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Legare S, Heide F, Gabir H, Rafiei F, Meier M, Padilla-Meier GP, Koch M, Stetefeld J. Identifying the molecular basis of Laminin N-terminal domain Ca 2+ binding using a hybrid approach. Biophys J 2024:S0006-3495(24)00388-6. [PMID: 38851889 DOI: 10.1016/j.bpj.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/13/2024] [Accepted: 06/06/2024] [Indexed: 06/10/2024] Open
Abstract
Ca2+ is a highly abundant ion involved in numerous biological processes, particularly in multicellular eukaryotic organisms where it exerts many of these functions through interactions with Ca2+ binding proteins. The laminin N-terminal (LN) domain is found in members of the laminin and netrin protein families where it plays a critical role in the function of these proteins. The LN domain of laminins and netrins is a Ca2+ binding domain and in many cases requires Ca2+ to perform its biological function. Here, we conduct a detailed examination of the molecular basis of the LN domain Ca2+ interaction combining structural, computational, bioinformatics, and biophysical techniques. By combining computational and bioinformatic techniques with x-ray crystallography we explore the molecular basis of the LN domain Ca2+ interaction and identify a conserved sequence present in Ca2+ binding LN domains. These findings enable a sequence-based prediction of LN domain Ca2+ binding ability. We use thermal shift assays and isothermal titration calorimetry to explore the biophysical properties of the LN domain Ca2+ interaction. We show that the netrin-1 LN domain exhibits a high affinity and specificity for Ca2+, which structurally stabilizes the LN domain. This study elucidates the molecular foundation of the LN domain Ca2+ binding interaction and provides a detailed functional characterization of this essential interaction, advancing our understanding of protein-Ca2+ dynamics within the context of the LN domain.
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Affiliation(s)
- Scott Legare
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Fabian Heide
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Haben Gabir
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Faride Rafiei
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Manuel Koch
- Center for Biochemistry II, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Institute for Dental Research and Oral Musculoskeletal Biology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
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Beauglehole AC, Roche Recinos D, Pegg CL, Lee YY, Turnbull V, Herrmann S, Marcellin E, Howard CB, Schulz BL. Recent advances in the production of recombinant factor IX: bioprocessing and cell engineering. Crit Rev Biotechnol 2022; 43:484-502. [PMID: 35430942 DOI: 10.1080/07388551.2022.2036691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Appropriate treatment of Hemophilia B is vital for patients' quality of life. Historically, the treatment used was the administration of coagulation Factor IX derived from human plasma. Advancements in recombinant technologies allowed Factor IX to be produced recombinantly. Successful recombinant production has triggered a gradual shift from the plasma derived origins of Factor IX, as it provides extended half-life and expanded production capacity. However, the complex post-translational modifications of Factor IX have made recombinant production at scale difficult. Considerable research has therefore been invested into understanding and optimizing the recombinant production of Factor IX. Here, we review the evolution of recombinant Factor IX production, focusing on recent developments in bioprocessing and cell engineering to control its post-translational modifications in its expression from Chinese Hamster Ovary (CHO) cells.
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Affiliation(s)
- Aiden C. Beauglehole
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD, Australia
- CSL Innovation, Parkville, Victoria, Australia
| | - Dinora Roche Recinos
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD, Australia
- CSL Innovation, Parkville, Victoria, Australia
| | - Cassandra L. Pegg
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | | | - Victor Turnbull
- CSL Innovation, Bio21 Institute of Molecular Science and Biotechnology, Parkville, Victoria, Australia
| | - Susann Herrmann
- CSL Innovation, Bio21 Institute of Molecular Science and Biotechnology, Parkville, Victoria, Australia
| | - Esteban Marcellin
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD, Australia
| | - Christopher B. Howard
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD, Australia
| | - Benjamin L. Schulz
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
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Geng K. Post-translational modifications of the ligands: Requirement for TAM receptor activation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 357:35-55. [PMID: 33234244 DOI: 10.1016/bs.ircmb.2020.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The Tyro3, Axl, and MerTK (TAM) receptors are three homologous Type I Receptor Tyrosine Kinases that have important homeostatic functions in multicellular organisms by regulating the clearance of apoptotic cells (efferocytosis). Pathologically, TAM receptors are overexpressed in a wide array of human cancers, and often associated with aggressive tumor grade and poor overall survival. In addition to their expression on tumor cells, TAMs are also expressed on infiltrating myeloid-derived cells in the tumor microenvironment, where they appear to act akin to negative immune checkpoints that impair host anti-tumor immunity. The ligands for TAMs are two endogenous proteins, Growth Arrest-Specific 6 (Gas6) and Protein S (Pros1), that function as bridging molecules between externalized phosphatidylserine (PtdSer) on apoptotic cells and the TAM ectodomains. One interesting feature of TAMs biology is that their ligand proteins require specific post-translational modifications to acquire activities. This chapter summarized these important modifications and explained the molecular mechanisms behind such phenomenon. Current evidences suggest that these modifications help Gas6/Pros1 to achieve optimal PtdSer-binding capacities. In addition, this chapter included recent discovery of regulating machineries of PtdSer dynamic across the plasma membrane, as well as their potential impacts in the tumor microenvironment. Taken together, this review highlights the importance of the upstream PtdSer and Gas6 in regulating TAMs' function and hope to provide researchers with new perspectives to inspire future studies of TAM receptors in human disease models.
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Affiliation(s)
- Ke Geng
- Public Health Research Institute, Rutgers Biomedical and Health Sciences, New Jersey Medical School, Newark, NJ, United States.
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Shuwen H, Xi Y, Qing Z, Jing Z, Wei W. Predicting biomarkers from classifier for liver metastasis of colorectal adenocarcinomas using machine learning models. Cancer Med 2020. [PMCID: PMC7520257 DOI: 10.1002/cam4.3289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Han Shuwen
- Department of Oncology Huzhou Central HospitalAffiliated Central Hospital Huzhou University Huzhou China
| | - Yang Xi
- Department of Oncology Huzhou Central HospitalAffiliated Central Hospital Huzhou University Huzhou China
| | - Zhou Qing
- Department of Nursing Huzhou Central HospitalAffiliated Central Hospital Huzhou University Huzhou China
| | - Zhuang Jing
- Graduate School of Nursing Huzhou university Huzhou China
| | - Wu Wei
- Department of Gastroenterology Huzhou Central Hospital Affiliated Central Hospital Huzhou University Huzhou China
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5
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Monitoring the hemostasis process through the electrical characteristics of a graphene-based field-effect transistor. Biosens Bioelectron 2020; 157:112167. [DOI: 10.1016/j.bios.2020.112167] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/05/2020] [Accepted: 03/20/2020] [Indexed: 11/18/2022]
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Zhou J, Oldfield CJ, Yan W, Shen B, Dunker AK. Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships. Protein Sci 2019; 28:1652-1663. [PMID: 31299122 DOI: 10.1002/pro.3680] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/29/2019] [Accepted: 07/03/2019] [Indexed: 02/05/2023]
Abstract
Disordered domains are long regions of intrinsic disorder that ideally have conserved sequences, conserved disorder, and conserved functions. These domains were first noticed in protein-protein interactions that are distinct from the interactions between two structured domains and the interactions between structured domains and linear motifs or molecular recognition features (MoRFs). So far, disordered domains have not been systematically characterized. Here, we present a bioinformatics investigation of the sequence-disorder-function relationships for a set of probable disordered domains (PDDs) identified from the Pfam database. All the Pfam seed proteins from those domains with at least one PDD sequence were collected. Most often, if a set contains one PDD sequence, then all members of the set are PDDs or nearly so. However, many seed sets have sequence collections that exhibit diverse proportions of predicted disorder and structure, thus giving the completely unexpected result that conserved sequences can vary substantially in predicted disorder and structure. In addition to the induction of structure by binding to protein partners, disordered domains are also induced to form structure by disulfide bond formation, by ion binding, and by complex formation with RNA or DNA. The two new findings, (a) that conserved sequences can vary substantially in their predicted disorder content and (b) that homologues from a single domain can evolve from structure to disorder (or vice versa), enrich our understanding of the sequence ➔ disorder ensemble ➔ function paradigm.
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Affiliation(s)
- Jianhong Zhou
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana.,School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
| | | | - Wenying Yan
- School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana
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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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8
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Plautz WE, Sekhar Pilli VS, Cooley BC, Chattopadhyay R, Westmark PR, Getz T, Paul D, Bergmeier W, Sheehan JP, Majumder R. Anticoagulant Protein S Targets the Factor IXa Heparin-Binding Exosite to Prevent Thrombosis. Arterioscler Thromb Vasc Biol 2018; 38:816-828. [PMID: 29419409 DOI: 10.1161/atvbaha.117.310588] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/16/2018] [Indexed: 01/20/2023]
Abstract
OBJECTIVE PS (protein S) is a plasma protein that directly inhibits the coagulation FIXa (factor IXa) in vitro. Because elevated FIXa is associated with increased risk of venous thromboembolism, it is important to establish how PS inhibits FIXa function in vivo. The goal of this study is to confirm direct binding of PS with FIXa in vivo, identify FIXa amino acid residues required for binding PS in vivo, and use an enzymatically active FIXa mutant that is unable to bind PS to measure the significance of PS-FIXa interaction in hemostasis. APPROACH AND RESULTS We demonstrate that PS inhibits FIXa in vivo by associating with the FIXa heparin-binding exosite. We used fluorescence tagging, immunohistochemistry, and protein-protein crosslinking to show in vivo interaction between FIXa and PS. Importantly, platelet colocalization required a direct interaction between the 2 proteins. FIXa and PS also coimmunoprecipitated from plasma, substantiating their interaction in a physiological milieu. PS binding to FIXa and PS inhibition of the intrinsic Xase complex required residues K132, K126, and R170 in the FIXa heparin-binding exosite. A double mutant, K132A/R170A, retained full activity but could not bind to PS. Crucially, Hemophilia B mice infused with FIXa K132A/R170A displayed an accelerated rate of fibrin clot formation compared with wild-type FIXa. CONCLUSIONS Our findings establish PS as an important in vivo inhibitor of FIXa. Disruption of the interaction between PS and FIXa causes an increased rate of thrombus formation in mice. This newly discovered function of PS implies an unexploited target for antithrombotic therapeutics.
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Affiliation(s)
- William E Plautz
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Vijaya Satish Sekhar Pilli
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Brian C Cooley
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Rima Chattopadhyay
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Pamela R Westmark
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Todd Getz
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - David Paul
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Wolfgang Bergmeier
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - John P Sheehan
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Rinku Majumder
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.).
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Justice ED, Barnum SJ, Kidd T. The WAGR syndrome gene PRRG4 is a functional homologue of the commissureless axon guidance gene. PLoS Genet 2017; 13:e1006865. [PMID: 28859078 PMCID: PMC5578492 DOI: 10.1371/journal.pgen.1006865] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/11/2017] [Indexed: 01/20/2023] Open
Abstract
WAGR syndrome is characterized by Wilm's tumor, aniridia, genitourinary abnormalities and intellectual disabilities. WAGR is caused by a chromosomal deletion that includes the PAX6, WT1 and PRRG4 genes. PRRG4 is proposed to contribute to the autistic symptoms of WAGR syndrome, but the molecular function of PRRG4 genes remains unknown. The Drosophila commissureless (comm) gene encodes a short transmembrane protein characterized by PY motifs, features that are shared by the PRRG4 protein. Comm intercepts the Robo axon guidance receptor in the ER/Golgi and targets Robo for degradation, allowing commissural axons to cross the CNS midline. Expression of human Robo1 in the fly CNS increases midline crossing and this was enhanced by co-expression of PRRG4, but not CYYR, Shisa or the yeast Rcr genes. In cell culture experiments, PRRG4 could re-localize hRobo1 from the cell surface, suggesting that PRRG4 is a functional homologue of Comm. Comm is required for axon guidance and synapse formation in the fly, so PRRG4 could contribute to the autistic symptoms of WAGR by disturbing either of these processes in the developing human brain.
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Affiliation(s)
- Elizabeth D. Justice
- Department of Biology/ms 314, University of Nevada, Reno, Nevada, United States of America
| | - Sarah J. Barnum
- Department of Biology/ms 314, University of Nevada, Reno, Nevada, United States of America
| | - Thomas Kidd
- Department of Biology/ms 314, University of Nevada, Reno, Nevada, United States of America
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Pabst TM, Wendeler M, Wang X, Bezemer S, Hermans P, Hunter AK. Camelid V H H affinity ligands enable separation of closely related biopharmaceuticals. Biotechnol J 2016; 12. [PMID: 27677057 PMCID: PMC5333455 DOI: 10.1002/biot.201600357] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/01/2016] [Accepted: 09/27/2016] [Indexed: 01/15/2023]
Abstract
Interest in new and diverse classes of molecules such as recombinant toxins, enzymes, and blood factors continues to grow for use a biotherapeutics. Compared to monoclonal antibodies, these novel drugs typically lack a commercially available affinity chromatography option, which leads to greater process complexity, longer development timelines, and poor platformability. To date, for both monoclonal antibodies and novel molecules, affinity chromatography has been mostly reserved for separation of process‐related impurities such as host cell proteins and DNA. Reports of affinity purification of closely related product variants and modified forms are much rarer. In this work we describe custom affinity chromatography development using camelid VHH antibody fragments as "tunable" immunoaffinity ligands for separation of product‐related impurities. One example demonstrates high selectivity for a recombinant immunotoxin where no binding was observed for an undesired deamidated species. Also discussed is affinity purification of a coagulation factor through specific recognition of the gamma‐carboxylglutamic acid domain.
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Affiliation(s)
- Timothy M Pabst
- MedImmune, Department of Purification Process Sciences, Gaithersburg, MD, USA
| | - Michaela Wendeler
- MedImmune, Department of Purification Process Sciences, Gaithersburg, MD, USA
| | - Xiangyang Wang
- MedImmune, Department of Purification Process Sciences, Gaithersburg, MD, USA
| | | | - Pim Hermans
- Thermo Fisher Scientific, Naarden, The Netherlands
| | - Alan K Hunter
- MedImmune, Department of Purification Process Sciences, Gaithersburg, MD, USA
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11
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Torres MP, Dewhurst H, Sundararaman N. Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease. Mol Cell Proteomics 2016; 15:3513-3528. [PMID: 27697855 PMCID: PMC5098047 DOI: 10.1074/mcp.m116.062331] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Indexed: 01/09/2023] Open
Abstract
Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable body of potential regulatory elements that impact hundreds of different biological processes important in eukaryotic biology and human health.
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Affiliation(s)
- Matthew P Torres
- From the School of Biological Sciences; Georgia Institute of Technology; Atlanta, Georgia 30332
| | - Henry Dewhurst
- From the School of Biological Sciences; Georgia Institute of Technology; Atlanta, Georgia 30332
| | - Niveda Sundararaman
- From the School of Biological Sciences; Georgia Institute of Technology; Atlanta, Georgia 30332
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12
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El-Brashy AEWS, El-Tanawy RM, Hassan WA, Shaban HM, Bhnasawy MMI. Potential role of vitamin K in radiological progression of early knee osteoarthritis patients. EGYPTIAN RHEUMATOLOGIST 2016. [DOI: 10.1016/j.ejr.2016.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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13
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Quade-Lyssy P, Abriss D, Milanov P, Ungerer C, Königs C, Seifried E, Schüttrumpf J. Next generation FIX muteins with FVIII-independent activity for alternative treatment of hemophilia A. J Thromb Haemost 2014; 12:1861-73. [PMID: 25224783 DOI: 10.1111/jth.12731] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 08/06/2014] [Indexed: 01/15/2023]
Abstract
BACKGROUND FVIII neutralizing antibodies are the main complication of substitution therapy in hemophilia A (HA); auto-antibodies against FVIII causing acquired HA can also occur. Treatment of inhibitor patients remains challenging because prophylactic treatment with existing FVIII bypassing agents, all based on constitutively active coagulation factors, is difficult due to their short half-life. OBJECTIVES To generate zymogenic FIX variants with FVIII-independent activity for gene- and protein-based therapy for HA. METHODS Modifications were introduced into FIX based on current knowledge of FIX structure and FVIII-independent function followed by random screening. Activity, thrombin generation and FX activation by FIX mutants were characterized in the presence and absence of FVIII. Phenotype correction of promising candidates was assessed by the tail-clip assay in FVIII-knockout mice. RESULTS About 1600 clones were screened and three mutations (L6F, S102N and E185D) identified, which improved FVIII-independent activity in combination with our previously described variant FIX-ITV. By systematic combination of all mutations, six FIX mutants with the desired bypassing activity were designed. Candidate mutants FIX-IDAV and FIX-FIAV demonstrated the most efficient thrombin generation in FVIII-deficient plasma and had considerably increased activities towards FX in the absence of FVIII, in that they showed an up to 5-fold increase in catalytic efficiency. Expression of FIX-IDAV in FVIII knockout mice reduced blood loss after the tail-clip assay, even in the presence of neutralizing FVIII antibodies. CONCLUSION Activatable bioengineered FIX molecules (as opposed to pre-activated coagulation factors) with FVIII-independent activity might be a promising tool for improving HA treatment, especially for patients with inhibitors.
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Affiliation(s)
- P Quade-Lyssy
- German Red Cross Blood Donor Service Baden-Württemberg-Hessen, Institute of Transfusion Medicine and Immunohematology of the Goethe University Clinics, Frankfurt am Main, Germany
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14
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Remko M, Broer R, Remková A, Van Duijnen PT. Acidity and metal (Mg 2+ , Ca 2+ , Zn 2+ ) affinity of l -γ-carboxyglutamic acid and its peptide analog. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.09.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Smiley DA, Becker RC. Factor IXa as a target for anticoagulation in thrombotic disorders and conditions. Drug Discov Today 2014; 19:1445-53. [PMID: 24998782 DOI: 10.1016/j.drudis.2014.06.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 06/26/2014] [Indexed: 10/25/2022]
Abstract
From acute coronary syndrome (ACS) to the prevention of cardioembolic events in patients with atrial fibrillation and thrombosis of mechanical heart valves, there is a quest to develop a new generation of anticoagulants. Perhaps the 'holy grail' of antithrombotic therapy is not only a drug that will prevent coagulation without promoting bleeding but also an anticoagulant that is easily reversible should the clinical need arise. Further, an optimally designed anticoagulant would have broad applications to include arterial, venous, hybrid conditions (atrial flutter and fibrillation) and nonbiological materials. Factor (F)IXa plays a pivotal part in tissue factor (TF)-mediated thrombin generation, and therefore represents a potentially promising target for drug development. FIXa activity has been targeted by multiple modalities, including oral inhibitors, RNA aptamers, monoclonal antibodies and synthetic active-site-blocking competitive inhibitors. Herein, we summarize the biochemistry of FIXa as it applies to thrombotic disorders and conditions, as well as the evolution of targeted therapies.
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Affiliation(s)
- Dia A Smiley
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Richard C Becker
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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16
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Disease-associated mutations disrupt functionally important regions of intrinsic protein disorder. PLoS Comput Biol 2012; 8:e1002709. [PMID: 23055912 PMCID: PMC3464192 DOI: 10.1371/journal.pcbi.1002709] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 08/14/2012] [Indexed: 01/01/2023] Open
Abstract
The effects of disease mutations on protein structure and function have been extensively investigated, and many predictors of the functional impact of single amino acid substitutions are publicly available. The majority of these predictors are based on protein structure and evolutionary conservation, following the assumption that disease mutations predominantly affect folded and conserved protein regions. However, the prevalence of the intrinsically disordered proteins (IDPs) and regions (IDRs) in the human proteome together with their lack of fixed structure and low sequence conservation raise a question about the impact of disease mutations in IDRs. Here, we investigate annotated missense disease mutations and show that 21.7% of them are located within such intrinsically disordered regions. We further demonstrate that 20% of disease mutations in IDRs cause local disorder-to-order transitions, which represents a 1.7–2.7 fold increase compared to annotated polymorphisms and neutral evolutionary substitutions, respectively. Secondary structure predictions show elevated rates of transition from helices and strands into loops and vice versa in the disease mutations dataset. Disease disorder-to-order mutations also influence predicted molecular recognition features (MoRFs) more often than the control mutations. The repertoire of disorder-to-order transition mutations is limited, with five most frequent mutations (R→W, R→C, E→K, R→H, R→Q) collectively accounting for 44% of all deleterious disorder-to-order transitions. As a proof of concept, we performed accelerated molecular dynamics simulations on a deleterious disorder-to-order transition mutation of tumor protein p63 and, in agreement with our predictions, observed an increased α-helical propensity of the region harboring the mutation. Our findings highlight the importance of mutations in IDRs and refine the traditional structure-centric view of disease mutations. The results of this study offer a new perspective on the role of mutations in disease, with implications for improving predictors of the functional impact of missense mutations. Intrinsically unstructured or disordered proteins have been implicated in the etiology of a wide spectrum of diseases. However, the molecular mechanisms that relate mutations in intrinsically disordered regions (IDRs) to disease pathogenesis have not been investigated. Disordered proteins do not conform to the prevailing view of deleterious mutations which equates function, structure and evolutionary conservation – intrinsically disordered regions are functional, but lack a fixed three-dimensional structure and in general have low sequence conservation. Here we demonstrate that >20% of disease-associated missense mutations affect IDRs and interfere with their functions. We further show that 20% of deleterious mutations in IDRs induce predicted disorder-to-order transitions. Our predictions are supported by accelerated molecular dynamics simulations that show an increase in helical propensity of the region harboring a disease disorder-to-order transition mutation of tumor protein p63. Our results refine the traditional structure-centric view of disease mutations and offer a new perspective on the role of non-synonymous mutations in disease. Our findings have broad implications for improving predictors of the functional impact of missense mutations, and for interpretation of novel variants identified in large genome sequencing projects that aim to provide a better understanding of human genetic variation and its relevance to common diseases.
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17
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Sen P, Clark CA, Gopalakrishnan R, Hedner U, Esmon CT, Pendurthi UR, Rao LVM. Factor VIIa binding to endothelial cell protein C receptor: differences between mouse and human systems. Thromb Haemost 2012; 107:951-61. [PMID: 22370814 PMCID: PMC3883592 DOI: 10.1160/th11-09-0672] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 01/16/2012] [Indexed: 11/05/2022]
Abstract
Recent in vitro studies have shown that the zymogen and activated form of factor (F)VII bind to endothelial cell protein C receptor (EPCR). At present, there is no evidence that FVIIa binds to EPCR on vascular endothelium in vivo in the presence of circulating protein C, a primary ligand for EPCR. The present study was carried out to investigate the interaction of murine and human ligands with murine EPCR both in vivo and in vitro . Measurement of endogenous plasma levels of FVII in wild-type, EPCR-deficient and EPCR-over expressing mice showed slightly lower levels of FVII in EPCR-over expressing mice. However, infusion of high concentrations of competing ligands, either human APCi or FVIIai, to EPCR-over expressing mice failed to increase plasma levels of mouse FVII whereas they increased the plasma levels of protein C by two- to three-fold. Examining the association of exogenously administered mouse FVIIa or human FVIIa by immunohistochemistry revealed that human, but not murine FVIIa, binds to the murine endothelium in an EPCR-dependent manner. In vitro binding studies performed using surface plasmon resonance and endothelial cells revealed that murine FVIIa binds murine EPCR negligibly. Human FVIIa binding to EPCR, particularly to mouse EPCR, is markedly enhanced by availability of Mg2+ ions. In summary, our data show that murine FVIIa binds poorly to murine EPCR, whereas human FVIIa binds efficiently to both murine and human EPCR. Our data suggest that one should consider the use of human FVIIa in mouse models to investigate the significance of FVIIa and EPCR interaction.
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Affiliation(s)
- Prosenjit Sen
- Center for Biomedical Research, The University of Texas Health Science Center at Tyler, Tyler, TX
| | - Curtis A. Clark
- Center for Biomedical Research, The University of Texas Health Science Center at Tyler, Tyler, TX
| | | | - Ulla Hedner
- Department of Medicine, Malmö University Hospital, University of Lund, Malmö, Sweden
| | - Charles T. Esmon
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Howard Hughes Medical Institute, Oklahoma City, OK
| | - Usha R. Pendurthi
- Center for Biomedical Research, The University of Texas Health Science Center at Tyler, Tyler, TX
| | - L. Vijaya Mohan Rao
- Center for Biomedical Research, The University of Texas Health Science Center at Tyler, Tyler, TX
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18
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Roser-Jones C, Chan M, Howard EL, Becker KCD, Rusconi CP, Becker RC. Factor IXa as a target for pharmacologic inhibition in acute coronary syndrome. Cardiovasc Ther 2011; 29:e22-35. [PMID: 21749674 DOI: 10.1111/j.1755-5922.2010.00134.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Anticoagulant therapy, combined with platelet-directed inhibitors, represents a standard-of-care in the management of patients with acute coronary syndrome, particularly those who require percutaneous coronary interventions. While a vast clinical experience, coupled with large clinical trials have collectively provided guidance, an optimal anticoagulant drug and applied strategy, defined as one that reduces thrombotic and hemorrhagic events consistently, with minimal off-target effects and active control of systemic anticoagulation according to patient and clinical-setting specific need, remains at large. An advancing knowledge of coagulation, hemostasis, and thrombosis suggests that factor IXa, a protease that governs thrombin generation in common thrombotic disorders may represent a prime target for pharmacologic inhibition.
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Affiliation(s)
- Christopher Roser-Jones
- Department of Medicine, Divisions of Cardiology and Hematology, Duke University Medical Center, Duke University School of Medicine and Duke Clinical Research Institute, Advanced Biomarkers Program, Durham, NC, USA
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19
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Complex assemblies of factors IX and X regulate the initiation, maintenance, and shutdown of blood coagulation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 99:51-103. [PMID: 21238934 DOI: 10.1016/b978-0-12-385504-6.00002-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Blood hemostasis is accomplished by a complex network of (anti-)coagulatory and fibrinolytic processes. These physiological processes are implemented by the assembly of multiprotein complexes involving both humoral and cellular components. Coagulation factor X, and particularly, factor IX, exemplify the dramatic enhancement that is obtained by the synergistic interaction of cell surface, inorganic and protein cofactors, protease, and substrate. With a focus on structure-function relationship, we review the current knowledge of activity modulation principles in the coagulation proteases factors IX and X and indicate future challenges for hemostasis research. This chapter is organized by describing the principles of hierarchical activation of blood coagulation proteases, including endogenous and exogenous protease activators, cofactor binding, substrate specificities, and protein inhibitors. We conclude by outlining pharmaceutical opportunities for unmet needs in hemophilia and thrombosis.
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20
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Woodruff B, Sullenger B, Becker RC. Antithrombotic Therapy in Acute Coronary Syndrome: How Far Up the Coagulation Cascade Will We Go? Curr Cardiol Rep 2010; 12:315-20. [DOI: 10.1007/s11886-010-0117-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Wu H, Xu X, Zhang L, Shen D, Peng L, Zhang Y, Song J. Mg(II)-induced binding of factor IX-binding protein from the venom of Agkistrodon Halys Pallas with factor Xa. Toxicon 2010; 55:1358-64. [PMID: 20156470 DOI: 10.1016/j.toxicon.2010.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 01/30/2010] [Accepted: 02/04/2010] [Indexed: 10/19/2022]
Abstract
Factor IX-binding protein (AHP IX-bp), a Ca2+- and Zn2+-binding protein from the venom of Agkistrodon Halys Pallas was reported to bind specifically with factor IX in a Zn2+-dependent manner. Here we have purified AHP IX-bp by a simple two-step of chromatography procedure and found that AHP IX-bp also binds factor Xa (FXa) with high binding-affinity in a Mg2+-dependent manner. Although Mg2+ ions have a significantly low binding-affinity for apo-AHP IX-bp as determined by isothermal titration calorimetry, they can induce the binding of apo-AHP IX-bp with FXa even in the absence of Ca2+ as determined by native PAGE and surface plasmon resonance. Mg2+ ions are required to maintain in vivo function of FX Gla domain for its recognition of AHP IX-bp. Both Ca2+ and Zn2+ ions fail to induce the binding between apo-AHP IX-bp and FXa. The abundant Mg2+ ions in blood play an important role in the anticoagulation of AHP IX-bp.
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Affiliation(s)
- Hao Wu
- Department of Chemistry, University of Science and Technology of China, No. 96, Jinzhai Road, Hefei 230026, PR China
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22
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Charbonneau S, Peng HT, Shek PN, Blostein MD. Amphipathic peptides can act as an anticoagulant by competing with phospholipid membranes for blood coagulation factors. Biochem Biophys Res Commun 2010; 391:1197-202. [DOI: 10.1016/j.bbrc.2009.12.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 12/08/2009] [Indexed: 10/20/2022]
Affiliation(s)
- S Charbonneau
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
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23
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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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24
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McCann JC, Ames BN. Vitamin K, an example of triage theory: is micronutrient inadequacy linked to diseases of aging? Am J Clin Nutr 2009; 90:889-907. [PMID: 19692494 DOI: 10.3945/ajcn.2009.27930] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The triage theory posits that some functions of micronutrients (the approximately 40 essential vitamins, minerals, fatty acids, and amino acids) are restricted during shortage and that functions required for short-term survival take precedence over those that are less essential. Insidious changes accumulate as a consequence of restriction, which increases the risk of diseases of aging. For 16 known vitamin K-dependent (VKD) proteins, we evaluated the relative lethality of 11 known mouse knockout mutants to categorize essentiality. Results indicate that 5 VKD proteins that are required for coagulation had critical functions (knockouts were embryonic lethal), whereas the knockouts of 5 less critical VKD proteins [osteocalcin, matrix Gla protein (Mgp), growth arrest specific protein 6, transforming growth factor beta-inducible protein (Tgfbi or betaig-h3), and periostin] survived at least through weaning. The VKD gamma-carboxylation of the 5 essential VKD proteins in the liver and the 5 nonessential proteins in nonhepatic tissues sets up a dichotomy that takes advantage of the preferential distribution of dietary vitamin K1 to the liver to preserve coagulation function when vitamin K1 is limiting. Genetic loss of less critical VKD proteins, dietary vitamin K inadequacy, human polymorphisms or mutations, and vitamin K deficiency induced by chronic anticoagulant (warfarin/coumadin) therapy are all linked to age-associated conditions: bone fragility after estrogen loss (osteocalcin) and arterial calcification linked to cardiovascular disease (Mgp). There is increased spontaneous cancer in Tgfbi mouse knockouts, and knockdown of Tgfbi causes mitotic spindle abnormalities. A triage perspective reinforces recommendations of some experts that much of the population and warfarin/coumadin patients may not receive sufficient vitamin K for optimal function of VKD proteins that are important to maintain long-term health.
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Affiliation(s)
- Joyce C McCann
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
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25
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Brosnan ME, Brosnan JT. Hepatic glutamate metabolism: a tale of 2 hepatocytes. Am J Clin Nutr 2009; 90:857S-861S. [PMID: 19625684 DOI: 10.3945/ajcn.2009.27462z] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Glutamate plays a central role in hepatic amino acid metabolism, both because of its role in the transdeamination of most amino acids and because the catabolism of arginine, ornithine, proline, histidine, and glutamine gives rise to glutamate. It is now appreciated that different hepatic functions are restricted to hepatocyte subpopulations within different acinar zones. This is also a feature of glutamate metabolism. Glutamine catabolism and synthesis are physically separated by zonation, with glutamine synthetase restricted to a narrow band of hepatocytes in zone 3 of the hepatic acinus, whereas glutaminase occurs in zone 1. Arginine and ornithine metabolism is also restricted to particular hepatocyte subpopulations. Ornithine aminotransferase, the regulated enzyme of arginine and ornithine catabolism, is restricted to the same zone 3 cells as glutamine synthetase, whereas the urea cycle is found in the remaining hepatocytes. This separation facilitates the independent regulation of these 2 different metabolic processes. We know the acinar localization of only a small fraction of the approximately 15,000 genes expressed in the liver. Knowledge of the acinar localization of metabolic processes is essential for an appreciation of their relation to other hepatic functions and their regulation.
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Affiliation(s)
- Margaret E Brosnan
- Department of Biochemistry, Memorial University of Newfoundland, St John's, Canada
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26
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Agah S, Bajaj SP. Role of magnesium in factor XIa catalyzed activation of factor IX: calcium binding to factor IX under physiologic magnesium. J Thromb Haemost 2009; 7:1426-8. [PMID: 19500239 PMCID: PMC3071651 DOI: 10.1111/j.1538-7836.2009.03506.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Kim WH, Kim JS, Yoon Y, Lee GM. Effect of Ca2+ and Mg2+ concentration in culture medium on the activation of recombinant factor IX produced in Chinese hamster ovary cells. J Biotechnol 2009; 142:275-8. [DOI: 10.1016/j.jbiotec.2009.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 05/28/2009] [Accepted: 06/03/2009] [Indexed: 10/20/2022]
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28
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Rajotte I, Hasanbasic I, Blostein M. Gas6-mediated signaling is dependent on the engagement of its gamma-carboxyglutamic acid domain with phosphatidylserine. Biochem Biophys Res Commun 2008; 376:70-3. [PMID: 18760998 DOI: 10.1016/j.bbrc.2008.08.083] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2008] [Accepted: 08/19/2008] [Indexed: 11/30/2022]
Abstract
Gas6 is a vitamin K-dependent protein containing gamma-carboxyglutamic acid (Gla) at its N-terminus and a receptor binding domain at its C-terminus. Gas6-Axl binding is necessary but not sufficient to support endothelial cell survival as decarboxylated gas6 inhibits the pro-survival function of gas6 by binding and inhibiting Axl, even though decarboxylated gas6 cannot support endothelial cell survival itself. It is hypothesized that interactions between the Gla domain of gas6 and phosphatidylserine (PS), though not required for gas6 binding to Axl, are necessary for gas6-Axl function. In support of this hypothesis are results showing that (1) two specific inhibitors of Gla-PS interactions, namely soluble PS and Annexin V, abrogate gas6-mediated endothelial cell survival and (2) Soluble PS inhibits Akt activation, a downstream intracellular event triggered by gas6-Axl binding. In conclusion, we propose a heretofore unknown function of Gla, where Gla-PS binding on the N-terminus of gas6 is necessary for a gas6 function mediated through its binding to Axl via its C-terminus.
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Affiliation(s)
- Isabelle Rajotte
- The Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, 3755 Cote Sainte Catherine, Montreal, Que., Canada H3T1E2
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29
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Crystal structure of human factor VIII: implications for the formation of the factor IXa-factor VIIIa complex. Structure 2008; 16:597-606. [PMID: 18400180 DOI: 10.1016/j.str.2008.03.001] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2008] [Revised: 02/27/2008] [Accepted: 03/01/2008] [Indexed: 11/24/2022]
Abstract
Factor VIII is a procofactor that plays a critical role in blood coagulation, and is missing or defective in hemophilia A. We determined the X-ray crystal structure of B domain-deleted human factor VIII. This protein is composed of five globular domains and contains one Ca(2+) and two Cu(2+) ions. The three homologous A domains form a triangular heterotrimer where the A1 and A3 domains serve as the base and interact with the C2 and C1 domains, respectively. The structurally homologous C1 and C2 domains reveal membrane binding features. Based on biochemical studies, a model of the factor IXa-factor VIIIa complex was constructed by in silico docking. Factor IXa wraps across the side of factor VIII, and an extended interface spans the factor VIII heavy and light chains. This model provides insight into the activation of factor VIII and the interaction of factor VIIIa with factor IXa on the membrane surface.
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Persson E. Protein disulfide isomerase has no stimulatory chaperone effect on factor X activation by factor VIIa-soluble tissue factor. Thromb Res 2008; 123:171-6. [PMID: 18550154 DOI: 10.1016/j.thromres.2008.04.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 03/27/2008] [Accepted: 04/21/2008] [Indexed: 11/26/2022]
Abstract
INTRODUCTION It was recently reported that protein disulfide isomerase (PDI) stimulates factor X (FX) activation by factor VIIa (FVIIa) bound to soluble tissue factor (sTF) in a purified system and that PDI may be responsible for activating cellular tissue factor (TF) and switching it between its roles in blood coagulation and cellular signalling. This study further investigates the former effect of PDI. METHOD FX activations by FVIIa-sTF(1-219) were carried out in the presence of different forms of PDI, with annexin V or detergent present in the system and using various forms of FVIIa and FX. In addition, FVIIa-lipidated TF was used as the FX activator. RESULTS Recombinant human PDI did not influence FX activation by FVIIa-sTF(1-219), whereas PDI purified from bovine liver enhanced the activation rate in a dose-dependent manner. The inclusion of annexin V or detergent abolished the stimulatory effect. Removal of the phospholipid-interactive gamma-carboxyglutamic acid (Gla)-containing domain from either FVIIa or FX obliterated the bovine PDI-induced enhancement of FX activation, as did the introduction of F4A or L8A mutation in FVIIa. The presence of 25 nM bovine PDI lowered the apparent K(m) for FX from far above 10 microM to 1-2 microM. No PDI effect was seen when FVIIa-lipidated TF was the FX activator. CONCLUSIONS FX activation is insensitive to PDI per se and a phospholipid contaminant in the bovine PDI preparation acts stimulatory when sTF, but not lipidated TF, is the cofactor. Strong support is provided by the lacking effect of bovine PDI after removal or modification of the Gla domain in either FVIIa or FX as well as by the effects of annexin V and detergents and the decreased K(m) value.
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Affiliation(s)
- Egon Persson
- Haemostasis Biochemistry, Novo Nordisk A/S, Novo Nordisk Park (G8.2.76), DK-2760 Måløv, Denmark.
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31
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Silva PJ, Ramos MJ. Reaction mechanism of the vitamin K-dependent glutamate carboxylase: a computational study. J Phys Chem B 2007; 111:12883-7. [PMID: 17935315 DOI: 10.1021/jp0738208] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the reaction cycle of glutamate carboxylase, vitamin K epoxidation by O2 has been proposed to generate a very strong base able to remove a proton from the gamma carbon of a Glu residue, thus yielding a Glu-based carbanion that readily reacts with CO2. We have used hybrid density functional theory to study this appealing mechanism. Our calculations show a very exergonic four-step mechanism with the reaction of (triplet) O2 with the singlet vitamin K anion as the rate-limiting step, with a rate similar to the experimental value. Our study also establishes the need to apply continuum models when performing the optimization of minimum-energy crossing points between potential energy surfaces of different multiplicities for enzyme model systems.
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Affiliation(s)
- Pedro J Silva
- REQUIMTE, Faculdade de Ciências da Saúde, Universidade Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150 Porto-Portugal
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32
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Gopinath S, Shikamoto Y, Mizuno H, Kumar P. Snake-venom-derived Factor IX-binding protein specifically blocks the gamma-carboxyglutamic acid-rich-domain-mediated membrane binding of human Factors IX and X. Biochem J 2007; 405:351-7. [PMID: 17407444 PMCID: PMC1904519 DOI: 10.1042/bj20061737] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A potent anticoagulant protein, IX-bp (Factor IX binding protein), has been isolated from the venom of Trimeresurus flavoviridis (habu snake) and is known to bind specifically to the Gla (gamma-carboxyglutamic acid-rich) domain of Factor IX. To evaluate the molecular basis for its anticoagulation activity, we assessed its interactions with various clotting factors. We found that the anticoagulation activity is primarily due to binding to the Gla domains of Factors IX and X, thus preventing these factors from recognizing phosphatidylserine on the plasma membrane. The present study suggests that ligands that bind to the Gla domains of Factors IX and X may have the potential to become novel anticoagulants.
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Affiliation(s)
- Subash C. B. Gopinath
- *Functional Nucleic Acids Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba City 305-8566, Ibaraki, Japan
| | - Yasuo Shikamoto
- †Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba City 305-8566, Ibaraki, Japan
| | - Hiroshi Mizuno
- *Functional Nucleic Acids Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba City 305-8566, Ibaraki, Japan
- ‡VALWAY Technology Center, NEC Soft Co. Ltd, 1-18-7, Shinkiba, Koto-ku, Tokyo 136-8627, Japan
| | - Penmetcha K. R. Kumar
- *Functional Nucleic Acids Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba City 305-8566, Ibaraki, Japan
- To whom correspondence should be addressed (email )
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Howard EL, Becker KCD, Rusconi CP, Becker RC. Factor IXa inhibitors as novel anticoagulants. Arterioscler Thromb Vasc Biol 2007; 27:722-7. [PMID: 17272750 DOI: 10.1161/01.atv.0000259363.91070.f1] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Currently available anticoagulants are limited by modest therapeutic benefits, narrow clinical applications, increased bleeding risk, and drug-induced thrombophilia. Because factor IX plays a pivotal role in tissue factor (TF)-mediated thrombin generation, it may represent a promising target for drug development. Several methods of attenuating factor IX activity, including monoclonal antibodies, synthetic active site-blocked competitive inhibitors, oral inhibitors, and RNA aptamers, have undergone investigation. This review summarizes present knowledge of factor IX inhibitors with emphasis on biology, pharmacology, preclinical data, and early-phase clinical experience in humans.
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Affiliation(s)
- Emily L Howard
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
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34
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Taboureau O, Olsen OH. Computational study of coagulation factor VIIa's affinity for phospholipid membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2006; 36:133-44. [PMID: 17131117 DOI: 10.1007/s00249-006-0114-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Revised: 09/12/2006] [Accepted: 10/31/2006] [Indexed: 11/28/2022]
Abstract
The interaction between the gamma-carboxyglutamic acid-rich domain of coagulation factor VIIa (FVIIa), a vitamin-K-dependent enzyme, and phospholipid membranes plays a major role in initiation of blood coagulation. However, despite a high sequence and structural similarity to the Gla domain of other vitamin-K-dependent enzymes with a high membrane affinity, its affinity for negatively charged phospholipids is poor. A few amino acid differences are responsible for this observation. Based on the X-ray structure of lysophosphatidylserine (lysoPS) bound to the Gla domain of bovine prothrombin (Prth), models of the Gla domain of wildtype FVIIa and mutated FVIIa Gla domains in complex with lysoPS were built. Molecular dynamics (MD) and steered molecular dynamics (SMD) simulations on the complexes were applied to investigate the significant difference in the binding affinity. The MD simulation approach provides a structural and dynamic support to the role of P10Q and K32E mutations in the improvement of the membrane contact. Hence, rotation of the Gly11 main chain generated during the MD simulation results in a hydrogen bond with Q10 side chain as well as the appearance of a hydrogen bond between E32 and Q10 forcing the loop harbouring Arg9 and Arg15 to shrink and thereby enhances the accessibility of the phospholipids to the calcium ions. Furthermore, the application of the SMD simulation method to dissociate C6-lysoPS from a series of Gla domain models exhibits a ranking of the rupture force that can be useful in the interpretation of the PS interaction with Gla domains. Finally, adiabatic mapping of Gla6 residue in FVIIa with or without insertion of Tyr4 confirms the critical role of the insertion on the conformation of the side chain Gla6 in FVIIa and the corresponding Gla7 in Prth.
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Affiliation(s)
- Olivier Taboureau
- Haemostasis Biochemistry, Novo Nordisk A/S, Novo Nordisk Park, Building G8.2.90, 2760 Måløv, Denmark
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35
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Birrell GW, Earl S, Masci PP, de Jersey J, Wallis TP, Gorman JJ, Lavin MF. Molecular Diversity in Venom from the Australian Brown Snake, Pseudonaja textilis. Mol Cell Proteomics 2006; 5:379-89. [PMID: 16284125 DOI: 10.1074/mcp.m500270-mcp200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Venom from the Australian elapid Pseudonaja textilis (Common or Eastern Brown snake), is the second most toxic snake venom known and is the most common cause of death from snake bite in Australia. This venom is known to contain a prothrombin activator complex, serine proteinase inhibitors, various phospholipase A2s, and pre- and postsynaptic neurotoxins. In this study, we performed a proteomic identification of the venom using two-dimensional gel electrophoresis, mass spectrometry, and de novo peptide sequencing. We identified most of the venom proteins including proteins previously not known to be present in the venom. In addition, we used immunoblotting and post-translational modification-specific enzyme stains and antibodies that reveal the complexity and regional diversity of the venom. Modifications observed include phosphorylation, gamma-carboxylation, and glycosylation. Glycoproteins were further characterized by enzymatic deglycosylation and by lectin binding specificity. The venom contains an abundance of glycoproteins with N-linked sugars that include glucose/mannose, N-acetylgalactosamine, N-acetylglucosamine, and sialic acids. Additionally there are multiple isoforms of mammalian coagulation factors that comprise a significant proportion of the venom. Indeed two of the identified proteins, a procoagulant and a plasmin inhibitor, are currently in development as human therapeutic agents.
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Affiliation(s)
- Geoff W Birrell
- The Queensland Institute of Medical Research, P. O. Royal Brisbane Hospital, Brisbane 4029, Australia
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36
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Furie B. P-selectin and blood coagulation: it's not only about inflammation any more. Arterioscler Thromb Vasc Biol 2005; 25:877-8. [PMID: 15863716 DOI: 10.1161/01.atv.0000161049.53535.5d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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Schmidt AE, Stewart JE, Mathur A, Krishnaswamy S, Bajaj SP. Na+ site in blood coagulation factor IXa: effect on catalysis and factor VIIIa binding. J Mol Biol 2005; 350:78-91. [PMID: 15913649 DOI: 10.1016/j.jmb.2005.04.052] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Revised: 04/20/2005] [Accepted: 04/25/2005] [Indexed: 11/17/2022]
Abstract
During blood coagulation, factor IXa (FIXa) activates factor X (FX) requiring Ca2+, phospholipid, and factor VIIIa (FVIIIa). The serine protease domain of FIXa contains a Ca2+ site and is predicted to contain a Na+ site. Comparative homology analysis revealed that Na+ in FIXa coordinates to the carbonyl groups of residues 184A, 185, 221A, and 224 (chymotrypsin numbering). Kinetic data obtained at several concentrations of Na+ and Ca2+ with increasing concentrations of a synthetic substrate (CH3-SO2-d-Leu-Gly-Arg-p-nitroanilide) were fit globally, assuming rapid equilibrium conditions. Occupancy by Na+ increased the affinity of FIXa for the synthetic substrate, whereas occupancy by Ca2+ decreased this affinity but increased k(cat) dramatically. Thus, Na+-FIXa-Ca2+ is catalytically more active than free FIXa. FIXa(Y225P), a Na+ site mutant, was severely impaired in Na+ potentiation of its catalytic activity and in binding to p-aminobenzamidine (S1 site probe) validating that substrate binding in FIXa is linked positively to Na+ binding. Moreover, the rate of carbamylation of NH2 of Val16, which forms a salt-bridge with Asp194 in serine proteases, was faster for FIXa(Y225P) and addition of Ca2+ overcame this impairment only partially. Further studies were aimed at delineating the role of the FIXa Na+ site in macromolecular catalysis. In the presence of Ca2+ and phospholipid, with or without saturating FVIIIa, FIXa(Y225P) activated FX with similar K(m) but threefold reduced k(cat). Further, interaction of FVIIIa:FIXa(Y225P) was impaired fourfold. Our previous data revealed that Ca2+ binding to the protease domain increases the affinity of FIXa for FVIIIa approximately 15-fold. The present data indicate that occupancy of the Na+ site further increases the affinity of FIXa for FVIIIa fourfold and k(cat) threefold. Thus, in the presence of Ca2+, phospholipid, and FVIIIa, binding of Na+ to FIXa increases its biologic activity by approximately 12-fold, implicating its role in physiologic coagulation.
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Affiliation(s)
- Amy E Schmidt
- UCLA/Orthopaedic Hospital, Department of Orthopaedic Surgery and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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38
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Oakhill JS, Sutton BJ, Gorringe AR, Evans RW. Homology modelling of transferrin-binding protein A from Neisseria meningitidis. Protein Eng Des Sel 2005; 18:221-8. [PMID: 15820975 DOI: 10.1093/protein/gzi024] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Neisseria meningitidis, a causative agent of bacterial meningitis, obtains transferrin-bound iron by expressing two outer membrane located transferrin-binding proteins, TbpA and TbpB. TbpA is thought to be an integral outer membrane pore that facilitates iron uptake. Evidence suggests that TbpA is a useful antigen for inclusion in a vaccine effective against meningococcal disease, hence the identification of regions involved in ligand binding is of paramount importance to design strategies to block uptake of iron. The protein shares sequence and functional similarities to the Escherichia coli siderophore receptors FepA and FhuA, whose structures have been determined. These receptors are composed of two domains, a 22-stranded beta-barrel and an N-terminal plug region that sits within the barrel and occludes the transmembrane pore. A three-dimensional TbpA model was constructed using FepA and FhuA structural templates, hydrophobicity analysis and homology modelling. TbpA was found to possess a similar architecture to the siderophore receptors. In addition to providing insights into the highly immunogenic nature of TbpA and allowing the prediction of potentially important ligand-binding epitopes, the model also reveals a narrow channel through its entire length. The relevance of this channel and the spatial arrangement of external loops, to the mechanism of iron translocation employed by TbpA is discussed.
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Affiliation(s)
- Jonathan S Oakhill
- Metalloprotein Research Group, Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK
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39
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Preston RJS, Villegas-Mendez A, Sun YH, Hermida J, Simioni P, Philippou H, Dahlbäck B, Lane DA. Selective modulation of protein C affinity for EPCR and phospholipids by Gla domain mutation. FEBS J 2004; 272:97-108. [PMID: 15634335 DOI: 10.1111/j.1432-1033.2004.04401.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Uniquely amongst vitamin K-dependent coagulation proteins, protein C interacts via its Gla domain both with a receptor, the endothelial cell protein C receptor (EPCR), and with phospholipids. We have studied naturally occurring and recombinant protein C Gla domain variants for soluble (s)EPCR binding, cell surface activation to activated protein C (APC) by the thrombin-thrombomodulin complex, and phospholipid dependent factor Va (FVa) inactivation by APC, to establish if these functions are concordant. Wild-type protein C binding to sEPCR was characterized with surface plasmon resonance to have an association rate constant of 5.23 x 10(5) m(-1).s(-1), a dissociation rate constant of 7.61 x 10(-2) s(-1) and equilibrium binding constant (K(D)) of 147 nm. It was activated by thrombin over endothelial cells with a K(m) of 213 nm and once activated to APC, rapidly inactivated FVa. Each of these interactions was dramatically reduced for variants causing gross Gla domain misfolding (R-1L, R-1C, E16D and E26K). Recombinant variants Q32A, V34A and D35A had essentially normal functions. However, R9H and H10Q/S11G/S12N/D23S/Q32E/N33D/H44Y (QGNSEDY) variants had slightly reduced (< twofold) binding to sEPCR, arising from an increased rate of dissociation, and increased K(m) (358 nm for QGNSEDY) for endothelial cell surface activation by thrombin. Interestingly, these variants had greatly reduced (R9H) or greatly enhanced (QGNSEDY) ability to inactivate FVa. Therefore, protein C binding to sEPCR and phospholipids is broadly dependent on correct Gla domain folding, but can be selectively influenced by judicious mutation.
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Affiliation(s)
- Roger J S Preston
- Department of Haematology, Division of Investigative Science, Hammersmith Campus, Imperial College London, UK
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40
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Grant MA, Baikeev RF, Gilbert GE, Rigby AC. Lysine 5 and Phenylalanine 9 of the Factor IX ω-Loop Interact with Phosphatidylserine in a Membrane-Mimetic Environment. Biochemistry 2004; 43:15367-78. [PMID: 15581349 DOI: 10.1021/bi049107f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding of factor IX to cell membranes requires a structured N-terminal omega-loop conformation that exposes hydrophobic residues for a highly regulated interaction with a phospholipid. We hypothesized that a peptide comprised of amino acids Gly4-Gln11 of factor IX (fIX(G4)(-)(Q11)) and constrained by an engineered disulfide bond would assume the native factor IX omega-loop conformation in the absence of Ca(2+). The small size and freedom from aggregation-inducing calcium interactions would make fIX(G4)(-)(Q11) suitable for structural studies for eliciting details about phospholipid interactions. fIX(G4)(-)(Q11) competes with factor IXa for binding sites on phosphatidylserine-containing membranes with a K(i) of 11 microM and inhibits the activation of factor X by the factor VIIIa-IXa complex with a K(i) of 285 microM. The NMR structure of fIX(G4)(-)(Q11) reveals an omega-loop backbone fold and side chain orientation similar to those found in the calcium-bound factor IX Gla domain, FIX(1-47)-Ca(2+). Dicaproylphosphatidylserine (C(6)PS) induces HN, Halpha backbone, and Hbeta chemical shift perturbations at residues Lys5, Leu6, Phe9, and Val10 of fIX(G4)(-)(Q11), while selectively protecting the NHzeta side chain resonance of Lys5 from solvent exchange. NOEs between the aromatic ring protons of Phe9 and specific acyl chain protons of C(6)PS indicate that these phosphatidylserine protons reside 3-6 A from Phe9. Stabilization of the phosphoserine headgroup and glycerol backbone of C(6)PS identifies that phosphatidylserine is in a protected environment that is spatially juxtaposed with fIX(G4)(-)(Q11). Together, these data demonstrate that Lys5, Leu6, Phe9, and Val10 preferentially interact with C(6)PS and allow us to correlate known hemophilia B mutations of factor IX at Lys5 or Phe9 with impaired phosphatidylserine interaction.
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Affiliation(s)
- Marianne A Grant
- Division of Hemostasis and Thrombosis, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, 330 Brookline Avenue, Boston, Massachusetts 02215, USA
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41
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Perera L, Darden TA, Duke RE, Venkateswarlu D, Pedersen LG. Early Unfolding Response of a Stable Protein Domain to Environmental Changes. J Phys Chem A 2004. [DOI: 10.1021/jp048385l] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lalith Perera
- High Performance Computing Group, Information Technology Services, CB#3455, and Department of Chemistry, CB#3290, University of North Carolina, Chapel Hill, North Carolina 27599, and Laboratory of Quantitative and Computational Biology, National Institute of Environmental Health Science, Research Triangle Park, North Carolina 27709
| | - Thomas A. Darden
- High Performance Computing Group, Information Technology Services, CB#3455, and Department of Chemistry, CB#3290, University of North Carolina, Chapel Hill, North Carolina 27599, and Laboratory of Quantitative and Computational Biology, National Institute of Environmental Health Science, Research Triangle Park, North Carolina 27709
| | - Robert E. Duke
- High Performance Computing Group, Information Technology Services, CB#3455, and Department of Chemistry, CB#3290, University of North Carolina, Chapel Hill, North Carolina 27599, and Laboratory of Quantitative and Computational Biology, National Institute of Environmental Health Science, Research Triangle Park, North Carolina 27709
| | - Divi Venkateswarlu
- High Performance Computing Group, Information Technology Services, CB#3455, and Department of Chemistry, CB#3290, University of North Carolina, Chapel Hill, North Carolina 27599, and Laboratory of Quantitative and Computational Biology, National Institute of Environmental Health Science, Research Triangle Park, North Carolina 27709
| | - Lee G. Pedersen
- High Performance Computing Group, Information Technology Services, CB#3455, and Department of Chemistry, CB#3290, University of North Carolina, Chapel Hill, North Carolina 27599, and Laboratory of Quantitative and Computational Biology, National Institute of Environmental Health Science, Research Triangle Park, North Carolina 27709
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42
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Grant MA, Hansson K, Furie BC, Furie B, Stenflo J, Rigby AC. The Metal-free and Calcium-bound Structures of a γ-Carboxyglutamic Acid-containing Contryphan from Conus marmoreus, Glacontryphan-M. J Biol Chem 2004; 279:32464-73. [PMID: 15155731 DOI: 10.1074/jbc.m313826200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glacontryphan-M, a novel calcium-dependent inhibitor of L-type voltage-gated Ca(2+) channels expressed in mouse pancreatic beta-cells, was recently isolated from the venom of the cone snail Conus marmoreus (Hansson, K., Ma, X., Eliasson, L., Czerwiec, E., Furie, B., Furie, B. C., Rorsman, P., and Stenflo, J. (2004) J. Biol. Chem. 278, 32453-32463). The conserved disulfide-bonded loop of the contryphan family of conotoxins including a D-Trp is present; however, unique to glacontryphan-M is a histidine within the intercysteine-loop and two gamma-carboxyglutamic acid (Gla) residues, formed by post-translational modification of glutamic acid. The two calcium-binding Gla residues are located in a four residue N-terminal extension of this contryphan. To better understand the structural and functional significance of these residues, we have determined the structure of glacontryphan-M using two-dimensional (1)H NMR spectroscopy in the absence and presence of calcium. Comparisons of the glacontryphan-M structures reveal that calcium binding induces structural perturbations within the Gla-containing N terminus and the Cys(11)-Cys(5)-Pro(6) region of the intercysteine loop. The backbone of N-terminal residues perturbed by calcium, Gla(2) and Ser(3), moves away from the His(8) and Trp(10) aromatic rings and the alignment of the D-Trp(7) and His(8) aromatic rings with respect to the Trp(10) rings is altered. The blockage of L-type voltage-gated Ca(2+) channel currents by glacontryphan-M requires calcium binding to N-terminal Gla residues, where presumably histidine and tryptophan may be accessible for interaction with the channel. The backbone C alpha conformation of the intercysteine loop of calcium-bound glacontryphan-M superimposes on known structures of contryphan-R and Vn (0.83 and 0.66 A, respectively). Taken together these data identify that glacontryphan-M possesses the canonical contryphan intercysteine loop structure, yet possesses critical determinants necessary for a calcium-induced functionally required conformation.
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Affiliation(s)
- Marianne A Grant
- Center for Hemostasis, Thrombosis, and Vascular Biology, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, USA
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43
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Huang M, Furie BC, Furie B. Crystal Structure of the Calcium-stabilized Human Factor IX Gla Domain Bound to a Conformation-specific Anti-factor IX Antibody. J Biol Chem 2004; 279:14338-46. [PMID: 14722079 DOI: 10.1074/jbc.m314011200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The binding of Factor IX to membranes during blood coagulation is mediated by the N-terminal gamma-carboxyglutamic acid-rich (Gla) domain, a membrane-anchoring domain found on vitamin K-dependent blood coagulation and regulatory proteins. Conformation-specific anti-Factor IX antibodies are directed at the calcium-stabilized Gla domain and interfere with Factor IX-membrane interaction. One such antibody, 10C12, recognizes the calcium-stabilized form of the Gla domain of Factor IX. We prepared the fully carboxylated Gla domain of Factor IX by solid phase peptide synthesis and crystallized Factor IX-(1-47) in complex with Fab fragments of the 10C12 antibody. The overall structure of the Gla domain in the Factor IX-(1-47)-antibody complex at 2.2 A is similar to the structure of the Factor IX Gla domain in the presence of calcium ions as determined by NMR spectroscopy (Freedman, S. J., Furie, B. C., Furie, B., and Baleja, J. D. (1995) Biochemistry 34, 12126-12137) and by x-ray crystallography (Shikamoto, Y., Morita, T., Fujimoto, Z., and Mizuno, H. (2003) J. Biol. Chem. 278, 24090-24094). The complex structure shows that the complementarity determining region loops of the 10C12 antibody form a hydrophobic pocket to accommodate the hydrophobic patch of the Gla domain consisting of Leu-6, Phe-9, and Val-10. Polar interactions also play an important role in the antibody-antigen recognition. Furthermore, the calcium coordination network of the Factor IX Gla domain is different than in Gla domain structures of other vitamin K-dependent proteins. We conclude that this antibody is directed at the membrane binding site in the omega loop of Factor IX and blocks Factor IX function by inhibiting its interaction with membranes.
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Affiliation(s)
- Mingdong Huang
- Center for Hemostasis, Thrombosis and Vascular Biology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts 02215, USA
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44
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Huang M, Rigby AC, Morelli X, Grant MA, Huang G, Furie B, Seaton B, Furie BC. Structural basis of membrane binding by Gla domains of vitamin K-dependent proteins. Nat Struct Mol Biol 2003; 10:751-6. [PMID: 12923575 DOI: 10.1038/nsb971] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2003] [Accepted: 07/24/2003] [Indexed: 11/09/2022]
Abstract
In a calcium-dependent interaction critical for blood coagulation, vitamin K-dependent blood coagulation proteins bind cell membranes containing phosphatidylserine via gamma-carboxyglutamic acid-rich (Gla) domains. Gla domain-mediated protein-membrane interaction is required for generation of thrombin, the terminal enzyme in the coagulation cascade, on a physiologic time scale. We determined by X-ray crystallography and NMR spectroscopy the lysophosphatidylserine-binding site in the bovine prothrombin Gla domain. The serine head group binds Gla domain-bound calcium ions and Gla residues 17 and 21, fixed elements of the Gla domain fold, predicting the structural basis for phosphatidylserine specificity among Gla domains. Gla domains provide a unique mechanism for protein-phospholipid membrane interaction. Increasingly Gla domains are being identified in proteins unrelated to blood coagulation. Thus, this membrane-binding mechanism may be important in other physiologic processes.
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Affiliation(s)
- Mingdong Huang
- Center for Hemostasis and Thrombosis Research, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, 330 Brookline Avenue, Boston, Massachusetts 02215, USA
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45
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Blostein MD, Furie BC, Rajotte I, Furie B. The Gla domain of factor IXa binds to factor VIIIa in the tenase complex. J Biol Chem 2003; 278:31297-302. [PMID: 12782629 DOI: 10.1074/jbc.m302840200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During blood coagulation factor IXa binds to factor VIIIa on phospholipid membranes to form an enzymatic complex, the tenase complex. To test whether there is a protein-protein contact site between the gamma-carboxyglutamic acid (Gla) domain of factor IXa and factor VIIIa, we demonstrated that an antibody to the Gla domain of factor IXa inhibited factor VIIIa-dependent factor IXa activity, suggesting an interaction of the factor IXa Gla domain with factor VIIIa. To study this interaction, we synthesized three analogs of the factor IXa Gla domain (FIX1-47) with Phe-9, Phe-25, or Val-46 replaced, respectively, with benzoylphenylalanine (BPA), a photoactivatable cross-linking reagent. These factor IX Gla domain analogs maintain native tertiary structure, as demonstrated by calcium-induced fluorescence quenching and phospholipid binding studies. In the absence of phospholipid membranes, FIX1-47 was able to inhibit factor IXa activity. This inhibition is dependent on the presence of factor VIIIa, suggesting a contact site between the factor IXa Gla domain and factor VIIIa. To demonstrate a direct interaction we did cross-linking experiments with FIX1-479BPA, FIX1-4725BPA, and FIX1-4746BPA. Covalent cross-linking to factor VIIIa was observed primarily with FIX1-4725BPA and to a much lesser degree with FIX1-4746BPA. Immunoprecipitation experiments with an antibody to the C2 domain of factor VIIIa indicate that the factor IX Gla domain cross-links to the A3-C1-C2 domain of factor VIIIa. These results suggest that the factor IXa Gla domain contacts factor VIIIa in the tenase complex through a contact site that includes phenylalanine 25 and perhaps valine 46.
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Affiliation(s)
- Mark D Blostein
- The Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, Quebec H3T 1A4, Canada.
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46
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Shikamoto Y, Morita T, Fujimoto Z, Mizuno H. Crystal structure of Mg2+- and Ca2+-bound Gla domain of factor IX complexed with binding protein. J Biol Chem 2003; 278:24090-4. [PMID: 12695512 DOI: 10.1074/jbc.m300650200] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Factor IX is an indispensable protein required in the blood coagulation cascade. It binds to the surface of phospholipid membrane by means of a gamma-carboxyglutamic acid (Gla) domain situated at the N terminus. Recently, we showed that physiological concentrations of Mg2+ ions affect the native conformation of the Gla domain and in doing so augment the biological activity of factor IXa and binding affinity with its binding protein even in the presence of Ca2+ ions. Here we report on the crystal structures of the Mg2+/Ca2+-bound and Ca2+-bound (Mg2+-free) factor IX Gla domain (IXGD1-46) in complex with its binding protein (IX-bp) at 1.55 and 1.80 A resolutions, respectively. Three Mg2+ and five Ca2+ ions were bound in the Mg2+/Ca2+-bound IXGD1-46, and the Mg2+ ions were replaced by Ca2+ ions in Mg2+-free IXGD1-46. Comparison of Mg2+/Ca2+-bound with Ca2+-bound structures of the complexes showed that Mg2+ ion, which formed a bridge between IXGD1-46 and IX-bp, forced IXGD1-46 to rotate 4 degrees relative to IX-bp and hence might be the cause of a more tight interaction between the molecules than in the case of the Mg2+-free structure. The results clearly suggest that Mg2+ ions are required to maintain native conformation and in vivo function of factor IX Gla domain during blood coagulation.
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Affiliation(s)
- Yasuo Shikamoto
- Department of Biochemistry, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
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47
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Aktimur A, Gabriel MA, Gailani D, Toomey JR. The factor IX gamma-carboxyglutamic acid (Gla) domain is involved in interactions between factor IX and factor XIa. J Biol Chem 2003; 278:7981-7. [PMID: 12496253 DOI: 10.1074/jbc.m212748200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During hemostasis, factor IX is activated to factor IXabeta by factor VIIa and factor XIa. The glutamic acid-rich gamma-carboxyglutamic acid (Gla) domain of factor IX is involved in phospholipid binding and is required for activation by factor VIIa. In contrast, activation by factor XIa is not phospholipid-dependent, raising questions about the importance of the Gla for this reaction. We examined binding of factors IX and IXabeta to factor XIa by surface plasmon resonance. Plasma factors IX and IXabeta bind to factor XIa with K(d) values of 120 +/- 11 nm and 110 +/- 8 nm, respectively. Recombinant factor IX bound to factor XIa with a K(d) of 107 nm, whereas factor IX with a factor VII Gla domain (rFIX/VII-Gla) and factor IX expressed in the presence of warfarin (rFIX-desgamma) did not bind. An anti-factor IX Gla monoclonal antibody was a potent inhibitor of factor IX binding to factor XIa (K(i) 34 nm) and activation by factor XIa (K(i) 33 nm). In activated partial thromboplastin time clotting assays, the specific activities of plasma and recombinant factor IX were comparable (200 and 150 units/mg), whereas rFIX/VII-Gla activity was low (<2 units/mg). In contrast, recombinant factor IXabeta and activated rFIX/VIIa-Gla had similar activities (80 and 60% of plasma factor IXabeta), indicating that both proteases activate factor X and that the poor activity of zymogen rFIX/VII-Gla was caused by a specific defect in activation by factor XIa. The data demonstrate that factor XIa binds with comparable affinity to factors IX and IXabeta and that the interactions are dependent on the factor IX Gla domain.
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Affiliation(s)
- Aysar Aktimur
- Department of Pathology, Vanderbilt University, Nashville, Tennessee 37232, USA
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Harvey SB, Stone MD, Martinez MB, Nelsestuen GL. Mutagenesis of the gamma-carboxyglutamic acid domain of human factor VII to generate maximum enhancement of the membrane contact site. J Biol Chem 2003; 278:8363-9. [PMID: 12506121 DOI: 10.1074/jbc.m211629200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Site-directed mutagenesis of the 40 N-terminal residues (gamma-carboxyglutamic acid domain) of blood clotting factor VII was carried out to identify sites that improve membrane affinity. Improvements and degree of change included P10Q (2-fold), K32E (13-fold), and insertion of Tyr at position 4 (2-fold). Two other beneficial changes, D33F (2-fold) and A34E (1.5-fold), may exert their impact via influence of K32E. The modification D33E (5.2-fold) also resulted in substantial improvement. The combined mutant with highest affinity, (Y4)P10Q/K32E/D33F/A34E, showed 150-296-fold enhancement over wild-type factor VIIa, depending on the assay used. Undercarboxylation of Glu residues at positions 33 and 34 may result in an underestimate of the true contributions of gamma-carboxyglutamic acid at these positions. Except for the Tyr(4) mutant, all other beneficial mutations were located on the same surface of the protein, suggesting a possible membrane contact region. An initial screening assay was developed that provided faithful evaluation of mutants in crude mixtures. Overall, the results suggest features of membrane binding by vitamin K-dependent proteins and provide reagents that may prove useful for research and therapy.
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Affiliation(s)
- Stephen B Harvey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis 55455, USA
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Joseph JS, Valiyaveettil M, Gowda DC, Kini RM. Occurrence of O-linked Xyl-GlcNAc and Xyl-Glc disaccharides in trocarin, a factor Xa homolog from snake venom. J Thromb Haemost 2003; 1:545-50. [PMID: 12871464 DOI: 10.1046/j.1538-7836.2003.00090.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Trocarin is a 46515-Da group D prothrombin-activating glycoprotein from the venom of the Australian elapid, Tropidechis carinatus. Amino acid sequencing and functional characterization of trocarin demonstrated that it is a structural and functional homolog of mammalian blood coagulation factor (F)Xa. In this study we show that, in contrast to mammalian Xa, which is not glycosylated, trocarin contains an O-linked carbohydrate moiety in its light chain and an N-linked carbohydrate oligosaccharide in its heavy chain. Mass spectrometry and sugar compositional analysis indicate that the O-linked carbohydrate moiety is a mixture of Xyl-GlcNAc-, GlcNAc-, Xyl-Glc- and Glc- structures linked to Ser 52. The N-linked carbohydrate on Asn 45 of the heavy chain is a sialylated, diantennary oligosaccharide that is located at the lip of the active site of the prothrombin activator.
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Affiliation(s)
- J S Joseph
- Department of Biochemistry, Faculty of Medicine, National University of Singapore, Singapore
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Rezende SM, Lane DA, Mille-Baker B, Samama MM, Conard J, Simmonds RE. Protein S Gla-domain mutations causing impaired Ca(2+)-induced phospholipid binding and severe functional protein S deficiency. Blood 2002; 100:2812-9. [PMID: 12351389 DOI: 10.1182/blood-2002-03-0909] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have identified 2 PROS1 missense mutations in the exon that encodes the vitamin K-dependent Gla domain of protein S (Gly11Asp and Thr37Met) in kindred with phenotypic protein S deficiency and thrombosis. In studies using recombinant proteins, substitution of Gly11Asp did not affect production of protein S but resulted in 15.2-fold reduced protein S activity in a factor Va inactivation assay. Substitution of Thr37Met reduced expression by 33.2% (P <.001) and activity by 3.6-fold. The Gly11Asp variant had 5.4-fold reduced affinity for anionic phospholipid vesicles (P <.0001) and decreased affinity for an antibody specific for the Ca(2+)-dependent conformation of the protein S Gla domain (HPS21). Examination of a molecular model suggested that this could be due to repositioning of Gla29. In contrast, the Thr37Met variant had only a modest 1.5-fold (P <.001), reduced affinities for phospholipid and HPS21. This mutation seems to disrupt the aromatic stack region. The proposita was a compound heterozygote with free protein S antigen levels just below the lower limit of the normal range, and this is now attributed to the partial expression defect of the Thr37Met mutation. The activity levels were strongly reduced to 15% of normal, probably reflecting the functional deficit of both protein S variants. Her son (who was heterozygous only for Thr37Met) had borderline levels of protein S antigen and activity, reflecting the partial secretion and functional defect associated with this mutation. This first characterization of natural protein S Gla-domain variants highlights the importance of the high affinity protein S-phospholipid interaction for its anticoagulant role.
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Affiliation(s)
- Suely M Rezende
- Department of Haematology, Division of Investigative Science, Hammersmith Campus, Imperial College of Science, Technology, and Medicine, London, United Kingdom
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