Transcriptomic and In Silico Analysis of Microplastic–Protein Interactions in the Tropical Krill Euphausia distinguenda

Microplastics (MPs) are pervasive in marine ecosystems, yet the molecular mechanisms underlying their sublethal effects on zooplankton remain poorly understood. Here, we integrated transcriptomic screening with sequence homology analysis, structural modeling, and molecular dynamics (MD) simulations to examine protein–polymer interaction behavior in the tropical euphausiid Euphausia distinguenda. Transcriptomic analysis identified three MP-responsive proteins; two isoforms (P1, P2) were consistently downregulated following exposure to polyethylene microspheres, while a third candidate (P3) was upregulated but excluded from modeling due to insufficient homology. Structural models of P1 and P2 were generated using AlphaFold2 (ColabFold implementation) and evaluated through comparative structural analyses. MD simulations (100 ns) were conducted using representative polymer oligomers LDPE used as a polyethylene analog and PET and PC included as contrast polymers, which revealed pronounced protein-specific differences and polymer-dependent modulation of interaction stability. Nonbonded Lennard–Jones and Coulomb interaction energies indicated substantially greater intermolecular contact stabilization for P2 than for P1 across all polymers, with LDPE yielding the lowest mean polymer RMSD for P2, and PET for P1. Together, these results indicate that MP–protein interactions in E. distinguenda are consistent with a dominant role of protein structural coherence and dynamic surface compatibility rather than by static structural complementarity or specific binding affinity and provide a reproducible basis for exploring molecular-scale responses to MP exposure in ecologically relevant zooplankton.