A Coarse-Grained MARTINI Model for Mucins

Highly glycosylated proteins known as mucins are the principal components of mucus, the gel-like secretion that protects and lubricates many tissues in the human body. Molecular dynamics (MD) simulations are a useful tool to investigate the nanoscale structure and function of proteins; however, the high molecular weight of mucins makes them a challenging target for atomistic MD simulations. To enable long-time MD simulations of large mucins, we develop and validate new coarse-grained force field parameters within the MARTINI 3 framework for the glycosylated domains of salivary mucin, MUC5B. We use atomistic MD simulations of segments of the protein backbone connected to O-glycans with the CHARMM36m force field to parameterize the bonded parameters. The structural properties of MUC5B from the MD simulations with MARTINI 3, including the radius of gyration, end-to-end distance, and solvent accessible surface area, agree well with the atomistic simulations. Our MARTINI 3 parameters reproduce the bottlebrush structure of MUC5B observed in atomistic MD simulations and previous experiments. The power-law scaling of the radius of gyration with molecular weight is within the range observed in previous experiments of mucins. Accordingly, the MARTINI 3 parameters developed and validated in this study will facilitate accurate and efficient MD simulations of mucins and other glycoproteins for a variety of application areas including food science, drug delivery, and biomaterials.