Hydrogels, three-dimensional crosslinked polymers formed from hydrophilic monomers, can absorb and retain up to 90% of their weight in water. Among different hydrogel chemistries, PEGylated hydrogels are widely studied as biomaterials for drug delivery and bioimplant applications due to their high biocompatibility and mechanical flexibility. Therefore, predictive modeling of the protein-hydrogel interactions is vital to understanding their behavior in biological environments and to the rational design of hydrogels with improved properties. Proteins consist of peptide chains of amino acids. Their interactions with hydrogels are determined both by the constituent amino acids and the three-dimensional complex structures proteins form in their native environments. In this work, we employed molecular dynamics simulations with atomistic forcefields to investigate the structures and interactions of PEGDA hydrogels. Three distinct hydrogel architectures were constructed with varying degrees of branching. We examined the structural and mechanical properties of the PEGDA hydrogels at different solvation levels and the interactions with water and individual amino acids of different types.