The influence of polar and non-polar interactions on the self-assembly of peptide nanomembranes and their applications: An atomistic study using classical molecular dynamics

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

In this work, nanomembranes formed by the I₃XGK (X = Q, S, or N) polar peptides are studied to characterize the average force and energy required to separate two neighboring β-sheets laterally joined by polar zippers. The results presented are obtained using a methodology (state of the art) involving the pulling umbrella method to generate the samples (umbrella sampling) and the potential of mean force (PMF) to evaluate the energetic variation evolved in the process of separating the polar zipper. It was observed that the maximum force required to separate the regions linked by polar zippers is 1.48 kJ/mol nm for the I₃NGK nanomembrane and 1.22 kJ/mol nm [1.30 kJ/mol nm] for the I₃QGK [I₃SGK] nanomembranes, emphasizing that polar zippers play an important role in the interaction that interconnects β-sheets in broad and robust two-dimensional structures (tapes and membranes), offering an agile route to the construction of distinct nanomaterials from β-sheets. Also, negative values were obtained for energy as a function of the reaction coordinate for the regions where the formation of polar zippers occurs, showing that the lateral union of neighboring β-sheets is energetically favorable, with a value up to -3.0 kJ/mol, in the case of I₃NGK nanomembranes.

Antimicrobial Peptide Analogs From Scorpions: Modifications and Structure-Activity

The rapid development of multidrug-resistant pathogens against conventional antibiotics is a global public health problem. The irrational use of antibiotics has promoted therapeutic limitations against different infections, making research of new molecules that can be applied to treat infections necessary. Antimicrobial peptides (AMPs) are a class of promising antibiotic molecules as they present broad action spectrum, potent activity, and do not easily induce resistance. Several AMPs from scorpion venoms have been described as a potential source for the development of new drugs; however, some limitations to their application are also observed. Here, we describe strategies used in several approaches to optimize scorpion AMPs, addressing their primary sequence, biotechnological potential, and characteristics that should be considered when developing an AMP derived from scorpion venoms. In addition, this review may contribute towards improving the understanding of rationally designing new molecules, targeting functional AMPs that may have a therapeutic application.

Updating atomic charge parameters of aliphatic amino acids: a quest to improve the performance of molecular modeling via sequential molecular dynamics and DFT-GIAO-NMR calculations

In this work, we observe the behavior of the dipole moment, atomic charges, solute-solvent interactions and NMR spectroscopy of aliphatic amino acids in a water solution via the computational simulations of classical molecular dynamics and DFT quantum calculations. Our results indicate that the convergence of the atomic charge of the solute, from an iterative process, together with the dipole moment of the amino acid, alters the lifetime of hydrogen bonds present in the first solvation shell, resulting in the modification of its structure and dynamics. Using GIAO-DFT-NMR calculations, we assessed the impact of these structural solute-solvent modifications on the magnetic shielding constants of the solute carbon atoms. In this sense, we evaluate the importance of an update in parameters that describe atomic charges present in the CHARMM36 force field.