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

Abstract

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.