Molecular Dynamics (MD) Simulation Data: Taurocholic Acid Transportation by OSTα/OSTβ

Human OSTα/OSTβ is a vital bile acid (BA) transporter. This study elucidated its structure and transport mechanism using cryo-EM and molecular dynamics.Cryo-EM revealed OSTα/OSTβ as a novel "dimer of heterodimers," with an OSTα homodimer core and peripheral OSTβs. OSTα, with a GPCR-fold, features a BA recognition site involving a cysteine-rich loop and transmembrane helices. A positive cavity facilitates BA translocation.Molecular dynamics (MD) simulations, including well-tempered metadynamics (wt-MetaD), detailed the taurocholic acid (TCA) transport pathway. It involves a "head-down" to "head-up" flip across the membrane, moving through intermediate states within a positive cavity. Polar residues guide the BA towards the extracellular side.This repository contains molecular dynamics (MD) simulation data aimed at elucidating the transportation of taurocholic acid (TCA) by the OSTα/OSTβ protein complex embedded within a POPC lipid bilayer.Directory StructureMD_system_parameters.csv: This file details the system composition and the simulation box dimensions used for all MD simulations.POPC_CMD/: This directory contains data from Conventional Molecular Dynamics (CMD) simulations.POPC_MetaD/: This directory contains data from Metadynamics (MetaD) simulations.Conventional Molecular Dynamics (CMD) Data (POPC_CMD/)This directory includes three independent conventional molecular dynamics simulation runs. These simulations provide insights into the dynamic behavior of the system under standard conditions.Files:runX_0ns.pdb: Initial PDB (Protein Data Bank) coordinate file for run X (where X is 1, 2, or 3) at 0 nanoseconds. These files represent the starting configuration for each simulation.runX_500ns.pdb: Final PDB coordinate file for run X (where X is 1, 2, or 3) after 500 nanoseconds of simulation. These files capture the system's configuration at the end of each run.runX_all_trj.xtc: Compressed trajectory file for the entire duration of run X (where X is 1, 2, or 3). These files contain atomic coordinates over time, allowing for detailed analysis of molecular motion and interactions throughout the simulation.Metadynamics (MetaD) Data (POPC_MetaD/)This directory includes data from a Metadynamics simulation. Metadynamics is a powerful enhanced sampling technique often used to explore complex free energy landscapes, particularly relevant for understanding transport processes and conformational changes.Files:Meta_ini.pdb: Initial PDB coordinate file used for the Metadynamics simulation. This represents the starting configuration for the enhanced sampling run.Meta_trj.xtc: Compressed trajectory file for the Metadynamics simulation. This trajectory can be analyzed to reconstruct free energy profiles and pathways related to TCA transportation.