Ligand-protein interaction plays a crucial role in regulating biological processes. The two basic steps of ligand-protein interactions are binding and dissociation, and these steps determine the binding affinity of a ligand to its receptor. Through the binding and dissociation of ligands to proteins such as enzymes, antibodies, and peptide hormones, essential biological functions are regulated through mechanisms that include enzyme catalysis, immunological responses, and signal transduction. Thus, understanding the molecular mechanisms helps gain insight into how protein-ligand interactions work to control biological processes.

A research team led by KAIST Professor Hak-Sung Kim and Doctor Moon-Hyeong Seo of the Department of Biological Sciences has newly discovered a mechanism that is involved in the binding and dissociation of ligands. The results of their study have been published online in Nature Communications on April 24 and is a follow-up to the paper published in Nature Chemical Biology last year. In their previous study, the research team conducted single-molecule fluorescence energy transfer (smFRET) on maltose-binding proteins (MBPs), thereby applying kinetic analysis to examine the relationship between ligand binding and a protein’s intrinsic conformational dynamics, and obtained evidence suggesting that MBPs recognize ligands through an induced-fit mechanism rather than a conformational selection mechanism as had been previously thought.

Researchers constructed a series of MBP mutants with different intrinsic dissociation constants for maltose by changing two amino acid residues in the hinge region. The ligand-binding interfaces were left intact, enabling the investigators to examine the role of conformational dynamics in ligand dissociation and binding affinity. Using smFRET, the team observed conformational changes in the MBP mutants and results indicating that a protein’s intrinsic opening rate dictates the rate of ligand dissociation, and in turn, the binding affinity.

The finding that protein conformational dynamics, or the intrinsic opening rate of a protein structure, plays a critical role in the determination of binding affinity provides deeper insight into understanding protein characteristics that regulate various biological phenomena. The results of this study could aid in controlling protein activity with more precision in the future, and contribute to the process of designing drugs and proteins.