Gluten Adhesion and Shearing in a Contact-Based Coarse-Grained Model

Abstract

We study adhesion of the gluten proteins during the shear and normal deformations as described by a coarse-grained molecular dynamics. We show that the two types of deformation have a different impact on the proteins. We also calculate the dynamic shear modulus and critical strain and find the results to be consistent with the slip-bond theory which assumes that the gluten proteins can be treated as an interconnected network of polymers. Graphical Abstract

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 wall displacement as a function of time was a sinusoid with an amplitude of 1 nm and an oscillation period of 40 µs. The residues were attracted to the walls with the Lennard-Jones potential [54]. Following five full oscillation cycles, the system underwent the next equilibration.…”

“…Finally, the simulation box with a well-equilibrated system was stretched in one direction to induce the rupture of the protein network. The same pair of box walls continually attracted protein residues, causing them to adhere to these walls and enabling the stretching of the entire system [54].…”

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

“…After the equilibration, the walls along the Z direction start to attract the proteins with Lenard–Jones potential with the depth (the same as for disulfide bonds), again in a quasi-adiabatic contact-switching manner (Mioduszewski and Cieplak 2021b ). The details of the adhesion process are also very important and we devoted an entire article to them (Mioduszewski and Cieplak 2021c ). After another (third) equilibration, when the attraction is already turned on, the box shape changes periodically (with the period 40,000 ) to recreate the shearing and normal strain (the box is no longer a square, but a parallelepiped - more details can be found in Mioduszewski and Cieplak 2021b ).…”