A fibrin knob-hole interaction is the binding of an exposed short peptide segment on one fibrin molecule to a complementary pocket on another molecule. Thrombin removes Fibrinopeptide A to expose the A knob and Fibrinopeptide B to expose the B knob. The corresponding a and b holes lie in different distal protein domains. These intermolecular contacts help assemble a fibrin network.[ref]
Polymerization of fibrin: specificity, strength, and stability of knob-hole interactions studied at the single-molecule level by Rustem I. Litvinov and others. Figure1: knob exposure and the locations of complementary holes
A decisive test uses a small competing peptide. The synthetic sequence Gly-Pro-Arg-Pro mimics the exposed A-knob end: it binds fibrinogen and its distal fragment D and inhibits fibrin polymerization. A soluble imitation can occupy a pocket without connecting two full-sized molecules, disrupting the assembly.[ref]
Synthetic peptide derivatives that bind to fibrinogen and prevent the polymerization of fibrin monomers by Andrew P. Laudano and Russell F. Doolittle. Abstract: binding to fibrinogen/fragment D, lack of binding to fragment E, and inhibition
Optical tweezers later measured individual rupture events, with forces around – under the study's conditions. Removing the required sites or adding the A-knob mimic suppressed the strong events. The assay supported specific A:a binding; it did not detect a comparable B-mediated force contribution under those conditions.[ref]
Polymerization of fibrin: specificity, strength, and stability of knob-hole interactions studied at the single-molecule level by Rustem I. Litvinov and others. Abstract: rupture-force distributions and peptide-inhibition controls
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