Fig 5. Dynamics in the D region of fibrinogen.

(a) Visualization of the ensemble of pathways of correlated motion connecting the a- and the b-hole at the two ends of the D region. Pathways connecting all residues in the gray regions have been considered, but only the residues in the blue regions can be actually connected. Residues are colored according to the fraction of pathways they belong to, from red (100%) to green (25%). Thus, all correlated motions occurring at the two ends of the D region involve the residues colored in red. (b) Structures of the D region with the largest (orange) and smallest (green) projection along the largest PCA mode. The picture shows the cleft hosting the P1 integrin binding site (in yellow). The two projections can be associated with the open (orange) and closed (green) state of the cleft, and help elucidating how dynamics in the D region may affect binding. (c) Structures of the D region and the C-terminal segment of the coiled-coil region (residues α125–189, β155–458 and γ100–394) with the largest and smallest projection along the second largest PCA mode. The picture shows how the opening of the b-hole, indicated by the arrow, is coordinated to the shift of the coiled-coil region away from the βC domain.