Design of peptides with strong binding affinity to poly(methyl methacrylate) resin by use of molecular simulation-based materials informatics

Abstract

Peptides with strong binding affinities for poly(methyl methacrylate) (PMMA) resin were designed by use of materials informatics technology based on molecular dynamics simulation for the purpose of covering the resin surface with adhesive peptides, which were expected to result in eco-friendly and biocompatible biomaterials. From the results of binding affinity obtained with this molecular simulation, it was confirmed that experimental values could be predicted with errors <10%. By analyzing the simulation data with the response-surface method, we found that three peptides (RWWRPWW, EWWRPWR, and RWWRPWR), which consist of arginine (R), tryptophan (W), and proline (P), have strong binding affinity to the PMMA resin. These amino acids were effective because arginine and tryptophan have strong binding affinities for methoxycarbonyl groups and methyl groups, which are the main constituents of the PMMA resin, and proline stabilizes the flat zigzag structures of the peptides in water. The strong binding affinities of the three peptides were confirmed by experiments (surface plasmon resonance methods).

Chemistry of Materials Nanoarchitectonics for Two-Dimensional Films: Langmuir–Blodgett, Layer-by-Layer Assembly, and Newcomers

“…However, nanoarchitectonics of such complex systems is difficult to advance based on a simple theoretical background or the experience of researchers. Fortunately, mankind has developed artificial intelligence and advanced methodologies such as machine learning − and materials informatics. − Such new technologies are expected to support thin film nanoarchitectonics, which consists of complex elements. In fact, a fusion of nanoarchitectonics and materials informatics for functional porous materials has been proposed .…”

Identification of the First Sulfobetaine Hydrogel‐Binding Peptides via Phage Display Assay

“…Molecular simulation‐based materials informatics also suggest that tryptophan plays a central role in the binding of peptides to PMMA hydrogels. [ 75 ] The binding affinities (binding free energies) were obtained with molecular simulations based on the response surface method (Kriging method). There, the calculated detachment energies of tryptophan from COOCH 3 and CH 3 were the highest of the biogenic amino acids.…”

An integrated chemical engineering approach to understanding microplastics

“…ML methods can navigate the design space and further confirm or elucidate the mechanisms behind the protein binding affinities. In Iwasaki et al, simulation‐based material informatic methods were used to probe why specific peptide sequences had such a high binding affinity to PMMA 73 . This approach has enhanced understanding of the structure–property relationship between plastic surfaces and proteins.…”

“…In Iwasaki et al, simulation-based material informatic methods were used to probe why specific peptide sequences had such a high binding affinity to PMMA. 73 This approach has enhanced understanding of the structure-property relationship between plastic surfaces and proteins. Such understanding would be beneficial in MP research, as it would help us identify which microbial species are most likely to adsorb to plastics or to design peptides that strongly bind to plastics for MP capture.…”