Phenylalanine Modification in Plasma-Driven Biocatalysis Revealed by Solvent Accessibility and Reactive Dynamics in Combination with Protein Mass Spectrometry

Biocatalysis is an emerging field that provides an environmentally
friendly alternative to conventional catalysis but still faces some
challenges. One of the major difficulties for biocatalysts that require
reactive species like H2O2 as cosubstrates lies
in the concentration of these reactive species. On the one hand, they
are used as reactants; on the other hand, they inactivate the enzymes
at high concentrations. When utilizing nonthermal 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 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
was confirmed experimentally by mass spectrometry, leading to the
discovery of plasma-mediated phenylalanine modifications. This result
underlines the utility of the SASA and MD-based screening approach
to direct time-consuming experiments and assist their interpretation.