Abstract
Oxidation of key methionine residues on fibrin leads to altered fibrin polymerization producing severely altered fibrin gel structure and function. This is important because fibrinogen and its modification by oxidative stress have been implicated as key contributors to both pathological thrombotic and hemorrhagic diseases ranging from cardiovascular thrombosis to the acute coagulopathy of trauma. However, how oxidation leads to altered fibrin polymerization remains poorly understood at the molecular level. We have applied a powerful and novel well-tempered ensemble parallel tempering (PT-WTE) technique along with conventional molecular dynamics (MD) simulation to investigate the molecular-level consequences of selective methionine oxidation of fibrinogen. We offer new insights into molecular mechanisms of oxidation-induced changes in fibrin polymerization, while focusing on the D region knob ‘B’ and hole ‘b’ interaction and αC-domain interactions, both of which are hypothesized to contribute to the lateral aggregation mechanism of fibrin fibrils. Methionine oxidation did not alter the native state or the stability of a bound knob ‘B’ surrogate when interacting with hole ‘b’ in the D region. However, applying PT-WTE simulation to a human homology model of the bovine N-terminal subdomain fragment from the αC-domain revealed that methionine oxidation altered the conformation of the hairpin-linking region to favor open rather than closed hairpin structures. We attribute this alteration to the disruption of the hairpin-linking region's conformation, with oxidation increasing the radius of gyration for this segment. This result is in agreement with experimental data demonstrating decreased fibrin protofibril lateral aggregation when methionine oxidation is present in the same αC-domain fragment. Therefore, single methionine oxidation within the αC-domain is a likely molecular mechanism.
Highlights
During blood clot formation, the plasma protein fibrinogen is normally converted by thrombin to fibrin monomers that selfpolymerize both linearly – forming long fibrils – and laterally, increasing fibrin fiber diameter and forming networks of fibers
Another recent study by Sutto and Gervasio applied this method to explore the conformational free-energy surface of a receptor tyrosine kinase enzyme and examined the effects of single and double mutations [41]. In contrast to these other studies, here we present the first use of PTWTE in an all-atom system without additional metadynamics bias on collective variables (CVs) related to our system configuration or modes of motion
We have hypothesized multiple mechanisms by which methionine oxidized to methionine sulfoxide may interrupt the proposed mechanism that are amenable to investigation by molecular dynamics (MD) simulation: methionine oxidation disrupts the conformation of the globular portion of the D region, disrupts the conformation of hole ‘b’, and/or creates an unfavorable interaction with knob ‘B’ and destabilizes its bound state
Summary
During blood clot formation, the plasma protein fibrinogen is normally converted by thrombin to fibrin monomers that selfpolymerize both linearly – forming long fibrils – and laterally, increasing fibrin fiber diameter and forming networks of fibers. Fibrinogen oxidation has been associated with increased cardiovascular events in chronic kidney disease patients [10,11] and fibrinogen nitration has been associated with myocardial infarction, possibly due to its induction of a prothrombotic fibrin clot phenotype [12]. This evidence highlights the potential for oxidative modification of fibrinogen to contribute to the mechanism of thrombotic cardiovascular diseases. Little is known of how the molecular events associated with oxidation can alter fibrin polymerization
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
