Coarse-Grained MD Trajectories of GPCR-Cholesterol Systems for the CHAMP Protocol

Coarse-Grained Molecular Dynamics (CG-MD) trajectories corresponding to two structures of the cannabinoid receptor 1 (CB1). One system corresponds to CB1 embedded in a POPC:cholesterol membrane, while the other contains the CB1 receptor bound to THC embedded in a POPC membrane mixed with the negative allosteric modulator Org27569.

Each directory includes the output trajectories after processing the structures using the Cholesterol Hotspot Automated Mapping Protocol (CHAMP, publicly available at the Urbino CAMD GitHub). The files provided are a reduced version of the originals where only relevant atoms (protein and cholesterol or Org27569) were retained for sharing purposes, and provide enough data to analyze them as indicated by the CHAMP method.

The starting atomistic structures that were processed are also provided, as well as the original Martini topologies and GROMACS .mdp files which led to the equilibration and simulation of the systems built.

本数据集包含对应于大麻素受体1（CB1）两种结构的粗粒度分子动力学（Coarse-Grained Molecular Dynamics, CG-MD）轨迹。其中一套体系为嵌入于1-棕榈酰-2-油酰-sn-甘油-3-磷酸胆碱（POPC）与胆固醇混合膜中的CB1受体；另一套体系为结合了四氢大麻酚（THC）的CB1受体，该受体嵌入于掺有负变构调节剂Org27569的POPC膜中。每个目录均包含采用胆固醇热点自动映射协议（CHAMP，可从乌尔比诺CAMD GitHub仓库公开获取）处理结构后得到的输出轨迹。本次提供的文件为原始数据的精简版本，仅保留了相关原子（蛋白质、胆固醇或Org27569）以方便共享，且数据量足以支持按照CHAMP方法开展相关分析。本次同时提供了经处理的初始全原子结构，以及用于构建并完成体系平衡与模拟的原始Martini拓扑文件与GROMACS .mdp参数文件。