Vesicular roundness and compound release in PC-12 cells

The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations

Antimicrobial cationic peptides (AMPs) are excellent candidates for use as therapeutic antimicrobial agents. Among them, short peptides possessing sequences of 9-11 amino acids have some advantages over long-sequence peptides. However, one of the main limitations of short peptides is that their mechanism of action at the molecular level is not well-known. In this article, we report a model based on multiscale molecular dynamics simulations of short peptides interacting with vesicles containing palmitoyl-oleoyl-phosphatidylglycerol (POPG)/palmitoyl-oleoyl-phosphatidylethanolamine (POPE). Simulations using this approach have allowed us to understand the different behaviors of peptides with antimicrobial activity with respect to those that do not produce this effect. We found remarkable agreement with a series of experimental results directly supporting our model. Moreover, these results allow us to understand the mechanism of action at the molecular level of these short peptides. Our simulations suggest that mechanical inhomogeneities appear in the membrane, promoting membrane rupture when a threshold concentration of peptides adsorbed on the membrane is achieved. These results explain the high structural demand for these peptides to maintain a delicate balance between the affinity for the bilayer surface, a low peptide-peptide repulsion (in order to reach the threshold concentration), and an acceptable tendency to penetrate into the bilayer. This mechanism is different from those proposed for peptides with long amino acid sequences. Such information is very useful from the medicinal chemistry point of view for the design of new small antimicrobial peptides.

Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape

The surface assessment via grid evaluation (SuAVE) software was developed to account for the effect of curvature in the calculations of structural properties of chemical interfaces regardless of the chemical composition, asymmetry, and level of atom coarseness. It employs differential geometry techniques, enabling the representation of chemical surfaces as fully differentiable. In this article, we present novel developments of SuAVE to treat closed surfaces and complex cavity shapes. These developments expand the repertoire of curvature-dependent analyses already available in the previous version of SuAVE (e.g., area per lipid, density profiles, membrane thickness, deuterium-order parameters, volume per lipid, and surface curvature angle) to include new functionalities applicable to soft matter (e.g., sphericity, average radius, principal moment of inertia, and roundness) and crystalline porous materials (e.g., pore diameter, internal void volume, total area, and the total void volume of the unit cell structure). SuAVE can accurately handle chemical systems with high and low atom density as demonstrated for two distinct chemical systems: the lipid A vesicle and a set of selected metal–organic frameworks. The SuAVE software v2.0 is fully parallel and benefits from a compiler that supports OpenMP. SuAVE is freely available from https://github.com/SuAVE-Software/source and https://www.biomatsite.net/.