Molecular Docking of Eco-MscL with DHS

Molecular docking was conducted as previous [22 (link)] using a representative structure of a 150-nanosecond molecular dynamics trajectory of Eco-MscL with a DHS molecule within the gated pore, described previously [20 (link)]. The binding pocket was identified by the SiteID module of the Sybyl-X2.11 software package [60 ]. Then flexible-ligand docking was performed for K05 with the Glide module of the Schrodinger software package following the standard procedure [61 ]. The top docking poses were manually examined and we found that the Top 2 docking poses are very similar and other docking poses have much worse docking scores (S2A Fig). Therefore, only the best docking pose was selected for further study.

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Wray R., Wang J., Iscla I, & Blount P. (2020). Novel MscL agonists that allow multiple antibiotics cytoplasmic access activate the channel through a common binding site. PLoS ONE, 15(1), e0228153.

Publication 2020

Glide module

Ligand Molecular structure

Corresponding Organization : University of Pittsburgh

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Variable analysis

independent variables

Molecular docking was conducted using a representative structure of a 150-nanosecond molecular dynamics trajectory of Eco-MscL with a DHS molecule within the gated pore
Flexible-ligand docking was performed for K05 with the Glide module of the Schrodinger software package

dependent variables

Binding pocket was identified by the SiteID module of the Sybyl-X2.11 software package
Top docking poses were manually examined

control variables

Molecular docking was conducted as previous [22 (link)]
Docking was performed following the standard procedure [61 (no link found)]

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