Fig. 6: Molecular dynamics analyses of C4S dp8 binding to Lcl-CTD. | Nature Communications

Fig. 6: Molecular dynamics analyses of C4S dp8 binding to Lcl-CTD.

From: The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans

Fig. 6: Molecular dynamics analyses of C4S dp8 binding to Lcl-CTD.

a Modified HADDOCK model (HM: C4S dp8 docked against a monomer of Lcl-CTD and reconstituted as a timer) used as a starting structure for MD simulations. Surface residues in close contact of C4S are annotated and coloured red (reduction >100% peak intensity by NMR), orange (reduction >85% peak intensity) or blue (lysine residues identified by ELISA). Chains are labelled A to C. b Spatial distribution function (sdf) of the sulfur atoms of C4S dp8 during the simulations. The purple isosurface connects the points with sdf = 20 × average value. The protein surface (initial MD structure) is represented in white with the positions of Lys369, Lys380, Lys385 and Lys391 coloured blue. c Frequency of occurrence (occupancy) of contacts between C4S dp8 and the Lcl-CTD during the simulations colour-mapped onto the protein surface (initial MD structure) from white (0–10%) to orange (40.9%). Residues with an occupancy >10% in chain A are annotated as (a) or black (identified from MD). Source data are available at https://doi.org/10.5281/zenodo.10974841.

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