mRNA lipid nanoparticle phase transition

The repository contains input files and data from the manuscript:

Trollmann, Marius F.W. and Böckmann, Rainer A. "mRNA lipid nanoparticle phase transition", Biophysical Journal (2022) https://doi.org/10.1016/j.bpj.2022.08.037

> Periodic membrane patches

Equilibrated structures, .mdp and .top files for the simulations of the periodic Comirnaty membrane patches. (microsecond = us)

>> periodic_patches/low_ph/single_patch: 

~ System A: Three replicas (4.1 us, 3.0 us and 3.0 us) of the self-assembled Comirnaty lipid mixture with the protonated aminolipid

>> periodic_patches/low_ph/quad_patch: 

System B: A quadruplicated system A patch simulated for 1.0 us

>> periodic_patches/dspc_chol:

System C: Binary membrane including DSPC and 43mol% cholesterol

>> periodic_patches/neutral_ph:

System D: A deprotonated system B patch simulated for 0.633 us

>> periodic_patches/mrna_selfassembly:

System E: Structures of the self-assembled Comirnaty lipid mixture with the modified mRNA strand

+ periodic_patches/mrna_selfassembly/selfassembly: Structures of the mRNA-lipid mixture after self-assembly with protonated aminolipids

+ periodic_patches/mrna_selfassembly/set1: Quadruplicated simulation systems after deprotonation of distant aminolipids (set 1, see paper)

 + periodic_patches/mrna_selfassembly/set2: Quadruplicated simulation systems after deprotonation of random aminolipids (set 2, see paper)

+ periodic_patches/mrna_selfassembly/set3: Simulation systems after deprotonated of all aminolipids (systems were not quadruplicated) (set 3, see paper)

> Lipid nanoparticles

Equilibrated structures, .mdp and .top files for the simulations of the lipid nanoparticles. (microsecond = us)

>> nanoparticles/lnp_nopegs:

System F: Structures of the lipid nanoparticles with capped PEGylated lipids

>> nanoparticles/lnp_pegs:

System G: Structure of the lipid nanoparticle with complete PEGylated lipids

> Topologies

- topology/DSPC.top - Parameters for the standard phospholipid from the CHARMM36 forcefield

- topology/CHOL.top - Parameters for cholesterol from the CHARMM36 forcefield

- topology/alc.itp, topology/alc.prm - Parametrization files of the PEG-ylated lipid ALC-0159 obtained from the CGenFF-Webserver

- topology/alc_neutral.itp - Parameters for the neutral aminolipid ALC-0315 obtained from the CGenFF-Webserver

- topology/alc_protonated.itp - Parameters for the protonated aminolipid ALC-0315 obtained from the CGenFF-Webserver

- topology/modRNA.top - Parameters for the short modified mRNA strand. Uridine was replaced with N1-Methylpseudouridine. The parameters were not included in the standard CHARMM36 forcefield (version July 2020) and were manually added to the forcefield.

- topology/ALC_SHORT_CORRECT_IDX.itp - Parameters for the capped PEG-ylated lipid ALC-0159 -> Parameters were manually adapted to fit the shortened structure.

- topology/charmm36-jul2020.ff - CHARMM36 forcefield parameters (version July 2020) with included parameters for N1-Methylpseudouridine.

- topology/cgenff_output - Output from the CGenFF-Webserver to parametrize the aminolipid (ALC-0315) and the PEGylated-lipid (ALC-0159)