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Nencini F, Bettiol A, Argento FR, Borghi S, Giurranna E, Emmi G, Prisco D, Taddei N, Fiorillo C, Becatti M. Post-translational modifications of fibrinogen: implications for clotting, fibrin structure and degradation. MOLECULAR BIOMEDICINE 2024; 5:45. [PMID: 39477884 PMCID: PMC11525374 DOI: 10.1186/s43556-024-00214-x] [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: 07/16/2024] [Accepted: 09/24/2024] [Indexed: 11/02/2024] Open
Abstract
Fibrinogen, a blood plasma protein with a key role in hemostasis and thrombosis, is highly susceptible to post-translational modifications (PTMs), that significantly influence clot formation, structure, and stability. These PTMs, which include acetylation, amidation, carbamylation, citrullination, dichlorination, glycation, glycosylation, guanidinylation, hydroxylation, homocysteinylation, malonylation, methylation, nitration, oxidation, phosphorylation and sulphation, can alter fibrinogen biochemical properties and affect its functional behavior in coagulation and fibrinolysis. Oxidation and nitration are notably associated with oxidative stress, impacting fibrin fiber formation and promoting the development of more compact and resistant fibrin networks. Glycosylation and glycation contribute to altered fibrinogen structural properties, often resulting in changes in fibrin clot density and susceptibility to lysis, particularly in metabolic disorders like diabetes. Acetylation and phosphorylation, influenced by medications such as aspirin, modulate clot architecture by affecting fiber thickness and clot permeability. Citrullination and homocysteinylation, although less studied, are linked to autoimmune conditions and cardiovascular diseases, respectively, affecting fibrin formation and stability. Understanding these modifications provides insights into the pathophysiology of thrombotic disorders and highlights potential therapeutic targets. This review comprehensively examines the current literature on fibrinogen PTMs, their specific sites, biochemical pathways, and their consequences on fibrin clot architecture, clot formation and clot lysis.
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Affiliation(s)
- Francesca Nencini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Firenze, Italy
| | - Alessandra Bettiol
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Flavia Rita Argento
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Firenze, Italy
| | - Serena Borghi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Firenze, Italy
| | - Elvira Giurranna
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Firenze, Italy
| | - Giacomo Emmi
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Domenico Prisco
- Department of Experimental and Clinical Medicine, University of Firenze, Firenze, Italy
| | - Niccolò Taddei
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Firenze, Italy
| | - Claudia Fiorillo
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Firenze, Italy
| | - Matteo Becatti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Firenze, Firenze, Italy.
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2
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Lee JH, Ward KR. Blood failure: traumatic hemorrhage and the interconnections between oxygen debt, endotheliopathy, and coagulopathy. Clin Exp Emerg Med 2024; 11:9-21. [PMID: 38018069 PMCID: PMC11009713 DOI: 10.15441/ceem.23.127] [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: 09/10/2023] [Accepted: 09/28/2023] [Indexed: 11/30/2023] Open
Abstract
This review explores the concept of "blood failure" in traumatic injury, which arises from the interplay of oxygen debt, the endotheliopathy of trauma (EoT), and acute traumatic coagulopathy (ATC). Traumatic hemorrhage leads to the accumulation of oxygen debt, which can further exacerbate hemorrhage by triggering a cascade of events when severe. Such events include EoT, characterized by endothelial glycocalyx damage, and ATC, involving platelet dysfunction, fibrinogen depletion, and dysregulated fibrinolysis. To manage blood failure effectively, a multifaceted approach is crucial. Damage control resuscitation strategies such as use of permissive hypotension, early hemorrhage control, and aggressive transfusion of blood products including whole blood aim to minimize oxygen debt and promote its repayment while addressing endothelial damage and coagulation. Transfusions of red blood cells, plasma, and platelets, as well as the use of tranexamic acid, play key roles in hemostasis and countering ATC. Whole blood, whether fresh or cold-stored, is emerging as a promising option to address multiple needs in traumatic hemorrhage. This review underscores the intricate relationships between oxygen debt, EoT, and ATC and highlights the importance of comprehensive, integrated strategies in the management of traumatic hemorrhage to prevent blood failure. A multidisciplinary approach is essential to address these interconnected factors effectively and to improve patient outcomes.
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Affiliation(s)
- Jae Hyuk Lee
- Department of Emergency Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Kevin R. Ward
- Department of Emergency Medicine, Max Harry Weil Institute for Critical Care Research and Innovation, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
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3
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D’Amore V, Donati G, Lenci E, Ludwig BS, Kossatz S, Baiula M, Trabocchi A, Kessler H, Di Leva FS, Marinelli L. Molecular View on the iRGD Peptide Binding Mechanism: Implications for Integrin Activity and Selectivity Profiles. J Chem Inf Model 2023; 63:6302-6315. [PMID: 37788340 PMCID: PMC10598797 DOI: 10.1021/acs.jcim.3c01071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Indexed: 10/05/2023]
Abstract
Receptor-selective peptides are widely used as smart carriers for specific tumor-targeted delivery. A remarkable example is the cyclic nonapeptide iRGD (CRGDKPGDC, 1) that couples intrinsic cytotoxic effects with striking tumor-homing properties. These peculiar features are based on a rather complex multistep mechanism of action, where the primary event is the recognition of RGD integrins. Despite the high number of preclinical studies and the recent success of a phase I trial for the treatment of pancreatic ductal adenocarcinoma (PDAC), there is little information available about the iRGD three-dimensional (3D) structure and integrin binding properties. Here, we re-evaluate the peptide's affinity for cancer-related integrins including not only the previously known targets αvβ3 and αvβ5 but also the αvβ6 isoform, which is known to drive cell growth, migration, and invasion in many malignancies including PDAC. Furthermore, we use parallel tempering in the well-tempered ensemble (PT-WTE) metadynamics simulations to characterize the in-solution conformation of iRGD and extensive molecular dynamics calculations to fully investigate its binding mechanism to integrin partners. Finally, we provide clues for fine-tuning the peptide's potency and selectivity profile, which, in turn, may further improve its tumor-homing properties.
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Affiliation(s)
- Vincenzo
Maria D’Amore
- Department
of Pharmacy, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Greta Donati
- Department
of Pharmacy, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Elena Lenci
- Department
of Chemistry “Ugo Schiff″, University of Florence, Via della Lastruccia 13, I-50019 Sesto Fiorentino, Florence, Italy
| | - Beatrice Stefanie Ludwig
- Department
of Nuclear Medicine, University Hospital Klinikum Rechts der Isar
and Central Institute for Translational Cancer Research (TranslaTUM), Technical University Munich, Munich 81675, Germany
| | - Susanne Kossatz
- Department
of Nuclear Medicine, University Hospital Klinikum Rechts der Isar
and Central Institute for Translational Cancer Research (TranslaTUM), Technical University Munich, Munich 81675, Germany
- Department
of Chemistry, Institute for Advanced Study, Technical University Munich, Garching 85748, Germany
| | - Monica Baiula
- Department
of Pharmacy and Biotechnology, University
of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Andrea Trabocchi
- Department
of Chemistry “Ugo Schiff″, University of Florence, Via della Lastruccia 13, I-50019 Sesto Fiorentino, Florence, Italy
| | - Horst Kessler
- Department
of Chemistry, Institute for Advanced Study, Technical University Munich, Garching 85748, Germany
| | - Francesco Saverio Di Leva
- Department
of Pharmacy, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
| | - Luciana Marinelli
- Department
of Pharmacy, Università degli Studi
di Napoli “Federico II”, Via D. Montesano 49, 80131 Naples, Italy
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4
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Kuang C, Li D, Zhou X, Lin H, Zhang R, Xu H, Huang S, Tang F, Liu F, Tang D, Dai Y. Proteomic analysis of lysine 2-hydroxyisobutyryl in SLE reveals protein modification alteration in complement and coagulation cascades and platelet activation Pathways. BMC Med Genomics 2023; 16:247. [PMID: 37845672 PMCID: PMC10577913 DOI: 10.1186/s12920-023-01656-y] [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: 05/17/2023] [Accepted: 09/06/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Post-translational modifications (PTMs) are considered to be an important factor in the pathogenesis of Systemic lupus erythematosus (SLE). Lysine 2-hydroxyisobutyryl (Khib), as an emerging post-translational modification of proteins, is involved in some important biological metabolic activities. However, there are poor studies on its correlation with diseases, especially SLE. OBJECTIVE We performed quantitative, comparative, and bioinformatic analysis of Khib proteins in Peripheral blood mononuclear cells (PBMCs) of SLE patients and PBMCs of healthy controls. Searching for pathways related to SLE disease progression and exploring the role of Khib in SLE. METHODS Khib levels in SLE patients and healthy controls were compared based on liquid chromatography tandem mass spectrometry, then proteomic analysis was conducted. RESULTS Compared with healthy controls, Khib in SLE patients was up-regulated at 865 sites of 416 proteins and down-regulated at 630 sites of 349 proteins. The site abundance, distribution and function of Khib protein were investigated further. Bioinformatics analysis showed that Complement and coagulation cascades and Platelet activation in immune-related pathways were significantly enriched, suggesting that differentially modified proteins among them may affect SLE. CONCLUSION Khib in PBMCs of SLE patients was significantly up- or down-regulated compared with healthy controls. Khib modification of key proteins in the Complement and coagulation cascades and Platelet activation pathways affects platelet activation and aggregation, coagulation functions in SLE patients. This result provides a new direction for the possible significance of Khib in the pathogenesis of SLE patients.
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Affiliation(s)
- Chaoying Kuang
- Nephrology Department, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong, 510632, China
- Department of Nephrology, The 924th Hospital of the Chinese People's Liberation Army Joint Logistic Support Force, Guilin, Guangxi, 541002, China
| | - Dandan Li
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, 518020, China
- Experimental Center, Shenzhen Pingle Orthopedic Hospital (Shenzhen Pingshan Traditional Chinese Medicine Hospital), Shenzhen, Guangdong, 518118, China
| | - Xianqing Zhou
- Department of Nephrology, The 924th Hospital of the Chinese People's Liberation Army Joint Logistic Support Force, Guilin, Guangxi, 541002, China
| | - Hua Lin
- Department of Nephrology, The 924th Hospital of the Chinese People's Liberation Army Joint Logistic Support Force, Guilin, Guangxi, 541002, China
| | - Ruohan Zhang
- Department of Nephrology, The 924th Hospital of the Chinese People's Liberation Army Joint Logistic Support Force, Guilin, Guangxi, 541002, China
| | - Huixuan Xu
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, 518020, China
| | - Shaoying Huang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, 518020, China
| | - Fang Tang
- Department of Nephrology, The 924th Hospital of the Chinese People's Liberation Army Joint Logistic Support Force, Guilin, Guangxi, 541002, China
| | - Fanna Liu
- Nephrology Department, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong, 510632, China.
| | - Donge Tang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, 518020, China.
| | - Yong Dai
- Department of Nephrology, The 924th Hospital of the Chinese People's Liberation Army Joint Logistic Support Force, Guilin, Guangxi, 541002, China.
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, 518020, China.
- The First Affiliated Hospital, School of Medicine, Anhui University of Science and Technology, Huainan, Anhui, 232001, China.
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5
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Han CY, Wang X, Ringgold KM, Bennett JC, St John AE, Berenson R, Stern SA, White NJ. A novel melanocortin fusion protein inhibits fibrinogen oxidation and degradation during trauma-induced coagulopathy. Blood 2023; 142:724-741. [PMID: 37363829 DOI: 10.1182/blood.2022019164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/04/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Immune cell inflammation is implicated in the pathophysiology of acute trauma-induced coagulopathy (TIC). We hypothesized that leukocyte inflammation contributes to TIC through the oxidation and proteolysis of fibrinogen. To test this hypothesis, antioxidants and a novel anti-inflammatory melanocortin fusion protein (AQB-565) were used to study the effects of interleukin-6 (IL-6)-stimulated human leukocytes on fibrinogen using single-cell imaging flow cytometry and multiplex fluorescent western blotting. We also studied the effects of AQB-565 on fibrinogen using an in vivo rat trauma model of native TIC. IL-6 induced cellular inflammation and mitochondrial superoxide production in human monocytes, causing fibrinogen oxidation and degradation in vitro. Antioxidants suppressing mitochondrial superoxide reduced oxidative stress and inflammation and protected fibrinogen. AQB-565 decreased inflammation, inhibited mitochondrial superoxide, and protected fibrinogen in vitro. Trauma with hemorrhagic shock increased IL-6 and other proinflammatory cytokines and chemokines, selectively oxidized and degraded fibrinogen, and induced TIC in rats in vivo. AQB-565, given at the onset of hemorrhage, blocked inflammation, protected fibrinogen from oxidation and degradation, and prevented TIC. Leukocyte activation contributes to TIC through the oxidation and degradation of fibrinogen, which involves mitochondrial superoxide and cellular inflammation. Suppression of inflammation by activation of melanocortin pathways may be a novel approach for the prevention and treatment of TIC.
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Affiliation(s)
- Chang Yeop Han
- Department of Emergency Medicine and Resuscitation Engineering Science Unit, University of Washington School of Medicine, Seattle, WA
| | - Xu Wang
- Department of Emergency Medicine and Resuscitation Engineering Science Unit, University of Washington School of Medicine, Seattle, WA
| | - Kristyn M Ringgold
- Department of Emergency Medicine and Resuscitation Engineering Science Unit, University of Washington School of Medicine, Seattle, WA
| | - Jennifer C Bennett
- Department of Emergency Medicine and Resuscitation Engineering Science Unit, University of Washington School of Medicine, Seattle, WA
| | - Alexander E St John
- Department of Emergency Medicine and Resuscitation Engineering Science Unit, University of Washington School of Medicine, Seattle, WA
| | | | - Susan A Stern
- Department of Emergency Medicine and Resuscitation Engineering Science Unit, University of Washington School of Medicine, Seattle, WA
| | - Nathan J White
- Department of Emergency Medicine and Resuscitation Engineering Science Unit, University of Washington School of Medicine, Seattle, WA
- Bloodworks Northwest Research Institute, Seattle, WA
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6
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Tracking oxidation-induced alterations in fibrin clot formation by NMR-based methods. Sci Rep 2021; 11:15691. [PMID: 34344919 PMCID: PMC8333047 DOI: 10.1038/s41598-021-94401-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
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 (T2i) 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.
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7
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Hutanu A, Hauser PC, Moritz B, Kiessig S, Noël A, Stracke JO, Wild M, Schwarz MA. Methionine oxidation of proteins analyzed by affinity capillary electrophoresis in presence of silver(I) and gold(III) ions. Electrophoresis 2021; 42:1209-1216. [PMID: 33651405 PMCID: PMC9291207 DOI: 10.1002/elps.202000355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/25/2021] [Accepted: 02/12/2021] [Indexed: 11/08/2022]
Abstract
Oxidative damage of biopharmaceuticals during manufacturing and storage is a key concern throughout pharmaceutical development. However, few simple and robust analytical methods are available for the determination of oxidation sites. Here, the potential of affinity capillary electrophoresis (ACE) in the separation of proteins with oxidized methionine (Met) residues is shown. Silver(I) and gold(I) ions have the attribute to selectively form complexes with thioethers over sulfoxides. The addition of these ions to the BGE leads to a selective complexation of Met residues and, thus, to a change of charge allowing separation of species according to the different oxidation states of Met. The mechanisms of these interactions are discussed and binding constants for peptides containing Met with silver(I) are calculated. Additionally, the proposed method can be used as an indicator of oxidative stress in large proteins. The presented technique is easily accessible, economical, and has rapid analysis times, adding new approaches to the analytical toolbox of Met sulfoxide detection.
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Affiliation(s)
- Andrei Hutanu
- Pharma Technical Development Europe (Biologics) Analytics, Basel, Switzerland.,Department of Chemistry, University of Basel, Basel, Switzerland
| | - Peter C Hauser
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Bernd Moritz
- Pharma Technical Development Europe (Biologics) Analytics, Basel, Switzerland
| | - Steffen Kiessig
- Pharma Technical Development Europe (Biologics) Analytics, Basel, Switzerland
| | - Aurélie Noël
- Pharma Technical Development Europe (Biologics) Analytics, Basel, Switzerland
| | - Jan O Stracke
- Pharma Technical Development Europe (Biologics) Analytics, Basel, Switzerland
| | - Markus Wild
- Pharma Technical Development Europe (Biologics) Analytics, Basel, Switzerland
| | - Maria A Schwarz
- Department of Chemistry, University of Basel, Basel, Switzerland.,Business Unit Biopharmaceuticals, Solvias AG, Kaiseraugst, Switzerland
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8
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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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9
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Smith J, McMullen P, Yuan Z, Pfaendtner J, Jiang S. Elucidating Molecular Design Principles for Charge-Alternating Peptides. Biomacromolecules 2019; 21:435-443. [DOI: 10.1021/acs.biomac.9b01191] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Josh Smith
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
| | - Patrick McMullen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
| | - Zhefan Yuan
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
| | - Shaoyi Jiang
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195-1750, United States
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10
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Yurina LV, Vasilyeva AD, Bugrova AE, Indeykina MI, Kononikhin AS, Nikolaev EN, Rosenfeld MA. Hypochlorite-Induced Oxidative Modification of Fibrinogen. DOKL BIOCHEM BIOPHYS 2019; 484:37-41. [DOI: 10.1134/s1607672919010101] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Indexed: 12/22/2022]
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11
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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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12
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Yurina L, Vasilyeva A, Indeykina M, Bugrova A, Biryukova M, Kononikhin A, Nikolaev E, Rosenfeld M. Ozone-induced damage of fibrinogen molecules: identification of oxidation sites by high-resolution mass spectrometry. Free Radic Res 2019; 53:430-455. [DOI: 10.1080/10715762.2019.1600686] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lyubov Yurina
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexandra Vasilyeva
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria Indeykina
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Anna Bugrova
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Marina Biryukova
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey Kononikhin
- Moskovskij Fiziko-Tehniceskij Institut, Dolgoprudnyi, Russian Federation
| | - Evgene Nikolaev
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Moscow, Russian Federation
| | - Mark Rosenfeld
- N.M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russian Federation
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13
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Becatti M, Emmi G, Bettiol A, Silvestri E, Di Scala G, Taddei N, Prisco D, Fiorillo C. Behçet's syndrome as a tool to dissect the mechanisms of thrombo-inflammation: clinical and pathogenetic aspects. Clin Exp Immunol 2018; 195:322-333. [PMID: 30472725 DOI: 10.1111/cei.13243] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2018] [Indexed: 01/01/2023] Open
Abstract
Behçet's syndrome (BS) is a complex disease with different organ involvement. The vascular one is the most intriguing, considering the existence of a specific group of patients suffering from recurrent vascular events involving the venous and, more rarely, the arterial vessels. Several clinical clues suggest the inflammatory nature of thrombosis in BS, especially of the venous involvement, thus BS is considered a model of inflammation-induced thrombosis. Unique among other inflammatory conditions, venous involvement (together with the arterial one) is currently treated with immunosuppressants, rather than with anti-coagulants. Although many in-vitro studies have suggested the different roles of the multiple players involved in clot formation, in-vivo models are crucial to study this process in a physiological context. At present, no clear mechanisms describing the pathophysiology of thrombo-inflammation in BS exist. Recently, we focused our attention on BS patients as a human in-vivo model of inflammation-induced thrombosis to investigate a new mechanism of clot formation. Indeed, fibrinogen displays a critical role not only in inflammatory processes, but also in clot formation, both in the fibrin network and in platelet aggregation. Reactive oxygen species (ROS)-derived modifications represent the main post-translational fibrinogen alterations responsible for structural and functional changes. Recent data have revealed that neutrophils (pivotal in the pathogenetic mechanisms leading to BS damage) promote fibrinogen oxidation and thrombus formation in BS. Altogether, these new findings may help understand the pathogenetic bases of inflammation-induced thrombosis and, more importantly, may suggest potential targets for innovative therapeutic approaches.
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Affiliation(s)
- M Becatti
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', University of Firenze, Italy
| | - G Emmi
- Department of Experimental and Clinical Medicine, University of Firenze, Italy
| | - A Bettiol
- Department of Experimental and Clinical Medicine, University of Firenze, Italy.,Department of Neurosciences, Psychology, Pharmacology and Child Health (NEUROFARBA), University of Firenze, Italy
| | - E Silvestri
- Department of Experimental and Clinical Medicine, University of Firenze, Italy
| | - G Di Scala
- Department of Experimental and Clinical Medicine, University of Firenze, Italy
| | - N Taddei
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', University of Firenze, Italy
| | - D Prisco
- Department of Experimental and Clinical Medicine, University of Firenze, Italy
| | - C Fiorillo
- Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', University of Firenze, Italy
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14
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Rosenfeld MA, Vasilyeva AD, Yurina LV, Bychkova AV. Oxidation of proteins: is it a programmed process? Free Radic Res 2017; 52:14-38. [DOI: 10.1080/10715762.2017.1402305] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mark A. Rosenfeld
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexandra D. Vasilyeva
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Lyubov V. Yurina
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Bychkova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
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15
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Bychkova AV, Vasilyeva AD, Bugrova AE, Indeykina MI, Kononikhin AS, Nikolaev EN, Konstantinova ML, Rosenfeld MA. Oxidation-induced modification of the fibrinogen polypeptide chains. DOKL BIOCHEM BIOPHYS 2017; 474:173-177. [PMID: 28726089 DOI: 10.1134/s1607672917030115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Indexed: 11/22/2022]
Abstract
By using the mass-spectrometry method, the oxidative modifications of the fibrinogen Aα, Bβ, and γ polypeptide chains induced by its oxidation have been studied. The αC-region has been proven to be the most vulnerable target for the oxidizer (ozone) as compared with the other structural elements of the Aα chain. The Bβ chain mapping shows that the oxidative sites are localized within all the structural elements of the chain in which the β-nodule exhibits high susceptibility to oxidation. The γ chains are the least vulnerable to the oxidizer action. The results obtained demonstrate convincingly that the self-assembly centers dealing with interactions of knob "A": hole "a" are not involved in oxidative modification. It is concluded that the numerous oxidative sites revealed are mainly responsible for inhibiting lateral aggregation of protofibrils. The part of amino acid residues subjected to oxidation is supposed to carry out the antioxidant function.
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Affiliation(s)
- A V Bychkova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia.
| | - A D Vasilyeva
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - A E Bugrova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - M I Indeykina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - A S Kononikhin
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia.,Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow oblast, Russia
| | - E N Nikolaev
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia.,Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,Skolkovo Institute of Science and Technology, ul. Novaya 100, Skolkovo, 143025, Russia
| | - M L Konstantinova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - M A Rosenfeld
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
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16
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Bjerkvig CK, Strandenes G, Eliassen HS, Spinella PC, Fosse TK, Cap AP, Ward KR. "Blood failure" time to view blood as an organ: how oxygen debt contributes to blood failure and its implications for remote damage control resuscitation. Transfusion 2017; 56 Suppl 2:S182-9. [PMID: 27100755 DOI: 10.1111/trf.13500] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 01/08/2023]
Abstract
Hemorrhagic shock is both a local and systemic disorder. In the context of systemic effects, blood loss may lead to levels of reduced oxygen delivery (DO2 ) sufficient to cause tissue ischemia. Similar to other physiologic debts such as sleep, it is not possible to incur a significant oxygen debt and suffer no consequences for lack of timely repayment. While the linkage between oxygen debt and traditional organ failure (renal, hepatic, lung, and circulation) has been long recognized, we should consider failure in two additional linked and very dynamic organ systems, the endothelium and blood. These systems are very sensitive to oxygen debt and at risk for failing, having further implications on all other organ systems. The degree of damage to the endothelium is largely modulated by the degree of oxygen debt. Thus hypoperfusion is believed to begin a cascade of events leading to acute traumatic coagulopathy (ATC). This combination of oxygen debt driven endothelial damage and ATC might be considered collectively as "blood failure" due to the highly connected networks between these drivers. This article presents the implications of oxygen debt for remote damage control resuscitation strategies, such as permissive hypotension and hemostatic resuscitation. We review the impact of whole blood resuscitation and red blood cell efficacy in mitigation of oxygen debt. At last, this article recognizes the need for simple and durable, lightweight equipment that can detect the adequacy of tissue DO2 and thus patient needs for resuscitative care. Point-of-care lactate measuring may be a predictive tool for identifying high-risk trauma patients and occult shock because it provides information beyond that of vital signs and mechanism of injury as it may help predict the level of oxygen debt accumulation and need for resuscitation. Serial measurements may also be valuable as a tool in guiding resuscitative efforts.
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Affiliation(s)
- Christopher K Bjerkvig
- Norwegian Naval Special Operations Command , Haukeland University Hospital, Bergen, Norway.,Department of Anesthesia and Intensive Care , Haukeland University Hospital, Bergen, Norway
| | - Geir Strandenes
- Norwegian Naval Special Operations Command , Haukeland University Hospital, Bergen, Norway.,Department of Immunology and Transfusion Medicine, Haukeland University Hospital, Bergen, Norway
| | - Håkon S Eliassen
- Department of Immunology and Transfusion Medicine, Haukeland University Hospital, Bergen, Norway
| | - Philip C Spinella
- Division of Pediatric Critical Care, Department of Pediatrics, Washington University in St Louis, St Louis, Missouri.,Coagulation and Blood Research, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas
| | - Theodor K Fosse
- Norwegian Naval Special Operations Command , Haukeland University Hospital, Bergen, Norway.,Department of Anesthesia and Intensive Care , Haukeland University Hospital, Bergen, Norway
| | - Andrew P Cap
- Blood Research Program, U.S. Army Institute of Surgical Research, Fort Sam Houston, Texas
| | - Kevin R Ward
- Michigan Center for Integrative Research in Critical Care; Department of Emergency Medicine, University of Michigan, Ann Arbor, Michigan
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17
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Han M, Xu J, Ren Y. Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method. J Mol Graph Model 2016; 72:136-147. [PMID: 28092832 DOI: 10.1016/j.jmgm.2016.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 12/18/2016] [Accepted: 12/23/2016] [Indexed: 10/20/2022]
Abstract
Intrinsically disordered proteins (IDPs) are a class of proteins that expected to be largely unstructured under physiological conditions. Due to their heterogeneous nature, experimental characterization of IDP is challenging. Temperature replica exchange molecular dynamics (T-REMD) is a widely used enhanced sampling method to probe structural characteristics of these proteins. However, its application has been hindered due to its tremendous computational cost, especially when simulating large systems in explicit solvent. Two methods, parallel tempering well-tempered ensemble (PT-WTE) and replica exchange with solute tempering (REST), have been proposed to alleviate the computational expense of T-REMD. In this work, we select three different IDP systems to compare the sampling characteristics and efficiencies of the two methods Both the two methods could efficiently sample the conformational space of IDP and yield highly consistent results for all the three IDPs. The efficiencies of the two methods: are compatible, with about 5-6 times better than the plain T-REMD. Besides, the advantages and disadvantages of each method are also discussed. Specially, the PT-WTE method could provide temperature dependent data of the system which could not be achieved by REST, while the REST method could readily be used to a part of the system, which is quite efficient to simulate some biological processes.
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Affiliation(s)
- Mengzhi Han
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Xu
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Ying Ren
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
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18
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Han M, Xu J, Ren Y. Compromise in competition between free energy and binding effect of intrinsically disordered protein p53 C-terminal domain. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1237023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Mengzhi Han
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, R.C. China
- University of Chinese Academy of Sciences, Beijing, R.C. China
| | - Ji Xu
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, R.C. China
| | - Ying Ren
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, R.C. China
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19
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White NJ, Wang Y, Fu X, Cardenas JC, Martin EJ, Brophy DF, Wade CE, Wang X, St John AE, Lim EB, Stern SA, Ward KR, López JA, Chung D. Post-translational oxidative modification of fibrinogen is associated with coagulopathy after traumatic injury. Free Radic Biol Med 2016; 96:181-9. [PMID: 27105953 PMCID: PMC4912420 DOI: 10.1016/j.freeradbiomed.2016.04.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/13/2016] [Accepted: 04/17/2016] [Indexed: 12/16/2022]
Abstract
Victims of trauma often develop impaired blood clot formation (coagulopathy) that contributes to bleeding and mortality. Fibrin polymerization is one critical component of clot formation that can be impacted by post-translational oxidative modifications of fibrinogen after exposure to oxidants. In vitro evidence suggests that Aα-C domain methionine sulfoxide formation, in particular, can induce conformational changes that prevent lateral aggregation of fibrin protofibrils during polymerization. We used mass spectrometry of plasma from trauma patients to find that fibrinogen Aα-C domain methionine sulfoxide content was selectively-increased in patients with coagulopathy vs. those without coagulopathy. This evidence supports a novel linkage between oxidative stress, coagulopathy, and bleeding after injury.
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Affiliation(s)
- Nathan J White
- University of Washington Division of Emergency Medicine, Harborview Medical Center, Box 359702, 325 9th Avenue, Seattle, WA 98104, USA; Bloodworks Northwest Research Institute, 1551 Eastlake Avenue E, Seattle, WA 98102, USA.
| | - Yi Wang
- Bloodworks Northwest Research Institute, 1551 Eastlake Avenue E, Seattle, WA 98102, USA
| | - Xiaoyun Fu
- Bloodworks Northwest Research Institute, 1551 Eastlake Avenue E, Seattle, WA 98102, USA
| | - Jessica C Cardenas
- Center for Translational Injury Research and Division of Acute Care Surgery, University of Texas Health Science Center at Houston, 6431 Fannin St. MSB 5.240, Houston, TX 77030, USA
| | - Erika J Martin
- Department of Pharmacotherapy & Outcomes Science, School of Pharmacy, 410 N 12th Street, P.O. Box 980533, Richmond, VA 23298, USA
| | - Donald F Brophy
- Department of Pharmacotherapy & Outcomes Science, School of Pharmacy, 410 N 12th Street, P.O. Box 980533, Richmond, VA 23298, USA
| | - Charles E Wade
- Center for Translational Injury Research and Division of Acute Care Surgery, University of Texas Health Science Center at Houston, 6431 Fannin St. MSB 5.240, Houston, TX 77030, USA
| | - Xu Wang
- University of Washington Division of Emergency Medicine, Harborview Medical Center, Box 359702, 325 9th Avenue, Seattle, WA 98104, USA
| | - Alexander E St John
- University of Washington Division of Emergency Medicine, Harborview Medical Center, Box 359702, 325 9th Avenue, Seattle, WA 98104, USA
| | - Esther B Lim
- University of Washington Division of Emergency Medicine, Harborview Medical Center, Box 359702, 325 9th Avenue, Seattle, WA 98104, USA
| | - Susan A Stern
- University of Washington Division of Emergency Medicine, Harborview Medical Center, Box 359702, 325 9th Avenue, Seattle, WA 98104, USA
| | - Kevin R Ward
- Michigan Center for Integrative Research in Critical Care, University of Michigan, Building 10-103A North Campus Research Complex 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| | - José A López
- Bloodworks Northwest Research Institute, 1551 Eastlake Avenue E, Seattle, WA 98102, USA
| | - Dominic Chung
- Bloodworks Northwest Research Institute, 1551 Eastlake Avenue E, Seattle, WA 98102, USA
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20
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Simulation of coupled folding and binding of an intrinsically disordered protein in explicit solvent with metadynamics. J Mol Graph Model 2016; 68:114-127. [PMID: 27423742 DOI: 10.1016/j.jmgm.2016.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 06/22/2016] [Accepted: 06/29/2016] [Indexed: 11/22/2022]
Abstract
The C-terminal domain of measles virus nucleoprotein is an intrinsically disordered protein that could bind to the X domain (XD) of phosphoprotein P to exert its physiological function. Experiments reveal that the minimal binding unit is a 21-residue α-helical molecular recognition element (α-MoRE-MeV), which adopts a fully helical conformation upon binding to XD. Due to currently limited computing power, direct simulation of this coupled folding and binding process with atomic force field in explicit solvent cannot be achieved. In this work, two advanced sampling methods, metadynamics and parallel tempering, are combined to characterize the free energy surface of this process and investigate the underlying mechanism. Starting from an unbound and partially folded state of α-MoRE-MeV, multiple folding and binding events are observed during the simulation and the energy landscape was well estimated. The results demonstrate that the isolated α-MoRE-MeV resembles a molten globule and rapidly interconverts between random coil and multiple partially helical states in solution. The coupled folding and binding process occurs through the induced fit mechanism, with the residual helical conformations providing the initial binding sites. Upon binding, α-MoRE-MeV can easily fold into helical conformation without obvious energy barriers. Two mechanisms, namely, the system tending to adopt the structure in which the free energy of isolated α-MoRE-MeV is the minimum, and the binding energy of α-MoRE-MeV to its partner protein XD tending to the minimum, jointly dominate the coupled folding and binding process. With the advanced sampling approach, more IDP systems could be simulated and common mechanisms concerning the coupled folding and binding process could be investigated in the future.
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21
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Rosenfeld MA, Bychkova AV, Shchegolikhin AN, Leonova VB, Kostanova EA, Biryukova MI, Sultimova NB, Konstantinova ML. Fibrin self-assembly is adapted to oxidation. Free Radic Biol Med 2016; 95:55-64. [PMID: 26969792 DOI: 10.1016/j.freeradbiomed.2016.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/29/2016] [Accepted: 03/07/2016] [Indexed: 10/22/2022]
Abstract
Fibrinogen is extremely susceptible to attack by reactive oxygen species (ROS). Having been suffered an oxidative modification, the fibrinogen molecules, now with altered spatial structure and function of fibrin network, affect hemostasis differently. However, the potential effects of the oxidative stress on the early stages of the fibrin self-assembly process remain unexplored. To clarify the damaging influence of ROS on the knob 'A': hole 'a' and the D:D interactions, the both are operating on the early stages of the fibrin polymerization, we have used a novel approach based on exploration of FXIIIa-mediated self-assembly of the cross-linked fibrin oligomers dissolved in the moderately concentrated urea solutions. The oligomers were composed of monomeric desA fibrin molecules created by cleaving the fibrinopeptides A off the fibrinogen molecules with a thrombin-like enzyme, reptilase. According to the UV-absorbance and fluorescence measurements data, the employed low ozone/fibrinogen ratios have induced only a slight fibrinogen oxidative modification that was accompanied by modest chemical transformations of the aromatic amino acid residues of the protein. Else, a slight consumption of the accessible tyrosine residues has been observed due to intermolecular dityrosine cross-links formation. The set of experimental data gathered with the aid of electrophoresis, elastic light scattering and analytical centrifugation has clearly witnessed that the oxidation can serve as an effective promoter for the observed enhanced self-assembly of the covalently cross-linked oligomers. At urea concentration of 1.20M, the pristine and oxidized fibrin oligomers were found to comprise a heterogeneous set of the double-stranded protofibrils that are cross-linked only by γ-γ dimers and the fibers consisting on average of four strands that are additionally linked by α polymers. The amounts of the oxidized protofibrils and the fibers accumulated in the system were higher than those of the non-oxidized counterparts. Moreover, the γ and α polypeptide chains of the oxidized molecules were more readily crosslinked by the FXIIIa. Upon increasing the urea solution concentration to 4.20M, the cross-linked double-stranded desA fibrin protofibrils have dissociated into the single-stranded fibrin oligomers, whereas the fibers dissociated into both the double-stranded desA fibrin oligomers, the structural integrity of the latter being maintained by means of the intermolecular α polymers, and the single-stranded fibrin oligomers cross-linked only by γ-γ dimers. The data we have obtained in this study indicate that the FXIIIa-mediated process of assembling the cross-linked protofibrils and the fibers constructed from the oxidized monomeric fibrin molecules was facilitated due to the strengthening of D:D interactions. The findings infer that the enhanced longitudinal D:D interactions become more essential in the assembly of soluble protofibrils when the interactions knobs 'A': holes 'a' are injured by oxidation. The new experimental findings presented here could be of help for elucidating the essential adaptive molecular mechanisms capable of mitigating the detrimental action of ROS in the oxidatively damaged fibrin self-assemblage processes.
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Affiliation(s)
- Mark A Rosenfeld
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia.
| | - Anna V Bychkova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
| | - Alexander N Shchegolikhin
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
| | - Vera B Leonova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
| | - Elizaveta A Kostanova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
| | - Marina I Biryukova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
| | - Natalia B Sultimova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
| | - Marina L Konstantinova
- N. M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4, Kosygina str., 119334 Moscow, Russia
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22
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Valsson O, Tiwary P, Parrinello M. Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint. Annu Rev Phys Chem 2016; 67:159-84. [DOI: 10.1146/annurev-physchem-040215-112229] [Citation(s) in RCA: 355] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Omar Valsson
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o Università della Swizzera Italiana Campus, 6900 Lugano, Switzerland;
- Facoltà di Informatica, Instituto di Scienze Computationali, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Pratyush Tiwary
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Michele Parrinello
- Department of Chemistry and Applied Biosciences, ETH Zurich, c/o Università della Swizzera Italiana Campus, 6900 Lugano, Switzerland;
- Facoltà di Informatica, Instituto di Scienze Computationali, Università della Svizzera Italiana, 6900 Lugano, Switzerland
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23
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Rosenfeld MA, Leonova VB, Bychkova AV, Kostanova EA, Biryukova MI, Sultimova NB, Konstantinova ML, Gorobets MG. The strengthening role of D:D interactions in fibrin self-assembly under oxidation. DOKL BIOCHEM BIOPHYS 2016; 466:28-31. [PMID: 27025482 DOI: 10.1134/s1607672916010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 11/23/2022]
Abstract
The effect on ozone-induced oxidation on the self-assembly of fibrin in the presence of fibrin-stabilizing factor FXIIIa of soluble cross-linked fibrin oligomers was studied in a medium containing moderate urea concentrations. It is established that fibrin oligomers were formed by the protofibrils cross-linked through γ-γ dimers and the fibrils additionally cross-linked by through α-polymers. The oxidation promoted both the accumulation of greater amounts of γ-γ dimers and the formation of protofibrils, fibrils, and their dissociation products emerging with increasing urea concentrations, which have a high molecular weight. It is concluded that the oxidation enhances the axial interactions between D-regions of fibrin molecules.
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Affiliation(s)
- M A Rosenfeld
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow, 117977, Russia.
| | - V B Leonova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow, 117977, Russia
| | - A V Bychkova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow, 117977, Russia
| | - E A Kostanova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow, 117977, Russia
| | - M I Biryukova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow, 117977, Russia
| | - N B Sultimova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow, 117977, Russia
| | - M L Konstantinova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow, 117977, Russia
| | - M G Gorobets
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow, 117977, Russia
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24
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Iron modulates the alpha chain of fibrinogen. Biometals 2016; 29:235-8. [DOI: 10.1007/s10534-016-9909-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/31/2015] [Indexed: 10/22/2022]
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25
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Regulation of thrombosis and vascular function by protein methionine oxidation. Blood 2015; 125:3851-9. [PMID: 25900980 DOI: 10.1182/blood-2015-01-544676] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/14/2015] [Indexed: 02/07/2023] Open
Abstract
Redox biology is fundamental to both normal cellular homeostasis and pathological states associated with excessive oxidative stress. Reactive oxygen species function not only as signaling molecules but also as redox regulators of protein function. In the vascular system, redox reactions help regulate key physiologic responses such as cell adhesion, vasoconstriction, platelet aggregation, angiogenesis, inflammatory gene expression, and apoptosis. During pathologic states, altered redox balance can cause vascular cell dysfunction and affect the equilibrium between procoagulant and anticoagulant systems, contributing to thrombotic vascular disease. This review focuses on the emerging role of a specific reversible redox reaction, protein methionine oxidation, in vascular disease and thrombosis. A growing number of cardiovascular and hemostatic proteins are recognized to undergo reversible methionine oxidation, in which methionine residues are posttranslationally oxidized to methionine sulfoxide. Protein methionine oxidation can be reversed by the action of stereospecific enzymes known as methionine sulfoxide reductases. Calcium/calmodulin-dependent protein kinase II is a prototypical methionine redox sensor that responds to changes in the intracellular redox state via reversible oxidation of tandem methionine residues in its regulatory domain. Several other proteins with oxidation-sensitive methionine residues, including apolipoprotein A-I, thrombomodulin, and von Willebrand factor, may contribute to vascular disease and thrombosis.
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26
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Abstract
PURPOSE OF REVIEW Hemorrhage is the leading cause of potentially preventable death following injury. Excessive and uncontrolled bleeding, commonly referred to as trauma-induced coagulopathy (TIC), affects a quarter of all trauma patients and is associated with substantial injuries, increased transfusion requirements, and poor outcomes. Recent data have contributed to our current understanding of the molecular mechanisms driving TIC. RECENT FINDINGS The current literature offers evidence supporting proposed mechanisms that induce TIC, such as platelet dysfunction, endogenous anticoagulation, endothelial activation, fibrinogen modifications, and hyperfibrinolysis. However, the majority of these data are mere associations; causative data are slowly unfolding through the utilization of animal models of hemorrhagic shock coupled with prospective observational clinical studies. SUMMARY As both clinical and basic science research expands our understanding of TIC, trauma patient care is improving substantially. Future studies should focus on the interplay between the coagulation pathways whose simultaneous or codependent dysregulation could offer the most advantageous points for intervention.
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27
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28
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Palazzesi F, Prakash MK, Bonomi M, Barducci A. Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States. J Chem Theory Comput 2014; 11:2-7. [DOI: 10.1021/ct500718s] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ferruccio Palazzesi
- Department
of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, CH-8093 Zurich, Switzerland
- Facoltá
di Informatica, Istituto di Scienze Computazionali, Universitá della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Meher K. Prakash
- Theoretical
Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur,
Bangalore, Karnataka, 500064, India
| | - Massimiliano Bonomi
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Alessandro Barducci
- Laboratoire
de Biophysique Statistique, Ècole Polytechnique Fèdèrale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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