Schematic representation of fibrin(ogen) molecules and their fragments used in this study as sources of knobs and holes. The drawing is based on crystallographic data and represents approximately the relative positions and dimensions of the molecular parts. A- and B-knobs are highly flexible and, hence, have not been visualized in the crystal structure to date. Gray and black circles represent fibrinopeptides A (FpA) and B (FpB), respectively. (A) Fibrinogen is 45 nm long and consists of 3 parts, namely 2 D regions and one E region. The D regions contain the distal portions of the coiled-coil and the C-terminal β- and γ-modules. The E region contains the central N-terminal part of the molecule and the proximal portions of both sets of coiled-coils. The E region has 2 pairs of binding sites, A- and B-knobs, that are masked and become exposed after cleavage of FpA and FpB. The D regions have constitutively open a- and b-holes located in the γ- and β-modules, respectively. (B) DesA-fibrin monomer with only A-knobs exposed, obtained from normal fibrinogen by selective cleavage of FpA using batroxobin. (C) DesB-fibrin monomer with only B-knobs exposed, obtained from fibrinogen variant AαR16C by selective cleavage of FpB by thrombin. (D) Fibrinogen variant γD364H with impaired nonfunctional a-holes. (E) Fragment D from normal fibrinogen has a- and b-holes. (F) Fragment D from fibrinogen γD364H with only b-holes. (G) D-dimer from fibrin representing 2 D regions of the adjacent monomer molecules covalently cross-linked through the C-termini of the γ-chains. (H) Recombinant fragment (β15-66)2 representing dimeric N-terminal portions of the β-chain bearing B-knobs.
