Grafting of functional motifs onto protein scaffolds identified by PDB screening - an efficient route to design optimizable protein binders

摘要

Artificial miniprotcins that arc able to target catalytic sites of matrix mctal-loprotcinascs (MMPs) were designed using a functional motif-grafting approach. The motif corresponded to the four N-terminal residues of TIMP-2, a broad-spectrum protein inhibitor of MMPs. Scaffolds that arc able to reproduce the functional topology of this motif were obtained by exhaustive screening of the Protein Data Bank (PDB) using stamps software (search for three-dimensional atom motifs in protein structures). Tenartificial protein binders were produced. The designed proteins bind catalytic sites of MMPs with affinities ranging from 450 ni to 450 im prior to optimization. The crystal structure of one artificial binder in complex with the catalytic domain of MMP-12 showed that the intcr-molccular interactions established by the functional motif in the artificial binder corresponded to those found in the MMP-14-TIMP-2 complex, albeit with some differences in geometry. Molecular dynamics simulations of the ten binders in complex with MMP-14 suggested that these scaffolds may allow partial reproduction of native intcr-molccular interactions, but differences in geometry and stability may contribute to the lower affinity of the artificial protein binders compared to the natural protein binder. Nevertheless, these results show that the in silica design method used provides sets of protein binders that target a specific binding site with a good rate of success. This approach may constitute the first step of an efficient hybrid computational/experimental approach to protein binder design.