Phenylalanine modification in plasma-driven biocatalysis revealed by solvent accessibility and reactive dynamics in combination with protein mass spectrometry

TL;DR

This study combines solvent accessibility analysis, reactive molecular dynamics simulations, and mass spectrometry to identify phenylalanine modifications in enzymes caused by plasma-generated reactive species, advancing understanding of plasma-driven biocatalysis.

Contribution

It introduces a combined computational and experimental approach to predict and verify amino acid modifications in enzymes due to plasma-generated reactive species.

Findings

Identification of phenylalanine residues modified by plasma species

Validation of computational predictions through mass spectrometry

Enhanced understanding of enzyme interactions with reactive plasma species

Abstract

Biocatalysis is an emerging field that provides an environmentally friendly alternative to conventional catalysis, but still it faces some challenges. One of the major difficulties for biocatalysts that require reactive species like H2O2 as co-substrates lies in the concentration of these reactive species. On the one hand, they are used as reactants, but on the other hand, they inactivate the enzymes at high concentrations. When utilizing non-thermal plasma to deliver H2O2 for biocatalysis, it is essential to understand the potential interactions between plasma-generated species (PGS) and enzymes. This is particularly important because, alongside \ch{H2O2}, other reactive species such as hydroxyl radicals, atomic oxygen, superoxide, and nitric oxide are also produced. The investigation of the localized reactivity of the solvent accessible surface area (SASA) of an enzyme, with certain species, is an important tool for predicting these interactions. In combination with reactive molecular dynamics (MD) simulations this enabled us to identify amino acid residues that are likely targets for modifications by the PGS. A subset of the theoretical predictions made in the present study were confirmed experimentally by mass spectrometry, underlining the utility of the SASA and MD based screening approach to direct time-consuming experiments and assist their interpretation.