M3B Lab
Published April 20, 2023 | Version v1
Journal article Open

Cellular uptake of rose bengal is mediated by OATP1B1/1B3 transporters

Creators

  • 1. Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland
  • 2. Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 141/143 Pomorska St., 90-236 Lodz, Poland; Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
  • 3. PolitoBIOMedLab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy
  • 4. Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, University of Lodz, Tamka 12, 91-403, Lodz, Poland

Description

This repositary contains the Molecular Dynamics simulation data for the paper "Cellular uptake of rose bengal is mediated by OATP1B1/1B3 transporters" (doi: 10.1016/j.bioelechem.2023.108449 ).

The input data, required to reproduce the results in the paper, is organized in the following folders:

  • MDP/
    • This folder contains the MD simulation parameters in GROMACS MDP format used for minimization, stepwise equilibration and production MD simulation.
  • Topologies/
    • This folder contains the molecular topologies for the simulated membrane (as obtained from CHARMM-GUI) and the CGenFF topology for Rose Bengal.
  • SimulationInput/
    • This folder contains the input coordinates (in both PDB and TPR format) for the production MD simulations (after NVT+NPT equilibration).

Notes

This work was supported by the National Science Centre, Poland (Project UMO-2017/25/B/NZ7/01304 ′′Phosphorus dendrimers as car- riers for photosensitizers - in vivo studies′′) and based upon work from COST Action ′′Nano2Clinic. Cancer Nanomedicine - from the bench to the bedside′′ CA17140 supported by COST (European Cooperation in Science and Technology). L.P. is grateful to the National Science Cen- tre, Poland (Project UMO-2021/43/O/ST4/01553)

Files

SimulationData.zip

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Additional details

Related works

Is supplement to
Journal article: 10.1016/j.bioelechem.2023.108449 (DOI)