Fig. 4: Molecular dynamics (MD) simulations of retinal- or decanoate-bound, and ligand-free proteoopsin (PO). | Nature Communications

Fig. 4: Molecular dynamics (MD) simulations of retinal- or decanoate-bound, and ligand-free proteoopsin (PO).

From: Structural insights into the mechanism and dynamics of proteorhodopsin biogenesis and retinal scavenging

Fig. 4: Molecular dynamics (MD) simulations of retinal- or decanoate-bound, and ligand-free proteoopsin (PO).The alternative text for this image may have been generated using AI.

Shared eigenspace defined by principal component (PC) analysis on aggregated MD simulations starting from lipid-embedded structures of PO (orange cross) or green-light absorbing proteorhodopsin (PDB ID: 7B03; green cross) bound to all-trans retinal by Schiff base (A), bound non-covalently to decanoate (B) or without ligand (apo; C). The conformational densities are represented by hexagons, with a higher colour intensity reflecting a larger number of states in each bin. Marginal distributions for each PC are displayed on the respective axes. Top view of PO structure (seen from extracellular side) with eigenvectors corresponding to PC1 (D) and PC2 (E) observed during the simulations represented as green arrows. The model is coloured to reflect the magnitude of the displacement, from small (white) to larger movement (red). Transmembrane α-helices are labelled (A–G) and loops were omitted for clarity. F Distribution of observed distances between residues L136 and P202 during the simulations to assess opening of the binding pocket. The same colours are used in (A–C) and (F) to represent the simulations of retinal-bound (red), decanoate-bound (orange) and ligand-free PO (apo; grey).

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