The mechanism by which proteins recognize ligands has long been a hot subject for discussion and investigation. Two primary models dominate the literature: induced fit and conformational selection. In the induced fit model, the ligand binds to the protein in its apo (unbound) state, and this interaction drives the conformational change toward the holo (bound) form. Conversely, the conformational selection model suggests that the protein naturally samples both apo and holo states, with the ligand selectively binding to the pre-existing holo form. The populations and interconversion rates between these conformers are influenced by environmental conditions such as pH, temperature, and salt concentration. In this model, ligand binding stabilizes the holo conformation without directly inducing the transition. Many prominent research groups worldwide are actively exploring these recognition pathways by using techniques like NMR spectroscopy, molecular dynamics simulations, and single-molecule studies.

One system receiving considerable scientific attention is the ubiquitin-proteasome pathway, which regulates the degradation of numerous cellular proteins and is often disrupted in various cancers. In this cascade, the E1 enzyme activates ubiquitin with ATP and then transfers it to E2. The E3 ligase then facilitates the transfer of ubiquitin from E2 to a substrate protein—a process termed “ubiquitination.” E3 ligases confer substrate specificity by directly recognizing target proteins through specific degradation signals, referred to as “degrons,” and attaching ubiquitin to their lysine residues. The GID4 subunit of the GID ubiquitin ligase plays a key role in recognizing the N-degrons, particularly those containing a proline residue at the second position. Structural studies of GID4 in both apo- and peptide-bound states show that this proline fits into a deep, narrow pocket formed by the subunit's β-barrel. Binding induces significant rearrangements in the L2 and L3 loops, which connect the β-strands, indicating a classical induced-fit mechanism.

In a recent study, Xiafei Hao and colleagues used all-atom molecular dynamics simulations, binding energy calculations, and mutational analyses to further dissect this recognition process. Their results reveal that peptide binding significantly reduces the intrinsic fluctuations of GID4. The hairpin loops, which directly contact the peptide, are more flexible than other regions and drive the binding pocket between open and closed conformations. These findings point to a hybrid mechanism involving elements of both conformational selection and induced fit.

Although structural data provide important snapshots of the binding interaction, this study highlights the necessity of integrating dynamic analyses to fully understand molecular recognition. As the saying goes, one cannot fully appreciate a dance performance by merely viewing still photographs of the dancer—no matter how beautiful the images may be.