Simulations for: Patched 1 regulates Smoothened by controlling sterol binding to its extracellular cysteine-rich domain.

<p><strong>Atomistic simulations of Smoothened:</strong></p> <p>Atomistic molecular dynamics simulations of glycosylated&nbsp;mouse Smoothened (mSMO) and human Smoothened (hSMO) in distinct liganded states:</p> <p>- mSMO in an apo state (mSMO_apo)</p> <p>-&nbsp;mSMO with TMD cholesterol bound (mSMO_chol_TMD)</p> <p>- mSMO with CRD cholesterol bound (mSMO_chol_CRD)</p> <p>- mSMO with cholesterol bound to the CRD and TMD (mSMO_2chol_TMD_CRD)</p> <p>- mSMO bound to CRD cholesterol and Smoothened agonist (SAG) (mSMO_chol_CRD_SAG)</p> <p>- mSMO bound to CRD and TMD cholesterols, SAG and an intracellular nanobody (mSMO_2chol_SAG_nanobody)</p> <p>- mSMO bound to CRD and TMD cholesterol and with an additional cholesterol bound at a proposed &#39;mid&#39; position (mSMO_3chol)</p> <p>- hSMO bound to CRD cholesterol and SAG (hSMO_chol_CRD_SAG)</p> <p>&nbsp;</p> <p>All simulations were run for 5x 300 ns. The active mSMO conformation was obtained from the Protein Data Bank (PDB ID: 6O3C). The hSMO structure was determined using X-ray crystallography as outlined&nbsp;within this study.&nbsp;&nbsp;</p> <p><strong>File description for each system:</strong></p> <p>- md_fit_firstframe.pdb : Initial frame used for atomistic simulations (replicate 1, each replicate equilibrated independently).&nbsp;</p> <p>- md_fit_<em>X</em>.xtc : Gromacs trajectory file for each replicate (X=replicate number).&nbsp;</p>