De novo designed peptides form a highly catalytic ordered nanoarchitecture on a graphite surface

Simulating chemical reactions promoted by self-assembled peptides with catalytic properties

Peptides that self-assemble exhibit distinct three-dimensional structures and attributes, positioning them as promising candidates for biocatalysts. Exploring their catalytic processes enhances our comprehension of the catalytic actions inherent to self-assembling peptides, laying a theoretical foundation for creating novel biocatalysts. The investigation into the intricate reaction mechanisms of these entities is rendered challenging due to the vast variability in peptide sequences, their aggregated formations, supportive elements, structures of active sites, types of catalytic reactions, and the interplay between these variables. This complexity hampers the elucidation of the linkage between sequence, structure, and catalytic efficiency in self-assembling peptide catalysts. This chapter delves into the latest progress in understanding the mechanisms behind peptide self-assembly, serving as a catalyst in hydrolysis and oxidation reactions, and employing computational analyses. It discusses the establishment of models, selection of computational strategies, and analysis of computational procedures, emphasizing the application of modeling techniques in probing the catalytic mechanisms of peptide self-assemblies. It also looks ahead to the potential future trajectories within this research domain. Despite facing numerous obstacles, a thorough investigation into the structural and catalytic mechanisms of peptide self-assemblies, combined with the ongoing advancement in computational simulations and experimental methodologies, is set to offer valuable theoretical insights for the development of new biocatalysts, thereby significantly advancing the biocatalysis field.

Rational Design and Self-Assembly of Histidine-Rich Peptides on a Graphite Surface

Histidine-rich peptides (HRPs) have been investigated to create functional biomolecules based on the nature of histidine, such as ion binding and catalytic activity. The organization of these HRPs on a solid surface can lead to surface functionalization with the well-known properties of HRPs. However, immobilization of HRPs on the surface has not been realized. Here, we design a series of octapeptides with histidine repeat units, aiming to establish their self-assembly on a graphite surface to produce a highly robust and active nanoscaffold. The new design has (XH)₄, and we incorporated various types of hydrophobic amino acids at X in the sequence to facilitate their interaction with the surface. The effect of the pair of amino acids on their self-assembly was investigated by atomic force microscopy. Contact angle measurement revealed that these assemblies functionalized graphite surfaces with different wetting chemistry. Moreover, the secondary structure of peptides was characterized by Fourier transform infrared spectroscopy (FTIR), which gives us further insights into the conformation of histidine repeat peptides on the surface. Our results showed a new approach to applying histidine-rich peptides on the surface and tuning the self-assembly behavior by introducing different counter amino acids that could be integrated with a wide range of biosensing and biotechnology applications.