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Vadivel K, Schreuder HA, Liesum A, Schmidt AE, Goldsmith G, Bajaj SP. Sodium-site in serine protease domain of human coagulation factor IXa: evidence from the crystal structure and molecular dynamics simulations study. J Thromb Haemost 2019; 17:574-584. [PMID: 30725510 PMCID: PMC6443445 DOI: 10.1111/jth.14401] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/24/2019] [Indexed: 01/03/2023]
Abstract
Essentials Consensus sequence and biochemical data suggest a Na+ -site in the factor (F) IXa protease domain. X-ray structure of the FIXa EGF2/protease domain at 1.37 Å reveals a Na+ -site not observed earlier. Molecular dynamics simulations data support that Na+ ± Ca2+ promote FIXa protease domain stability. Sulfate ions found in the protease domain mimic heparin sulfate binding mode in FIXa. SUMMARY: Background Activated coagulation factor IX (FIXa) consists of a γ-carboxyglutamic acid domain, two epidermal growth factor-like (EGF) domains, and a C-terminal protease domain. Consensus sequence and biochemical data support the existence of a Na+ -site in the FIXa protease domain. However, soaking experiments or crystals grown in high concentration of ammonium sulfate did not reveal a Na+ -site in wild-type or mutant FIXa EGF2/protease domain structure. Objective Determine the structure of the FIXa EGF2/protease domain in the presence of Na+ ; perform molecular dynamics (MD) simulations to explore the role of Na+ in stabilizing FIXa structure. Methods Crystallography, MD simulations, and modeling heparin binding to FIXa. Results Crystal structure at 1.37-Å resolution revealed that Na+ is coordinated to carbonyl groups of residues 184A, 185, 221A, and 224 in the FIXa protease domain. The Na+ -site in FIXa is similar to that of FXa and is linked to the Asp189 S1-site. In MD simulations, Na+ reduced fluctuations in residues 217-225 (Na+ -loop) and 70-80 (Ca2+ -loop), whereas Ca2+ reduced fluctuations only in residues of the Ca2+ -loop. Ca2+ and Na+ together reduced fluctuations in residues of the Ca2+ -loop and Na+ -loop (residues 70-80, 183-194, and 217-225). Moreover, we observed four sulfate ions that make salt bridges with FIXa protease domain Arg/Lys residues, which have been implicated in heparin binding. Based upon locations of the sulfate ions, we modeled heparin binding to FIXa, which is similar to the heparin binding in thrombin. Conclusions The FIXa Na+ -site in association with Ca2+ contributes to stabilization of the FIXa protease domain. The heparin binding mode in FIXa is similar to that in thrombin.
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Affiliation(s)
- Kanagasabai Vadivel
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA
| | | | - Alexander Liesum
- Sanofi-Aventis Pharma Deutschland GmbH, Frankfurt am Main, Germany
| | - Amy E Schmidt
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA
| | | | - S Paul Bajaj
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
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Tokutake T, Baba H, Shimada Y, Takeda W, Sato K, Hiroshima Y, Kirihara T, Shimizu I, Nakazawa H, Kobayashi H, Ishida F. Exogenous Magnesium Chloride Reduces the Activated Partial Thromboplastin Times of Lupus Anticoagulant-Positive Patients. PLoS One 2016; 11:e0157835. [PMID: 27355205 PMCID: PMC4927146 DOI: 10.1371/journal.pone.0157835] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/06/2016] [Indexed: 11/19/2022] Open
Abstract
The activated partial thromboplastin time (APTT) assay is a basic hemostatic assay based on the time it takes for clots to form in plasma samples after the addition of calcium chloride. It is used to screen for various coagulation disorders. Several previous reports have suggested that magnesium (Mg) might contribute to coagulation reactions by binding to specific coagulation proteins. We investigated the effects of Mg on the APTT. In healthy controls, the APTT was significantly prolonged in proportion to the increase in the concentration of magnesium chloride in the range from 2.1 to 16.7 mmol/L. Among eight samples from patients with various disorders that exhibited prolonged APTT, two samples demonstrated shorter APTT when Mg was added, both of which were from patients that were positive for lupus anticoagulant. When we examined 206 clinical APTT samples, we found that Mg shortened the APTT of two samples. These two samples were also from lupus anticoagulant-positive patients (p-value: <0.003). Our findings regarding the unique effects of exogenous Mg on the APTT of lupus anticoagulant-positive patients might shed light on the role of Mg in APTT assays and lead to the development of a novel screening method for lupus anticoagulant.
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Affiliation(s)
- Takayoshi Tokutake
- Department of Clinical Laboratory, Nagano Red Cross Hospital, Nagano, Japan
| | - Hisami Baba
- Department of Clinical Laboratory, Nagano Red Cross Hospital, Nagano, Japan
| | - Yuji Shimada
- Department of Clinical Laboratory, Nagano Red Cross Hospital, Nagano, Japan
| | - Wataru Takeda
- Department of Hematology, Nagano Red Cross Hospital, Nagano, Japan
| | - Keijiro Sato
- Department of Hematology, Nagano Red Cross Hospital, Nagano, Japan
| | - Yuki Hiroshima
- Department of Hematology, Nagano Red Cross Hospital, Nagano, Japan
| | | | - Ikuo Shimizu
- Department of Hematology, Nagano Red Cross Hospital, Nagano, Japan
- Center for Medical Education, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hideyuki Nakazawa
- Department of Hematology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hikaru Kobayashi
- Department of Clinical Laboratory, Nagano Red Cross Hospital, Nagano, Japan
- Department of Hematology, Nagano Red Cross Hospital, Nagano, Japan
| | - Fumihiro Ishida
- Department of Hematology, Shinshu University School of Medicine, Matsumoto, Japan
- Department of Biomedical Laboratory Sciences, School of Health Sciences, Shinshu University School of Medicine, Matsumoto, Japan
- * E-mail:
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Both acute delivery of and storage with magnesium sulfate promote cold-stored platelet aggregation and coagulation function. J Trauma Acute Care Surg 2015; 79:S139-45. [DOI: 10.1097/ta.0000000000000739] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Vanderslice NC, Messer AS, Vadivel K, Bajaj SP, Phillips M, Fatemi M, Xu W, Velander WH. Quantifying vitamin K-dependent holoprotein compaction caused by differential γ-carboxylation using high-pressure size exclusion chromatography. Anal Biochem 2015; 479:6-14. [PMID: 25804408 PMCID: PMC4428943 DOI: 10.1016/j.ab.2015.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/09/2015] [Accepted: 03/15/2015] [Indexed: 11/19/2022]
Abstract
This study uses high-pressure size exclusion chromatography (HPSEC) to quantify divalent metal ion (X(2+))-induced compaction found in vitamin K-dependent (VKD) proteins. Multiple X(2+) binding sites formed by the presence of up to 12 γ-carboxyglutamic acid (Gla) residues are present in plasma-derived FIX (pd-FIX) and recombinant FIX (r-FIX). Analytical ultracentrifugation (AUC) was used to calibrate the Stokes radius (R) measured by HPSEC. A compaction of pd-FIX caused by the filling of Ca(2+) and Mg(2+) binding sites resulted in a 5 to 6% decrease in radius of hydration as observed by HPSEC. The filling of Ca(2+) sites resulted in greater compaction than for Mg(2+) alone where this effect was additive or greater when both ions were present at physiological levels. Less X(2+)-induced compaction was observed in r-FIX with lower Gla content populations, which enabled the separation of biologically active r-FIX species from inactive ones by HPSEC. HPSEC was sensitive to R changes of approximately 0.01nm that enabled the detection of FIX compaction that was likely cooperative in nature between lower avidity X(2+) sites of the Gla domain and higher avidity X(2+) sites of the epidermal growth factor 1 (EGF1)-like domain.
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Affiliation(s)
- Nicholas C Vanderslice
- Protein Purification and Characterization Laboratories, Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Amanda S Messer
- Protein Purification and Characterization Laboratories, Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Protein Science Laboratory, UCLA/Orthopaedic Hospital, Department of Orthopaedic Surgery and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kanagasabai Vadivel
- Protein Science Laboratory, UCLA/Orthopaedic Hospital, Department of Orthopaedic Surgery and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - S Paul Bajaj
- Protein Science Laboratory, UCLA/Orthopaedic Hospital, Department of Orthopaedic Surgery and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Martin Phillips
- UCLA-DOE Biochemistry Instrumentation Facility, Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mostafa Fatemi
- Protein Purification and Characterization Laboratories, Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Weijie Xu
- Protein Purification and Characterization Laboratories, Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - William H Velander
- Protein Purification and Characterization Laboratories, Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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Vadivel K, Agah S, Messer AS, Cascio D, Bajaj MS, Krishnaswamy S, Esmon CT, Padmanabhan K, Bajaj SP. Structural and functional studies of γ-carboxyglutamic acid domains of factor VIIa and activated Protein C: role of magnesium at physiological calcium. J Mol Biol 2013; 425:1961-1981. [PMID: 23454357 DOI: 10.1016/j.jmb.2013.02.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/10/2013] [Accepted: 02/14/2013] [Indexed: 11/28/2022]
Abstract
Crystal structures of factor (F) VIIa/soluble tissue factor (TF), obtained under high Mg(2+) (50mM Mg(2+)/5mM Ca(2+)), have three of seven Ca(2+) sites in the γ-carboxyglutamic acid (Gla) domain replaced by Mg(2+) at positions 1, 4, and 7. We now report structures under low Mg(2+) (2.5mM Mg(2+)/5mM Ca(2+)) as well as under high Ca(2+) (5mM Mg(2+)/45 mM Ca(2+)). Under low Mg(2+), four Ca(2+) and three Mg(2+) occupy the same positions as in high-Mg(2+) structures. Conversely, under low Mg(2+), reexamination of the structure of Gla domain of activated Protein C (APC) complexed with soluble endothelial Protein C receptor (sEPCR) has position 4 occupied by Ca(2+) and positions 1 and 7 by Mg(2+). Nonetheless, in direct binding experiments, Mg(2+) replaced three Ca(2+) sites in the unliganded Protein C or APC. Further, the high-Ca(2+) condition was necessary to replace Mg4 in the FVIIa/soluble TF structure. In biological studies, Mg(2+) enhanced phospholipid binding to FVIIa and APC at physiological Ca(2+). Additionally, Mg(2+) potentiated phospholipid-dependent activations of FIX and FX by FVIIa/TF and inactivation of activated factor V by APC. Since APC and FVIIa bind to sEPCR involving similar interactions, we conclude that under the low-Mg(2+) condition, sEPCR binding to APC-Gla (or FVIIa-Gla) replaces Mg4 by Ca4 with an attendant conformational change in the Gla domain ω-loop. Moreover, since phospholipid and sEPCR bind to FVIIa or APC via the ω-loop, we predict that phospholipid binding also induces the functional Ca4 conformation in this loop. Cumulatively, the data illustrate that Mg(2+) and Ca(2+) act in concert to promote coagulation and anticoagulation.
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Affiliation(s)
- Kanagasabai Vadivel
- UCLA/Orthopaedic Hospital Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA
| | - Sayeh Agah
- UCLA/Orthopaedic Hospital Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA
| | - Amanda S Messer
- UCLA/Orthopaedic Hospital Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Madhu S Bajaj
- Division of Pulmonology and Critical Care, Department of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Sriram Krishnaswamy
- Department of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Charles T Esmon
- Oklahoma Medical Research Foundation, Howard Hughes Medical Institute, Oklahoma City, OK 73104, USA
| | - Kaillathe Padmanabhan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - S Paul Bajaj
- UCLA/Orthopaedic Hospital Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
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Vadivel K, Bajaj SP. Structural biology of factor VIIa/tissue factor initiated coagulation. Front Biosci (Landmark Ed) 2012; 17:2476-94. [PMID: 22652793 DOI: 10.2741/4066] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Factor VII (FVII) consists of an N-terminal gamma-carboxyglutamic acid domain followed by two epidermal growth factor-like (EGF1 and EGF2) domains and the C-terminal protease domain. Activation of FVII results in a two-chain FVIIa molecule consisting of a light chain (Gla-EGF1-EGF2 domains) and a heavy chain (protease domain) held together by a single disulfide bond. During coagulation, the complex of tissue factor (TF, a transmembrane glycoprotein) and FVIIa activates factor IX (FIX) and factor X (FX). FVIIa is structurally "zymogen-like" and when bound to TF, it is more "active enzyme-like." FIX and FX share structural homology with FVII. Three structural biology aspects of FVIIa/TF are presented in this review. One, regions in soluble TF (sTF) that interact with FVIIa as well as mapping of Ca2+, Mg2+, Na+ and Zn2+ sites in FVIIa and their functions; two, modeled interactive regions of Gla and EGF1 domains of FXa and FIXa with FVIIa/sTF; and three, incompletely formed oxyanion hole in FVIIa/sTF and its induction by substrate/inhibitor. Finally, an overview of the recognition elements in TF pathway inhibitor is provided.
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Affiliation(s)
- Kanagasabai Vadivel
- Protein Science Laboratory, UCLA/Orthopaedic Hospital, Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095-1795, USA
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Abstract
The proverb that probably best exemplifies my career in research is attributable to Yogi Berra (http://www.yogiberra.com/), ie, “when you come to a fork in the road … take it.” My career is a consequence of chance interactions with great mentors and talented students and the opportunities provided by a succession of ground-breaking improvements in technology.
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Messer AS, Velander WH, Bajaj SP. Contribution of magnesium in binding of factor IXa to the phospholipid surface: implications for vitamin K-dependent coagulation proteins. J Thromb Haemost 2009; 7:2151-3. [PMID: 19817987 PMCID: PMC2885445 DOI: 10.1111/j.1538-7836.2009.03634.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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