Molecular dynamics simulations of ligand binding to the MsepPR3/Orco receptor

This dataset contains the structural prediction–derived ligand position data and molecular dynamics (MD) simulation input files used in the study of ligand interactions with the MsepPR3/Orco receptor complex. The repository is organized into two compressed archives: AlphaFold3-derived ligand position data and MD simulation input data. 1. AlphaFold3 prediction–derived ligand position data The archive AF3_predict_results.zip contains the ligand coordinate datasets derived from AlphaFold3 predictions of the MsepPR3/Orco tetramer in complex with pheromone and aromatic ligands.These files do not contain the predicted structural models themselves, but instead include the ligand center-of-mass (COM) coordinates extracted from the predicted models, which were used to generate the ligand distribution density plots in the manuscript. Two subfolders correspond to predictions performed with different aromatic ligands: MsepPR3_Orco_Z&BA – predictions involving Z11-16:Ald and benzaldehyde (BA) MsepPR3_Orco_Z&MBA – predictions involving Z11-16:Ald and isoamyl alcohol (MBA) Within each subfolder, ligand coordinate data are provided for three binding scenarios: Single-ligand conditionThe receptor tetramer bound to one Z11-16:Ald molecule Dual-ligand conditionThe tetramer bound to one Z11-16:Ald and one BA/MBA molecule Multiple-ligand conditionThe tetramer bound to one Z11-16:Ald and ten BA/MBA molecules For each condition, the files contain the ligand center-of-mass (COM) coordinates extracted from all AlphaFold3-predicted models, which were used to construct the two-dimensional kernel density estimation (KDE) plots of ligand occupancy. These datasets correspond to: Figure 7 – Z11-16:Ald and BA systems Figure S5 – Z11-16:Ald and MBA systems 2. Molecular dynamics simulation inputs The archive MD_input_information.zip contains the input files used to perform the molecular dynamics simulations of ligand binding to the MsepPR3/Orco complex. Four simulation systems are provided: MsepPR3_Orco_onlyZ_pocket MsepPR3_Orco_Z&BA These correspond to the simulations shown in Figure 7. Additional simulations used to evaluate alternative ligand-binding starting positions are provided in: MsepPR3_Orco_onlyZ_TM2TM7 MsepPR3_Orco_onlyZ_TM5TM6 These correspond to Figure S6. Each simulation system contains three independent replicate runs: rep1/rep2/rep3/ Each replicate folder includes the following files: run.sh – shell script used to execute the MD simulation input.gro – initial structure generated using CHARMM-GUI md.mdp – MD simulation parameter file topol.top – system topology file toppar.zip – force-field and topology parameter files The simulations were performed using GROMACS, with system preparation conducted using CHARMM-GUI.本数据集包含用于研究配体与MsepPR3/Orco受体复合物相互作用的、由结构预测得到的配体位置数据，以及分子动力学（MD）模拟输入文件。本存储库分为两个压缩归档包：分别为AlphaFold3预测得到的配体位置数据，与MD模拟输入数据。 1. AlphaFold3预测得到的配体位置数据 归档文件AF3_predict_results.zip 包含了由AlphaFold3对结合了信息素与芳香族配体的MsepPR3/Orco四聚体进行预测所得到的配体坐标数据集。本文件不包含预测得到的结构模型本身，仅包含从预测模型中提取的配体质心（COM）坐标，这些坐标用于绘制论文中的配体分布密度图。 本归档包含两个子文件夹，对应使用不同芳香族配体完成的预测任务： MsepPR3_Orco_Z&BA：涉及Z11-16:Ald与苯甲醛（BA）的预测 MsepPR3_Orco_Z&MBA：涉及Z11-16:Ald与异戊醇（MBA）的预测 在每个子文件夹中，针对三种结合场景提供了配体坐标数据： 单配体条件：受体四聚体结合1个Z11-16:Ald分子 双配体条件：四聚体结合1个Z11-16:Ald与1个BA/MBA分子 多配体条件：四聚体结合1个Z11-16:Ald与10个BA/MBA分子 针对每种条件，文件中包含从所有AlphaFold3预测模型中提取的配体质心坐标，用于构建配体占据率的二维核密度估计（KDE）图。 本数据集对应以下图表： 图7 —— Z11-16:Ald与BA体系 图S5 —— Z11-16:Ald与MBA体系 2. 分子动力学模拟输入文件 归档文件MD_input_information.zip 包含了用于开展配体与MsepPR3/Orco复合物结合模拟的分子动力学模拟输入文件。 本归档提供了四类模拟体系： MsepPR3_Orco_onlyZ_pocket MsepPR3_Orco_Z&BA 上述体系对应图7中展示的模拟实验。 用于评估替代配体结合起始位置的额外模拟实验归档于： MsepPR3_Orco_onlyZ_TM2TM7 MsepPR3_Orco_onlyZ_TM5TM6 上述体系对应图S6。 每个模拟体系包含3组独立重复运行：rep1/rep2/rep3/ 每个重复运行文件夹包含以下文件： run.sh —— 用于执行MD模拟的Shell脚本 input.gro —— 由CHARMM-GUI生成的初始结构文件 md.mdp —— MD模拟参数文件 topol.top —— 系统拓扑文件 toppar.zip —— 力场与拓扑参数文件 本模拟实验使用GROMACS完成，系统构建流程采用CHARMM-GUI实现。