXZ (69), 2ZXE (70), 3B8C (71), 3B8E (72), whereas the ATP10D intensive model used PDB entries 1MHS (66), 3B9B (68), 3IXZ (69), 2ZXE (70), 3B8C (71), and 3B8E(72).
ATP10D & Dnf2 Structures: