Elucidating the impact of red blood cell membrane components on melittin-induced pore formation with molecular dynamics simulations

Understanding the membrane-disrupting mode of action of antimicrobial peptides (AMPs) in complex biological membranes is critical for the design of therapeutically viable AMPs that are both active against microbial pathogens and nontoxic to human cells. To assess human toxicity in AMP design studies, melittin (MEL) – a highly charged 26-amino acid AMP sourced from bee venom – is often used as the positive control in experimental human red blood cell (RBC) hemolysis assays. Molecular dynamics (MD) simulations have proved invaluable in elucidating the pore-formation mechanism of MEL in single-lipid zwitterionic membranes. However, modeling pore formation in lipid bilayers containing multiple lipid species, like RBC membranes, has been limited due to the challenges of using atomistic MD simulations to capture long-timescale membrane restructuring events that depend on lipid heterogeneity, leaflet asymmetry, and cholesterol content. To address these challenges and access larger time scales,..., , # Data from: Elucidating the impact of red blood cell membrane components on melittin-induced pore formation with molecular dynamics simulations

Dataset DOI: [10.5061/dryad.ttdz08m92](10.5061/dryad.ttdz08m92)

## Description of the data and file structure

### Overview

This work implements the nucleation collective variable ξ proposed by Hub et. al (10.1021/acs.jctc.7b00106) to expand on our recently developed coarse-grained to atomistic backmapping and umbrella sampling methodology (10.1021/acs.jpcb.4c03276) to rapidly resolve free energy profiles for melittin-lined pores in red blood cell (RBC) lipid membranes with molecular dynamics (MD) simulations. All simulations were run with [Gromacs 2021.5](https://manual.gromacs.org/2021.5/user-guide/getting-started.html) patched with PLUMED 2.8.

### Folder Structure

The provided tarball (Supporting_Data.tar.gz) contains the following folders to aid with the reproducibility of the results of this work:

* **analysis_output** --> Stores all...,