The human microbiome-derived antibiotic lugdunin self-regulates its biosynthesis by a feed-forward mechanism
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1.
German Center for Infection Research
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2.
University of Eastern Finland
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3.
Universitätsklinikum Tübingen
Description
Molecular dynamics simulation trajectories for LugL and LugR generated using Desmond implemented on Maestro2022.4. We used OPLS4 force-field, cubic PBC box of 13Ang axis filled with TIP3P water molecules. Details can be found in the publication.
Systems are labelled as follows:
1092- LugL_4G6Qbased 13x3A OPLS4 apostructure
1093- LugR_4W97based 13x3A OPLS4 apostructure
1094- lugR_4w97based_s-ludgdunin 13x3A OPLS4
1095- lugR_4w97based_r-ludgdunin 13x3A OPLS4
1097- LugL_4G6Qbased - r-ludgdunin 13x3A OPLS4
1098- LugL_4G6Qbased - s-ludgdunin 13x3A OPLS4
1114- LugR_based 5GPC with dsDNA, 13A3, TIP3, OPLS4, Maestro 2022.4
1115- LugL_4G6Qbased Thr40Ala apostructure
1116- LugR_based 5GPC with dsDNA (frame 250 from 1114) with r-ludgdunin pose 1, 13A3, TIP3, OPLS4, Maestro 2022.4
1117- LugR_based 5GPC with dsDNA (frame 250 from 1114) with r-ludgdunin pose 2, 13A3, TIP3, OPLS4, Maestro 2022.4
1118- LugR_based 5GPC with dsDNA (frame 250 from 1114) with s-ludgdunin pose 1, 13A3, TIP3, OPLS4, Maestro 2022.4
1119- LugR_based 5GPC with dsDNA (frame 250 from 1114) with s-ludgdunin pose 2, 13A3, TIP3, OPLS4, Maestro 2022.4
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