MD_MAITcellLigands_MDvi_2020

The broadly designed study of molecular dynamics (MD) of receptor complexes of natural MAIT cell ligands, their ethinylated or fluorescence-labelled derivatives generated data that give insights beyond analysis of interactions observed in crystal structures of ternary ligand/MR1/TCR complexes. The data permit a MD weighted appreciation of the crystallographically observed interactions, thereby supporting drug design of MAIT cell ligand. They were notably generated from models of both, binary and ternary complexes of MAIT cell ligands to give insights into the formation of the ternary complexes. Analysis of torsional angles evinces induced-fit of the ligand in binary MR1 complexes upon formation of the corresponding ternary complexes. Radial distribution functions of water around the ethinylated ligands in binary MR1 complexes show that fluorescence labeling by copper(I)-catalyzed azide-alkyne cycloaddition can occur on covalently bound ligand. They also provide a first step to the risk assessment of photon-induced electron transfer (PET) in fluorophore-labelled ligand/MR1 complexes.
The dataset contains:
* Simulation Interactions Diagram Reports (pdf) and statistics of non-covalent interaction counts (xlsx) of molecular dynamics simulations of natural MAIT cell ligands and their ethinylated or fluorophore-reacted analogs in ternary and binary MR1/TCR and MR1 complexes, respectively.
* Raw data of the molecular dynamics simulations: Desmond input and output files as generated by the implementation in Maestro molecular modelling package commercialized by Schrödinger Inc.; compressed; tar archives;
The trajectory files found in the directories [MDsimulation_name]_trj have to be decompressed prior to visualization. The 4 simulations of the binary and ternary complexes of 5OERU and 5OPRU are found in archive_natural_ligands_5OERU.tar and archive_natural_ligands_5OPRU.tar. The 4 simulations of the ternary complexes of the R and S stereoisomers of their ethinylated analogues are contained in archive_ethinylated_ligands_SSRR_ternary.tar and archive_ethinylated_ligands_SSRS_ternary.tar while the simulations of the corresponding binary complexes are in archive_ethinylated_ligands_binary.tar. The 4 simulations of the binary complexes of the two stereoisomers of the fluorophore-reacted products are accessible in archive_fluorescent_ligands.tar.

Links to other parts of the dataset:
https://data.mendeley.com/drafts/txms2vk6jb http://dx.doi.org/10.17632/txms2vk6jb.1 (MD_MAITcellLigands_i_2020)
https://data.mendeley.com/drafts/wwxnsj66ks http://dx.doi.org/10.17632/wwxnsj66ks.1 (MD_MAITcellLigands_ii_2020)
https://data.mendeley.com/drafts/d9byds5hs6 http://dx.doi.org/10.17632/d9byds5hs6.1 (MD_MAITcellLigands_iii_2020)
https://data.mendeley.com/drafts/kbvs2cdyjg http://dx.doi.org/10.17632/kbvs2cdyjg.1 (MD_MAITcellLigands_iv_2020)
https://data.mendeley.com/drafts/tp62zb6rg4 http://dx.doi.org/10.17632/tp62zb6rg4.1 (MD_MAITcellLigands_v_2020)

本研究针对天然黏膜相关恒定T细胞（mucosa-associated invariant T cell, MAIT）配体的受体复合物，及其炔基化或荧光标记衍生物开展了系统性分子动力学（molecular dynamics, MD）模拟，所获数据可提供超出三元配体/MR1/TCR复合物晶体结构相互作用分析范畴的认知。该数据支持通过分子动力学加权解析晶体学观测到的相互作用，进而助力MAIT细胞配体的药物开发。
本数据集基于MAIT细胞配体的二元与三元复合物模型生成，可用于解析三元复合物的形成机制。扭转角分析结果表明，二元MR1复合物中的配体在对应三元复合物形成时发生了诱导契合。二元MR1复合物中炔基化配体周围水分子的径向分布函数分析显示，通过铜(I)催化叠氮-炔环加成（copper(I)-catalyzed azide-alkyne cycloaddition）实现的荧光标记可结合在共价连接的配体上。本数据集同时为荧光标记配体/MR1复合物中的光诱导电子转移（photon-induced electron transfer, PET）风险评估提供了首个研究基础。
本数据集包含以下内容：
* 天然MAIT细胞配体及其炔基化、荧光基团反应类似物分别在三元MR1/TCR复合物与二元MR1复合物中进行分子动力学模拟的模拟相互作用图解报告（PDF格式）与非共价相互作用计数统计文件（XLSX格式）；
* 分子动力学模拟原始数据：由Schrödinger公司商业化的Maestro分子建模软件包所生成的Desmond输入与输出文件，均已压缩为tar归档包；
位于[MDsimulation_name]_trj目录下的轨迹文件需先解压后方可进行可视化操作。针对5OERU与5OPRU的二元及三元复合物的4组模拟数据，分别存放在archive_natural_ligands_5OERU.tar与archive_natural_ligands_5OPRU.tar归档包中；针对其炔基化衍生物的R、S立体异构体的4组三元复合物模拟数据，分别存放在archive_ethinylated_ligands_SSRR_ternary.tar与archive_ethinylated_ligands_SSRS_ternary.tar归档包中，对应二元复合物的模拟数据则存放在archive_ethinylated_ligands_binary.tar中；针对荧光基团反应产物的两种立体异构体的4组二元复合物模拟数据，可在archive_fluorescent_ligands.tar归档包中获取。
本数据集其他部分的访问链接如下：
https://data.mendeley.com/drafts/txms2vk6jb http://dx.doi.org/10.17632/txms2vk6jb.1（MD_MAITcellLigands_i_2020）
https://data.mendeley.com/drafts/wwxnsj66ks http://dx.doi.org/10.17632/wwxnsj66ks.1（MD_MAITcellLigands_ii_2020）
https://data.mendeley.com/drafts/d9byds5hs6 http://dx.doi.org/10.17632/d9byds5hs6.1（MD_MAITcellLigands_iii_2020）
https://data.mendeley.com/drafts/kbvs2cdyjg http://dx.doi.org/10.17632/kbvs2cdyjg.1（MD_MAITcellLigands_iv_2020）
https://data.mendeley.com/drafts/tp62zb6rg4 http://dx.doi.org/10.17632/tp62zb6rg4.1（MD_MAITcellLigands_v_2020）