Published December 6, 2023
| Version v1
Dataset
Open
Molecular dynamics simulation of MFSD1 in apo, His-Ala, Lys-Ala and Leu-Ala bound
Authors/Creators
-
1.
European Molecular Biology Laboratory
Contributors
Contact person:
Description
The MFSD1 structures were placed in a heterogenous bilayer composed of POPE (20%), 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC, 30%), Cholesterol (30%), and N-Palmitoyl-sphingomyelin (SPM, 20%) using CHARMM-GUI scripts and all simulations were performed using GROMACS 2021.3.
Substrates were fitted into the binding site based on non-protein density observed in the outward-open Cryo-EM structure of GLMP-MFSD1+HisAla.
Here, inital structures and 500 ns simulations for each replicate (Rep1-3) with the respective ligands and its starting conformation (Conf1 or Conf2) are given in PDB-format.
The following ligands were used for the molecular dynamics simulations:
- LA - Leucyl-alanine dipeptide: both termini are charged
- KA - Lysyl-alanine dipeptide: both termini are charged, side chain of lysine is positively charged
- H0A - Histidyl-alanine dipeptide: both termini are charged, side chain of histidine is neutral
- HA - Histidyl-alanine dipeptide: both termini are charged, side chain of histidine is positively charged
Files
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