Fig 1.
Workflow of LIR predictions using AlphaFold2-multimer.
(a) The amino acid sequence of the candidate protein (here the human selective autophagy receptor p62/SQSTM1) and the ATG8 protein (here human LC3B) are entered into AlphaFold2-multimer, (b) which then provides the predicted structures of the two proteins in complex. They are docked together with the LIR motif positioned into the hydrophobic pockets HP1 and HP2 in the so-called LIR docking site of LC3B as shown in the zoomed inset in b, lower right. This allows both identification of the LIR motif of p62/SQSTM1 (see looking glass in a), which is the already verified LIR motif and a structural model of how the tryptophan (W) and leucine (L) residues of the core LIR motif fits into HP1 and HP2. (c) A sequence logo was generated by WebLogo from verified LIR motifs found in 24 autophagy proteins with acidic amino acids indicated in red, basic ones in blue, phosphorylatable serines (S) and threonines (T) in green, and hydrophobic amino acids in black.