Protein-Protein Docking and Molecular Dynamics Simulations Elucidated Binding Modes of FUBI-p62 UBA Complex

The cytosolic Fau protein, a precursor of antimicrobial peptide, composes of ubiquitin-like domain FUBI at N-terminus and ribosomal protein rpS30 at C-terminus. Fau has been important in killing of intracellular Mycobacterium tuberculosis infection through autophagy-targeting p62 mechanism. The p62 adapter protein delivered microbicidal protein rpS30 to autolysosome where it was converted into antimicrobial peptides capable of killing M. tuberculosis in mycobacterial phagosome. Recently, direct interaction of FUBI and p62 UBA domain has been established using immunoprecipitation. In the absence of experimental complex structure of FUBI and p62 UBA, understanding of binding interaction could be extensively characterized using molecular modeling techniques. The aim of this study was to elucidate the binding mode of FUBI interacting with the p62 UBA. Base on the conserved hydrophobic binding regions of FUBI and p62 UBA domain, 334 docked poses were predicted using the ZDOCK and RDOCK protein-protein docking algorithms. Five binding modes of complex structures were clustered and only two were stable after 15 ns of molecular dynamics simulations. The binding free energy was elucidated using MM-PBSA method and the best FUBI-p62 UBA complex was determined. The key binding residues of FUBI and p62 UBA domain were elucidated using protein interface and alanine scanning. Gly405 and Phe406 in the MGF hydrophobic area and certain residues in loop 1, helix 2 and helix 3 of the p62 UBA domain were bound with FUBI domain. The results enable us to understand how p62 and Fau interact which is a crucial step of autophagy-targeting p62 mechanism for antimycobacterial action.