LNP-endosome stalk system: unbiased MD with all MC3 deprotonated (spontaneous siRNA release)

Kazi Amirul Hossain,Mariana Valério,Pedro Medina,Paulo C. T. Souza,Modesto Orozco

Created 20 Oct 2026Updated 20 Oct 2026

MD-A00C6E

Description

All-atom (CHARMM36) system of a HER2-siRNA lipid nanoparticle fused through a stalk with an endosomal-like membrane (MC3, DSPC, cholesterol, PC/PE/PI/SM lipids) in water with 100 mM KCl, in which all ionizable MC3 lipids are neutral (deprotonated). Unbiased MD showing spontaneous siRNA translocation/release (Figure 4 and Fig. S17 of the paper). Trajectory without solvent.

Molecular system

Program: GROMACS

Sequences

Sequence 1Nucleic acid · 10 residues

CUCACAGAGA

Sequence 2Nucleic acid · 10 residues

UCUCUGUGAG

Run	Outputs
allDeproto_endoLNP_spontenousRNArelease_dry	Trajectory Analyses

Files

20 files · 1.5 GB

All files1.5 GB

trajectory.binBIN
pca_trajectory_01.binBIN
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pca_trajectory_05.binBIN
pca_trajectory_06.binBIN
pca_trajectory_07.binBIN
pca_trajectory_08.binBIN
pca_trajectory_09.binBIN

Acknowledgements

Supported by Instituto de Salud Carlos III, the Spanish Ministry of Science, Innovation and Universities (including FPU), CDTI, Generalitat de Catalunya (AGAUR), CNRS and a research collaboration agreement with Sanofi. Computing resources from EuroHPC, Barcelona Supercomputing Center, GENCI (IDRIS, CINES, TGCC) and PSMN/Centre Blaise Pascal.