Conformational entropy of a single peptide controlled under force governs protease recognition and catalysis

Significance In the cell, enzymes such as proteases target peptides with specific amino acid sequences. The mechanism of specificity is typically examined by looking at the peptide structure in complex with the enzyme. However, a question remains: How do enzymes recognize a free peptide that can adopt a large number of geometries before the association? Here, we propose a method to control the peptide flexibility by stretching it under force. In our assay, we can follow the substrate elongation and its catalytic cleavage by a single protease. Finally, we designed a computational model to describe all possible geometries of a free peptide that acts as an elastic under force and assessed the impact of peptide flexibility upon the specific recognition.