UC San Diego

Creation of synthetic structures with an enzyme-like mechanism and turnover remains a significant challenge. In this study, peptides containing a cysteine thiol and histidine imidazole group were designed to mimic the active site of the cysteine protease papain. Ellman's reagent trapping experiments showed that rapid acetyl group exchange exists between the thiol and imidazole groups. This exchange rate increased significantly in peptides with bulky R-groups (phenylalanine) between the cysteine and histidine. A reduction of the cysteine thiol pKa and NMR results further support closer proximity of the thiol and imidazole groups in peptides with faster acetyl group exchange. We have also used NAMD and VMD simulation to determine the distance between these catalytic groups and the overall mechanical flexibility of the peptides. We found important correlations between the Cys-His distance deviation, which determines the flexibility between the two molecules, and its relationship to the deacylation rate. We found that generally, shorter Cys-His distance deviations allow for a higher deacylation rate constant, meaning that greater confinement of the two residues will allow a higher frequency of the acetyl exchange between the cysteine thiol and histidine imidazole R-groups. This may be the key to future design of peptide structures with molecular mechanical properties that lead to viable enzyme mimics. End of this study include our initial attempts in stabilizing the peptides with the use of nanoparticles, micelles, and functionalized surfaces. We have also shown our initial concept which utilizes electric field in order to control the negatively charged cysteine thiol and the positively charged histidine imidazole to achieve a truly mechanically controlled molecular system to produce catalytic effects. Although much work needs to be done, our preliminary results show promise in the growth of new techniques that can be built upon in the future