Understanding the stability of polypeptide membranes in ionic liquids: a theoretical molecular dynamics study

Abstract

Stability analysis of polypeptide membranes in ionic liquids can make possible new applications of these membranes in energy storage and ionic solution separation.

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; 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 . As previously described, our estimate is that the average number of HBs between peptides increases by about 0.6 HBs/peptide.…”

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

“…Each one of the 150 configurations was submitted to an independent separation process because by using different initial configurations we can evaluate the effect of the conformations between the REF and PUL groups during the separation process. The pull umbrella process was performed using the directional technique with the application of a harmonic force in the direction of the reaction coordinate (ξ) with a constant equal to 2 × 10 3 kJ/mol nm 2 at an application rate of 0.05 nm/ps and parameters extracted from previous studies involving the extraction of peptides in peptide and lipid membranes. , Thus, each configuration X ( i ) was subjected to the separation process between REF-PUL regions obtaining the force F ( i ) as a function of time (and distance). Therefore, individual information from each X ( i ) configuration and average information considering all the 150 configurations was computed during the procedure.…”

Molecular dynamic simulations, GIAO‐NMR and TD‐DFT spectroscopy analyze for zwitterionic isoleucine (ILE)N, 1 ≤ N ≤ 6, in water solution

“…In recent years, there has been an increase in interest for biological molecules especially amino acids, which has had great appeal for the manufacture of new nanomaterials and applications. In this regard, the determination of spectroscopic properties and the possible dependence of these properties on amino acid chain growth becomes an important point for applications of these new nanomaterials whether in the membranes research [1][2][3][4] or self-assemble properties [5][6][7][8] , energy storage 9 or even pharmaceutical applications [10][11][12] . In this article, we focus on the amino acid Isoleucine (ILE) which has a characteristic hydrophobic structure and has a high β-sheet formation potential compared to the other amino acids.…”