Self-assembly mechanism of rice glutelin amyloid fibril aggregates obtained through experimental and molecular dynamics simulation analysis

Abstract

In this study, intermolecular interactions and the self-assembly mechanism of rice glutelin amyloid fibril aggregates (RAFA) were studied using a combination of experimental and computer simulation methods. Based on the results of Thioflavin T fluorescence intensity, particle size measurement, and atomic force microscopy, the addition of NaCl and SDS accelerated the agglomeration of the RAFA, whereas adding urea caused the degradation of fibril clusters and the depolymerization of amyloid fibrils. The formation of the common cross β-sheet structure in the RAFA was primarily driven by hydrogen bonding, hydrophobic and electrostatic interaction were also involved. Visual molecular dynamics simulations indicated that randomly distributed peptides, hydrolyzed from rice glutelin, experienced aggregation, dispersion, structural rearrangements, and positional modifications to form the RAFA, which was compatible with the nucleation-elongation mechanism. The study supports for clarifying the self-assembly pattern of amyloid fibril aggregates derived from food protein, which is crucial for the denovo design and practical application of protein-amyloid fibril aggregates.