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John L, Vijay R. Role of TAM Receptors in Antimalarial Humoral Immune Response. Pathogens 2024; 13:298. [PMID: 38668253 PMCID: PMC11054553 DOI: 10.3390/pathogens13040298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/29/2024] Open
Abstract
Immune response against malaria and the clearance of Plasmodium parasite relies on germinal-center-derived B cell responses that are temporally and histologically layered. Despite a well-orchestrated germinal center response, anti-Plasmodium immune response seldom offers sterilizing immunity. Recent studies report that certain pathophysiological features of malaria such as extensive hemolysis, hypoxia as well as the extrafollicular accumulation of short-lived plasmablasts may contribute to this suboptimal immune response. In this review, we summarize some of those studies and attempt to connect certain host intrinsic features in response to the malarial disease and the resultant gaps in the immune response.
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Affiliation(s)
- Lijo John
- Department of Veterinary Biochemistry, Kerala Veterinary and Animal Sciences University, Pookode 673576, Kerala, India
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60047, USA
| | - Rahul Vijay
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60047, USA
- Department of Microbiology and Immunology, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60047, USA
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2
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Miao YR, Rankin EB, Giaccia AJ. Therapeutic targeting of the functionally elusive TAM receptor family. Nat Rev Drug Discov 2024; 23:201-217. [PMID: 38092952 DOI: 10.1038/s41573-023-00846-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2023] [Indexed: 03/07/2024]
Abstract
The TAM receptor family of TYRO3, AXL and MERTK regulates tissue and immune homeostasis. Aberrant TAM receptor signalling has been linked to a range of diseases, including cancer, fibrosis and viral infections. Specifically, the dysregulation of TAM receptors can enhance tumour growth and metastasis due to their involvement in multiple oncogenic pathways. For example, TAM receptors have been implicated in the epithelial-mesenchymal transition, maintaining the stem cell phenotype, immune modulation, proliferation, angiogenesis and resistance to conventional and targeted therapies. Therapeutically, multiple TAM receptor inhibitors are in preclinical and clinical development for cancers and other indications, with those targeting AXL being the most clinically advanced. Although there has been notable clinical advancement in recent years, challenges persist. This Review aims to provide both biological and clinical insights into the current therapeutic landscape of TAM receptor inhibitors, and evaluates their potential for the treatment of cancer and non-malignant diseases.
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Affiliation(s)
- Yu Rebecca Miao
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Erinn B Rankin
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
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3
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Alniss HY, Witzel II, Semreen MH, Panda PK, Mishra YK, Ahuja R, Parkinson JA. Investigation of the Factors That Dictate the Preferred Orientation of Lexitropsins in the Minor Groove of DNA. J Med Chem 2019; 62:10423-10440. [DOI: 10.1021/acs.jmedchem.9b01534] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hasan Y. Alniss
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Ini-Isabée Witzel
- Core Technology Platform, New York University of Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Mohammad H. Semreen
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Sharjah Institute for Medical Research, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Pritam Kumar Panda
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala Sweden
| | - Yogendra Kumar Mishra
- Functional Nanomaterials, Institute for Materials Science, Kiel University, Kaiserstraße 2, D-24143 Kiel, Germany
| | - Rajeev Ahuja
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120, Uppsala Sweden
- Department of Materials and Engineering, Royal Institute of Technology (KTH), SE-10044 Stockholm Sweden
| | - John A. Parkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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Ma YC, Yang B, Wang X, Zhou L, Li WY, Liu WS, Lu XH, Zheng ZH, Ma Y, Wang RL. Identification of novel inhibitor of protein tyrosine phosphatases delta: structure-based pharmacophore modeling, virtual screening, flexible docking, molecular dynamics simulation, and post-molecular dynamics analysis. J Biomol Struct Dyn 2019; 38:4432-4448. [PMID: 31625456 DOI: 10.1080/07391102.2019.1682050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Owing to their unique functions in regulating the synapse activity of protein tyrosine phosphatases delta (PTPδ) that has drawn special attention for developing drugs to autism spectrum disorders (ASDs). In this study, the PTPδ pharmacophore was first established by the structure-based pharmacophore method. Subsequently, 10 compounds contented Lipinski's rule of five was acquired by the virtual screening of the PTPδ pharmacophore against ZINC and PubChem databases. Then, the 10 identified molecules were discovered that had better binding affinity than a known PTPδ inhibitors compound SCHEMBL16375396. Two compounds SCHEMBL16375408 and ZINC19796658 with high binding score, low toxicity were gained. They were observed by docking analysis and molecular dynamics simulations that the novel potential inhibitors not only possessed the same function as SCHEMBL16375396 did in inhibiting PTPδ, but also had more favorable conformation to bind with the catalytic active regions. This study provides a new method for identify PTPδ inhibitor for the treatment of ASDs disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yang-Chun Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Bing Yang
- Department of Cell Biology, School of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Xin Wang
- Tasly Pharmaceutical Group Co., Ltd., Tianjin, China
| | - Liang Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wen-Shan Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xin-Hua Lu
- New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering and Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Zhi-Hui Zheng
- New Drug Research and Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering and Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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5
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Smart SK, Vasileiadi E, Wang X, DeRyckere D, Graham DK. The Emerging Role of TYRO3 as a Therapeutic Target in Cancer. Cancers (Basel) 2018; 10:cancers10120474. [PMID: 30501104 PMCID: PMC6316664 DOI: 10.3390/cancers10120474] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022] Open
Abstract
The TAM family (TYRO3, AXL, MERTK) tyrosine kinases play roles in diverse biological processes including immune regulation, clearance of apoptotic cells, platelet aggregation, and cell proliferation, survival, and migration. While AXL and MERTK have been extensively studied, less is known about TYRO3. Recent studies revealed roles for TYRO3 in cancer and suggest TYRO3 as a therapeutic target in this context. TYRO3 is overexpressed in many types of cancer and functions to promote tumor cell survival and/or proliferation, metastasis, and resistance to chemotherapy. In addition, higher levels of TYRO3 expression have been associated with decreased overall survival in patients with colorectal, hepatocellular, and breast cancers. Here we review the physiological roles for TYRO3 and its expression and functions in cancer cells and the tumor microenvironment, with emphasis on the signaling pathways that are regulated downstream of TYRO3 and emerging roles for TYRO3 in the immune system. Translational agents that target TYRO3 are also described.
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Affiliation(s)
- Sherri K Smart
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA.
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA.
| | - Eleana Vasileiadi
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA.
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA.
| | - Xiaodong Wang
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Deborah DeRyckere
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA.
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA.
| | - Douglas K Graham
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA.
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA 30322, USA.
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6
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Li W, Wei H, Sun Y, Zhou H, Ma Y, Wang R. Exploring the effect of E76K mutation on SHP2 cause gain‐of‐function activity by a molecular dynamics study. J Cell Biochem 2018; 119:9941-9956. [DOI: 10.1002/jcb.27316] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/29/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Wei‐Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics) School of Pharmacy, Tianjin Medical University Tianjin China
| | - Hui‐Yu Wei
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics) School of Pharmacy, Tianjin Medical University Tianjin China
- Eye Hospital, School of Optometry and Ophthalmology, Tianjin Medical University Tianjin China
| | - Ying‐Zhan Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics) School of Pharmacy, Tianjin Medical University Tianjin China
| | - Hui Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics) School of Pharmacy, Tianjin Medical University Tianjin China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics) School of Pharmacy, Tianjin Medical University Tianjin China
| | - Run‐Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics) School of Pharmacy, Tianjin Medical University Tianjin China
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7
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Prakash A, Dixit G, Meena NK, Singh R, Vishwakarma P, Mishra S, Lynn AM. Elucidation of stable intermediates in urea-induced unfolding pathway of human carbonic anhydrase IX. J Biomol Struct Dyn 2017; 36:2391-2406. [DOI: 10.1080/07391102.2017.1355847] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Amresh Prakash
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Gunjan Dixit
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Naveen Kumar Meena
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ruhar Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Poonam Vishwakarma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Smriti Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Andrew M. Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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8
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Abstract
The interaction between Axl receptor tyrosine kinase and its main ligand Gas6 has been implicated in the progression of a wide number of malignancies. More recently, overexpression of Axl has emerged as a key molecular determinant underlying the development of acquired resistance to targeted anticancer agents. The activation of Axl is overexpression-dependent and controls a number of hallmarks of cancer progression including proliferation, migration, resistance to apoptosis and survival through a complex network of intracellular second messengers. Axl has been noted to influence clinically meaningful end points including metastatic recurrence and survival in the vast majority of tumour types. With Axl inhibitors having gained momentum as novel anticancer therapies, we provide an overview of the biological and clinical relevance of this molecular pathway, outlining the main directions of research.
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Affiliation(s)
- Matthew Brown
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - James R M Black
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Rohini Sharma
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Justin Stebbing
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - David J Pinato
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
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9
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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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10
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Karimi Z, Falsafi-Zade S, Galehdari H. The role of Ca(2+) ions in the complex assembling of protein Z and Z-dependent protease inhibitor: A structure and dynamics investigation. Bioinformation 2012; 8:407-11. [PMID: 22715309 PMCID: PMC3374369 DOI: 10.6026/97320630008407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 04/18/2012] [Indexed: 11/29/2022] Open
Abstract
We investigated the solution structure and dynamics of the human anti-coagulation protein Z (PZ) in the complex with protein Zdependent protease inhibitor (ZPI) to order to understand key structural changes in the presence and absence of Ca(2+). Structural features of the complete complex of PZ-ZPI are poorly understood due to lack of complete atomic model of the PZ-ZPI complex. We have constructed a model of the complete PZ-ZPI complex and molecular dynamics (MD) simulation of the solvated PZ-ZPI complex with and without Ca(2+) was achieved for 100ns. It is consider that the Ω-loop of GLA domains interacts with negatively charged biological membranes in the presence of Ca(2+) ions. The PZ exerts its role as cofactor in a similar way. However, we used solvent-equilibrated dynamics to show structural features of the PZ-ZPI complex in the presence and the absence of Ca(2+)ions. We observed that the distance between the interacting sites of the ZPI with the PZ and the GLA domain decreases in the presence of Ca(2+) ions. Further, we postulated that the calculated distance between the dominant plane of the Ca(2+) ions and Ser196 of the pseudo-catalytic triad of the PZ is similar to the equivalent distance of FXa. This suggests that the central role of the PZ in the blood coagulation may be to align the inhibitory site of the ZPI with the active site of the FXa, which is depends on the interaction of the calcium bound GLA domain of the PZ with the active membrane.
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Affiliation(s)
- Zahra Karimi
- Bioinformatics unit, Department of Genetics, Shahid Chamran University, Ahvaz, Iran
| | - Sajad Falsafi-Zade
- Bioinformatics unit, Department of Genetics, Shahid Chamran University, Ahvaz, Iran
| | - Hamid Galehdari
- Department of Genetics, Shahid Chamran University, Ahvaz, Iran
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11
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Reif MM, Kräutler V, Kastenholz MA, Daura X, Hünenberger PH. Molecular dynamics simulations of a reversibly folding beta-heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions. J Phys Chem B 2009; 113:3112-28. [PMID: 19228001 DOI: 10.1021/jp807421a] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Eight 100-ns molecular dynamics simulations of a beta-heptapeptide in methanol at 340 K (within cubic periodic computational boxes of about 6-nm edge) are reported and compared. These simulations were performed with three different charge-state combinations at the peptide termini, one of them with or without a neutralizing chloride counterion, and using either the lattice-sum (LS) or reaction-field (RF) scheme to handle electrostatic interactions. The choice of the electrostatic scheme has essentially no influence on the folding-unfolding equilibrium when the peptide termini are uncharged and only a small influence when the peptide is positively charged at its N-terminus (with or without inclusion of a neutralizing chloride counterion). However, when the peptide is zwitterionic, the LS scheme leads to preferential sampling of the high-dipole folded helical state, whereas the RF scheme leads to preferential sampling of a low-dipole unfolded salt-bridged state. A continuum electrostatics analysis based on the sampled configurations (zwitterionic case) suggests that the LS scheme stabilizes the helical state through artificial periodicity, but that the magnitude of this perturbation is essentially negligible (compared to the thermal energy) for the large box size and relatively polar solvent considered. The results thus provide clear evidence (continuum electrostatics analysis) for the absence of LS artifacts and some indications (still not definitive because of the limited sampling of the folding-unfolding transition) for the presence of RF artifacts in this specific system.
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Affiliation(s)
- Maria M Reif
- Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
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12
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Hafizi S, Dahlbäck B. Gas6 and protein S. Vitamin K-dependent ligands for the Axl receptor tyrosine kinase subfamily. FEBS J 2006; 273:5231-44. [PMID: 17064312 DOI: 10.1111/j.1742-4658.2006.05529.x] [Citation(s) in RCA: 257] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gas6 and protein S are two homologous secreted proteins that depend on vitamin K for their execution of a range of biological functions. A discrete subset of these functions is mediated through their binding to and activation of the receptor tyrosine kinases Axl, Sky and Mer. Furthermore, a hallmark of the Gas6-Axl system is the unique ability of Gas6 and protein S to tether their non receptor-binding regions to the negatively charged membranes of apoptotic cells. Numerous studies have shown the Gas6-Axl system to regulate cell survival, proliferation, migration, adhesion and phagocytosis. Consequently, altered activity/expression of its components has been detected in a variety of pathologies such as cancer and vascular, autoimmune and kidney disorders. Moreover, Axl overactivation can equally occur without ligand binding, which has implications for tumorigenesis. Further knowledge of this exquisite ligand-receptor system and the circumstances of its activation should provide the basis for development of novel therapies for the above diseases.
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Affiliation(s)
- Sassan Hafizi
- Lund University, Department of Laboratory Medicine, Section for Clinical Chemistry, Wallenberg Laboratory, University Hospital Malmö, Sweden.
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Stenhoff J, Dahlbäck B, Hafizi S. Vitamin K-dependent Gas6 activates ERK kinase and stimulates growth of cardiac fibroblasts. Biochem Biophys Res Commun 2004; 319:871-8. [PMID: 15184064 DOI: 10.1016/j.bbrc.2004.05.070] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Indexed: 11/20/2022]
Abstract
The protein product of growth arrest specific gene 6 (Gas6), is the biological ligand for the Axl subfamily of receptor tyrosine kinases. We investigated the effects of exogenous Gas6 on growth of cardiac fibroblasts isolated from genetically Gas6-deficient mice. Recombinant Gas6, containing N terminal gamma-carboxyglutamic acid residues formed from a vitamin K-dependent reaction, stimulated both DNA synthesis and proliferation of cardiac fibroblasts under serum-free conditions. Gas6 also markedly enhanced survival of cells during prolonged serum starvation. Gas6 stimulated tyrosine phosphorylation of Axl as well as phosphorylation of ERK kinase. The mitogenic effects of Gas6 were inhibited by neutralising anti-Gas6 antibodies and by a soluble Axl ectodomain fusion protein. In contrast, recombinant Gas6 from cells treated with warfarin, which prevents the gamma-carboxylation reaction, neither stimulated fibroblast proliferation nor activated Axl tyrosine phosphorylation. Gas6-induced cell proliferation was additive to the effects of epidermal growth factor, suggesting activation of discrete signalling pathways. In conclusion, Gas6 appears to be a unique growth factor for fibroblasts and post-translational gamma-carboxylation is necessary for its biological activity. These findings implicate vitamin K-dependent biochemical reactions in growth processes in development and in disease.
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Affiliation(s)
- Jonas Stenhoff
- Department of Clinical Chemistry, Lund University, Wallenberg Laboratory, University Hospital Malmö, Malmö SE-205 02, Sweden
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14
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Perera L, Darden TA, Pedersen LG. Predicted solution structure of zymogen human coagulation FVII. J Comput Chem 2002; 23:35-47. [PMID: 11913388 DOI: 10.1002/jcc.1155] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A model solution structure for the complete tissue factor-free calcium ion-bound human zymogen FVII (residues 1-406) (FVII) has been constructed to study possible conformational changes associated with the activation process and tissue factor (TF) binding. The initial structure for the present model was constructed using the X-ray crystallographic structure of human coagulation FVIIa/TF complex bound with calcium ions (Banner et al., Nature 1996, 380, 41-46). This model was subsequently subjected to lengthy molecular dynamics simulations. The Amber force field in conjunction with the PME electrostatic summation method was employed. The estimated TF free solution structure was then compared with the currently available X-ray crystal structures of FVIIa (with or without TF, variable inhibitor bound) to estimate the restructuring of FVII due to TF binding and activation. The solution structure of the zymogen FVII in the absence of TF is predicted to be an extended domain structure similar to that of the TF-bound X-ray crystal structure. An additional extension of the serine protease (SP) domain of the zymogen above a reference lipid surface by approximately 7 A was in agreement with experiment. Significant Gla-EGF1 and EGF1-EGF2 interdomain motions in the zymogen were observed. Carbohydrate dimers attached to Ser-52 and Ser-60 did not cause restructuring in this domain. Minimal restructuring of the SP domain is found upon inference of the zymogen from the activated form. The catalytic triad residues maintain the H-bonded network while Lys-341 occupies the S1 specific site in the zymogen.
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Affiliation(s)
- Lalith Perera
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290, USA
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15
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Jin J, Perera L, Stafford D, Pedersen L. Four loops of the catalytic domain of factor viia mediate the effect of the first EGF-like domain substitution on factor viia catalytic activity. J Mol Biol 2001; 307:1503-17. [PMID: 11292356 DOI: 10.1006/jmbi.2001.4556] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The presence of tissue factor is essential for factor VIIa (FVIIa) to reach its full catalytic potential. The previous work in this laboratory demonstrated that substitution of the EGF1 domain of factor VIIa with that of factor IX (FVII((IXegf1))a) results in a substantial decrease in TF-binding affinity and catalytic activity. Supporting simulations of the solution structures of Ca(2+)-bound factor VIIa and FVII((IXegf1))a with tissue factor are provided. Mutants are generated, based on the simulation model, to study the effect of EGF1 substitution on catalytic activity. The simulations show larger Gla-EGF1 and EGF1-EGF2 inter-domain motions for FVII((IXegf1))a than for factor VIIa. The catalytic domain of the chimeric factor VIIa has been disturbed and several surface loops in the catalytic domain of FVII((IXegf1))a (Loop 170s (170-182), Loop 1 (185-188) and Loop 2 (221A-225)) manifest larger position fluctuations than wild-type. The position of Loop 140s (142-152) of FVII((IXegf1))a, near the N terminus insertion site of the catalytic domain, shifts relative to factor VIIa, resulting in a slight alteration of the active site. The results suggest that these four loops mediate the effect of the EGF1 domain substitution on the S1 site and catalytic residues. To test the model, we prepared mutations of these surface loops, including four FVII mutants, D186A, K188A, L144A and R147A, a FVII mutant with multiple mutations (MM3: L144A+R147A+D186A) and a FVII mutant with Loop 170s partially deleted, Loop 170s(del). The catalytic activities towards a small peptidyl substrate decreased 2.4, 4.5 and 9-fold for Loop 170s(del)a (a, activated), L144Aa and D186Aa, respectively, while MM3a lost almost all catalytic activity. The combined results of the simulations and mutants provide insight into the mechanism by which tissue factor enhances factor VIIa catalytic activity.
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Affiliation(s)
- J Jin
- Department of Biology, University of North Carolina at Chapel Hill, 27599, USA
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16
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Abstract
A solution structure for the complete zymogen form of human coagulation protein C is modeled. The initial core structure is based on the x-ray crystallographic structure of the gamma-carboxyglutamic acid (Gla)-domainless activated form. The Gla domain (residues 1-48) is modeled from the x-ray crystal coordinates of the factor VII(a)/tissue factor complex and oriented with the epidermal growth factor-1 domain to yield an initial orientation consistent with the x-ray crystal structure of porcine factor IX(a). The missing C-terminal residues in the light chain (residues 147-157) and the activation peptide residues 158-169 were introduced using homology modeling so that the activation peptide residues directly interact with the residues in the calcium binding loop. Molecular dynamics simulations (Amber-particle-mesh-Ewald) are used to obtain the complete calcium-complexed solution structure. The individual domain structures of protein C in solution are largely unaffected by solvation, whereas the Gla-epidermal growth factor-1 orientation evolves to a form different from both factors VII(a) and IX(a). The solution structure of the zymogen protein C is compared with the crystal structures of the existing zymogen serine proteases: chymotrypsinogen, proproteinase, and prethrombin-2. Calculated electrostatic potential surfaces support the involvement of the serine protease calcium ion binding loop in providing a suitable electrostatic environment around the scissile bond for II(a)/thrombomodulin interaction.
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Affiliation(s)
- L Perera
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.
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Perera L, Darden TA, Pedersen LG. Probing the structural changes in the light chain of human coagulation factor VIIa due to tissue factor association. Biophys J 1999; 77:99-113. [PMID: 10388743 PMCID: PMC1300315 DOI: 10.1016/s0006-3495(99)76875-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The crystallographic structure of human coagulation factor VIIa/tissue factor complex bound with calcium ions was used to model the solution structure of the light chain of factor VIIa (residues 1-142) in the absence of tissue factor. The Amber force field in conjunction with the particle mesh Ewald summation method to accommodate long-range electrostatic interactions was used in the trajectory calculations. The estimated TF-free solution structure was then compared with the crystal structure of factor VIIa/tissue factor complex to estimate the restructuring of factor VIIa due to tissue factor binding. The solution structure of the light chain of factor VIIa in the absence of tissue factor is predicted to be an extended domain structure similar to that of the tissue factor-bound crystal. Removal of the EGF1-bound calcium ion is shown by simulation to lead to minor structural changes within the EGF1 domain, but also leads to substantial relative reorientation of the Gla and EGF1 domains.
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Affiliation(s)
- L Perera
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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Perera L, Darden TA, Pedersen LG. Trans-cis isomerization of proline 22 in bovine prothrombin fragment 1: a surprising result of structural characterization. Biochemistry 1998; 37:10920-7. [PMID: 9692984 DOI: 10.1021/bi980263u] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The calcium ion-mediated interaction of bovine prothrombin (BF1) with negatively charged phospholipid membranes is assumed to be largely via the Gla domain of BF1 with the fold of the Gla domain essential for binding. It has been reported that Pro22 undergoes classical trans to cis isomerization in the presence of calcium ions with the cis conformation of Pro22 of BF1 responsible for membrane binding [Evans, T. C., Jr., and Nelsestuen, G. L. (1996) Biochemistry 35, 8210-8215]. However, Pro22 was found to be in the trans conformation in the crystal structure of BF1. In the present work, we have used molecular dynamics simulations to investigate the relative importance of the two conformations of Pro22 to the structural and dynamical properties of BF1. The initial trans conformation of Pro22 in BF1 was slowly converted to cis-Pro22 using constrained dynamics. The second-generation AMBER force field in conjunction with the particle mesh Ewald method to accommodate long-range interaction was employed in the trajectory calculations. Comparison of the BF1(trans-Pro22) and BF1(cis-Pro22) equilibrated structures reveals surprisingly that the overall structural changes associated with the trans-cis isomerization is minimal and only minor modifications to the hydrogen bond network and the network of N-terminus Ala1 take place. The calculated electrostatic potential energy surfaces of the two protein structures also appear to be very similar, indicating the near equality of the local interaction site environments in the protein prior to lipid binding.
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Affiliation(s)
- L Perera
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290, USA
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