Developing Isomeric Peptides for Mimicking the Sequence–Activity Landscapes of Enzyme Evolution

Abstract

Enzymes catalyze almost all material conversion processes within living organisms, yet their natural evolution remains unobserved. Short peptides, derived from proteins and featuring active sites, have emerged as promising building blocks for constructing bioactive supramolecular materials that mimic native proteins through self-assembly. Herein, we employ histidine-containing isomeric tetrapeptides KHFF, HKFF, KFHF, HFKF, FKHF, and FHKF to craft supramolecular selfassemblies, aiming to explore the sequence−activity landscapes of enzyme evolution. Our investigations reveal the profound impact of peptide sequence variations on both assembly behavior and catalytic activity as hydrolytic simulation enzymes. During self-assembly, a delicate balance of multiple intermolecular interactions, particularly hydrogen bonding and aromatic− aromatic interactions, influences nanostructure formation, yielding various morphologies (e.g., nanofibers, nanospheres, and nanodiscs). Furthermore, the analysis of the structure−activity relationship demonstrates a strong correlation between the distribution of the His active site on the nanostructures and the formation of the catalytic microenvironment. This investigation of the sequence−structure−activity paradigm reflects how natural enzymes enhance catalytic activity by adjusting the primary structure during evolution, promoting fundamental research related to enzyme evolutionary processes.

Efficiently solving the curse of feature-space dimensionality for improved peptide classification

“…For example, nitrogen atoms are present in the main chain of all peptides (every amino acid has at least one nitrogen atom) and are found in side chains of arginine, histidine, and lysine, as well as asparagine, glutamine, and tryptophan. Recently, lysine was identified as the amino acid that promotes the catalytic activity of short peptide sequences, through its side chain amino group, 52,53 which points in the same direction as F3. The importance of F3 could be related to its specific position within the molecule, as the topological features F1, F2, and F4 might suggest; however, it remains inconclusive as its relation to a specific amino acid is unknown.…”