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.

Exploring How System Dimensions and Periodic Boundary Conditions Influence the Molecular Dynamics Simulation of A6H Peptide Self-Assembly Nanostructures

“…For the average number of HBs, we can compare the results obtained for membrane systems composed mainly of alanines. Previous studies show that the average number of HBs in these systems is approximately 7.84, 6.92, and 4.50 HBs/peptide depending on the membrane structure formed by A 6 R; 50 around 7.8 HBs/peptide in A 6 D-type structures; and about 8.2 HBs/peptide in membrane structures formed by A 6 K. 51 As previously described, our estimate is that the average number of HBs between peptides increases by about 0.6 HBs/peptide. Therefore, the values described for the highlighted composite systems can be adjusted, estimating a result free from PBCs and reflecting an increase that may range from 7 to 13%.…”

Polar Zipper on a Peptide Nanomembrane: A Characterization by Potential of Mean Force

“…Among the architectures found in the peptide scenario, ,,,,,− the nanomembranes stand out. In addition to having several applications, ,− understanding the nanomembranes’ self-organization can help in the formation of more complex architectures .…”