1
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Feller T, McPherson HR, Connell SD, Ariëns RAS. Fibrinogen αC-region acts as a functional safety latch: implications for a fibrin biomechanical behaviour model. Acta Biomater 2024:S1742-7061(24)00588-9. [PMID: 39393660 DOI: 10.1016/j.actbio.2024.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 10/02/2024] [Accepted: 10/03/2024] [Indexed: 10/13/2024]
Abstract
Fibrin has unique biomechanical properties which are essential for its role as a scaffold for blood clots. Fibrin is highly extensible and demonstrates significant strain stiffening behaviour, which is essential for stress-distribution in the network. Yet the exact structures of fibrin at the sub-fibre level that contribute to its unique biomechanical characteristic are unknown. Here we show how truncations of the fibrinogen αC-region impact the biomechanical properties of fibrin fibres. Surprisingly, absence of the complete αC-region did not influence the low strain modulus of fibrin fibres but led to premature fibre rupture and decreased extensibility. Intermediate effects were observed with partial deletion of the αC-region, reflected by intermediate rupture stress and toughness. However, overall strain-stiffening behaviour remained even in absence of the αC-region, indicating that strain stiffening is not due to stress being transferred from the αC-region to the protofibril backbone. Upon stress-relaxation, decay constants and their relative contribution to the total relaxation remained similar at all strains, showing that a distinct relaxation process is present until fibre rupture. However, relative contribution of fast relaxation was maximal only in crosslinked fibres if the flexible αC-connector was present. These data show that the αC-region is not the main load-bearing structure within fibrin fibres and point to a critical role for the protofibril backbone instead. We present a revised structural model based on protofibril branching that fully explains the unique biomechanical behaviour of fibrin fibres, while the αC-region primarily acts as a safety latch at the highest of strains. STATEMENT OF SIGNIFICANCE: The findings presented in this paper reveal critically important details about how the molecular structure of fibrin contributes to its unique mechanical properties which are essential to fulfil its function as the scaffold of blood clots. In this work we used engineered proteins with alterations in an important but highly disordered area of the molecule called αC-region and we provide direct evidence for the first time for how the absence of either the globular αC-domain, or the complete αC-region impacts the mechanical behaviour of individual fibrin fibres. Using these results we developed a new structural model of protofibril organisation within fibrin fibres that fully explains their strain stiffening, relatively low modulus and their high, largely variable, extensibility.
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Affiliation(s)
- Tímea Feller
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, UK; Molecular and Nanoscale Physics Group, School of Physics, University of Leeds, UK.
| | - Helen R McPherson
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, UK
| | - Simon D Connell
- Molecular and Nanoscale Physics Group, School of Physics, University of Leeds, UK
| | - Robert A S Ariëns
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, UK
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2
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Wolberg AS. Fibrinogen and fibrin: synthesis, structure, and function in health and disease. J Thromb Haemost 2023; 21:3005-3015. [PMID: 37625698 PMCID: PMC10592048 DOI: 10.1016/j.jtha.2023.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
Fibrinogen is an extraordinary molecule by any estimation. It is large, structurally intricate, and circulates at high concentrations. Its biological end product, insoluble fibrin(ogen) or fibrin, can assume a diverse array of conformations with the ability to interact with numerous plasma proteins and cells and withstand biochemical and biomechanical disruption to facilitate wound healing. Quantitative and qualitative defects in fibrinogen or fibrin are associated with bleeding, thrombosis, inflammation, and diseases affected by these processes. Numerous studies investigating mechanisms by which fibrin(ogen) and fibrin contribute to health and disease have been published. This review for the 20th-anniversary series in the Journal of Thrombosis and Haemostasis summarizes interesting aspects of fibrin(ogen) biology, biochemistry, biophysics, and physiology and highlights exciting findings published in the past 2 decades.
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Affiliation(s)
- Alisa S Wolberg
- Department of Pathology and Laboratory Medicine, UNC Blood Research Center, University of North Carolina, Chapel Hill, North Carolina, USA.
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3
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Hughes MDG, Cussons S, Hanson BS, Cook KR, Feller T, Mahmoudi N, Baker DL, Ariëns R, Head DA, Brockwell DJ, Dougan L. Building block aspect ratio controls assembly, architecture, and mechanics of synthetic and natural protein networks. Nat Commun 2023; 14:5593. [PMID: 37696784 PMCID: PMC10495373 DOI: 10.1038/s41467-023-40921-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/16/2023] [Indexed: 09/13/2023] Open
Abstract
Fibrous networks constructed from high aspect ratio protein building blocks are ubiquitous in nature. Despite this ubiquity, the functional advantage of such building blocks over globular proteins is not understood. To answer this question, we engineered hydrogel network building blocks with varying numbers of protein L domains to control the aspect ratio. The mechanical and structural properties of photochemically crosslinked protein L networks were then characterised using shear rheology and small angle neutron scattering. We show that aspect ratio is a crucial property that defines network architecture and mechanics, by shifting the formation from translationally diffusion dominated to rotationally diffusion dominated. Additionally, we demonstrate that a similar transition is observed in the model living system: fibrin blood clot networks. The functional advantages of this transition are increased mechanical strength and the rapid assembly of homogenous networks above a critical protein concentration, crucial for in vivo biological processes such as blood clotting. In addition, manipulating aspect ratio also provides a parameter in the design of future bio-mimetic and bio-inspired materials.
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Affiliation(s)
- Matt D G Hughes
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, UK
| | - Sophie Cussons
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Benjamin S Hanson
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, UK
| | - Kalila R Cook
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, UK
| | - Tímea Feller
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - Najet Mahmoudi
- ISIS Neutron and Muon Spallation Source, STFC Rutherford Appleton Laboratory, Oxfordshire, UK
| | - Daniel L Baker
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, UK
| | - Robert Ariëns
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - David A Head
- School of Computing, Faculty of Engineering and Physical Science, University of Leeds, Leeds, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Lorna Dougan
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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4
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Maksudov F, Kliuchnikov E, Marx KA, Purohit PK, Barsegov V. Mechanical fatigue testing in silico: Dynamic evolution of material properties of nanoscale biological particles. Acta Biomater 2023; 166:326-345. [PMID: 37142109 DOI: 10.1016/j.actbio.2023.04.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/01/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
Biological particles have evolved to possess mechanical characteristics necessary to carry out their functions. We developed a computational approach to "fatigue testing in silico", in which constant-amplitude cyclic loading is applied to a particle to explore its mechanobiology. We used this approach to describe dynamic evolution of nanomaterial properties and low-cycle fatigue in the thin spherical encapsulin shell, thick spherical Cowpea Chlorotic Mottle Virus (CCMV) capsid, and thick cylindrical microtubule (MT) fragment over 20 cycles of deformation. Changing structures and force-deformation curves enabled us to describe their damage-dependent biomechanics (strength, deformability, stiffness), thermodynamics (released and dissipated energies, enthalpy, and entropy) and material properties (toughness). Thick CCMV and MT particles experience material fatigue due to slow recovery and damage accumulation over 3-5 loading cycles; thin encapsulin shells show little fatigue due to rapid remodeling and limited damage. The results obtained challenge the existing paradigm: damage in biological particles is partially reversible owing to particle's partial recovery; fatigue crack may or may not grow with each loading cycle and may heal; and particles adapt to deformation amplitude and frequency to minimize the energy dissipated. Using crack size to quantitate damage is problematic as several cracks might form simultaneously in a particle. Dynamic evolution of strength, deformability, and stiffness, can be predicted by analyzing the cycle number (N) dependent damage, [Formula: see text] , where α is a power law and Nf is fatigue life. Fatigue testing in silico can now be used to explore damage-induced changes in the material properties of other biological particles. STATEMENT OF SIGNIFICANCE: Biological particles possess mechanical characteristics necessary to perform their functions. We developed "fatigue testing in silico" approach, which employes Langevin Dynamics simulations of constant-amplitude cyclic loading of nanoscale biological particles, to explore dynamic evolution of the mechanical, energetic, and material properties of the thin and thick spherical particles of encapsulin and Cowpea Chlorotic Mottle Virus, and the microtubule filament fragment. Our study of damage growth and fatigue development challenge the existing paradigm. Damage in biological particles is partially reversible as fatigue crack might heal with each loading cycle. Particles adapt to deformation amplitude and frequency to minimize energy dissipation. The evolution of strength, deformability, and stiffness, can be accurately predicted by analyzing the damage growth in particle structure.
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Affiliation(s)
- Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States
| | - Evgenii Kliuchnikov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States
| | - Kenneth A Marx
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States
| | - Prashant K Purohit
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, PA, United States
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States.
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Vottero P, Tavernini S, Santin AD, Scheim DE, Tuszynski JA, Aminpour M. Computational Prediction of the Interaction of Ivermectin with Fibrinogen. Int J Mol Sci 2023; 24:11449. [PMID: 37511206 PMCID: PMC10380762 DOI: 10.3390/ijms241411449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/08/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Hypercoagulability and formation of extensive and difficult-to-lyse microclots are a hallmark of both acute COVID-19 and long COVID. Fibrinogen, when converted to fibrin, is responsible for clot formation, but abnormal structural and mechanical clot properties can lead to pathologic thrombosis. Recent experimental evidence suggests that the spike protein (SP) from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may directly bind to the blood coagulation factor fibrinogen and induce structurally abnormal blood clots with heightened proinflammatory activity. Accordingly, in this study, we used molecular docking and molecular dynamics simulations to explore the potential activity of the antiparasitic drug ivermectin (IVM) to prevent the binding of the SARS-CoV-2 SP to fibrinogen and reduce the occurrence of microclots. Our computational results indicate that IVM may bind with high affinity to multiple sites on the fibrinogen peptide, with binding more likely in the central, E region, and in the coiled-coil region, as opposed to the globular D region. Taken together, our in silico results suggest that IVM may interfere with SP-fibrinogen binding and, potentially, decrease the formation of fibrin clots resistant to degradation. Additional in vitro studies are warranted to validate whether IVM binding to fibrinogen is sufficiently stable to prevent interaction with the SP, and potentially reduce its thrombo-inflammatory effect in vivo.
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Affiliation(s)
- Paola Vottero
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB T6G 1Z2, Canada; (P.V.); (M.A.)
| | - Scott Tavernini
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada;
| | - Alessandro D. Santin
- Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, P.O. Box 208063, New Haven, CT 06520-8063, USA;
| | - David E. Scheim
- US Public Health Service, Commissioned Corps, Inactive Reserve, Blacksburg, VA 24060-6367, USA;
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, Edmonton, AB T6G 1Z2, Canada
- DIMEAS, Politecnico di Torino, 10129 Turin, Italy
- Department of Data Science and Engineering, The Silesian University of Technology, 44-100 Gliwice, Poland
| | - Maral Aminpour
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB T6G 1Z2, Canada; (P.V.); (M.A.)
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6
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Nzulumike ANO, Thormann E. Fibrin Adsorption on Cardiovascular Biomaterials and Medical Devices. ACS APPLIED BIO MATERIALS 2023. [PMID: 37368548 DOI: 10.1021/acsabm.2c01057] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Medical devices that are inserted in blood vessels always risk eliciting thrombosis, and the surface properties of such devices are thus of major importance. The initiating step for surface-induced pathological coagulation has been associated with adsorption of fibrinogen protein on biomaterial surfaces and subsequent polymerization into an insoluble fibrin clot. This issue gives rise to an inherent challenge in biomaterial design as varied surface materials must fulfill specialized roles while also minimizing thrombotic complications from spontaneous fibrin(ogen) recruitment. We have aimed to characterize the thrombogenic properties of state-of-the-art cardiovascular biomaterials and medical devices by quantifying the relative surface-dependent adsorption and formation of fibrin followed by analysis of the resulting morphologies. We identified stainless steel and amorphous fluoropolymer as comparatively preferable biomaterials based on their low fibrin(ogen) recruitment, in comparison to other metallic and polymeric biomaterials, respectively. In addition, we observed a morphological trend that fibrin forms fiber structures on metallic surfaces and fractal branched structures on polymeric surfaces. Finally, we used vascular guidewires as clotting substrates and found that fibrin adsorption depends on parts of the guidewire that are exposed, and we correlated the morphologies on uncoated guidewires with those formed on raw stainless-steel biomaterials.
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Affiliation(s)
- Achebe N O Nzulumike
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Department of Civil and Mechanical Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Esben Thormann
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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7
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Pinelo JEE, Manandhar P, Popovic G, Ray K, Tasdelen MF, Nguyen Q, Iavarone AT, Offenbacher AR, Hudson NE, Sen M. Systematic mapping of the conformational landscape and dynamism of soluble fibrinogen. J Thromb Haemost 2023; 21:1529-1543. [PMID: 36746319 PMCID: PMC10407912 DOI: 10.1016/j.jtha.2023.01.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
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.
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Affiliation(s)
- Jose E E Pinelo
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Pragya Manandhar
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Grega Popovic
- Department of Chemistry, East Carolina University, Greenville, North Carolina, USA
| | - Katherine Ray
- Department of Chemistry, East Carolina University, Greenville, North Carolina, USA
| | - Mehmet F Tasdelen
- Department of Computer Science, University of Houston, Houston, Texas, USA
| | - Quoc Nguyen
- Department of Mathematics, University of Houston, Houston, Texas, USA
| | - Anthony T Iavarone
- QB3/Chemistry/Mass Spectrometry Facility, University of California, Berkeley, California, USA
| | - Adam R Offenbacher
- Department of Chemistry, East Carolina University, Greenville, North Carolina, USA
| | - Nathan E Hudson
- Department of Physics, East Carolina University, Greenville, North Carolina, USA
| | - Mehmet Sen
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA.
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8
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Jimenez JM, Tuttle T, Guo Y, Miles D, Buganza-Tepole A, Calve S. Multiscale mechanical characterization and computational modeling of fibrin gels. Acta Biomater 2023; 162:292-303. [PMID: 36965611 PMCID: PMC10313219 DOI: 10.1016/j.actbio.2023.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/28/2023] [Accepted: 03/17/2023] [Indexed: 03/27/2023]
Abstract
Fibrin is a naturally occurring protein network that forms a temporary structure to enable remodeling during wound healing. It is also a common tissue engineering scaffold because the structural properties can be controlled. However, to fully characterize the wound healing process and improve the design of regenerative scaffolds, understanding fibrin mechanics at multiple scales is necessary. Here, we present a strategy to quantify both the macroscale (1-10 mm) stress-strain response and the deformation of the mesoscale (10-1000 µm) network structure during unidirectional tensile tests. The experimental data were then used to inform a computational model to accurately capture the mechanical response of fibrin gels. Simultaneous mechanical testing and confocal microscopy imaging of fluorophore-conjugated fibrin gels revealed up to an 88% decrease in volume coupled with increase in volume fraction in deformed gels, and non-affine fiber alignment in the direction of deformation. Combination of the computational model with finite element analysis enabled us to predict the strain fields that were observed experimentally within heterogenous fibrin gels with spatial variations in material properties. These strategies can be expanded to characterize and predict the macroscale mechanics and mesoscale network organization of other heterogeneous biological tissues and matrices. STATEMENT OF SIGNIFICANCE: Fibrin is a naturally-occurring scaffold that supports cellular growth and assembly of de novo tissue and has tunable material properties. Characterization of meso- and macro-scale mechanics of fibrin gel networks can advance understanding of the wound healing process and impact future tissue engineering approaches. Using structural and mechanical characteristics of fibrin gels, a theoretical and computational model that can predict multiscale fibrin network mechanics was developed. These data and model can be used to design gels with tunable properties.
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Affiliation(s)
- Julian M Jimenez
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, IN 47907, United States
| | - Tyler Tuttle
- Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, 1111 Engineering Dr, Boulder, CO 80309, United States
| | - Yifan Guo
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, United States
| | - Dalton Miles
- Chemical and Biological Engineering, University of Colorado Boulder, 3415 Colorado Ave, Boulder, CO 80303, United States
| | - Adrian Buganza-Tepole
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, IN 47907, United States; School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, United States.
| | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, IN 47907, United States; Paul M. Rady Department of Mechanical Engineering, University of Colorado Boulder, 1111 Engineering Dr, Boulder, CO 80309, United States.
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9
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Pietsch K, Storm‐Johannsen L, Schmidt‐Thomée A, Pompe T. Correlation between Fibrin Fibrillation Kinetics and the Resulting Fibrin Network Microstructure. Adv Healthc Mater 2023; 12:e2202231. [PMID: 36494086 PMCID: PMC11468976 DOI: 10.1002/adhm.202202231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/27/2022] [Indexed: 12/14/2022]
Abstract
Fibrin, the prominent extracellular matrix in early wound tissue, is discussed to influence immune cells and healing. The nature of fibrinogen/fibrin to form fibrillary networks is frequently exploited to engineer microenvironments for cellular analysis. This study focuses on revealing the correlation of fibril formation kinetic and the resulting network microstructure of engineered 3D fibrin networks. Different concentrations of fibrinogen (1-3 mg mL-1 ), thrombin (0.01-0.15 U mL-1 ), sodium chloride (40-120 mm), and calcium chloride (1-10 mm) are applied to assess the impact on the fibril growth kinetics by turbidity analysis and on the resulting fibril and pore diameter by laser scanning microscopy. The results highlight a direct influence of the sodium chloride concentration on fibrillation kinetics and reveal a strong correlation between fibrillation kinetics and network microstructure. With the assumption of a first-order growth kinetic, an increase of the growth constant k (0.015-0.04 min-1 ) is found to correlate to a decrease in fibril diameter (1-0.65 µm) and pore diameter (11-5 µm). The new findings enable an easy prediction of 3D fibrin network microstructure by the fibril formation kinetic and contribute to an improved engineering of defined scaffolds for tissue engineering and cell culture applications.
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Affiliation(s)
- Katja Pietsch
- Institute of BiochemistryLeipzig UniversityJohannisallee 21‐2304103LeipzigGermany
| | - Lisa Storm‐Johannsen
- Institute of BiochemistryLeipzig UniversityJohannisallee 21‐2304103LeipzigGermany
| | | | - Tilo Pompe
- Institute of BiochemistryLeipzig UniversityJohannisallee 21‐2304103LeipzigGermany
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10
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Stohnii Y, Yatsenko T, Nikulina V, Kucheriavyi Y, Hrabovskyi O, Slominskyi O, Savchenko K, Garmanchuk L, Varbanets L, Tykhomyrov A, Chernyshenko V. Functional properties of individual sub-domains of the fibrin(ogen) αC-domains. BBA ADVANCES 2023; 3:100072. [PMID: 37082262 PMCID: PMC10074951 DOI: 10.1016/j.bbadva.2023.100072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Background Fibrinogen is a large polyfunctional plasma protein consisting of a number of structural and functional domains. Among them, two αC-domains, each formed by the amino acid residues Аα392-610, are involved in fibrin polymerization, activation of fibrinolysis, platelet aggregation, and interaction with different cell types. Previous study revealed that each fibrinogen αC-domain consists of the N-terminal and C-terminal sub-domains. The major objections of the present study were to test functional role of these sub-domains in the above mentioned processes. Methods To achieve these objections, we used specific proteases to prepare two truncated forms of fibrinogen, fibrinogen desAα505-610 and fibrinogen desAα414-610, missing their N-terminal and both N- and C-terminal sub-domains, respectively. Results Our study with these truncated forms using turbidity measurements and electron microscopy revealed that the N- and C-terminal subdomains both contribute to protofibril formation and their lateral aggregation into fibers during fibrin polymerization process. These two sub-domains also contributed to platelet aggregation with the N-terminal sub-domains playing a more significant role in this process. At the same time, the C-terminal sub-domains make the major contribution to the plasminogen activation process. Further, our experiments revealed that the C-terminal sub-domains are involved in endothelial cell viability and migration of cancer cells. Conclusions Thus, the results obtained establish the functional role of individual sub-domains of the αC-domains in fibrin polymerization, activation of fibrinolytic system, platelet aggregation, and cellular interactions. General significance The present study expands our understanding of the functional role of individual fibrinogen domains and their specific portions in various fibrin(ogen)-dependent processes.
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11
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Spiewak R, Gosselin A, Merinov D, Litvinov RI, Weisel JW, Tutwiler V, Purohit PK. Biomechanical origins of inherent tension in fibrin networks. J Mech Behav Biomed Mater 2022; 133:105328. [PMID: 35803206 PMCID: PMC9434494 DOI: 10.1016/j.jmbbm.2022.105328] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/02/2022] [Accepted: 06/18/2022] [Indexed: 10/17/2022]
Abstract
Blood clots form at the site of vascular injury to seal the wound and prevent bleeding. Clots are in tension as they perform their biological functions and withstand hydrodynamic forces of blood flow, vessel wall fluctuations, extravascular muscle contraction and other forces. There are several mechanisms that generate tension in a blood clot, of which the most well-known is the contraction/retraction caused by activated platelets. Here we show through experiments and modeling that clot tension is generated by the polymerization of fibrin. Our mathematical model is built on the hypothesis that the shape of fibrin monomers having two-fold symmetry and off-axis binding sites is ultimately the source of inherent tension in individual fibers and the clot. As the diameter of a fiber grows during polymerization the fibrin monomers must suffer axial twisting deformation so that they remain in register to form the half-staggered arrangement characteristic of fibrin protofibrils. This deformation results in a pre-strain that causes fiber and network tension. Our results for the pre-strain in single fibrin fibers is in agreement with experiments that measured it by cutting fibers and measuring their relaxed length. We connect the mechanics of a fiber to that of the network using the 8-chain model of polymer elasticity. By combining this with a continuum model of swellable elastomers we can compute the evolution of tension in a constrained fibrin gel. The temporal evolution and tensile stresses predicted by this model are in qualitative agreement with experimental measurements of the inherent tension of fibrin clots polymerized between two fixed rheometer plates. These experiments also revealed that increasing thrombin concentration leads to increasing internal tension in the fibrin network. Our model may be extended to account for other mechanisms that generate pre-strains in individual fibers and cause tension in three-dimensional proteinaceous polymeric networks.
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Affiliation(s)
- Russell Spiewak
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew Gosselin
- Department of Biomedical Engineering, Rutgers - The State University of New Jersey, 599 Taylor Road, Room 209, Piscataway, NJ 08854, USA
| | - Danil Merinov
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, 1154 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104-6058, USA
| | - Rustem I Litvinov
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, 1154 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104-6058, USA
| | - John W Weisel
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, 1154 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104-6058, USA.
| | - Valerie Tutwiler
- Department of Biomedical Engineering, Rutgers - The State University of New Jersey, 599 Taylor Road, Room 209, Piscataway, NJ 08854, USA.
| | - Prashant K Purohit
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Fibrin protofibril packing and clot stability are enhanced by extended knob-hole interactions and catch-slip bonds. Blood Adv 2022; 6:4015-4027. [PMID: 35561308 PMCID: PMC9278297 DOI: 10.1182/bloodadvances.2022006977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/03/2022] [Indexed: 11/25/2022] Open
Abstract
Fibrin polymerization involves thrombin-mediated exposure of knobs on one monomer that bind to holes available on another, leading to the formation of fibers. In silico evidence has suggested that the classical A:a knob-hole interaction is enhanced by surrounding residues not directly involved in the binding pocket of hole a, via noncovalent interactions with knob A. We assessed the importance of extended knob-hole interactions by performing biochemical, biophysical, and in silico modeling studies on recombinant human fibrinogen variants with mutations at residues responsible for the extended interactions. Three single fibrinogen variants, γD297N, γE323Q, and γK356Q, and a triple variant γDEK (γD297N/γE323Q/γK356Q) were produced in a CHO (Chinese Hamster Ovary) cell expression system. Longitudinal protofibril growth probed by atomic force microscopy was disrupted for γD297N and enhanced for the γK356Q mutation. Initial polymerization rates were reduced for all variants in turbidimetric studies. Laser scanning confocal microscopy showed that γDEK and γE323Q produced denser clots, whereas γD297N and γK356Q were similar to wild type. Scanning electron microscopy and light scattering studies showed that fiber thickness and protofibril packing of the fibers were reduced for all variants. Clot viscoelastic analysis showed that only γDEK was more readily deformable. In silico modeling suggested that most variants displayed only slip-bond dissociation kinetics compared with biphasic catch-slip kinetics characteristics of wild type. These data provide new evidence for the role of extended interactions in supporting the classical knob-hole bonds involving catch-slip behavior in fibrin formation, clot structure, and clot mechanics.
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13
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Pancaldi F, Kim OV, Weisel JW, Alber M, Xu Z. Computational Biomechanical Modeling of Fibrin Networks and Platelet-Fiber Network Interactions. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2022; 22:100369. [PMID: 35386550 PMCID: PMC8979495 DOI: 10.1016/j.cobme.2022.100369] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fibrin deformation and interaction of fibrin with other blood components play critical roles in hemostasis and thrombosis. In this review, computational and mathematical biomechanical models of fibrin network deformation and contraction at different spatio-temporal scales as well as challenges in developing and calibrating multiscale models are discussed. There are long standing challenges. For instance, applicability of models to identify and test potential mechanisms of the biomechanical processes mediating interactions between platelets and fiber networks in blood clot stretching and contraction needs to be examined carefully. How the structural and mechanical properties of major blood clot components influences biomechanical responses of the entire clot subjected to external forces, such as blood flow or vessel wall deformations needs to be investigated thoroughly.
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Affiliation(s)
- Francesco Pancaldi
- Department of Mathematics, University of California Riverside, Riverside, CA 92505, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92505, USA
| | - Oleg V. Kim
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - John W. Weisel
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Mark Alber
- Department of Mathematics, University of California Riverside, Riverside, CA 92505, USA
- Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92505, USA
| | - Zhiliang Xu
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, IN 46556, USA
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14
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Maksudov F, Daraei A, Sesha A, Marx KA, Guthold M, Barsegov V. Strength, deformability and toughness of uncrosslinked fibrin fibers from theoretical reconstruction of stress-strain curves. Acta Biomater 2021; 136:327-342. [PMID: 34606991 PMCID: PMC8627496 DOI: 10.1016/j.actbio.2021.09.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/31/2021] [Accepted: 09/27/2021] [Indexed: 10/20/2022]
Abstract
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.
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Affiliation(s)
- Farkhad Maksudov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States
| | - Ali Daraei
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109, United States
| | - Anuj Sesha
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States
| | - Kenneth A Marx
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States
| | - Martin Guthold
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109, United States.
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, Lowell, MA 01854, United States.
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15
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Takeishi N, Shigematsu T, Enosaki R, Ishida S, Ii S, Wada S. Development of a mesoscopic framework spanning nanoscale protofibril dynamics to macro-scale fibrin clot formation. J R Soc Interface 2021; 18:20210554. [PMID: 34753310 PMCID: PMC8580471 DOI: 10.1098/rsif.2021.0554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/14/2021] [Indexed: 11/23/2022] Open
Abstract
Thrombi form a micro-scale fibrin network consisting of an interlinked structure of nanoscale protofibrils, resulting in haemostasis. It is theorized that the mechanical effect of the fibrin clot is caused by the polymeric protofibrils between crosslinks, or to their dynamics on a nanoscale order. Despite a number of studies, however, it is still unknown, how the nanoscale protofibril dynamics affect the formation of the macro-scale fibrin clot and thus its mechanical properties. A mesoscopic framework would be useful to tackle this multi-scale problem, but it has not yet been established. We thus propose a minimal mesoscopic model for protofibrils based on Brownian dynamics, and performed numerical simulations of protofibril aggregation. We also performed stretch tests of polymeric protofibrils to quantify the elasticity of fibrin clots. Our model results successfully captured the conformational properties of aggregated protofibrils, e.g., strain-hardening response. Furthermore, the results suggest that the bending stiffness of individual protofibrils increases to resist extension.
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Affiliation(s)
- Naoki Takeishi
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama Toyonaka, Osaka 560-8531, Japan
| | - Taiki Shigematsu
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama Toyonaka, Osaka 560-8531, Japan
| | - Ryogo Enosaki
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama Toyonaka, Osaka 560-8531, Japan
| | - Shunichi Ishida
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Satoshi Ii
- Graduate School of Systems Design, Tokyo Metropolitan University, 1-1 Minami-Osawa Hachioji, Tokyo 192-0397, Japan
| | - Shigeo Wada
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama Toyonaka, Osaka 560-8531, Japan
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16
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Barinov NA, Tolstova AP, Bersenev EA, Ivanov DA, Dubrovin EV, Klinov DV. Molecular patterns of oligopeptide hydrocarbons on graphite. Colloids Surf B Biointerfaces 2021; 206:111921. [PMID: 34157520 DOI: 10.1016/j.colsurfb.2021.111921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 05/19/2021] [Accepted: 06/13/2021] [Indexed: 10/21/2022]
Abstract
Graphitic materials including graphene, carbon nanotubes and fullerenes, are promising for use in nanotechnology and biomedicine. Non-covalent functionalization by peptides and other organic molecules allows changing the properties of graphitic surfaces in a controlled manner and represents a big potential for fundamental research and applications. Recently described oligopeptide-hydrocarbon derivative N,N'-(decane-1,10-diyl)bis(tetraglycineamide) (GM) is highly prospective for the development of graphitic interfaces in biosensor application as well as in structural biology for improving the quality of high-resolution atomic force microscopy (AFM) visualization of individual biomacromolecules. However, molecular organization of GM on graphitic surfaces is still unknown. In this work, the molecular model of GM at the water/highly oriented pyrolytic graphite (HOPG) interface has been developed basing on the high-resolution AFM and full-atom molecular modeling data. This model explains two periodicities observed in AFM images by GM self-assembly on a HOPG surface with formation of the stacks with the lateral shifts. The obtained results reveal the particular patterns and dynamics of GM molecules adsorbed on graphite and unravel the puzzle of peptide self-assembly on graphitic surfaces.
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Affiliation(s)
- Nikolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow 119435 Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340, Sochi, Russian Federation
| | - Anna P Tolstova
- Engelhardt Institute of Molecular Biology, Vavilova 32, 119991, Moscow, Russian Federation
| | - Egor A Bersenev
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka 142432, Russian Federation
| | - Dmitry A Ivanov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340, Sochi, Russian Federation; Institut de Sciences des Matériaux de Mulhouse-IS2M, CNRS UMR 7361, 15, rue Jean Starcky, F-68057 Mulhouse, France
| | - Evgeniy V Dubrovin
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow 119435 Russian Federation; Lomonosov Moscow State University, Leninskie Gory 1 Bld. 2, 119991 Moscow, Russian Federation.
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya 1a, Moscow 119435 Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340, Sochi, Russian Federation.
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17
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Abstract
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.
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18
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Alshammari RH, Rajesh UC, Morgan DG, Zaleski JM. Au-Cu@PANI Alloy Core Shells for Aerobic Fibrin Degradation under Visible Light Exposure. ACS APPLIED BIO MATERIALS 2020; 3:7631-7638. [PMID: 35019503 DOI: 10.1021/acsabm.0c00833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fibrin plays a critical role in wound healing and hemostasis, yet it is also the main case of cardiovascular diseases and thrombosis. Here, we show the unique design of Au-Cu@PANI alloy core-shell rods for fibrin clot degradation. Microscopic (transmission electron microscopy (TEM), scanning transmission electron microscopy-energy-dispersive X-ray (STEM-EDX)) and structural characterizations (powder X-ray diffraction (PXRD), X-ray photoelectron spectroscopy (XPS)) of the Au-Cu@PANI hybrid material reveal the formation of Au-Cu heterogeneous alloy core rods (aspect ratio = 3.7) with thin Cu2O and PANI shells that create a positive surface charge (ζ-potential = +22 mV). This architecture is supported by the survey XPS spectrum showing the presence of Cu 2p, N 1s, and C 1s features with binding energies of 934.8, 399.7, and 284.8 eV, respectively. Upon photolysis (λ ≥ 495 or 590 nm), these hybrid composite nanorods provide sufficient excited-state redox potential to generate reactive oxygen species (ROS) for degradation of model fibrin clots within 5-7 h. Detailed scanning electron microscopy (SEM) analysis of the fibrin network shows significant morphology modification including formation of large voids and strand termini, indicating degradation of fibrin protofibril by Au-Cu@PANI. The dye 1,3-diphenylisobenzofuran (DPBF) used to detect the presence of 1O2 shows a 27% bleaching of the absorption at λ = 418 nm within 75 min of irradiation of an aqueous Au-Cu@PANI solution in air. Moreover, electron paramagnetic resonance (EPR) spin-trapping experiments reveal a hyperfine-coupled triplet signature at room temperature with intensities 1:1:1: and g-value = 2.0057, characteristic of the reaction between the spin probe 4-Oxo-TEMP and 1O2 during irradiation. Controlled 1O2 scavenging experiments by NaN3 show 82% reduction in the spin-trapped EPR signal area. Both DPBF bleaching and EPR spin trapping indicate that in situ generated 1O2 is responsible for fibrin strand scission. This unique nanomaterial function via use of ubiquitous oxygen as a reagent could open creative avenues for future in vivo biomedical applications to treat fibrin clot diseases.
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Affiliation(s)
- Riyadh H Alshammari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States.,Department of Chemistry, King Saud University, Riyadh 11451, Saudi Arabia
| | - U Chinna Rajesh
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - David Gene Morgan
- Electron Microscopy Center, Indiana University, Bloomington, Indiana 47405, United States
| | - Jeffrey M Zaleski
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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19
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Jansen KA, Zhmurov A, Vos BE, Portale G, Hermida-Merino D, Litvinov RI, Tutwiler V, Kurniawan NA, Bras W, Weisel JW, Barsegov V, Koenderink GH. Molecular packing structure of fibrin fibers resolved by X-ray scattering and molecular modeling. SOFT MATTER 2020; 16:8272-8283. [PMID: 32935715 DOI: 10.1039/d0sm00916d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
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.
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Affiliation(s)
- Karin A Jansen
- AMOLF, Biological Soft Matter Group, Amsterdam, The Netherlands and UMC Utrecht, Department of Pathology, 3508 GA Utrecht, The Netherlands
| | - Artem Zhmurov
- KTH Royal Institute of Technology, Stockholm, Sweden and Sechenov University, Moscow 119991, Russian Federation
| | - Bart E Vos
- AMOLF, Biological Soft Matter Group, Amsterdam, The Netherlands and Institute of Cell Biology, Center of Molecular Biology of Inflammation, University of Münster, Münster, Germany
| | - Giuseppe Portale
- Macromolecular Chemistry and New Polymeric Materials, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Daniel Hermida-Merino
- Netherlands Organization for Scientific Research (NWO), DUBBLE CRG at the ESRF, 71 Avenue des Martyrs, 38000 Grenoble Cedex, France
| | - Rustem I Litvinov
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA and Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya St., Kazan 420008, Russian Federation
| | - Valerie Tutwiler
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicholas A Kurniawan
- AMOLF, Biological Soft Matter Group, Amsterdam, The Netherlands and Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Wim Bras
- Netherlands Organization for Scientific Research (NWO), DUBBLE CRG at the ESRF, 71 Avenue des Martyrs, 38000 Grenoble Cedex, France and Chemical Sciences Division, Oak Ridge National Laboratory, One Bethel Valley Road, Oak Ridge Tennessee, 37831, USA
| | - John W Weisel
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Valeri Barsegov
- Department of Chemistry, University of Massachusetts, 1 University Ave., Lowell, MA, 01854, USA.
| | - Gijsje H Koenderink
- AMOLF, Biological Soft Matter Group, Amsterdam, The Netherlands and Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, The Netherlands.
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20
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Duval C, Profumo A, Aprile A, Salis A, Millo E, Damonte G, Gauer JS, Ariëns RAS, Rocco M. Fibrinogen αC-regions are not directly involved in fibrin polymerization as evidenced by a "Double-Detroit" recombinant fibrinogen mutant and knobs-mimic peptides. J Thromb Haemost 2020; 18:802-814. [PMID: 31889430 PMCID: PMC7186824 DOI: 10.1111/jth.14725] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Fibrin polymerization, following fibrinopeptides A and B (FpA, FpB) cleavage, relies on newly exposed α- and β-chains N-termini (GPR, GHR; A-, B-knobs, respectively) engaging preexistent a and b pockets in other fibrin(ogen) molecules' γ- and (B)β-chains C-terminal regions. A role for mostly disordered (A)α-chains C-terminal regions "bridging" between fibrin molecules/fibrils has been proposed. OBJECTIVES Fibrinogen Detroit is a clinically observed mutation (AαR19 → S) with nonengaging GPS A-knobs. By analogy, a similar Bβ-chain mutation, BβR17 → S, should produce nonengaging GHS B-knobs. A homozygous "Double-Detroit" mutant (AαR19 → S, BβR17 → S; DD-FG) was developed: with A-a and B-b engagements endogenously blocked, other interactions would become apparent. METHODS DD-FG, wild-type recombinant (WT-FG), and human plasma (hp-FG) fibrinogen self-association was studied by turbidimetry coupled with fibrinopeptides release high-performance liquid chromatography (HPLC)/mass spectrometry analyses, and by light-scattering following size-exclusion chromatography (SE-HPLC). RESULTS In contrast to WT-FG and hp-FG, DD-FG produced no turbidity increase, irrespective of thrombin concentration. The SE-HPLC profile of concentrated DD-FG was unaffected by thrombin treatment, and light-scattering, at lower concentration, showed no intensity and hydrodynamic radius changes. Compared with hp-FG, both WT-FG and DD-FG showed no FpA cleavage difference, while ~50% FpB was not recovered. Correspondingly, SDS-PAGE/Western-blots revealed partial Bβ-chain N-terminal and Aα-chain C-terminal degradation. Nevertheless, ~70% DD-FG molecules bearing (A)αC-regions potentially able to associate were available. Higher-concentration, nearly intact hp-FG with 500-fold molar excess GPRP-NH2 /GHRP-NH2 knobs-mimics experiments confirmed these no-association findings. CONCLUSIONS (A)αC-regions interactions appear too weak to assist native fibrin polymerization, at least without knobs engagement. Their role in all stages should be carefully reconsidered.
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Affiliation(s)
- Cédric Duval
- Leeds Thrombosis CollectiveDiscovery and Translational Science DepartmentLeeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | - Aldo Profumo
- Biopolimeri e ProteomicaIRCCS Ospedale Policlinico San MartinoGenovaItaly
| | - Anna Aprile
- Biopolimeri e ProteomicaIRCCS Ospedale Policlinico San MartinoGenovaItaly
| | - Annalisa Salis
- Department of Experimental MedicineCenter of Excellence for Biomedical Research (CEBR)University of GenovaGenovaItaly
| | - Enrico Millo
- Department of Experimental MedicineCenter of Excellence for Biomedical Research (CEBR)University of GenovaGenovaItaly
| | - Gianluca Damonte
- Department of Experimental MedicineCenter of Excellence for Biomedical Research (CEBR)University of GenovaGenovaItaly
| | - Julia S. Gauer
- Leeds Thrombosis CollectiveDiscovery and Translational Science DepartmentLeeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | - Robert A. S. Ariëns
- Leeds Thrombosis CollectiveDiscovery and Translational Science DepartmentLeeds Institute of Cardiovascular and Metabolic MedicineUniversity of LeedsLeedsUK
| | - Mattia Rocco
- Biopolimeri e ProteomicaIRCCS Ospedale Policlinico San MartinoGenovaItaly
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21
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Sachs L, Denker C, Greinacher A, Palankar R. Quantifying single-platelet biomechanics: An outsider's guide to biophysical methods and recent advances. Res Pract Thromb Haemost 2020; 4:386-401. [PMID: 32211573 PMCID: PMC7086474 DOI: 10.1002/rth2.12313] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/10/2019] [Accepted: 01/07/2020] [Indexed: 01/30/2023] Open
Abstract
Platelets are the key cellular components of blood primarily contributing to formation of stable hemostatic plugs at the site of vascular injury, thus preventing excessive blood loss. On the other hand, excessive platelet activation can contribute to thrombosis. Platelets respond to many stimuli that can be of biochemical, cellular, or physical origin. This drives platelet activation kinetics and plays a vital role in physiological and pathological situations. Currently used bulk assays are inadequate for comprehensive biomechanical assessment of single platelets. Individual platelets interact and respond differentially while modulating their biomechanical behavior depending on dynamic changes that occur in surrounding microenvironments. Quantitative description of such a phenomenon at single-platelet regime and up to nanometer resolution requires methodological approaches that can manipulate individual platelets at submicron scales. This review focusses on principles, specific examples, and limitations of several relevant biophysical methods applied to single-platelet analysis such as micropipette aspiration, atomic force microscopy, scanning ion conductance microscopy and traction force microscopy. Additionally, we are introducing a promising single-cell approach, real-time deformability cytometry, as an emerging biophysical method for high-throughput biomechanical characterization of single platelets. This review serves as an introductory guide for clinician scientists and beginners interested in exploring one or more of the above-mentioned biophysical methods to address outstanding questions in single-platelet biomechanics.
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Affiliation(s)
- Laura Sachs
- Institute of Immunology and Transfusion MedicineUniversity Medicine GreifswaldGreifswaldGermany
| | | | - Andreas Greinacher
- Institute of Immunology and Transfusion MedicineUniversity Medicine GreifswaldGreifswaldGermany
| | - Raghavendra Palankar
- Institute of Immunology and Transfusion MedicineUniversity Medicine GreifswaldGreifswaldGermany
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22
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Sovová Ž, Štikarová J, Kaufmanová J, Májek P, Suttnar J, Šácha P, Malý M, Dyr JE. Impact of posttranslational modifications on atomistic structure of fibrinogen. PLoS One 2020; 15:e0227543. [PMID: 31995579 PMCID: PMC6988951 DOI: 10.1371/journal.pone.0227543] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/20/2019] [Indexed: 01/09/2023] Open
Abstract
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.
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Affiliation(s)
- Žofie Sovová
- Department of Biochemistry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
- * E-mail:
| | - Jana Štikarová
- Department of Biochemistry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jiřina Kaufmanová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Pavel Májek
- Department of Biochemistry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Jiří Suttnar
- Department of Biochemistry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Pavel Šácha
- Proteases of Human Pathogens, Institute of Organic Chemistry and Biochemistry ASCR, v.v.i., Prague, Czech Republic
| | - Martin Malý
- Military University Hospital, Charles University in Prague, Prague, Czech Republic
| | - Jan E. Dyr
- Department of Biochemistry, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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23
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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; 117:1976-1987. [PMID: 31924745 PMCID: PMC6995014 DOI: 10.1073/pnas.1911785117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Fibrinogen hexamers are major components of blood clots. After release of fibrinopeptides resulting in fibrin monomers, clot formation occurs through fibrin oligomerization followed by lateral aggregation, packing into fibrin fibers, and consequent branching. Shedding light on fibrin clots by in situ cross-linking mass spectrometry and structural modeling extends our current knowledge of the structure of fibrin with regard to receptor-binding hotspots. Further restraint-driven molecular docking reveals how fibrin oligomers laterally aggregate into clots and uncovers the molecular architecture of the clot to albumin interaction. We hypothesize this interaction is involved in the prevention of clot degradation. Mapping known mutations validates the generated structural model and, for a subset, brings their molecular mechanisms into view. 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).
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24
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Pederson EN, Interlandi G. Oxidation-induced destabilization of the fibrinogen αC-domain dimer investigated by molecular dynamics simulations. Proteins 2019; 87:826-836. [PMID: 31134660 DOI: 10.1002/prot.25746] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 12/20/2022]
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. Oxidation of Met476 located within the αC domain is thought to hinder 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 Met476 . Analysis of the trajectories revealed that multiple stable binding modes were sampled between two αC domains while oxidation decreased the likelihood of dimer formation. Furthermore, the side chain of Met476 was observed to act as a docking spot for the binding and this function was impaired by its conversion to methionine sulfoxide.
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Affiliation(s)
- Eric N Pederson
- Department of Bioengineering, University of Washington, Seattle, Washington
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25
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Schmitt LR, Henderson R, Barrett A, Darula Z, Issaian A, D'Alessandro A, Clendenen N, Hansen KC. Mass spectrometry-based molecular mapping of native FXIIIa cross-links in insoluble fibrin clots. J Biol Chem 2019; 294:8773-8778. [PMID: 31028172 DOI: 10.1074/jbc.ac119.007981] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/22/2019] [Indexed: 12/31/2022] Open
Abstract
The roles of factor XIIIa-specific cross-links in thrombus formation, regression, or probability for embolization are largely unknown. A molecular understanding of fibrin architecture at the level of these cross-links could inform the development of therapeutic strategies to prevent the sequelae of thromboembolism. Here, we present an MS-based method to map native factor XIIIa cross-links in the insoluble matrix component of whole-blood or plasma-fibrin clots and in in vivo thrombi. Using a chaotrope-insoluble digestion method and quantitative cross-linking MS, we identified the previously mapped fibrinogen peptides that are responsible for covalent D-dimer association, as well as dozens of novel cross-links in the αC region of fibrinogen α. Our findings expand the known native cross-linked species from one to over 100 and suggest distinct antiparallel registries for interprotofibril association and covalent attachment of serpins that regulate clot dissolution.
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Affiliation(s)
| | - Rachel Henderson
- Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado 80045 and
| | | | - Zsuzsanna Darula
- Laboratory of Proteomics Research, Biological Research Center of the Hungarian Academy of Sciences, H-6701 Szeged, Hungary
| | - Aaron Issaian
- From the Departments of Biochemistry and Molecular Genetics and
| | | | - Nathan Clendenen
- Anesthesiology, University of Colorado School of Medicine, Aurora, Colorado 80045 and
| | - Kirk C Hansen
- From the Departments of Biochemistry and Molecular Genetics and
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