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$$^3$$ 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.

The Role of Cavities in Biological Structures

“…For the simulated plant storage protein systems, we correlated changes in the size and number of cavities after periodic deformation with the "loops and trains" theory [57]. This enabled us to demonstrate that, even in an implicit solvent model, cavities can serve as a measure of the hydration level [52], and processes like solvent expulsion can be simulated using only geometric constraints [54]. The variations in the number of cavities also contributed to confirming the unique nature of the viscoelastic gluten protein network [53].…”

“…The viscoelastic properties of storage proteins depend on their hydration levels [52]. In a coarsegrained model with an implicit solvent [53], water molecules cannot be represented explicitly.…”

“…Our simulations were conducted in several steps. Initially, the simulation box was compressed to achieve the desired protein concentration of 3.5 residues per cubic nanometer, as detailed in [52]. In the next step, the system was equilibrated in prepa- ration for periodic box deformations.…”