MD_MAITcellLigands_MDv_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/4d96x29xkp http://dx.doi.org/10.17632/4d96x29xkp.1 (MD_MAITcellLigands_vi_2020)

针对天然黏膜相关恒定T细胞（MAIT cell）配体受体复合物及其炔基化、荧光标记衍生物的分子动力学(MD)系统性研究，所生成的数据可提供超越三元配体/MR1/TCR复合物晶体结构相互作用分析的认知视角。该数据可通过分子动力学加权评估晶体学观测到的相互作用，进而为MAIT细胞配体的药物设计提供支撑。本研究的数据特别基于MAIT细胞配体的二元与三元复合物模型生成，以阐明三元复合物的形成机制。对扭转角的分析表明，在对应三元复合物形成过程中，二元MR1复合物内的配体存在诱导契合现象。二元MR1复合物中炔基化配体周围的水径向分布函数显示，通过铜(I)催化叠氮-炔环加成实现的荧光标记可发生于共价结合的配体之上。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(PET)风险评估提供了初步基础。

本数据集包含：
* 天然MAIT细胞配体及其炔基化或荧光标记衍生物分别在三元MR1/TCR复合物、二元MR1复合物中进行分子动力学模拟的相互作用图报告（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：由施罗丁格公司（Schrödinger Inc.）商业化推出的Maestro分子建模套件中集成的Desmond模块生成的Desmond输入与输出文件，均为压缩tar归档格式；位于[MDsimulation_name]_trj目录下的轨迹文件需先解压方可进行可视化操作。
5-OERU与5-OPRU的二元、三元复合物共4组模拟数据分别存储于archive_natural_ligands_5OERU.tar与archive_natural_ligands_5OPRU.tar归档文件中。其炔基化类似物的R、S立体异构体的三元复合物共4组模拟数据存储于archive_ethinylated_ligands_SSRR_ternary.tar与archive_ethinylated_ligands_SSRS_ternary.tar归档文件中，对应二元复合物的模拟数据则存储于archive_ethinylated_ligands_binary.tar。荧光标记产物的两种立体异构体的二元复合物共4组模拟数据可从archive_fluorescent_ligands.tar归档文件中获取。

本数据集其余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/4d96x29xkp http://dx.doi.org/10.17632/4d96x29xkp.1 (MD_MAITcellLigands_vi_2020)