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Mapping the Prothrombin Binding Site of Pseutarin C by Site-directed PEGylation. Blood 2022; 139:2972-2982. [PMID: 35148539 PMCID: PMC9101250 DOI: 10.1182/blood.2021014878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/26/2022] [Indexed: 11/24/2022] Open
Abstract
Results support our previously published model and reveal the surprising role of the a1-loop in presenting Arg320 for initial cleavage. Using pseutarin C as model prothrombinase, the interaction site for prothrombin was probed by site-directed PEGylation and other mutations.
The prothrombinase complex processes prothrombin to thrombin through sequential cleavage at Arg320 followed by Arg271 when cofactor, factor (f) Va, protease, fXa, and substrate, prothrombin, are all bound to the same membrane surface. In the absence of the membrane or cofactor, cleavage occurs in the opposite order. For the less favorable cleavage site at Arg320 to be cleaved first, it is thought that prothrombin docks on fVa in a way that presents Arg320 and hides Arg271 from the active site of fXa. Based on the crystal structure of the prothrombinase complex from the venom of the Australian eastern brown snake, pseutarin C, we modeled an initial prothrombin docking mode, which involved an interaction with discrete portions of the A1 and A2 domains of fV and the loop connecting the 2 domains, known as the a1-loop. We interrogated the proposed interface by site-directed PEGylation and by swapping the a1-loop in pseutarin C with that of human fV and fVIII and measuring the effect on rate and pathway of thrombin generation. PEGylation of residues within our proposed binding site greatly reduced the rate of thrombin generation, without affecting the pathway, whereas those outside the proposed interface had no effect. PEGylation of residues within the a1-loop also reduced the rate of thrombin generation. The sequence of the a1-loop was found to play a critical role in prothrombin binding and in the presentation of Arg320 for initial cleavage.
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Ohkubo YZ, Madsen JJ. Uncovering Membrane-Bound Models of Coagulation Factors by Combined Experimental and Computational Approaches. Thromb Haemost 2021; 121:1122-1137. [PMID: 34214998 PMCID: PMC8432591 DOI: 10.1055/s-0040-1722187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In the life sciences, including hemostasis and thrombosis, methods of structural biology have become indispensable tools for shedding light on underlying mechanisms that govern complex biological processes. Advancements of the relatively young field of computational biology have matured to a point where it is increasingly recognized as trustworthy and useful, in part due to their high space–time resolution that is unparalleled by most experimental techniques to date. In concert with biochemical and biophysical approaches, computational studies have therefore proven time and again in recent years to be key assets in building or suggesting structural models for membrane-bound forms of coagulation factors and their supramolecular complexes on membrane surfaces where they are activated. Such endeavors and the proposed models arising from them are of fundamental importance in describing and understanding the molecular basis of hemostasis under both health and disease conditions. We summarize the body of work done in this important area of research to drive forward both experimental and computational studies toward new discoveries and potential future therapeutic strategies.
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Affiliation(s)
- Y Zenmei Ohkubo
- Department of Bioinformatics, School of Life and Natural Sciences, Abdullah Gül University, Kayseri, Turkey
| | - Jesper J Madsen
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida, United States
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3
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Zhang DL, Xue F, Dou XQ, Liu XF, Fu RF, Chen YF, Liu W, Jia YJ, Wang YH, Xiao ZJ, Zhang L, Yang RC. [Clinical and genetic analyses of hereditary factor Ⅴ deficiency cases]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2021; 42:302-307. [PMID: 33979974 PMCID: PMC8120128 DOI: 10.3760/cma.j.issn.0253-2727.2021.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 11/05/2022]
Abstract
Objective: To analyze the clinical phenotype and molecular pathogenesis of nine patients with hereditary factor Ⅴ (FⅤ) deficiency. Methods: Nine patients with hereditary FⅤ deficiency who were admitted to the Institute of Hematology and Blood Diseases Hospital from April 1999 to September 2019 were analyzed. The activated partial thromboplastin time, prothrombin time, and FⅤ procoagulant activity (FⅤ∶C) were measured for phenotypic diagnosis. High-throughput sequencing was employed for the F5 gene mutation screening, Sanger sequencing was adopted to confirm candidate variants and parental carrying status, Swiss-model was used for three-dimensional structure analysis, and ClustalX v.2.1 was used for homologous analysis. Results: The FⅤ∶C of the nine patients ranged from 0.1 to 10.6. Among them, eight had a hemorrhage history, with kin/mucosal bleeding as the most common symptom (three cases, 37.5%) , whereas one case had no bleeding symptom. There were five homozygotes and four compound heterozygotes. A total of 12 pathogenic or likely pathogenic mutations were detected, of which c.6100C>A/p.Pro2034Thr, c.6575T>C/p.Phe2192Ser, c.1600_1601delinsTG/p. Gln534*, c.4713C>A/p.Tyr1571*, and c.952+5G>C were reported for the first time. Conclusion: The newly discovered gene mutations enriched the F5 gene mutation spectrum associated with hereditary FⅤ deficiency. High-throughput sequencing could be an effective method to detect F5 gene mutations.
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Affiliation(s)
- D L Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - F Xue
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - X Q Dou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - X F Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - R F Fu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Y F Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - W Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Y J Jia
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Y H Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Z J Xiao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - L Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - R C Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
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Gierula M, Salles‐Crawley II, Santamaria S, Teraz‐Orosz A, Crawley JTB, Lane DA, Ahnström J. The roles of factor Va and protein S in formation of the activated protein C/protein S/factor Va inactivation complex. J Thromb Haemost 2019; 17:2056-2068. [PMID: 31364267 PMCID: PMC6916587 DOI: 10.1111/jth.14594] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/26/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Activated protein C (APC)-mediated inactivation of factor (F)Va is greatly enhanced by protein S. For inactivation to occur, a trimolecular complex among FVa, APC, and protein S must form on the phospholipid membrane. However, direct demonstration of complex formation has proven elusive. OBJECTIVES To elucidate the nature of the phospholipid-dependent interactions among APC, protein S, and FVa. METHODS We evaluated binding of active site blocked APC to phospholipid-coated magnetic beads in the presence and absence of protein S and/or FVa. The importance of protein S and FV residues were evaluated functionally. RESULTS Activated protein C alone bound weakly to phospholipids. Protein S mildly enhanced APC binding to phospholipid surfaces, whereas FVa did not. However, FVa together with protein S enhanced APC binding (>14-fold), demonstrating formation of an APC/protein S/FVa complex. C4b binding protein-bound protein S failed to enhance APC binding, agreeing with its reduced APC cofactor function. Protein S variants (E36A and D95A) with reduced APC cofactor function exhibited essentially normal augmentation of APC binding to phospholipids, but diminished APC/protein S/FVa complex formation, suggesting involvement in interactions dependent upon FVa. Similarly, FVaNara (W1920R), an APC-resistant FV variant, also did not efficiently incorporate into the trimolecular complex as efficiently as wild-type FVa. FVa inactivation assays suggested that the mutation impairs its affinity for phospholipid membranes and with protein S within the complex. CONCLUSIONS FVa plays a central role in the formation of its inactivation complex. Furthermore, membrane proximal interactions among FVa, APC, and protein S are essential for its cofactor function.
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Affiliation(s)
| | | | | | | | | | - David A. Lane
- Centre for HaematologyImperial College LondonLondonUK
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Schreuder M, Reitsma PH, Bos MHA. Blood coagulation factor Va's key interactive residues and regions for prothrombinase assembly and prothrombin binding. J Thromb Haemost 2019; 17:1229-1239. [PMID: 31102425 PMCID: PMC6851895 DOI: 10.1111/jth.14487] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 05/02/2019] [Accepted: 05/07/2019] [Indexed: 11/28/2022]
Abstract
Blood coagulation factor Va serves an indispensable role in hemostasis as cofactor for the serine protease factor Xa. In the presence of an anionic phospholipid membrane and calcium ions, factors Va and Xa assemble into the prothrombinase complex. Following formation of the ternary complex with the macromolecular zymogen substrate prothrombin, the latter is rapidly converted into thrombin, the key regulatory enzyme of coagulation. Over the years, multiple binding sites have been identified in factor Va that play a role in the interaction of the cofactor with factor Xa, prothrombin, or the anionic phospholipid membrane surface. In this review, an overview of the currently available information on these interactive sites in factor Va is provided, and data from biochemical approaches and 3D structural protein complex models are discussed. The structural models have been generated in recent years and provide novel insights into the molecular requirements for assembly of both the prothrombinase and the ternary prothrombinase-prothrombin complexes. Integrated knowledge of functionally important regions in factor Va will allow for a better understanding of factor Va cofactor activity.
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Affiliation(s)
- Mark Schreuder
- Division of Thrombosis and HemostasisEinthoven Laboratory for Vascular and Regenerative MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Pieter H. Reitsma
- Division of Thrombosis and HemostasisEinthoven Laboratory for Vascular and Regenerative MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Mettine H. A. Bos
- Division of Thrombosis and HemostasisEinthoven Laboratory for Vascular and Regenerative MedicineLeiden University Medical CenterLeidenThe Netherlands
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Chaves R, Dahmane S, Odorico M, Nicolaes G, Pellequer JL. Factor Va alternative conformation reconstruction using atomic force microscopy. Thromb Haemost 2017; 112:1167-73. [DOI: 10.1160/th14-06-0481] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 07/15/2014] [Indexed: 01/15/2023]
Abstract
SummaryProtein conformational variability (or dynamics) for large macromolecules and its implication for their biological function attracts more and more attention. Collective motions of domains increase the ability of a protein to bind to partner molecules. Using atomic force microscopy (AFM) topographic images, it is possible to take snapshots of large multi-component macromolecules at the single molecule level and to reconstruct complete molecular conformations. Here, we report the application of a reconstruction protocol, named AFM-assembly, to characterise the conformational variability of the two C domains of human coagulation factor Va (FVa). Using AFM topographic surfaces obtained in liquid environment, it is shown that the angle between C1 and C2 domains of FVa can vary between 40° and 166°. Such dynamical variation in C1 and C2 domain arrangement may have important implications regarding the binding of FVa to phospholipid membranes.
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Abstract
Human coagulation FXa (Factor Xa) plays a key role in blood coagulation by activating prothrombin to thrombin on 'stimulated' platelet membranes in the presence of its cofactor FVa (Factor Va). PS (phosphatidylserine) exposure on activated platelet membranes promotes prothrombin activation by FXa by allosterically regulating FXa. To identify the structural basis of this allosteric regulation, we used FRET to monitor changes in FXa length in response to (i) soluble short-chain PS [C6PS (dicaproylphosphatidylserine)], (ii) PS membranes, and (iii) FVa in the presence of C6PS and membranes. We incorporated a FRET pair with donor (fluorescein) at the active site and acceptor (Alexa Fluor® 555) at the FXa N-terminus near the membrane. The results demonstrated that FXa structure changes upon binding of C6PS to two sites: a regulatory site at the N-terminus [identified previously as involving the Gla (γ-carboxyglutamic acid) and EGFN (N-terminus of epidermal growth factor) domains] and a presumptive protein-recognition site in the catalytic domain. Binding of C6PS to the regulatory site increased the interprobe distance by ~3 Å (1 Å=0.1 nm), whereas saturation of both sites increased the distance by a further ~6.4 Å. FXa binding to a membrane produced a smaller increase in length (~1.4 Å), indicating that FXa has a somewhat different structure on a membrane from when bound to C6PS in solution. However, when both FVa2 (a FVa glycoform) and either C6PS- or PS-containing membranes were bound to FXa, the overall change in length was comparable (~5.6-5.8 Å), indicating that C6PS- and PS-containing membranes in conjunction with FVa2 have comparable regulatory effects on FXa. We conclude that the similar functional regulation of FXa by C6PS or membranes in conjunction with FVa2 correlates with similar structural regulation. The results demonstrate the usefulness of FRET in analysing structure-function relationships in FXa and in the FXa·FVa2 complex.
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9
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Bravo MC, Orfeo T, Mann KG, Everse SJ. Modeling of human factor Va inactivation by activated protein C. BMC SYSTEMS BIOLOGY 2012; 6:45. [PMID: 22607732 PMCID: PMC3403913 DOI: 10.1186/1752-0509-6-45] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 05/20/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND Because understanding of the inventory, connectivity and dynamics of the components characterizing the process of coagulation is relatively mature, it has become an attractive target for physiochemical modeling. Such models can potentially improve the design of therapeutics. The prothrombinase complex (composed of the protease factor (F)Xa and its cofactor FVa) plays a central role in this network as the main producer of thrombin, which catalyses both the activation of platelets and the conversion of fibrinogen to fibrin, the main substances of a clot. A key negative feedback loop that prevents clot propagation beyond the site of injury is the thrombin-dependent generation of activated protein C (APC), an enzyme that inactivates FVa, thus neutralizing the prothrombinase complex. APC inactivation of FVa is complex, involving the production of partially active intermediates and "protection" of FVa from APC by both FXa and prothrombin. An empirically validated mathematical model of this process would be useful in advancing the predictive capacity of comprehensive models of coagulation. RESULTS A model of human APC inactivation of prothrombinase was constructed in a stepwise fashion by analyzing time courses of FVa inactivation in empirical reaction systems with increasing number of interacting components and generating corresponding model constructs of each reaction system. Reaction mechanisms, rate constants and equilibrium constants informing these model constructs were initially derived from various research groups reporting on APC inactivation of FVa in isolation, or in the presence of FXa or prothrombin. Model predictions were assessed against empirical data measuring the appearance and disappearance of multiple FVa degradation intermediates as well as prothrombinase activity changes, with plasma proteins derived from multiple preparations. Our work integrates previously published findings and through the cooperative analysis of in vitro experiments and mathematical constructs we are able to produce a final validated model that includes 24 chemical reactions and interactions with 14 unique rate constants which describe the flux in concentrations of 24 species. CONCLUSION This study highlights the complexity of the inactivation process and provides a module of equations describing the Protein C pathway that can be integrated into existing comprehensive mathematical models describing tissue factor initiated coagulation.
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Affiliation(s)
- Maria Cristina Bravo
- Cell and Molecular Biology Program, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405, USA
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10
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Lee CJ, Wu S, Pedersen LG. A revisit to the one-form kinetic model of prothrombinase: A comment on the rebuttal. Biophys Chem 2012. [DOI: 10.1016/j.bpc.2011.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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11
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Lee CJ, Wu S, Pedersen LG. A proposed ternary complex model of prothrombinase with prothrombin: protein-protein docking and molecular dynamics simulations. J Thromb Haemost 2011; 9:2123-6. [PMID: 21827606 DOI: 10.1111/j.1538-7836.2011.04463.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Paraboschi EM, Kayiran SM, Özbek N, Gürakan B, Peyvandi F, Guella I, Duga S, Asselta R. Functional characterization of a novel missense mutation identified in a Turkish patient affected by severe coagulation factor V deficiency. Haemophilia 2011; 18:205-10. [PMID: 21777354 DOI: 10.1111/j.1365-2516.2011.02621.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Factor V (FV) deficiency is a rare coagulation disorder, characterized by a bleeding phenotype varying from mild to severe. To date, 115 mutations have been described along the gene encoding for FV (F5) but only few of them have been functionally characterized. Aim of this study was the identification and the molecular characterization of genetic defects underlying severe FV deficiency in a 7-month-old Turkish patient. Mutation detection was performed by sequencing the whole F5 coding region, exon-intron boundaries and about 300 bp of the promoter region. Functional analysis of the identified missense mutation was conducted by transient expression of wild-type and mutant FV recombinant molecules in COS-1 cells. Two novel mutations: a missense (Pro132Arg) and a 1-bp deletion (Ile1890TyrfsX19) were identified in the F5 gene. While the frameshift mutation is responsible for the introduction of a premature stop codon, likely triggering F5 mRNA to nonsense-mediated mRNA degradation, the demonstration of the pathogenic role of the Pro132Arg mutation required an experimental validation. Expression experiments showed that the missense mutation causes a significant reduction in FV secretion and in the specific activity of the residual secreted molecule (77% and 78% decrease, respectively). This paper reports the identification of two novel mutations responsible for FV deficiency, thus widening the mutational spectrum of the F5 gene. The Pro132Arg mutation adds to the only other two functionally characterized missense defects in the FV A1 domain.
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Affiliation(s)
- E M Paraboschi
- Dipartimento di Biologia e Genetica per Scienze Mediche, Università degli Studi di Milano, Milan, Italy
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Pedersen LG. Lee Pedersen’s work in theoretical and computational chemistry and biochemistry. World J Biol Chem 2011; 2:35-8. [PMID: 21537488 PMCID: PMC3083993 DOI: 10.4331/wjbc.v2.i2.35] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 01/18/2011] [Accepted: 01/25/2011] [Indexed: 02/05/2023] Open
Abstract
Nature at the lab level in biology and chemistry can be described by the application of quantum mechanics. In many cases, a reasonable approximation to quantum mechanics is classical mechanics realized through Newton’s equations of motion. Dr. Pedersen began his career using quantum mechanics to describe the properties of small molecular complexes that could serve as models for biochemical systems. To describe large molecular systems required a drop-back to classical means and this led surprisingly to a major improvement in the classical treatment of electrostatics for all molecules, not just biological molecules. Recent work has involved the application of quantum mechanics for the putative active sites of enzymes to gain greater insight into the key steps in enzyme catalysis.
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Affiliation(s)
- Lee G Pedersen
- Lee G Pedersen, Department of Chemistry, University of North Carolina at Chapel Hill, CB#3290, Chapel Hill, NC 27599, United States
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14
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A revisit to the one form kinetic model of prothrombinase. Biophys Chem 2010; 149:28-33. [PMID: 20435402 DOI: 10.1016/j.bpc.2010.03.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/11/2010] [Accepted: 03/12/2010] [Indexed: 11/22/2022]
Abstract
Thrombin is generated enzymatically from prothrombin by two pathways with the intermediates of meizothrombin and prethrombin-2. Experimental concentration profiles from two independent groups for these two pathways have been re-analyzed. By rationally combining the independent data sets, a simple mechanism can be established and rate constants determined. A structural model is consistent with the data-derived finding that mechanisms that feature channeling or ratcheting are not necessary to describe thrombin production.
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Lee CJ, Chandrasekaran V, Wu S, Duke RE, Pedersen LG. Recent estimates of the structure of the factor VIIa (FVIIa)/tissue factor (TF) and factor Xa (FXa) ternary complex. Thromb Res 2010; 125 Suppl 1:S7-S10. [PMID: 20156644 DOI: 10.1016/j.thromres.2010.01.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The putative structure of the Tissue Factor/Factor VIIa/Factor Xa (TF/FVIIa/FXa) ternary complex is reconsidered. Two independently derived docking models proposed in 2003 (one for our laboratory: CHeA and one from the Scripps laboratory: Ss) are dynamically equilibrated for over 10 ns in an electrically neutral solution using all-atom molecular dynamics. Although the dynamical models (CHeB and Se) differ in atomic detail, there are similarities in that TF is found to interact with the gamma-carboxyglutamic acid (Gla) and Epidermal Growth Factor-like 1 (EGF-1) domains of FXa, and FVIIa is found to interact with the Gla, EGF-2 and serine protease (SP) domains of FXa in both models. FVIIa does not interact with the FXa EGF-1 domain in Se and the EGF domains of FVIIa do not interact with FXa in the CHeB. Both models are consistent with experimentally suggested contacts between the SP domain of FVIIa with the EGF-2 and SP domains of FXa.
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Affiliation(s)
- Chang Jun Lee
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA
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16
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Buddai SK, Layzer JM, Lu G, Rusconi CP, Sullenger BA, Monroe DM, Krishnaswamy S. An anticoagulant RNA aptamer that inhibits proteinase-cofactor interactions within prothrombinase. J Biol Chem 2009; 285:5212-23. [PMID: 20022942 DOI: 10.1074/jbc.m109.049833] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction of factor Xa with factor Va on membranes to form prothrombinase profoundly increases the rate of the proteolytic conversion of prothrombin to thrombin. We present the characterization of an RNA aptamer (RNA(11F7t)) selected from a combinatorial library based on its ability to bind factor Xa. We show that RNA(11F7t) inhibits thrombin formation catalyzed by prothrombinase without obscuring the active site of Xa within the enzyme complex. Selective inhibition of protein substrate cleavage arises from the ability of the aptamer to bind to factor Xa and exclude interactions between the proteinase and cofactor within prothrombinase. Competition for enzyme complex assembly results from the binding of RNA(11F7t) to factor Xa with nanomolar affinity in a Ca(2+)-dependent interaction. RNA(11F7t) binds equivalently to the zymogen factor X as well as derivatives lacking gamma-carboxyglutamic acid residues. We suggest that the ability of RNA(11F7t) to compete for the Xa-Va interaction with surprisingly high affinity likely reflects a significant contribution from its ability to indirectly impact regions of Xa that participate in the proteinase-cofactor interaction. Thus, despite the complexity of the macromolecular interactions that underlie the assembly of prothrombinase, efficient inhibition of enzyme complex assembly and thrombin formation can be achieved by tight binding ligands that target factor Xa in a discrete manner.
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Affiliation(s)
- Sai K Buddai
- Joseph Stokes Research Institute, Children's Hospital of Philadelphia, Pennsylvania 19104, USA
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17
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Bradford HN, Micucci JA, Krishnaswamy S. Regulated cleavage of prothrombin by prothrombinase: repositioning a cleavage site reveals the unique kinetic behavior of the action of prothrombinase on its compound substrate. J Biol Chem 2009; 285:328-38. [PMID: 19858193 DOI: 10.1074/jbc.m109.070334] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prothrombinase converts prothrombin to thrombin via cleavage at Arg(320) followed by cleavage at Arg(271). Exosite-dependent binding of prothrombin to prothrombinase facilitates active site docking by Arg(320) and initial cleavage at this site. Precise positioning of the Arg(320) site for cleavage is implied by essentially normal cleavage at Arg(320) in recombinant prothrombin variants bearing additional Arg side chains either one or two residues away. However, mutation of Arg(320) to Gln reveals that prothrombinase can cleave prothrombin following Arg side chains shifted by as many as two residues N-terminal to the 320 position at near normal rates. Further repositioning leads to a loss in cleavage at this region with an abrupt shift toward slow cleavage at Arg(271). In contrast, the binding constant for the active site docking step is strongly dependent on the sequence preceding the scissile bond as well as position. Large effects on binding only yield minor changes in rate until the binding constant passes a threshold value. This behavior is expected for a substrate that can engage the enzyme through mutually exclusive active site docking reactions followed by cleavage to yield different products. Cleavage site specificity as well as the ordered action of prothrombinase on its compound substrate is regulated by the thermodynamics of active site engagement of the individual sites as well as competition between alternate cleavage sites for active site docking.
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Affiliation(s)
- Harlan N Bradford
- Joseph Stokes Research Institute, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Differential contributions of Glu96, Asp102 and Asp111 to coagulation Factor V/Va metal ion binding and subunit stability. Biochem J 2009; 422:257-64. [DOI: 10.1042/bj20090405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Blood coagulation FV (Factor V) is activated by thrombin-mediated excision of the B domain, resulting in a non-covalent heterodimer, FVa (activated FV). Previous studies implicated Glu96, Asp102 and Asp111 in the essential Ca2+-dependent FVa subunit interaction. In the present study, FV E96A, D102A and D111A were purified and evaluated for function, subunit dissociation and metal ion binding. Chromogenic and clotting assays in the presence of procoagulant vesicles showed that each variant was inhibited (∼20–40%). D111A was further inhibited (>90%) after cleavage by thrombin. Comparable function was observed on activated platelets. D111A inhibition correlated to spontaneous subunit dissociation and severely impaired Ca2+ binding. The Cu2+ interaction was also inhibited, suggesting interdependent Ca2+ and Cu2+ binding to FV. The parental FV (FV-810; wild-type human FV missing residues 811–1491) used here is fully active without proteolysis because the B domain is truncated. Therefore, a FVa-like functional configuration exists for intact D111A independent of normal metal ion interactions. Unlike D111A, the thrombin-mediated FVa derived from E96A and D102A had only moderately enhanced subunit dissociation upon chelation and had normal metal ion binding. For FV-810-, E96A- and D102A-derived FVa, loss of function after chelation significantly preceded subunit dissociation. This study defines the highly conserved segment spanning Glu96–Asp111 in FV as multifunctional. Of the three amino acids evaluated, Asp111 is essential and probably functions through direct and indirect effects on Ca2+ and Cu2+ interactions. Glu96 and Asp102 individually influence FV/FVa by more subtle effects, possibly at the metal ion-dependent subunit interface.
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A phosphatidylserine binding site in factor Va C1 domain regulates both assembly and activity of the prothrombinase complex. Blood 2008; 112:2795-802. [PMID: 18587009 DOI: 10.1182/blood-2008-02-138941] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tightly associated factor V(a) (FVa) and factor X(a) (FXa) serve as the essential prothrombin-activating complex that assembles on phosphatidylserine (PS)-containing platelet membranes during blood coagulation. We have previously shown that (1) a soluble form of PS (C6PS) triggers assembly of a fully active FVa-FXa complex in solution and (2) that 2 molecules of C6PS bind to FVa light chain with one occupying a site in the C2 domain. We expressed human factor V(a) (rFVa) with mutations in either the C1 domain (Y1956,L1957)A, the C2 domain (W2063,W2064)A, or both C domains (Y1956,L1957,W2063,W2064)A. Mutations in the C1 and C1-C2 domains of rFVa reduced the rate of activation of prothrombin to thrombin by FXa in the presence of 400 muM C6PS by 14 000- to 15 000-fold relative to either wild-type or C2 mutant factor rFVa. The K(d')s of FXa binding with rFVa (wild-type, C2 mutant, C1 mutant, and C1-C2 mutant) were 3, 4, 564, and 624 nM, respectively. Equilibrium dialysis experiments detected binding of 4, 3, and 2 molecules of C6PS to wild-type rFVa, C1-mutated, and C1,C2-mutated rFVa, respectively. Because FVa heavy chain binds 2 molecules of C6PS, we conclude that both C2 and C1 domains bind one C6PS, with binding to the C1 domain regulating prothrombinase complex assembly.
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Segers K, Dahlbäck B, Rosing J, Nicolaes GAF. Identification of surface epitopes of human coagulation factor Va that are important for interaction with activated protein C and heparin. J Biol Chem 2008; 283:22573-81. [PMID: 18519572 DOI: 10.1074/jbc.m801724200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Inactivation of factor Va (FVa) by activated protein C (APC) is a key reaction in the down-regulation of thrombin formation. FVa inactivation by APC is correlated with a loss of FXa cofactor activity as a result of three proteolytic cleavages in the FVa heavy chain at Arg306, Arg506, and Arg679. Recently, we have shown that heparin specifically inhibits the APC-mediated cleavage at Arg506 and stimulates cleavage at Arg306. Three-dimensional molecular models of APC docked at the Arg306 and Arg506 cleavage sites in FVa have identified several FVa amino acids that may be important for FVa inactivation by APC in the absence and presence of heparin. Mutagenesis of Lys320, Arg321, and Arg400 to Ala resulted in an increased inactivation rate by APC at Arg306, which indicates the importance of these residues in the FVa-APC interaction. No heparin-mediated stimulation of Arg306 cleavage was observed for these mutants, and stimulation by protein S was similar to that of wild type FVa. With this, we have now demonstrated that a cluster of basic residues in FVa comprising Lys320, Arg321, and Arg400 is required for the heparin-mediated stimulation of cleavage at Arg306 by APC. Furthermore, mutations that were introduced near the Arg506 cleavage site had a significant but modest effect on the rate of APC-catalyzed FVa inactivation, suggesting an extended interaction surface between the FVa Arg506 site and APC.
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Affiliation(s)
- Kenneth Segers
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, 6200MD, The Netherlands
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