MD_MAITcellLigands_i_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/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)
https://data.mendeley.com/drafts/4d96x29xkp http://dx.doi.org/10.17632/4d96x29xkp.1 (MD_MAITcellLigands_vi_2020)