Department: NanoEngineering
Faculty Advisor(s): Michael Heller

Primary Student
Name: Tsukasa Takahashi
Email: tstakaha@ucsd.edu
Phone: 858-603-3395
Grad Year: 2012

Student Collaborators
Michelle Cheung, mcheung@ucsd.edu

Enzymes are unique protein structures that catalyze the transformation of all biomolecules, build cellular structures, carryout energy conversions and provide the animation and dynamics of living organisms. Enzymes are nanomachines that do chemistry, and they are truly the very essence of life. Over the past four decades considerable efforts have been made to study and mimic enzyme catalysis using a variety of synthetic constructs known as "synzymes". In spite of these large efforts, almost all biomimetic synzyme approaches have failed. A few efforts have produced marginal results, but they would barely be considered catalytic. The ability to mimic enzyme catalysis requires an understanding of intramolecular mechanism of the enzyme and its interaction with its substrate. Here we report measurements for the catalytic activities of novel peptide synzyme structures consisting of a series of nine amino acids that mimic the active catalytic site of proteases which utilizes serine/hydroxyl, cysteine/sulfhydryl, histidine/imidazole and aspartate/carboxyl groups for catalysis. In cysteine proteases such as papain, the thiol group of cysteine serves as a primary nucleophile, cleaving the ester or amide linkage of the substrate with the resultant formation of an acyl-thiol intermediate. The imidazole moiety of histidine is thought to assist the deacylation of the acyl-enzyme required to regenerate or turnover of the catalyst. While papain, and other proteases (trypsin, chymotrypsin) have very high turn-over rates (100 substrate molecules per second), to date no one has successfully developed a synzyme which has any significant turnover. In our present work, we are closely studying the hydrolysis of p-nitrophenyl acetate esters using peptides with different combinations of cysteine and histidine. We are also using acetic anhydride and Ellman's reagent to investigate the deacylation of acetyl cysteine by the closely positioned imadazole group of histidine. The acetylation and the deacylation kinetics are being studied through molecular modeling of the synzyme peptide, UV/Vis spectrophotometry and the use of NMR to confirm the locations of protons and H-bonding interactions through chemical shift. To date, our synzyme peptide with phenylalanines, between the cysteine and histidine yields a significantly higher deacylation rate, suggesting the large bulky R-groups of phenylalanine bends the backbone of the peptide bringing the cysteine thiol group and the histidine imadazole group closer for acetyl exchange. Our newest work now includes novel methods which may allow us to incorporate dynamic mechanistic properties into our peptide synzyme structures.

« Back to Posters or Search Results