Following protein conformational fluctuations during ligand binding, catalysis, and inhibition

A single-molecule nanocircuit technique is applied to trace protein conformational fluctuations that control dynamic interactions between a single enzyme lysozyme and various ligands including peptidoglycan substrates and synthetic peptide inhibitors. The electronic recordings directly revealed the ligand-dependent, wide conformational fluctuations such as precluded catalytically important conformation states and their timing or additional conformational states. We have identified several kinetic parameters and compared them for each ligand to elucidate the role of such fluctuations for enzyme activities such as binding, catalysis, and inhibition. These results help understand the molecular mechanism governing lysozyme’s interaction with inhibitors as well as design more effective drugs, such as mechanism-based inhibitors.