Choosing the right density for a concentrated protein system like gluten in a coarse-grained model

Abstract

Large coarse-grained simulations are often conducted with an implicit solvent, which makes it hard to assess the water content of the sample and the effective concentration of the system. Here the number and the size of cavities and entanglements in the system, together with density profiles, are used to asses the homogeneity and interconnectedness of gluten. This is a continuation of an earlier article, "Viscoelastic properties of wheat gluten in a molecular dynamics study" (Mioduszewski and Cieplak 2021b). It turns out there is a wide range of densities (between 1 residue per cubic nanometer and 3 residues/nm\(^3\)) where the system is interconnected, but not homogeneous: there are still large empty spaces, surrounded by an entangled protein network. Those findings should be of importance to any coarse-grained simulation of large protein systems.