Simulations for: The Energetics and Ion Coupling of Cholesterol Transport Through Patched1

Free energy profiles: Coarse-grained (CG) potential of mean force (PMF) free energy and histogram outputs, obtained via the gromacs weighted-histogram analysis method (WHAM). PMF profile numbers match those described in the accompanying manuscript for cholesterol movement between the: - PTCH1-molA ECD base and the sterol binding domain (SBD) (PMF_1a_PTCH1_molA-SHH_cholesterol) - PTCH1-molB ECD base and the SBD (PMF_1a_PTCH1_molB-free_cholesterol) - PTCH1-molA ECD base and the sterol sensing domain (SSD) (PMF_1b_PTCH1_molA-SHH_cholesterol) - PTCH1-molA SSD and the membrane (PMF_2_PTCH1_molA-SSD_cholesterol_OHup) - PTCH1-molB SSD and the membrane (PMF_2_PTCH1_molB-SSD_cholesterol_OHup) - PTCH1-molB SSD and the membrane in a flipped conformation (PMF_2_PTCH1_molB-SSD_cholesterol_OHdown) - Membrane and solvent (PMF_3_Membrane_cholesterol) - PTCH1-molA SBD and the solvent (PMF_4_PTCH1_molA-SSH_cholesterol) - PTCH1-molB SBD and the solvent (PMF_4_PTCH1_molB-free_cholesterol) 2000 rounds of Bayesian Bootstrapping were performed. File description for each system: - histo.xvg: umbrella window histograms - bsres.xvg: Average free energy profile and computed bootstrapping error. Atomistic simulations: Subset of atomistic molecular dynamics simulations of wild-type (WT) Patched1 (PTCH1) and Dispatched1 (DISP1) in distinct ion-bound states: - PTCH1 with Na+ bound at Site 1 initially (PTCH1_WT_Na_Site1) - PTCH1 apo in 0.15 M NaCl (PTCH1_WT_apo_inNaCl) - PTCH1 apo in 0.15 M KCl (PTCH1_WT_apo_inKCl) - PTCH1 with 3 x Na+ ions bound to anionic triad residues (PTCH1_WT_3xNa) - PTCH1 with 3 x K+ ions bound to anionic triad residues (PTCH1_WT_3xK) - DISP1 apo in 0.15 M NaCl (DISP1_WT_apo) - DISP1 with 3 x Na+ ions bound to anionic triad residues (DISP1_WT_3xNa) - DISP1 with 2 x Na+ ions bound, generated by sequential ion removal from the end of DISP1_WT_3xNa simulations (DISP1_WT_2xNa) - DISP1 with 1 x Na+ ion bound, generated by sequential ion removal from the end of DISP1_WT_2xNa simulations (DISP1_WT_1xNa) - DISP1 without Na+ bound, generated by sequential ion removal from the end of DISP1_WT_1xNa simulations (DISP1_WT_0xNa) All simulations were run for 3 x 100 ns except for PTCH1_WT_apo_inNaCl which was run for 3 x 50 ns. The PTCH1 and DISP1 conformations were obtained from the Protein Data Bank (PDB IDs: 6DMY, 7RPH). File description for each system: - md_fit_firstframe.pdb : Initial frame used for atomistic simulations (replicate 1, each replicate equilibrated independently). - md_fit_X.xtc : Gromacs trajectory file for each replicate (X=replicate number).

自由能剖面数据集：本数据集包含通过GROMACS加权直方图分析方法（weighted-histogram analysis method, WHAM）计算得到的粗粒度（Coarse-grained, CG）平均力势（potential of mean force, PMF）自由能及直方图输出结果。所有PMF剖面的编号与随附手稿中描述的胆固醇在以下区域间移动的场景一一对应：
- PTCH1-molA的胞外结构域（extracellular domain, ECD）基部与甾醇结合结构域（sterol binding domain, SBD）之间（PMF_1a_PTCH1_molA-SHH_cholesterol）
- PTCH1-molB的ECD基部与SBD之间（PMF_1a_PTCH1_molB-free_cholesterol）
- PTCH1-molA的ECD基部与甾醇感应结构域（sterol sensing domain, SSD）之间（PMF_1b_PTCH1_molA-SHH_cholesterol）
- PTCH1-molA的SSD与细胞膜之间（PMF_2_PTCH1_molA-SSD_cholesterol_OHup）
- PTCH1-molB的SSD与细胞膜之间（PMF_2_PTCH1_molB-SSD_cholesterol_OHup）
- 翻转构象下PTCH1-molB的SSD与细胞膜之间（PMF_2_PTCH1_molB-SSD_cholesterol_OHdown）
- 细胞膜与溶剂之间（PMF_3_Membrane_cholesterol）
- PTCH1-molA的SBD与溶剂之间（PMF_4_PTCH1_molA-SSH_cholesterol）
- PTCH1-molB的SBD与溶剂之间（PMF_4_PTCH1_molB-free_cholesterol）
本数据集已完成2000轮贝叶斯自举（Bayesian Bootstrapping）分析。各体系配套文件说明如下：
- histo.xvg：伞形采样窗口直方图文件
- bsres.xvg：平均自由能剖面与计算得到的自举误差文件

全原子分子动力学模拟子集：本部分包含野生型（wild-type, WT）Patched1（PTCH1）与Dispatched1（DISP1）在不同离子结合状态下的全原子分子动力学模拟，具体体系如下：
- PTCH1_WT_Na_Site1：初始在位点1结合Na+的PTCH1
- PTCH1_WT_apo_inNaCl：于0.15 M NaCl缓冲液中孵育的无配体PTCH1
- PTCH1_WT_apo_inKCl：于0.15 M KCl缓冲液中孵育的无配体PTCH1
- PTCH1_WT_3xNa：3个Na+结合至阴离子三联体残基的PTCH1
- PTCH1_WT_3xK：3个K+结合至阴离子三联体残基的PTCH1
- DISP1_WT_apo：于0.15 M NaCl缓冲液中孵育的无配体DISP1
- DISP1_WT_3xNa：3个Na+结合至阴离子三联体残基的DISP1
- DISP1_WT_2xNa：从DISP1_WT_3xNa模拟终点依次移除离子得到的结合2个Na+的DISP1
- DISP1_WT_1xNa：从DISP1_WT_2xNa模拟终点依次移除离子得到的结合1个Na+的DISP1
- DISP1_WT_0xNa：从DISP1_WT_1xNa模拟终点依次移除离子得到的无Na+结合的DISP1

所有模拟体系均运行3组100 ns时长的独立模拟，仅PTCH1_WT_apo_inNaCl体系运行3组50 ns时长的独立模拟。PTCH1与DISP1的初始构象获取自蛋白质数据银行（Protein Data Bank, PDB），对应PDB编号为6DMY、7RPH。各体系配套文件说明如下：
- md_fit_firstframe.pdb：用于全原子模拟的初始结构帧（对应重复1，每个重复均独立完成平衡化处理）
- md_fit_X.xtc：对应每个重复的GROMACS轨迹文件（X为重复编号）