FIGURE 5.

Computational reconstruction of the non-covalent coupling of the central nodule (bearing sites ‘A’) and the γ-nodules (bearing sites ‘a’). A, ribbon representation of the initial structure (before equilibration) of the double-D fragment of abutted fibrin molecules containing two γ- and two β-nodules. The residues in site ‘a’ form binding contacts with the residues of site ‘A’ emanating from the central nodule of the third fibrin monomer between the coiled coil connectors. B shows the translocation of the central nodule following formation of the A:a knob-hole bonds observed at the end of the simulation run. Also shown is the magnified view of electrostatic contacts between residues γGlu³²³ in loop I, γLys³⁵⁶ in the interior region, and γAsp²⁹⁷ in the moveable flap (all residues belong to site ‘a’ in the γ-nodule) and residues βLys⁵⁸, βAsp⁶¹, and βHis⁶⁷ in the N-terminal portion of the β chain in the central nodule (the GPR motif has been suppressed for clarity). In the central nodule, the residues colored in red represent negatively charged amino acids, whereas the residues colored in blue represent positively charged amino acids.