Conformational entropy of a single peptide controlled under force governs protease recognition and catalysis
We created a single molecule assay where mechanical force both activates the reaction and controls precisely the energy landscape of the disordered substrate peptide modulating its kinetics of recognition with distinct orders of magnitude. Furthermore, we built an energetic model with atomistic details that successfully predicts the impact of substrate entropy on the enzymatic recognition and allows, beyond the scope of this study, for new interpretations of biopolymer chemistry and mechanochemistry of proteins.
Guerin ME, Stirnemann G, Giganti D.
Proc Natl Acad Sci U S A 2018 Nov; 115: 11525.
An immense repertoire of protein chemical modifications catalyzed by enzymes is available as proteomics data. Quantifying the impact of the conformational dynamics of the modified peptide remains challenging to understand the decisive kinetics and amino acid sequence specificity of these enzymatic reactions in vivo, because the target peptide must be disordered to accommodate the specific enzyme-binding site. Here, we were able to control the conformation of a single-molecule peptide chain by applying mechanical force to activate and monitor its specific cleavage by a model protease. We found that the conformational entropy impacts the reaction in two distinct ways. First, the flexibility and accessibility of the substrate peptide greatly increase upon mechanical unfolding. Second, the conformational sampling of the disordered peptide drives the specific recognition, revealing force-dependent reaction kinetics. These results support a mechanism of peptide recognition based on conformational selection from an ensemble that we were able to quantify with a torsional free-energy model. Our approach can be used to predict how entropy affects site-specific modifications of proteins and prompts conformational and mechanical selectivity.
PubMed: 30341218. Doi: 10.1073/pnas.1803872115. Free PMC article
