Stability and structural analysis of A6R polypeptide nanosheets: a theoretical study using the classical molecular dynamics simulation

Abstract

In this work, we have investigated the interactions of polypeptides composed of the sequence of six alanines and one arginine (A6R) grouped in three nanosheet structures with maximum, intermediate, and minimal spatial overlap of polyalanine–arginine peptide molecules, allowing an evaluation of their porosity in water solution. Our results obtained through molecular dynamics show a well-equilibrated structure for the final configuration of A6R nanosheets with maximum spatial overlap indicating a low porosity, whereas the model with intermediate nanosheet separation presents greater infiltration, despite maintaining the membrane structure. The electrically charged A6R model with minimal spatial overlap did not maintain the membrane structure. With only one agglomerate having large water infiltration, the alanines still remained in the inner part of this agglomerate, whereas the arginines are located outside, characterizing amorphous blocks. By extracting a peptide from the membrane through pulling methodology, we have observed how membrane stiffness is established with the self-organization of the peptides in the membrane, associating such results with the infiltration of water molecules in the structure.