Conformational Flexibility and Self-Association of Fibrinogen in Concentrated Solutions

Pathogenic Mechanisms in Congenital Afibrinogenemia: A Systematic Review of Genetic Variants

INTRODUCTION

Congenital afibrinogenemia is a rare bleeding disorder characterized by the complete absence of plasma fibrinogen, primarily caused by homozygous or compound heterozygous mutations in the FGA, FGB and FGG genes.

AIM

To deepen our understanding of the pathogenic mechanisms of afibrinogenemia through the study of natural variants.

METHODS

We conducted a literature review of all publications up to 2024 that report cases of afibrinogenemia with confirmed genetic diagnoses, focusing on the impact of mutations on fibrinogen synthesis, assembly and secretion.

RESULTS

We classified the pathogenic mechanisms of afibrinogenemia into the following seven categories: (1) Chromosomal structural variations, such as large deletions, disrupt the integrity of the fibrinogen gene cluster. (2) Splice site mutations interfere with the proper splicing of precursor mRNA, resulting in abnormal transcripts that cannot encode functional fibrinogen chains. (3) Start codon mutations prevent the initiation of translation, halting the synthesis of fibrinogen polypeptides. (4) Nonsense and frameshift mutations introduce termination codons, resulting in truncated fibrinogen chains. (5) Signal peptide mutations disrupt the targeting of polypeptides to the endoplasmic reticulum, preventing further post-translational modifications. (6) Mutations affecting disulphide bonds in the coiled-coil region hinder the assembly of fibrinogen chains, preventing the formation of complete hexamers. (7) Mutations affecting the correct conformation of β and γ nodules cause intra-cellular retention of fibrinogen and prevent its secretion.

CONCLUSIONS

This review provides a comprehensive summary of mutations associated with afibrinogenemia, offering insights that contribute to the phenotypic prediction of novel mutations and providing a framework for understanding the molecular mechanisms of afibrinogenemia.

Impact of Temperature on the Self-Assembly of Fibrinogen in Thrombin-Free Solutions

Self-assembly of thrombin-free solutions of fibrinogen can be triggered not only by a drop in the ionic strength but also by an appropriate decrease in temperature. Accordingly, an in situ study of self-assembly of fibrinogen in saline buffered solution is carried out by means of time-resolved light scattering providing the molar mass, geometric size, and hydrodynamic radius of the growing intermediates. The resulting data provide access to the morphology of the intermediates and to the mechanism in which these intermediates grow during the early stages of self-assembly. Modeling the results of concentration dependent experiments based on temperature gradients in terms of a chain growth mechanism leads to the corresponding molar standard enthalpy and entropy of aggregation.

Protein translational diffusion as a way to detect intermolecular interactions

In this work, we analyze the information on the protein intermolecular interactions obtained from macromolecular diffusion. We have shown that the most hopeful results are given by our approach based on analysis of protein translational self-diffusion and collective diffusion obtained by dynamic light scattering and pulsed-field gradient NMR (PFG NMR) spectroscopy with the help of Vink's approach to analyze diffusion motion of particles by frictional formalism of non-equilibrium thermodynamics and the usage of the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of colloid particles interactions in electrolyte solutions. Early we have shown that integration of Vink's theory with DLVO provides a reliable basis for uniform interpreting of PFG NMR and DLS experiments on concentration dependence of diffusion coefficients. Basic details of theoretical and mathematical procedures and a broad analysis of experimental attestation of proposed conception on proteins of various structural form, size, and shape are presented. In the present review, the main capabilities of our approach obtain the details of intermolecular interactions of proteins with different shapes, internal structures, and mass. The universality of Vink's approach is experimentally shown, which gives the appropriate description of experimental results for proteins of complicated structure and shape.

Systematic mapping of the conformational landscape and dynamism of soluble fibrinogen

BACKGROUND

Fibrinogen is a soluble, multisubunit, and multidomain dimeric protein, which, upon its proteolytic cleavage by thrombin, is converted to insoluble fibrin, initiating polymerization that substantially contributes to clot growth. Fibrinogen contains numerous, transiently accessible "cryptic" epitopes for hemostatic and immunologic proteins, suggesting that fibrinogen exhibits conformational flexibility, which may play functional roles in its temporal and spatial interactions. Hitherto, there have been limited integrative approaches characterizing the solution structure and internal flexibility of fibrinogen.

METHODS

Here, utilizing a multipronged, biophysical approach involving 2 solution-based techniques, temperature-dependent hydrogen-deuterium exchange mass spectrometry and small angle X-ray scattering, corroborated by negative stain electron microscopy, we present a holistic, conformationally dynamic model of human fibrinogen in solution.

RESULTS

Our data reveal 4 major and distinct conformations of fibrinogen accommodated by a high degree of internal protein flexibility along its central scaffold. We propose that the fibrinogen structure in the solution consists of a complex, conformational landscape with multiple local minima. This is further supported by the location of numerous point mutations that are linked to dysfibrinogenemia and posttranslational modifications, residing near the identified fibrinogen flexions.

CONCLUSION

This work provides a molecular basis for the structural "dynamism" of fibrinogen that is expected to influence the broad swath of its functionally diverse macromolecular interactions and fine-tune the structural and mechanical properties of blood clots.

Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics

Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of information about their structures. While PMOs have been approved by the US Food and Drug Administration for treatment of Duchenne muscular dystrophy, no structural information on these unique, charge-neutral, and stable molecules is available. We performed circular dichroism and solution viscosity measurements combined with molecular dynamics simulations and machine learning to resolve solution structures of 22-mer, 25-mer, and 30-mer length PMOs. The PMO conformational dynamics are defined by the competition between non-polar nucleobases and uncharged phosphorodiamidate groups for shielding from solvent exposure. PMO molecules form non-canonical, partially helical, stable folded structures with a small 1.4- to 1.7-nm radius of gyration, low count of three to six base pairs and six to nine base stacks, characterized by -34 to -51 kcal/mol free energy, -57 to -103 kcal/mol enthalpy, and -23 to -53 kcal/mol entropy for folding. The 4.5- to 6.2-cm³/g intrinsic viscosity and Huggins constant of 4.5-9.9 are indicative of extended and aggregating systems. The results obtained highlight the importance of the conformational ensemble view of PMO solution structures, thermodynamic stability of their non-canonical structures, and concentration-dependent viscosity properties. These principles form a paradigm to understand the structure-properties-function relationship for therapeutic PMOs to advance the design of new RNA-mimic-based drugs.

Fibrin-Rhamnogalacturonan I Composite Gel for Therapeutic Enzyme Delivery to Intestinal Tumors

Therapy of colorectal cancer with protein drugs, including targeted therapy using monoclonal antibodies, requires the preservation of the drug's structure and activity in the gastrointestinal tract or bloodstream. Here, we confirmed experimentally the fundamental possibility of creating composite protein-polysaccharide hydrogels based on non-degrading rhamnogalacturonan I (RG) and fibrin as a delivery vehicle for antitumor RNase binase. The method is based on enzymatic polymerization of fibrin in the presence of RG with the inclusion of liposomes, containing an encapsulated enzyme drug, into the gel network. The proposed method for fabricating a gel matrix does not require the use of cytotoxic chemical cross-linking agents and divalent cations, and contains completely biocompatible and biodegradable components. The process proceeds under physiological conditions, excluding the effect of high temperatures, organic solvents and ultrasound on protein components. Immobilization of therapeutic enzyme binase in the carrier matrix by encapsulating it in liposomes made from uncharged lipid made it possible to achieve its prolonged release with preservation of activity for a long time. The release time of binase from the composite carrier can be regulated by variation of the fibrin and RG concentration.

A mechanistic model of cross-bridge migration in RBC aggregation and disaggregation

Red blood cells (RBCs) clump together under low flow conditions in a process called RBC aggregation, which can alter RBC perfusion in a microvascular network. As elevated RBC aggregation is commonly associated with cardiovascular and inflammatory diseases, a better understanding of aggregation is essential. Unlike RBC aggregation in polymer solutions which can be well explained by polymer depletion theory, plasma-mediated RBC aggregation has features that best match explanations with cross-bridging mechanisms. Previous studies have demonstrated the dominant role of fibrinogen (Fg) in promoting aggregate formation and recent cell-force spectroscopy (CFS) experiments on interacting RBC doublets in plasma have reported an inverse relationship between disaggregation force and the adhesive contact area between RBCs. This has led investigators to revisit the hypothesis of inter-RBC cross-bridging which involves cross-bridge migration under interfacial tension during the forced disaggregation of RBC aggregates. In this study, we developed the cross-bridge migration model (CBMM) in plasma that mechanistically represents the migrating cross-bridge hypothesis. Transport of mobile Fg cross-bridges (mFg) was calculated using a convection-diffusion transport equation with our novel introduction of convective cross-bridge drift that arises due to intercellular friction. By parametrically transforming the diffusivity of mFg in the CBMM, we were able to match experimental observations of both RBC doublet formation kinematics and RBC doublet disaggregation forces under optical tweezers tension. We found that non-specific cross-bridging promotes spontaneous growth of adhesion area between RBC doublets whereas specific cross-bridging tends to prevent adhesion area growth. Our CBMM was also able to correlate Fg concentration shifts from healthy population blood plasma to SLE (lupus) condition blood plasma with the observed increase in doublet disaggregation forces for the RBC doublets in SLE plasma.

Effect of Protein–Protein Interactions on Translational Diffusion of Spheroidal Proteins

One of the commonly accepted approaches to estimate protein–protein interactions (PPI) in aqueous solutions is the analysis of their translational diffusion. The present review article observes a phenomenological approach to analyze PPI effects via concentration dependencies of self- and collective translational diffusion coefficient for several spheroidal proteins derived from the pulsed field gradient NMR (PFG NMR) and dynamic light scattering (DLS), respectively. These proteins are rigid globular α-chymotrypsin (ChTr) and human serum albumin (HSA), and partly disordered α-casein (α-CN) and β-lactoglobulin (β-Lg). The PPI analysis enabled us to reveal the dominance of intermolecular repulsion at low ionic strength of solution (0.003–0.01 M) for all studied proteins. The increase in the ionic strength to 0.1–1.0 M leads to the screening of protein charges, resulting in the decrease of the protein electrostatic potential. The increase of the van der Waals potential for ChTr and α-CN characterizes their propensity towards unstable weak attractive interactions. The decrease of van der Waals interactions for β-Lg is probably associated with the formation of stable oligomers by this protein. The PPI, estimated with the help of interaction potential and idealized spherical molecular geometry, are in good agreement with experimental data.

Myeloperoxidase-induced fibrinogen unfolding and clotting

Due to its unique properties and high biomedical relevance fibrinogen is a promising protein for the development of various matrixes and scaffolds for biotechnological applications. Fibrinogen molecules may form extensive clots either upon specific cleavage by thrombin or in thrombin-free environment, for example, in the presence of different salts. Here, we report the novel type of non-conventional fibrinogen clot formation, which is mediated by myeloperoxidase and takes place even at low fibrinogen concentrations (<0.1 mg/ml). We have revealed fibrillar nature of myeloperoxidase-mediated fibrinogen clots, which differ morphologically from fibrin clots. We have shown that fibrinogen clotting is mediated by direct interaction of myeloperoxidase molecules with the outer globular regions of fibrinogen molecules followed by fibrinogen unfolding from its natural trinodular to a fibrillar structure. We have demonstrated a major role of the Debye screening effect in regulating of myeloperoxidase-induced fibrinogen clotting, which is facilitated by small ionic strength. While fibrinogen in an aqueous solution with myeloperoxidase undergoes changes, the enzymatic activity of myeloperoxidase is not inhibited in excess of fibrinogen. The obtained results open new insights into fibrinogen clotting, give new possibilities for the development of fibrinogen-based functional biomaterials, and provide the novel concepts of protein unfolding.

Strength, deformability and toughness of uncrosslinked fibrin fibers from theoretical reconstruction of stress-strain curves

Structural mechanisms underlying the mechanical properties of fibrin fibers are elusive. We combined tensile testing of uncrosslinked fibrin polymers in vitro and in silico to explore their material properties. The experimental stress (σ) - strain (ε) curves for fibrin fibers are characterized by elastic deformations with a weaker elastic response for ε<160% due to unraveling of αC tethers and straightening of fibrin protofibrils, and a stronger response for ε>160% owing to unfolding of the coiled coils and γ nodules in fibrin monomers. Fiber rupture for strains ε>212% is due to dissociation of the knob-hole bonds and rupture of D:D interfaces. We developed the Fluctuating Bilinear Spring model to interpret the σ-ε profiles in terms of the free energy for protofibril alignment ΔG0 = 10.1-11.5 kBT, Young's moduli for protofibril alignment Yu = 1.9-3.2 MPa and stretching Ya = 5.7-9.7 MPa, strain scale ε˜≈ 12-40% for fiber rupture, and protofibril cooperativity m= 3.6-8. We applied the model to characterize the fiber strength σcr≈ 12-13 MPa, deformability εcr≈ 222%, and rupture toughness U≈ 9 MJ/m3, and to resolve thermodynamic state functions, 96.9 GJ/mol entropy change for protofibril alignment (at room temperature) and 113.6 GJ/mol enthalpy change for protofibril stretching, which add up to 210.5 GJ/mol free-energy change. Fiber elongation is associated with protofibril dehydration and sliding mechanism to create an ordered protofibril array. Fibrin fibers behave like a hydrogel; protofibril dehydration and water expulsion account for ∼94-98% of the total free-energy changes for fiber elongation and rupture. STATEMENT OF SIGNIFICANCE: Structural mechanisms underlying the mechanical properties of fibrin fibers, major components of blood clots and obstructive thrombi, are elusive. We performed tensile testing of uncrosslinked fibrin polymers in vitro and in silico to explore their material properties. Fluctuating Bilinear Spring theory was developed to interpret the stress-strain profiles in terms of the energy for protofibril alignment, elastic moduli for protofibril alignment and stretching, and strain scale for fiber rupture, and to probe the limits of fiber strength, extensibility and toughness. Fibrin fibers behave like a hydrogel. Fiber elongation is defined by the protofibril dehydration and sliding. Structural rearrangements in water matrix control fiber elasticity. These results contribute to fundamental understanding of blood clot breakage that underlies thrombotic embolization.

Influence of Divalent Metal Ions on the Precipitation of the Plasma Protein Fibrinogen

Fibrinogen nanofibers are very attractive biomaterials to mimic the native blood clot architecture. Previously, we reported the self-assembly of fibrinogen nanofibers in the presence of monovalent salts and have now studied how divalent salts influence fibrinogen precipitation. Although the secondary fibrinogen structure was significantly altered with divalent metal ions, morphological analysis revealed exclusively smooth fibrinogen precipitates. In situ monitoring of the surface roughness facilitated predicting the tendency of various salts to form fibrinogen fibers or smooth films. Analysis of the chemical composition revealed that divalent salts were removed from smooth fibrinogen films upon rinsing while monovalent Na⁺ species were still present in fibrinogen fibers. Therefore, we assume that the decisive factor controlling the morphology of fibrinogen precipitates is direct ion-protein contact, which requires disruption of the ion-surrounding hydration shells. We conclude that in fibrinogen aggregates, this mechanism is effective only for monovalent ions, whereas divalent ions are limited to indirect fibrinogen adsorption.

The Role of pH and Ionic Strength in the Attraction-Repulsion Balance of Fibrinogen Interactions

Fibrinogen (Fg) self-assembly is sensitive to the physicochemical properties of an environment like pH and ionic strength. These parameters tune the direction and strength of noncovalent physical driving forces determining protein intermolecular interactions. The attraction-repulsion balance in intermolecular interactions of the multidomain protein Fg at pH values 3.5, 7.4, and 9.5 and varying ionic strengths of the water medium has been analyzed by the complex diffusive approach, proposed by us previously. The concentration dependence of protein collective diffusion was analyzed within the phenomenological approach, based on the frictional formalism of nonequilibrium thermodynamics proposed by H. Vink. The analysis of protein diffusion data has shown the fundamental difference in the physical nature and direction of interaction forces between protein molecules at different conditions. The paired interaction potential of protein molecules was characterized in terms of second virial coefficients and Hamaker constants within the Deryaguin-Landau-Verwey-Overbeek theory and the "porous" colloid particle model. Our results indicated the maximum Hamaker constant and dominance of the van der Waals attraction between Fg molecules at pH 7.4. The increase in pH up to 9.5 results in the zero values of the second virial coefficient and Hamaker constant, corresponding to the full reciprocal compensation for electrostatic repulsion and van der Waals attraction. In the acidic medium (pH 3.5), the strong electrostatic repulsion substantially exceeds the van der Waals attraction. A high ionic strength is characterized by a significant decrease of all intermolecular interactions, which is expressed in almost zero values of virial coefficients and the Hamaker constant. Thus, it is experimentally shown that the physiological conditions of the Fg environment (pH 7.4 and slight ionic strength) provide a high probability for peak physical attraction between fibrinogen molecules, which is used in nature to facilitate blood clotting.

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

Plasma fibrinogen is an important coagulation factor and susceptible to post-translational modification by oxidants. We have reported impairment of fibrin polymerization after exposure to hypochlorous acid (HOCl) and increased methionine oxidation of fibrinogen in severely injured trauma patients. Molecular dynamics suggests that methionine oxidation poses a mechanistic link between oxidative stress and coagulation through protofibril lateral aggregation by disruption of AαC domain structures. However, experimental evidence explaining how HOCl oxidation impairs fibrinogen structure and function has not been demonstrated. We utilized polymerization studies and two dimensional-nuclear magnetic resonance spectrometry (2D-NMR) to investigate the hypothesis that HOCl oxidation alters fibrinogen conformation and T₂ relaxation time of water protons in the fibrin gels. We have demonstrated that both HOCl oxidation of purified fibrinogen and addition of HOCl-oxidized fibrinogen to plasma fibrinogen solution disrupted lateral aggregation of protofibrils similarly to competitive inhibition of fibrin polymerization using a recombinant AαC fragment (AαC 419–502). DOSY NMR measurement of fibrinogen protons demonstrated that the diffusion coefficient of fibrinogen increased by 17.4%, suggesting the oxidized fibrinogen was more compact and fast motion in the prefibrillar state. 2D-NMR analysis reflected that water protons existed as bulk water (T₂) and intermediate water (T_2i) in the control plasma fibrin. Bulk water T₂ relaxation time was increased twofold and correlated positively with the level of HOCl oxidation. However, T₂ relaxation of the oxidized plasma fibrin gels was dominated by intermediate water. Oxidation induced thinner fibers, in which less water is released into the bulk and water fraction in the hydration shell was increased. We have confirmed that T₂ relaxation is affected by the self-assembly of fibers and stiffness of the plasma fibrin gel. We propose that water protons can serve as an NMR signature to probe oxidative rearrangement of the fibrin clot.

Adsorption properties of albumin and fibrinogen on hydrophilic/hydrophobic TiO2 surfaces: A molecular dynamics study

In serval experimental researches, UV-induced hydrophilicity enabled better hemocompatibility in the TiO₂ surface, which was considered to be caused by the removal of the carboxylic acid contamination from the surface. In this paper, we altered the surface wetting property by applying the formate contamination on the rutile (110) surface, and systematically investigated the adsorption properties of albumin and fibrinogen on hydrophilic/hydrophobic TiO₂ surface. Unique contacts were found between the charged residues and the hydrophilic surface, anchoring the protein on the surface. The small size and the heart shape of albumin make it easy to cross the stable water layers near the surface. Besides, albumin has a higher proportion of charged residues, so it can form more unique contacts on the hydrophilic surface. Therefore, the albumin tends to adsorb on the hydrophilic surface. For the hydrophobic surface, the water layers near the surface are weakened, which helps the fibrinogen diffusing to the surface and adjusting its orientation. Although the hydrophobic surface cannot form the unique contacts, the larger size of fibrinogen can provide more residues to form enough ordinary contacts after adjusting, and then achieves stable adsorption. Therefore, fibrinogen tends to adsorb on the hydrophobic surface.

Principles of Fibrinogen Fiber Assembly In Vitro

Fibrinogen nanofibers hold great potential for applications in wound healing and personalized regenerative medicine due to their ability to mimic the native blood clot architecture. Although versatile strategies exist to induce fibrillogenesis of fibrinogen in vitro, little is known about the underlying mechanisms and the associated length scales. Therefore, in this manuscript the current state of research on fibrinogen fibrillogenesis in vitro is reviewed. For the first time, the manifold factors leading to the assembly of fibrinogen molecules into fibers are categorized considering three main groups: substrate interactions, denaturing and non-denaturing buffer conditions. Based on the meta-analysis in the review it is concluded that the assembly of fibrinogen is driven by several mechanisms across different length scales. In these processes, certain buffer conditions, in particular the presence of salts, play a predominant role during fibrinogen self-assembly compared to the surface chemistry of the substrate material. Yet, to tailor fibrous fibrinogen scaffolds with defined structure-function-relationships for future tissue engineering applications, it still needs to be understood which particular role each of these factors plays during fiber assembly. Therefore, the future combination of experimental and simulation studies is proposed to understand the intermolecular interactions of fibrinogen, which induce the assembly of soluble fibrinogen into solid fibers.

Fibrinogen and Fibrin

Fibrinogen is a large glycoprotein, synthesized primarily in the liver. With a normal plasma concentration of 1.5-3.5 g/L, fibrinogen is the most abundant blood coagulation factor. The final stage of blood clot formation is the conversion of soluble fibrinogen to insoluble fibrin, the polymeric scaffold for blood clots that stop bleeding (a protective reaction called hemostasis) or obstruct blood vessels (pathological thrombosis). Fibrin is a viscoelastic polymer and the structural and mechanical properties of the fibrin scaffold determine its effectiveness in hemostasis and the development and outcome of thrombotic complications. Fibrin polymerization comprises a number of consecutive reactions, each affecting the ultimate 3D porous network structure. The physical properties of fibrin clots are determined by structural features at the individual fibrin molecule, fibrin fiber, network, and whole clot levels and are among the most important functional characteristics, enabling the blood clot to withstand arterial blood flow, platelet-driven clot contraction, and other dynamic forces. This chapter describes the molecular structure of fibrinogen, the conversion of fibrinogen to fibrin, the mechanical properties of fibrin as well as its structural origins and lastly provides evidence for the role of altered fibrin clot properties in both thrombosis and bleeding.

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

Fibrin is the major extracellular component of blood clots and a proteinaceous hydrogel used as a versatile biomaterial. Fibrin forms branched networks built of laterally associated double-stranded protofibrils. This multiscale hierarchical structure is crucial for the extraordinary mechanical resilience of blood clots, yet the structural basis of clot mechanical properties remains largely unclear due, in part, to the unresolved molecular packing of fibrin fibers. Here the packing structure of fibrin fibers is quantitatively assessed by combining Small Angle X-ray Scattering (SAXS) measurements of fibrin reconstituted under a wide range of conditions with computational molecular modeling of fibrin protofibrils. The number, positions, and intensities of the Bragg peaks observed in the SAXS experiments were reproduced computationally based on the all-atom molecular structure of reconstructed fibrin protofibrils. Specifically, the model correctly predicts the intensities of the reflections of the 22.5 nm axial repeat, corresponding to the half-staggered longitudinal arrangement of fibrin molecules. In addition, the SAXS measurements showed that protofibrils within fibrin fibers have a partially ordered lateral arrangement with a characteristic transverse repeat distance of 13 nm, irrespective of the fiber thickness. These findings provide fundamental insights into the molecular structure of fibrin clots that underlies their biological and physical properties.

Impact of posttranslational modifications on atomistic structure of fibrinogen

Oxidative stress in humans is related to various pathophysiological processes, which can manifest in numerous diseases including cancer, cardiovascular diseases, and Alzheimer’s disease. On the atomistic level, oxidative stress causes posttranslational modifications, thus inducing structural and functional changes into the proteins structure. This study focuses on fibrinogen, a blood plasma protein that is frequently targeted by reagents causing posttranslational modifications in proteins. Fibrinogen was in vitro modified by three reagents, namely sodium hypochlorite, malondialdehyde, and 3-morpholinosydnonimine that mimic the oxidative stress in diseases. Newly induced posttranslational modifications were detected via mass spectrometry. Electron microscopy was used to visualize changes in the fibrin networks, which highlight the extent of disturbances in fibrinogen behavior after exposure to reagents. We used molecular dynamics simulations to observe the impact of selected posttranslational modifications on the fibrinogen structure at the atomistic level. In total, 154 posttranslational modifications were identified, 84 of them were in fibrinogen treated with hypochlorite, 51 resulted from a reaction of fibrinogen with malondialdehyde, and 19 were caused by 3-morpholinosydnonimine. Our data reveal that the stronger reagents induce more posttranslational modifications in the fibrinogen structure than the weaker ones, and they extensively alter the architecture of the fibrin network. Molecular dynamics simulations revealed that the effect of posttranslational modifications on fibrinogen secondary structure varies from negligible alternations to serious disruptions. Among the serious disruptions is the oxidation of γR375 resulting in the release of Ca²⁺ ion that is necessary for appropriate fibrin fiber formation. Folding of amino acids γE72–γN77 into a short α-helix is a result of oxidation of γP76 to glutamic acid. The study describes behaviour of fibrinogen coiled-coil connecter in the vicinity of plasmin and hementin cleavage sites.

Targeting Human Thrombus by Liposomes Modified with Anti-Fibrin Protein Binders

Development of tools for direct thrombus imaging represents a key step for diagnosis and treatment of stroke. Nanoliposomal carriers of contrast agents and thrombolytics can be functionalized to target blood thrombi by small protein binders with selectivity for fibrin domains uniquely formed on insoluble fibrin. We employed a highly complex combinatorial library derived from scaffold of 46 amino acid albumin-binding domain (ABD) of streptococcal protein G, and ribosome display, to identify variants recognizing fibrin cloth in human thrombus. We constructed a recombinant target as a stretch of three identical fibrin fragments of 16 amino acid peptide of the Bβ chain fused to TolA protein. Ribosome display selection followed by large-scale Enzyme-Linked ImmunoSorbent Assay (ELISA) screening provided four protein variants preferentially binding to insoluble form of human fibrin. The most specific binder variant D7 was further modified by C-terminal FLAG/His-Tag or double His-tag for the attachment onto the surface of nanoliposomes via metallochelating bond. D7-His-nanoliposomes were tested using in vitro flow model of coronary artery and their binding to fibrin fibers was demonstrated by confocal and electron microscopy. Thus, we present here the concept of fibrin-targeted binders as a platform for functionalization of nanoliposomes in the development of advanced imaging tools and future theranostics.

Direct interaction of fibrinogen with lipid microparticles modulates clotting kinetics and clot structure

Extensive studies revealed the role of blood lipid microparticles (liposomes, microvesicles) in activation of coagulation cascade. The direct interaction of fibrinogen/fibrin with lipid surfaces and its consequence for hemostasis received much less attention. We observed pronounced changes in both clot morphology and kinetics of fibrin clotting in the presence of artificial liposomes. The evidence was obtained that lipid microparticles per se present a diffusion barrier to the three-dimensional fibril assembling and pose spatial restrictions for fiber elongation. On the other hand, fibrinogen adsorption results in its high local concentration on liposome surface that accelerates fibrin polymerization. Adsorption induces Fg secondary structure alterations which may contribute to the abnormal clot morphology. In dependence on lipid composition and size of microparticles, the interplay of all the outlined mechanisms determines functionally important changes of clot morphology. The obtained results contribute to the knowledge of clotting mechanisms in the presence of artificial and natural lipid microparticles.

Translational diffusion of unfolded and intrinsically disordered proteins

Translational (or self-diffusion) coefficient in dilute solution is inversely proportional to the size of a diffusing molecule, and hence self-diffusion coefficient measurements have been applied to determine the effective hydrodynamic radii for a range of native and nonnative protein conformations. In particular, translational diffusion coefficient measurements are useful to estimate the hydrodynamic radius of natively (or intrinsically) disordered proteins in solution, and, thereby, probe the compactness of a protein as well as its change when environmental parameters such as temperature, solution pH, or protein concentration are varied. The situation becomes more complicated in concentrated solutions. In this review, we discuss the translational diffusion of disordered proteins in dilute and crowded solutions, focusing primarily on the information provided by pulsed-field gradient NMR technique, and draw analogies to well-structured globular proteins and synthetic polymers.

The Native Monomer of Bacillus Pumilus Ribonuclease Does Not Exist Extracellularly

Supported by crystallography studies, secreted ribonuclease of Bacillus pumilus (binase) has long been considered to be monomeric in form. Recent evidence obtained using native polyacrylamide gel electrophoresis and size-exclusion chromatography suggests that binase is in fact dimeric. To eliminate ambiguity and contradictions in the data we have measured conformational changes, hypochromic effect, and hydrodynamic radius of binase. The immutability of binase secondary structure upon transition from low to high protein concentration was registered, suggesting the binase dimerization immediately after translocation through the cell membrane and leading to detection of binase dimers only in the culture fluid regardless of ribonuclease concentration. Our results made it necessary to take a fresh look at the binase stability and cytotoxicity towards virus-infected or tumor cells.

Atomic Structural Models of Fibrin Oligomers

The space-filling fibrin network is a major part of clots and thrombi formed in blood. Fibrin polymerization starts when fibrinogen, a plasma protein, is proteolytically converted to fibrin, which self-assembles to form double-stranded protofibrils. When reaching a critical length, these intermediate species aggregate laterally to transform into fibers arranged into branched fibrin network. We combined multiscale modeling in silico with atomic force microscopy (AFM) imaging to reconstruct complete atomic models of double-stranded fibrin protofibrils with γ-γ crosslinking, A:a and B:b knob-hole bonds, and αC regions-all important structural determinants not resolved crystallographically. Structures of fibrin oligomers and protofibrils containing up to 19 monomers were successfully validated by quantitative comparison with high-resolution AFM images. We characterized the protofibril twisting, bending, kinking, and reversibility of A:a knob-hole bonds, and calculated hydrodynamic parameters of fibrin oligomers. Atomic structures of protofibrils provide a basis to understand mechanisms of early stages of fibrin polymerization.

How viscoelastic is human blood plasma?

Blood plasma has been considered a Newtonian fluid for decades. Recent experiments (Brust et al., Phys. Rev. Lett., 2013, 110) revealed that blood plasma has a pronounced viscoelastic behavior. This claim was based on purely elastic effects observed in the collapse of a thin plasma filament and the fast flow of plasma inside a contraction-expansion microchannel. However, due to the fact that plasma is a solution with very low viscosity, conventional rotational rheometers are not able to stretch the proteins effectively and thus, provide information about the viscoelastic properties of plasma. Using computational rheology and a molecular-based constitutive model, we predict accurately the rheological response of human blood plasma in strong extensional and constriction complex flows. The complete rheological characterization of plasma yields the first quantitative estimation of its viscoelastic properties in shear and extensional flows. We find that although plasma is characterized by a spectrum of ultra-short relaxation times (on the order of 10-3-10-5 s), its elastic nature dominates in flows that feature high shear and extensional rates, such as blood flow in microvessels. We show that plasma exhibits intense strain hardening when exposed to extensional deformations due to the stretch of the proteins in its bulk. In addition, using simple theoretical considerations we propose fibrinogen as the main candidate that attributes elasticity to plasma. These findings confirm that human blood plasma features bulk viscoelasticity and indicate that this non-Newtonian response should be seriously taken into consideration when examining whole blood flow.