Structural Basis of Interfacial Flexibility in Fibrin Oligomers

Abstract

SUMMARY Fibrin is a filamentous network made in blood to stem bleeding; it forms when fibrinogen is converted into fibrin monomers that self-associate into oligomers and then to polymers. To gather structural insights into fibrin formation and properties, we combined high-resolution atomic force microscopy of fibrin(ogen) oligomers and molecular modeling of crystal structures of fibrin(ogen) and its fragments. We provided a structural basis for the intermolecular flexibility of single-stranded fibrin(ogen) oligomers and identified a hinge region at the D:D inter-monomer junction. Following computational reconstruction of the missing portions, we recreated the full-atomic structure of double-stranded fibrin oligomers that was validated by quantitative comparison with the experimental images. We characterized previously unknown intermolecular binding contacts at the D:D and D:E:D interfaces, which drive oligomerization and reinforce the intra- and inter-strand connections in fibrin besides the known knob-hole bonds. The atomic models provide valuable insights into the submolecular mechanisms of fibrin polymerization.

Recombinant fibrinogen reveals the differential roles of α‐ and γ‐chain cross‐linking and molecular heterogeneity in fibrin clot strain‐stiffening

“…Here we report l p = 75 nm, which is smaller than l p values predicted by modeling protofibrils as homogeneous elastic rods . However, recent atomistic molecular dynamics simulations point to the existence of hinge points within fibrinogen coiled‐coil regions and in the D : D interface between fibrin monomers within single‐stranded oligomers that may make protofibrils more flexible than anticipated.…”

Fibrin Formation, Structure and Properties

“…Moreover, a much larger piece of fibrin molecule from the central part (bearing knobs ‘A’) interacted with fibrinogen (bearing holes ‘a’) with even higher affinity ( K d = 5.8 ± 1.1 μM; Geer et al 2007), suggesting that the ‘A-a’ interactions are not limited to the Gly-Pro-Arg motif. There must be additional interface beyond the ‘A-a’ bonds that has substantially higher binding strength, which has been confirmed using structural modeling (Kononova et al 2013; Zhmurov et al 2016). …”

“…The hot spots of holes ‘a’ directly involved in the binding of the GPRP peptide were identified as residues γTrp315-Trp330, γTrp335-Asn365, and γPhe295-Thr305. However, using molecular dynamics simulations, it has been shown that during fibrin oligomerization the D:E interface includes binding sites beyond the ‘A-a’ knob-hole associations, confirming the existence of intermolecular binding sites ‘A’ and ‘a’ that are not limited to knobs ‘A’ and holes ‘a’ (Zhmurov et al 2016). Nevertheless, release of FpA and formation of knobs ‘A’ are necessary and sufficient to induce fibrin polymerization, resulting in formation of the so-called desA-fibrin.…”

Molecular packing structure of fibrin fibers resolved by X-ray scattering and molecular modeling

“…The flexible Cterminal portions of the Aα chains known as the αC regions form compact αC-domains that are tethered to the molecule by flexible αC-connectors 62 . Fibrin oligomers were reconstructed in silico using CHARMM 63 , complete with A:a and B:a knob-hole bonds, γ-γ covalent crosslinking, and αC chains, as described elsewhere 25 . One of the general features to note is that in all structural models, the two strands inside the protofibril are twisted around one another, forming a superhelical structure.…”

“…The structure of the monomers has been elucidated by X-ray crystallography 13 , electron microscopy 14 and atomic force microscopy [15][16] and has been modeled by full-atom molecular dynamics (MD) simulations [17][18][19][20][21] . The structure and assembly mechanism of fibrin protofibrils has likewise been studied by electron microscopy and atomic force microscopy [22][23][24] and through full-atom MD simulations 22,25 . The structure at the network level has been characterized mostly by light scattering 23,[26][27][28] , confocal light microscopy [29][30] , and scanning electron microscopy 31 .…”