Missing regions within the molecular architecture of human fibrin clots structurally resolved by XL-MS and integrative structural modeling

Proc Natl Acad Sci U S A. 2020 Jan 28;117(4):1976-1987. doi: 10.1073/pnas.1911785117. Epub 2020 Jan 10.


Upon activation, fibrinogen forms large fibrin biopolymers that coalesce into clots which assist in wound healing. Limited insights into their molecular architecture, due to the sheer size and the insoluble character of fibrin clots, have restricted our ability to develop novel treatments for clotting diseases. The, so far resolved, disparate structural details have provided insights into linear elongation; however, molecular details like the C-terminal domain of the α-chain, the heparin-binding domain on the β-chain, and other functional domains remain elusive. To illuminate these dark areas, we applied cross-linking mass spectrometry (XL-MS) to obtain biochemical evidence in the form of over 300 distance constraints and combined this with structural modeling. These restraints additionally define the interaction network of the clots and provide molecular details for the interaction with human serum albumin (HSA). We were able to construct the structural models of the fibrinogen α-chain (excluding two highly flexible regions) and the N termini of the β-chain, confirm these models with known structural arrangements, and map how the structure laterally aggregates to form intricate lattices together with the γ-chain. We validate the final model by mapping mutations leading to impaired clot formation. From a list of 22 mutations, we uncovered structural features for all, including a crucial role for βArg'169 (UniProt: 196) in lateral aggregation. The resulting model can potentially serve for research on dysfibrinogenemia and amyloidosis as it provides insights into the molecular mechanisms of thrombosis and bleeding disorders related to fibrinogen variants. The structure is provided in the PDB-DEV repository (PDBDEV_00000030).

Keywords: DSSO; XlinkX; cross-linking mass spectrometry; fibrin clot; fibrinogen.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Albumins / chemistry
  • Albumins / metabolism*
  • Cross-Linking Reagents / metabolism*
  • Fibrin / chemistry*
  • Fibrin / genetics
  • Fibrin / metabolism*
  • Humans
  • Mass Spectrometry / methods*
  • Models, Structural*
  • Mutation
  • Protein Conformation
  • Thrombosis / physiopathology*


  • Albumins
  • Cross-Linking Reagents
  • Fibrin