Schematic representation of a short oligomer formed by 3 fibrin monomers based on the x-ray crystallographic structure of fibrinogen (Protein Data Bank entry: 3GHG). Shown for each monomer are the central nodule (blue), coiled-coil connectors (red), the γ- and β-nodules (green), which make up the main part of the lateral D region, and the αC regions (orange). The molecules are shown with the addition of the missing parts of the crystal structure reconstructed from molecular dynamics simulations, namely the amino terminal ends of the α-chains in the central nodule and the αC regions. A:a knob-hole bonds that are the major basis of fibrin polymerization maintain the third (lower) monomer in a half-staggered arrangement. The intermolecular noncovalent coupling and the covalent cross-linking at the D-D interface hold the two (upper) monomers in a linear arrangement. Created by and published with permission from A. Zhmurov, O. Kononova, and V. Barsegov, University of Massachusetts–Lowell.