In silico modeling of the LMX1B–LC3B interaction. (A) Frames from a computer simulation of the LIR-dependent LMX1B-LC3B interaction (see Video 1) showing the dynamics of the putative LMX1B LIR motif docked by molecular replacement in the position adopted by the FYCO1 LIR (5d94.pdb). LC3B in cyan; LMX1B LIR in magenta. (B) LMX1B LIR (cyan) overlaid upon a space-filling model of LC3B (5d94.pdb) in final simulation pose, showing docking of the key LIR residues at P0 and P3 within hydrophobic pockets (HP) 1 and 2 of LC3B, respectively. (C) Current Alphafold prediction of the LMX1B structure showing the location of the LIR domain within a region of low/very low confidence for structure. Inherently unstructured regions in proteins requiring a cognate ligand to induce/stabilize folds will continue to pose a problem for protein structure prediction. (D) Ribbon structure of human LC3B (gray) in complex with the FYCO1 LIR (magenta; 5d94.pdb) overlayed with the final model simulation pose of LC3B (green) and LMX1B LIR (cyan). Close alignment between FYCO1 and LMX1B is seen within the core LIR binding region. (E) Side-by-side comparison of the LMX1B (left) and FYCO1 (right) LIRs docked at HP2 of LC3B (5d94.pdb) to show how LMX1B Q316 and FYCO1 E1287 fold back toward HP2 in both structures to stabilize LIR binding. (F) Comparison of the final LMX1B LIR pose and the position of the N-terminal ATG4B LIR identified in the ATG4B/lC3B crystal lattice.
