Oxidation-induced destabilization of the fibrinogenαC-domain dimer investigated by molecular dynamics simulations

Abstract

Pederson et al., Oxidation of fibrinogen αC domain 2 Abstract Upon activation, fibrinogen is converted to insoluble fibrin, which assembles into long strings called protofibrils. These aggregate laterally to form a fibrin matrix that stabilizes a blood clot. Lateral aggregation of protofibrils is mediated by the αC domain, a partially structured fragment located in a disordered region of fibrinogen. Polymerization of αC domains links multiple fibrin molecules with each other enabling the formation of thick fibrin fibers and a fibrin matrix that is stable but can also be digested by enzymes. However, oxidizing agents produced during the inflammatory response have been shown to cause thinner fibrin fibers resulting in denser clots, which are harder to proteolyze and pose the risk of deep vein thrombosis and lung embolism. It has been postulated that oxidation of Met 476 located within the αC domain hinders its ability to polymerize disrupting the lateral aggregation of protofibrils and leading to the observed thinner fibers. How αC domains assemble into polymers is still unclear and yet this knowledge would shed light on the mechanism through which oxidation weakens the lateral aggregation of protofibrils.This study used temperature replica exchange molecular dynamics simulations to investigate the αC-domain dimer and how this is affected by oxidation of Met 476 . The results suggest that multiple binding modes between two alphaC domains can occur and that oxidation decreases the likelihood of dimer formation. Furthermore, the side chain of Met 476 acts as a docking spot between αC domains and this function is abrogated by its conversion to methionine sulfoxide.

Tracking oxidation-induced alterations in fibrin clot formation by NMR-based methods

“…Our results showed that the effect on clot turbidity was nearly identical to that seen with oxidation. This observation supports MD simulations pointing towards a potential mechanism by which oxidation of the AαC domain inhibits lateral proto bril aggregation due to partial burying of local polymerization binding sites 26 making lateral aggregation of brin monomers energetically unfavorable 33,34 .…”

“…For instance, an increase of T 2 was detected in articular cartilage degraded by collagen and loss of proteoglycan, resulting in an abnormal structural collage network 38 . Applying this approach to study brin clot structure after oxidation, we found that HOCl oxidation made brinogen less accessible to water molecules and prevented water-protein interactions, which may have direct effects of burying the active binding sites in the alpha C domains and inhibiting dimerization between brinogen molecules 33,34 . The total T 1 /T 2 ratio of water protons was increased upon conversion of brinogen solution to plasma brin gel (refer to Fig.…”

Fibrinogen αC‐regions are not directly involved in fibrin polymerization as evidenced by a “Double‐Detroit” recombinant fibrinogen mutant and knobs‐mimic peptides

“…The consensus picture was that the αC‐regions following FpB cleavage extend further and help the lateral aggregation of fibrils by binding to each other. Furthermore, a very recent molecular dynamics simulation investigated the role of a particular residue, AαM476, located in the β‐hairpin present within the only (partially) structured domain so far identified in the αC‐region.…”

Re-mining serum proteomics data reveals extensive post-translational modifications upon Zika and dengue infection

“…Further, six methionine oxidized fibrinogen peptides were more abundant in ZIKV patients. Methionine oxidation in fibrinogen can change protein structure and impair aggregation and coagulation (Weigandt et al 2012; White et al 2016; Pederson and Interlandi 2019). The known modification sites were consistent with one of the modifications we identified in Fibrinogen A (residue 495) which was significantly less abundant in ZIKV patients.…”