LNP-endosome stalk system: unbiased MD with all MC3 protonated and reoriented siRNA

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

Created 20 Oct 2026Updated 20 Oct 2026

MD-A00C6F

Description

All-atom (CHARMM36) system of a HER2-siRNA lipid nanoparticle fused through a stalk with an endosomal-like membrane in water with 100 mM KCl, with all ionizable MC3 lipids protonated and the siRNA reoriented. Unbiased MD studying siRNA translocation (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
stalk_LNP_endosome_AA_reorientedRNA	Trajectory Analyses

Files

22 files · 801 MB

All files801 MB

trajectory.binBIN
pca_trajectory_01.binBIN
pca_trajectory_02.binBIN
pca_trajectory_03.binBIN
pca_trajectory_04.binBIN
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.