Figure 5
All-atoms partial heterotetrameric FXIIIIA2B (S1–S4 S8–S10)2 model.
(Panel A) Heterotetrameric FXIIIIA2B (S1–S4 antiparallel S8–S10)2 model. FXIIIA subunit shown as molecular surface rendering (grey); Sushi domains from apposed FXIIIB monomers shown in alpha-carbon trace (ribbons) format. (colored according to secondary structure: beta-strand (red), extended loop (cyan), random coil (green), alpha-helix (blue); dashed arrow marks the mirror symmetry of both FXIIIA (grey) and FXIIIB (cyan) subunits. (Panel B) Schematic diagram of putative interface residues forming physical contacts between the FXIIIA and FXIIIB subunits of the heterotetrameric FXIIIIA2B (S1–S4 antiparallel S8–S10)2 model. The dashed lines represent inter-residue contacts while the multiple colored oval structures represent the participating residues. (Panel C) FXIIIB S1 Sushi domain interaction with the FXIII-AP N-terminal region. Backbone alpha-carbon trace (left panel, ribbons: S1 domain, blue; FXIII-AP, grey). Middle panel shows electrostatic potential (negative, red; positive, blue) superimposed on molecular surface view for same domains depicted in left panel. The electrostatic surface potential was calculated and graphically depicted using Adaptive Poisson-Boltzmann Solver (integrated within YASARA). Right panel shows hydrophobicity (minimum, purple; maximum, green) for the same molecular view as in left and middle panels. (Panel D) Close up view of aligned models from simulation snapshots. Pre- (green) and post-SMD (red) alpha-carbon backbone traces (ribbons) from 80 ns simulation of FXIIIB dissociation from FXIIIA in the vicinity of FXIII-AP.
