Computational molecular modeling. (A) Complete atomic structure of the A:a knob-hole complex (in ribbon representation), extracted from the structures of fibrin oligomers^6,36  at pH 7.0 and 25°C, showing hole a with the following binding determinants: the interior region (residues γTrp335-Asn365; shown in green), loop I (γTrp315-Trp330; in blue), and movable flap (γPhe295-Thr305; in red) in the γ-nodule, and knob A (residues αGly17-Cys36; shown in orange). Also shown are the setup for the dynamic force experiments in silico, for example, the constrained residue γLys159 in the γ-nodule in hole a and tagged residue αCys36 in knob A, and the direction of pulling force (indicated by the arrow), and single-point mutations corresponding to variants γD297N, γE323Q, and γK356Q (small arrows). (B) The average bond-rupture forces and SDs (mean ± SD, N = 5 simulation runs) for WT and variants γD297N. γE323Q, γK356Q, and γDEK extracted from the simulations. (C-D) The side view (C) and top view (D) of a structural fragment of 2-stranded fibrin oligomer inside its hydrodynamic volume, displaying the α chain (in red color), β chain (in blue), and γ chain (in green). Also shown are the D:D self-association interface, the D:E:D complex with the A:a and B:b knob-hole bonds, the coiled coils, and carbohydrate moieties. These structures reveal the positions of mutated residues relative to the body of fibrin oligomer, which can be correlated with their propensities to form the intra-protofibril vs inter-protofibril contacts. (E) The same structure as in panel D but with another protofibril added to the picture to help visualize the lateral packing with the inter-protofibril contacts corresponding to the crystal contacts in structure 1FZC¹⁹  from the protein data bank.