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Rosenfeld MA, Yurina LV, Gavrilina ES, Vasilyeva AD. Post-Translational Oxidative Modifications of Hemostasis Proteins: Structure, Function, and Regulation. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S14-S33. [PMID: 38621742 DOI: 10.1134/s0006297924140025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 04/17/2024]
Abstract
Reactive oxygen species (ROS) are constantly generated in a living organism. An imbalance between the amount of generated reactive species in the body and their destruction leads to the development of oxidative stress. Proteins are extremely vulnerable targets for ROS molecules, which can cause oxidative modifications of amino acid residues, thus altering structure and function of intra- and extracellular proteins. The current review considers the effect of oxidation on the structural rearrangements and functional activity of hemostasis proteins: coagulation system proteins such as fibrinogen, prothrombin/thrombin, factor VII/VIIa; anticoagulant proteins - thrombomodulin and protein C; proteins of the fibrinolytic system such as plasminogen, tissue plasminogen activator and plasminogen activator inhibitor-1. Structure and function of the proteins, oxidative modifications, and their detrimental consequences resulting from the induced oxidation or oxidative stress in vivo are described. Possible effects of oxidative modifications of proteins in vitro and in vivo leading to disruption of the coagulation and fibrinolysis processes are summarized and systematized, and the possibility of a compensatory mechanism in maintaining hemostasis under oxidative stress is analyzed.
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Affiliation(s)
- Mark A Rosenfeld
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Lyubov V Yurina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Elizaveta S Gavrilina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Alexandra D Vasilyeva
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
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Puzari U, Goswami M, Rani K, Patra A, Mukherjee AK. Computational and in vitro analyses to identify the anticoagulant regions of Echicetin, a snake venom anticoagulant C-type lectin (snaclec): possibility to develop anticoagulant peptide therapeutics? J Biomol Struct Dyn 2023; 41:15569-15583. [PMID: 36994880 DOI: 10.1080/07391102.2023.2191138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/05/2023] [Indexed: 03/31/2023]
Abstract
Snake venom C-type lectins (Snaclecs) display anticoagulant and platelet-modulating activities; however, their interaction with the critical components of blood coagulation factors was unknown. Computational analysis revealed that Echicetin (Snaclec from Echis carinatus venom) interacted with heavy chain of thrombin, and heavy and light chains of factor Xa (FXa). Based on FXa and thrombin binding regions of Echicetin, the two synthetic peptides (1A and 1B) were designed. The in silico binding studies of the peptides with thrombin and FXa showed that peptide 1B interacted with both heavy and light chains of thrombin and, peptide 1A interacted with only heavy chain of thrombin. Similarly, peptide 1B interacted with both heavy and light chains of FXa; however, peptide 1A interacted only with heavy chain of FXa. Alanine screening predicted the hot-spots residues for peptide 1A (Aspartic acid6, Valine8, Valine9, and Tyrosine17 with FXa, and Isoleucine14, Lysine15 with thrombin) and peptide 1B (Valine16 with FXa). Spectrofluorometric interaction study showed a lower Kd value for peptide 1B binding with both FXa and thrombin than peptide 1A, indicating higher binding strength of the former peptide. The circular dichroism spectroscopy also established the interaction between thrombin and the custom peptides. The in vitro study demonstrated higher anticoagulant activity of peptide 1B than peptide 1A due to higher inhibition of thrombin and FXa. Inhibition of anticoagulant activity of the peptides by respective anti-peptide antibodies corroborates our hypothesis that peptides 1A and 1B represent the anticoagulant regions of Echicetin and may be developed as antithrombotic peptide drug prototypes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Upasana Puzari
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Mahasweta Goswami
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Komal Rani
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | - Aparup Patra
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
| | - Ashis K Mukherjee
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
- Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, Assam, India
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3
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Li S, Wang W, Lin L, Yang L, Cai Y, Yang X, Zhang T, Xiao C, Yan H, Gao N, Zhao J. Oligosaccharide Blocks PAR1 (Proteinase-Activated Receptor 1)-PAR4-Mediated Platelet Activation by Binding to Thrombin Exosite II and Impairs Thrombosis. Arterioscler Thromb Vasc Biol 2023; 43:253-266. [PMID: 36519467 DOI: 10.1161/atvbaha.122.318085] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Inappropriate activation and aggregation of platelets can lead to arterial thrombosis. Thrombin is the most potent platelet agonist that activates human platelets via two PARs (proteinase-activated receptors), PAR1 and PAR4. The aim is to study the activity and mechanism of an oligosaccharide HS-11 (the undecasaccharide, derived from sea cucumber Holothuria fuscopunctata) in inhibiting thrombin-mediated platelet activation and aggregation and to evaluate its antithrombotic activity. METHODS Platelet activation was analyzed by detecting CD62P/P-selectin expression using flow cytometry. The HS-11-thrombin interaction and the binding site were studied by biolayer interferometry. Intracellular Ca2+ mobilization of platelets was measured by FLIPR Tetra System using Fluo-4 AM (Fluo-4 acetoxymethyl). Platelet aggregation, thrombus formation, and bleeding Assay were assessed. RESULTS An oligosaccharide HS-11, depolymerized from fucosylated glycosaminoglycan from sea cucumber Holothuria fuscopunctata blocks the interaction of thrombin with PAR1 and PAR4 complex by directly binding to thrombin exosite II, and completely inhibits platelet signal transduction, including intracellular Ca2+ mobilization and protein phosphorylation. Furthermore, HS-11 potently inhibits thrombin-PARs-mediated platelet aggregation and reduces thrombus formation in a model of ex vivo thrombosis. CONCLUSIONS The study firstly report that the fucosylated glycosaminoglycan oligosaccharide has antiplatelet activity by binding to thrombin exosite II, and demonstrates that thrombin exosite II plays an important role in the simultaneous activation of PAR1 and PAR4, which may be a potential antithrombotic target for effective treatment of arterial thrombosis.
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Affiliation(s)
- Sujuan Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.).,University of Chinese Academy of Sciences, Beijing, China (S.L., W.W., L.L., Y.C., T.Z.)
| | - Weili Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.).,University of Chinese Academy of Sciences, Beijing, China (S.L., W.W., L.L., Y.C., T.Z.)
| | - Lisha Lin
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.).,University of Chinese Academy of Sciences, Beijing, China (S.L., W.W., L.L., Y.C., T.Z.)
| | - Lian Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.)
| | - Ying Cai
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.).,University of Chinese Academy of Sciences, Beijing, China (S.L., W.W., L.L., Y.C., T.Z.)
| | - Xingzhi Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.)
| | - Taocui Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.).,University of Chinese Academy of Sciences, Beijing, China (S.L., W.W., L.L., Y.C., T.Z.)
| | - Chuang Xiao
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, China (C.X.)
| | - Hui Yan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.)
| | - Na Gao
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China (N.G., J.Z.)
| | - Jinhua Zhao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences (S.L., W.W., L.L., L.Y., Y.C., X.Y., T.Z., H.Y., J.Z.).,School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China (N.G., J.Z.)
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Urra FA, Vivas-Ruiz DE, Sanchez EF, Araya-Maturana R. An Emergent Role for Mitochondrial Bioenergetics in the Action of Snake Venom Toxins on Cancer Cells. Front Oncol 2022; 12:938749. [PMID: 35924151 PMCID: PMC9343075 DOI: 10.3389/fonc.2022.938749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/14/2022] [Indexed: 01/09/2023] Open
Abstract
Beyond the role of mitochondria in apoptosis initiation/execution, some mitochondrial adaptations support the metastasis and chemoresistance of cancer cells. This highlights mitochondria as a promising target for new anticancer strategies. Emergent evidence suggests that some snake venom toxins, both proteins with enzymatic and non-enzymatic activities, act on the mitochondrial metabolism of cancer cells, exhibiting unique and novel mechanisms that are not yet fully understood. Currently, six toxin classes (L-amino acid oxidases, thrombin-like enzymes, secreted phospholipases A2, three-finger toxins, cysteine-rich secreted proteins, and snake C-type lectin) that alter the mitochondrial bioenergetics have been described. These toxins act through Complex IV activity inhibition, OXPHOS uncoupling, ROS-mediated permeabilization of inner mitochondrial membrane (IMM), IMM reorganization by cardiolipin interaction, and mitochondrial fragmentation with selective migrastatic and cytotoxic effects on cancer cells. Notably, selective internalization and direct action of snake venom toxins on tumor mitochondria can be mediated by cell surface proteins overexpressed in cancer cells (e.g. nucleolin and heparan sulfate proteoglycans) or facilitated by the elevated Δψm of cancer cells compared to that non-tumor cells. In this latter case, selective mitochondrial accumulation, in a Δψm-dependent manner, of compounds linked to cationic snake peptides may be explored as a new anti-cancer drug delivery system. This review analyzes the effect of snake venom toxins on mitochondrial bioenergetics of cancer cells, whose mechanisms of action may offer the opportunity to develop new anticancer drugs based on toxin scaffolds.
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Affiliation(s)
- Félix A. Urra
- Laboratorio de Plasticidad Metabólica y Bioenergética, Programa de Farmacología Clínica y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Network for Snake Venom Research and Drug Discovery, Santiago, Chile
- Interdisciplinary Group on Mitochondrial Targeting and Bioenergetics (MIBI), Talca, Chile
- *Correspondence: Félix A. Urra,
| | - Dan E. Vivas-Ruiz
- Network for Snake Venom Research and Drug Discovery, Santiago, Chile
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Ciudad Universitaria, Lima, Peru
| | - Eladio Flores Sanchez
- Network for Snake Venom Research and Drug Discovery, Santiago, Chile
- Laboratory of Biochemistry of Proteins from Animal Venoms, Research and Development Center, Ezequiel Dias Foundation, Belo Horizonte, Brazil
| | - Ramiro Araya-Maturana
- Network for Snake Venom Research and Drug Discovery, Santiago, Chile
- Interdisciplinary Group on Mitochondrial Targeting and Bioenergetics (MIBI), Talca, Chile
- Laboratorio de Productos Bioactivos, Instituto de Química de Recursos Naturales, Universidad de Talca, Talca, Chile
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5
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Stewart V, Ronald PC. Sulfotyrosine residues: interaction specificity determinants for extracellular protein-protein interactions. J Biol Chem 2022; 298:102232. [PMID: 35798140 PMCID: PMC9372746 DOI: 10.1016/j.jbc.2022.102232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
Tyrosine sulfation, a post-translational modification, can determine and often enhance protein–protein interaction specificity. Sulfotyrosyl residues (sTyrs) are formed by the enzyme tyrosyl-protein sulfotransferase during protein maturation in the Golgi apparatus and most often occur singly or as a cluster within a six-residue span. With both negative charge and aromatic character, sTyr facilitates numerous atomic contacts as visualized in binding interface structural models, thus there is no discernible binding site consensus. Found exclusively in secreted proteins, in this review, we discuss the four broad sequence contexts in which sTyr has been observed: first, a solitary sTyr has been shown to be critical for diverse high-affinity interactions, such as between peptide hormones and their receptors, in both plants and animals. Second, sTyr clusters within structurally flexible anionic segments are essential for a variety of cellular processes, including coreceptor binding to the HIV-1 envelope spike protein during virus entry, chemokine interactions with receptors, and leukocyte rolling cell adhesion. Third, a subcategory of sTyr clusters is found in conserved acidic sequences termed hirudin-like motifs that enable proteins to interact with thrombin; consequently, many proven and potential therapeutic proteins derived from blood-consuming invertebrates depend on sTyrs for their activity. Finally, several proteins that interact with collagen or similar proteins contain one or more sTyrs within an acidic residue array. Refined methods to direct sTyr incorporation in peptides synthesized both in vitro and in vivo, together with continued advances in mass spectrometry and affinity detection, promise to accelerate discoveries of sTyr occurrence and function.
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Affiliation(s)
- Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, USA.
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, USA; Genome Center, University of California, Davis, USA.
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6
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Vecchio FL, Bisceglia P, Imbimbo BP, Lozupone M, Latino RR, Resta E, Leone M, Solfrizzi V, Greco A, Daniele A, Watling M, Panza F, Seripa D. Are apolipoprotein E fragments a promising new therapeutic target for Alzheimer’s disease? Ther Adv Chronic Dis 2022; 13:20406223221081605. [PMID: 35321401 PMCID: PMC8935560 DOI: 10.1177/20406223221081605] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/28/2022] [Indexed: 11/17/2022] Open
Abstract
Human apolipoprotein E (ApoE) is a 299-amino acid secreted glycoprotein that binds cholesterol and phospholipids. ApoE exists as three common isoforms (ApoE2, ApoE3, and ApoE4) and heterozygous carriers of the ε4 allele of the gene encoding ApoE (APOE) have a fourfold greater risk of developing Alzheimer’s disease (AD). The enzymes thrombin, cathepsin D, α-chymotrypsin-like serine protease, and high-temperature requirement serine protease A1 are responsible for ApoE proteolytic processing resulting in bioactive C-terminal-truncated fragments that vary depending on ApoE isoforms, brain region, aging, and neural injury. The objectives of the present narrative review were to describe ApoE processing, discussing current hypotheses about the potential role of various ApoE fragments in AD pathophysiology, and reviewing the current development status of different anti-ApoE drugs. The exact mechanism by which APOE gene variants increase/decrease AD risk and the role of ApoE fragments in the deposition are not fully understood, but APOE is known to directly affect tau-mediated neurodegeneration. ApoE fragments co-localize with neurofibrillary tangles and amyloid β (Aβ) plaques, and may cause neurodegeneration. Among anti-ApoE approaches, a fascinating strategy may be to therapeutically overexpress ApoE2 in APOE ε4/ε4 carriers through vector administration or liposomal delivery systems. Another approach involves reducing ApoE4 expression by intracerebroventricular antisense oligonucleotides that significantly decreased Aβ pathology in transgenic mice. Differences in the proteolytic processing of distinct ApoE isoforms and the use of ApoE fragments as mimetic peptides in AD treatment are also under investigation. Treatment with peptides that mimic the structural and biological properties of native ApoE may reduce Aβ deposition, tau hyperphosphorylation, and glial activation in mouse models of Aβ pathology. Alternative strategies involve the use of ApoE4 structure correctors, passive immunization to target a certain form of ApoE, conversion of the ApoE4 aminoacid sequence into that of ApoE3 or ApoE2, and inhibition of the ApoE-Aβ interaction.
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Affiliation(s)
- Filomena Lo Vecchio
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia 71013, Italy
| | - Paola Bisceglia
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Madia Lozupone
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Raffaela Rita Latino
- Complex Structure of Neurology, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Emanuela Resta
- Translational Medicine and Management of Health Systems, University of Foggia, Foggia, Italy
| | - Maurizio Leone
- Complex Structure of Neurology, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Vincenzo Solfrizzi
- ‘Cesare Frugoni’ Internal and Geriatric Medicine and Memory Unit, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Antonio Greco
- Department of Neuroscience, Catholic University of the Sacred Heart, Rome, Italy; Neurology Unit, IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Mark Watling
- CNS & Pain Department, TranScrip Ltd, Reading, UK
| | - Francesco Panza
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
- Population Health Unit, Healthy Aging Phenotypes Research Unit, ‘Salus in Apulia Study’, National Institute of Gastroenterology ‘Saverio de Bellis’, Research Hospital, Castellana Grotte, Bari 70013, Italy
| | - Davide Seripa
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Hematology and Stem Cell Transplant Unit, ‘Vito Fazzi’ Hospital, Lecce, Italy
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Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands. Int J Mol Sci 2021; 22:ijms221910803. [PMID: 34639143 PMCID: PMC8509272 DOI: 10.3390/ijms221910803] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Thrombin is the key enzyme of the entire hemostatic process since it is able to exert both procoagulant and anticoagulant functions; therefore, it represents an attractive target for the developments of biomolecules with therapeutic potential. Thrombin can perform its many functional activities because of its ability to recognize a wide variety of substrates, inhibitors, and cofactors. These molecules frequently are bound to positively charged regions on the surface of protein called exosites. In this review, we carried out extensive analyses of the structural determinants of thrombin partnerships by surveying literature data as well as the structural content of the Protein Data Bank (PDB). In particular, we used the information collected on functional, natural, and synthetic molecular ligands to define the anatomy of the exosites and to quantify the interface area between thrombin and exosite ligands. In this framework, we reviewed in detail the specificity of thrombin binding to aptamers, a class of compounds with intriguing pharmaceutical properties. Although these compounds anchor to protein using conservative patterns on its surface, the present analysis highlights some interesting peculiarities. Moreover, the impact of thrombin binding aptamers in the elucidation of the cross-talk between the two distant exosites is illustrated. Collectively, the data and the work here reviewed may provide insights into the design of novel thrombin inhibitors.
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8
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Yang Z, Wan Y, E J, Luo Z, Guan S, Wang S, Zhang H. Structural basis of different surface-modified fullerene derivatives as novel thrombin inhibitors: insight into the inhibitory mechanism through molecular modelling studies. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1943028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Zhijie Yang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Yongfeng Wan
- Institute of Atomic and Molecular Physics, Jilin University, Changchun, People’s Republic of China
| | - Jingwen E
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Zhijian Luo
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Shanshan Guan
- College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun, People’s Republic of China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, People’s Republic of China
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9
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2D titanium carbide nanosheets based fluorescent aptasensor for sensitive detection of thrombin. Talanta 2021; 228:122219. [PMID: 33773725 DOI: 10.1016/j.talanta.2021.122219] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/02/2021] [Accepted: 02/13/2021] [Indexed: 01/06/2023]
Abstract
The emerging two-dimensional titanium carbides (MXenes) have a large potential in biomedical sensing owing to their excellent electrical and optical properties. Herein, a fluorescence resonance energy transfer (FRET) aptasensor with high sensitivity and specificity was constructed with single layer Ti3C2 MXene for quantitative detection of thrombin. The dye labelled thrombin-binding aptamer (TBA) was deposited on the surface of Ti3C2, and the fluorescence of which was efficiently quenched owing to the FRET between the dye and Ti3C2. The fact that thrombin forms quadruplex with TBA on Ti3C2 surface is due to the high electronic affinity between thrombin and Ti3C2. This process will cause the subsequent detachment of dye from the surface of Ti3C2, resulting in the recovery of fluorescence. Because of the special structure and high fluorescence quenching efficiency of Ti3C2 MXene, the aptasensor shows a high sensitivity with a low detection limit for thrombin at 5.27 pM. Three different aptamers were compared, and the aptamer HD22 is most sensitive for detection of thrombin originated from its great specificity in the human plasma. Importantly, this Ti3C2 MXene-based FRET aptasensor can detect thrombin in human serum accurately. These results suggest that the Ti3C2 MXene-based FRET aptasensor hold a great prospect in clinical diagnosis in the real-world applications.
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Kovach IM. Proton Bridging in Catalysis by and Inhibition of Serine Proteases of the Blood Cascade System. Life (Basel) 2021; 11:396. [PMID: 33925363 PMCID: PMC8146069 DOI: 10.3390/life11050396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
Inquiries into the participation of short hydrogen bonds in stabilizing transition states and intermediate states in the thrombin, factor Xa, plasmin and activated protein C-catalyzed reactions revealed that specific binding of effectors at Sn, n = 1-4 and S'n, n = 1-3 and at remote exosites elicit complex patterns of hydrogen bonding and involve water networks. The methods employed that yielded these discoveries include; (1) kinetics, especially partial or full kinetic deuterium solvent isotope effects with short cognate substrates and also with the natural substrates, (2) kinetic and structural probes, particularly low-field high-resolution nuclear magnetic resonance (1H NMR), of mechanism-based inhibitors and substrate-mimic peptide inhibitors. Short hydrogen bonds form at the transition states of the catalytic reactions at the active site of the enzymes as they do with mechanism-based covalent inhibitors of thrombin. The emergence of short hydrogen bonds at the binding interface of effectors and thrombin at remote exosites has recently gained recognition. Herein, I describe our contribution, a confirmation of this discovery, by low-field 1H NMR. The principal conclusion of this review is that proton sharing at distances below the sum of van der Waals radii of the hydrogen and both donor and acceptor atoms contribute to the remarkable catalytic prowess of serine proteases of the blood clotting system and other enzymes that employ acid-base catalysis. Proton bridges also play a role in tight binding in proteins and at exosites, i.e., allosteric sites, of enzymes.
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Affiliation(s)
- Ildiko M Kovach
- Department of Chemistry, The Catholic University of America, Washington, DC 20064, USA
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Xu S, Fan F, Liu H, Cheng S, Tu M, Du M. Novel Anticoagulant Peptide from Lactoferrin Binding Thrombin at the Active Site and Exosite-I. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:3132-3139. [PMID: 32064873 DOI: 10.1021/acs.jafc.9b08094] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Thrombin is currently one of the important targets for the treatment and prevention of thrombosis. At present, there are few reports on the application of lactoferrin peptides in anticoagulation. In this study, a peptide with the amino acid sequence of LRPVAAEIY (LF-LR) derived from lactoferrin was shown to possess antithrombotic activity. LF-LR (5 mM) significantly prolonged activated partial thromboplastin time, prothrombin time, and thrombin time for 13.4, 1.7, and 5.1 s, respectively. It prolonged the coagulation time of fibrinogen from 15.3 ± 0.4 to 20.2 ± 0.5 s by affecting the conformation of thrombin. Using circular dichroism analysis, LF-LR can increase the α-helix content of thrombin from 25.6 to 56.7% and made the β-sheet disappear. In addition, LF-LR also quenched fluorescence of thrombin at about 346 nm (λEx = 280 nm). By means of molecular docking, it was found that LF-LR could bind to both the active site and the exosite-I of thrombin, and the combined LYS60F, TRP60D, ASP189, LYS36, and ARG77A are typical amino acids in the two domains, respectively.
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Affiliation(s)
- Shiqi Xu
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian Liaoning, 116034, China
| | - Fengjiao Fan
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210046, China
| | - Hanxiong Liu
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian Liaoning, 116034, China
| | - Shuzhen Cheng
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian Liaoning, 116034, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Maolin Tu
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian Liaoning, 116034, China
| | - Ming Du
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian Liaoning, 116034, China
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12
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Chen F, Huang G. Mechanism and inhibition kinetics of peptide P13 as thrombin inhibitor. Int J Biol Macromol 2019; 150:1046-1052. [PMID: 31743711 DOI: 10.1016/j.ijbiomac.2019.10.109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/22/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022]
Abstract
Excessive coagulation can easily lead to arterial and venous thrombosis, which is the main reason for the evolution of myocardial infarction and cerebrovascular accidents. As a key coagulation factor for the coagulation pathway, thrombin has become a remarkable target for the control of thrombosis. The synthesized peptide P13 with amino acid sequence of N-RGDAGFAGDDAPR was expected to be an inhibitor with higher antithrombotic activity. The results showed that the IC50 (50% inhibition of thrombin activity) of the peptide P13 was determined by colorimetric method to be 115 µM. And enzyme kinetic experiments showed that P13 was a competitive inhibitor of thrombin with Ki = 106 µM. Fluorescence spectra and three-dimensional fluorescence showed that P13 could alter the secondary structure of thrombin and the microenvironment of certain chromogenic amino acids. P13 can spontaneously bind with thrombin exosite 1 in the form of 1:1 mainly through hydrogen bonding and van der Waals force. And the optimal docking mode of P13 and thrombin was revealed by molecular docking with "-CDOCKER_Energy" of 178.679 kcal mol-1. This study revealed P13 may become a potential anticoagulant drug widely used after further studies in preclinical and clinical trials.
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Affiliation(s)
- Fangyuan Chen
- Key Lab of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Guangrong Huang
- Key Lab of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, China.
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13
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Identification and in silico analysis of antithrombotic peptides from the enzymatic hydrolysates of Tenebrio molitor larvae. Eur Food Res Technol 2019. [DOI: 10.1007/s00217-019-03381-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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14
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Zhong S, Huang K, Xiao Z, Sheng X, Li Y, Duan L. Binding Mechanism of Thrombin–Ligand Systems Investigated by a Polarized Protein-Specific Charge Force Field and Interaction Entropy Method. J Phys Chem B 2019; 123:8704-8716. [DOI: 10.1021/acs.jpcb.9b08064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Susu Zhong
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Kaifang Huang
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Zhengrong Xiao
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Xiehuang Sheng
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Yuchen Li
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
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15
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Aviñó A, Jorge AF, Huertas CS, Cova TFGG, Pais A, Lechuga LM, Eritja R, Fabrega C. Aptamer-peptide conjugates as a new strategy to modulate human α-thrombin binding affinity. Biochim Biophys Acta Gen Subj 2019; 1863:1619-1630. [PMID: 31265898 DOI: 10.1016/j.bbagen.2019.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/20/2019] [Accepted: 06/27/2019] [Indexed: 12/23/2022]
Abstract
Aptamers are single-stranded RNA or DNA molecules that specifically recognize their targets and have proven valuable for functionalizing sensitive biosensors. α-thrombin is a trypsin-like serine proteinase which plays a crucial role in haemostasis and thrombosis. An abnormal activity or overexpression of this protein is associated with a variety of diseases. A great deal of attention was devoted to the construction of high-throughput biosensors for accurately detect thrombin for the early diagnosis and treatment of related diseases. Herein, we propose a new approach to modulate the interaction between α-thrombin and the aptamer TBA15. To this end, TBA15 was chemically conjugated to two peptide sequences (TBA-G3FIE-Ac and TBA-G3EIF-Ac) corresponding to a short fragment of the acidic region of the human factor V, which is known to interact directly with exosite I. Surface Plasmon Resonance (SPR) results showed enhanced analytical performances of thrombin with TBA-G3EIF-Ac than with TBA wild-type, reaching a limit of detection as low as 44.9 pM. Electrophoresis mobility shift assay (EMSA) corroborated the SPR results. Molecular dynamics (MD) simulations support experimental evidences and provided further insight into thrombin/TBA-peptide interaction. Our findings demonstrate that the combination of TBA15 with key interacting peptides offers good opportunities to produce sensitive devices for thrombin detection and potential candidates to block thrombin activity.
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Affiliation(s)
- Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Andreia F Jorge
- CQC, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - César S Huertas
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, ICN2 Building, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Tânia F G G Cova
- CQC, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Alberto Pais
- CQC, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Laura M Lechuga
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, ICN2 Building, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain.
| | - Carme Fabrega
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain.
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16
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Liu H, Tu M, Cheng S, Chen H, Wang Z, Du M. An anticoagulant peptide from beta-casein: identification, structure and molecular mechanism. Food Funct 2019; 10:886-892. [DOI: 10.1039/c8fo02235f] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A bioactive peptide is identified from casein hydrolysates.
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Affiliation(s)
- Hanxiong Liu
- School of Food Science and Technology
- National Engineering Research Center of Seafood
- Dalian Polytechnic University
- Dalian 116034
- China
| | - Maolin Tu
- Department of Chemistry and Chemical Engineering
- Harbin Institute of Technology
- Harbin 150090
- China
| | - Shuzhen Cheng
- School of Food Science and Technology
- National Engineering Research Center of Seafood
- Dalian Polytechnic University
- Dalian 116034
- China
| | - Hui Chen
- School of Food Science and Technology
- National Engineering Research Center of Seafood
- Dalian Polytechnic University
- Dalian 116034
- China
| | - Zhenyu Wang
- School of Food Science and Technology
- National Engineering Research Center of Seafood
- Dalian Polytechnic University
- Dalian 116034
- China
| | - Ming Du
- School of Food Science and Technology
- National Engineering Research Center of Seafood
- Dalian Polytechnic University
- Dalian 116034
- China
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17
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Qiao M, Tu M, Chen H, Mao F, Yu C, Du M. Identification and In Silico Prediction of Anticoagulant Peptides from the Enzymatic Hydrolysates of Mytilus edulis Proteins. Int J Mol Sci 2018; 19:ijms19072100. [PMID: 30029529 PMCID: PMC6073223 DOI: 10.3390/ijms19072100] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 01/13/2023] Open
Abstract
Mytilus edulis is a typical marine bivalve mollusk. Many kinds of bioactive components with nutritional and pharmaceutical activities in Mytilus edulis were reported. In this study, eight different parts of Mytilus edulis tissues, i.e., the foot, byssus, pedal retractor muscle, mantle, gill, adductor muscle, viscera, and other parts, were separated and the proteins from these tissues were prepared. A total of 277 unique peptides from the hydrolysates of different proteins were identified by UPLC-Q-TOF-MS/MS, and the molecular weight distribution of the peptides in different tissues was investigated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The bioactivity of the peptides was predicted through the Peptide Ranker database and molecular docking. Moreover, the peptides from the adductor muscle were chosen to do the active validation of anticoagulant activity. The active mechanism of three peptides from the adductor muscle, VQQELEDAEERADSAEGSLQK, RMEADIAAMQSDLDDALNGQR, and AAFLLGVNSNDLLK, were analyzed by Discovery Studio 2017, which also explained the anticoagulant activity of the hydrolysates of proteins from adductor muscle. This study optimized a screening and identification method of bioactive peptides from enzymatic hydrolysates of different tissues in Mytilus edulis.
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Affiliation(s)
- Meiling Qiao
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Maolin Tu
- Department of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Hui Chen
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Fengjiao Mao
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Cuiping Yu
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
| | - Ming Du
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China.
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18
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Qiao M, Tu M, Wang Z, Mao F, Chen H, Qin L, Du M. Identification and Antithrombotic Activity of Peptides from Blue Mussel (Mytilus edulis) Protein. Int J Mol Sci 2018; 19:E138. [PMID: 29300301 PMCID: PMC5796087 DOI: 10.3390/ijms19010138] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/14/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022] Open
Abstract
The blue mussel (Mytilus edulis) reportedly contains many bioactive components of nutritional value. Water-, salt- and acid-soluble M. edulis protein fractions were obtained and the proteins were trypsinized. The resultant peptides were analyzed by ultra-performance liquid chromatography quadrupole time of flight tandem mass spectrometry (UPLC-Q-TOF-MS/MS). 387 unique peptides were identified that matched 81 precursor proteins. Molecular mass distributions of the proteins and peptides were analyzed by sodium dodecyl sulfate-polyacryl amide gel electrophoresis (SDS-PAGE). The differences between the three protein samples were studied by Venn diagram of peptide and protein compositions. Toxicity, allergic and antithrombotic activity of peptides was predicted using database website and molecular docking respectively. The antithrombotic activity of enzymatic hydrolysate from water-, salt- and acid-soluble M. edulis protein were 40.17%, 85.74%, 82.00% at 5 mg/mL, respectively. Active mechanism of antithrombotic peptide (ELEDSLDSER) was also research about amino acid binding sites and interaction, simultaneously.
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Affiliation(s)
- Meiling Qiao
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Maolin Tu
- Department of Food Science and Engineering, Harbin Institute of Technology, Harbin 150090, China.
| | - Zhenyu Wang
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Fengjiao Mao
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Hui Chen
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Lei Qin
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
| | - Ming Du
- School of Food Science and Technology, Dalian Polytechnic University, National Engineering Research Center of Seafood, Dalian 116034, China.
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19
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Xiao J, Salsbury FR. Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin. J Biomol Struct Dyn 2017; 35:3354-3369. [PMID: 27794633 PMCID: PMC6876308 DOI: 10.1080/07391102.2016.1254682] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/21/2016] [Indexed: 01/11/2023]
Abstract
Thrombin is an attractive target for antithrombotic therapy due to its central role in thrombosis and hemostasis as well as its role in inducing tumor growth, metastasis, and tumor invasion. The thrombin-binding DNA aptamer (TBA), is under investigation for anticoagulant drugs. Although aptamer binding experiments have been revealed various effects on thrombin's enzymatic activities, the detailed picture of the thrombin's allostery from TBA binding is still unclear. To investigate thrombin's response to the aptamer-binding at the molecular level, we compare the mechanical properties and free energy landscapes of the free and aptamer-bound thrombin using microsecond-scale all-atom GPU-based molecular dynamics simulations. Our calculations on residue fluctuations and coupling illustrate the allosteric effects of aptamer-binding at the atomic level, highlighting the exosite II, 60s, γ and the sodium loops, and the alpha helix region in the light chains involved in the allosteric changes. This level of details clarifies the mechanisms of previous experimentally demonstrated phenomena, and provides a prediction of the reduced autolysis rate after aptamer-binding. The shifts in thrombin's ensemble of conformations and free energy surfaces after aptamer-binding demonstrate that the presence of bound-aptamer restricts the conformational freedom of thrombin suggesting that conformational selection, i.e. generalized allostery, is the dominant mechanism of thrombin-aptamer binding. The profound perturbation on thrombin's mechanical and thermodynamic properties due to the aptamer-binding, which was revealed comprehensively as a generalized allostery in this work, may be exploited in further drug discovery and development.
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Affiliation(s)
- Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, NC, USA
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20
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Tu M, Feng L, Wang Z, Qiao M, Shahidi F, Lu W, Du M. Sequence analysis and molecular docking of antithrombotic peptides from casein hydrolysate by trypsin digestion. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.03.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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21
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Iyer JK, Koh CY, Kazimirova M, Roller L, Jobichen C, Swaminathan K, Mizuguchi J, Iwanaga S, Nuttall PA, Chan MY, Kini RM. Avathrin: a novel thrombin inhibitor derived from a multicopy precursor in the salivary glands of the ixodid tick,
Amblyomma variegatum. FASEB J 2017; 31:2981-2995. [DOI: 10.1096/fj.201601216r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/13/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Janaki Krishnamoorthy Iyer
- Protein Science LaboratoryDepartment of Biological SciencesNational University of Singapore Singapore
- Department of Pathology and Molecular MedicineMcMaster UniversityHamilton Ontario Canada
| | - Cho Yeow Koh
- Protein Science LaboratoryDepartment of Biological SciencesNational University of Singapore Singapore
| | - Maria Kazimirova
- Institute of ZoologySlovak Academy of SciencesBratislava Slovakia
| | - Ladislav Roller
- Institute of ZoologySlovak Academy of SciencesBratislava Slovakia
| | - Chacko Jobichen
- Protein Science LaboratoryDepartment of Biological SciencesNational University of Singapore Singapore
| | | | - Jun Mizuguchi
- The Chemo‐Sero‐Therapeutic Research InstituteKumamoto Japan
| | | | | | - Mark Y. Chan
- Yong Loo Lin School of MedicineNational University of Singapore Singapore
- Department of CardiologyNational University Heart Centre Singapore
| | - R. Manjunatha Kini
- Protein Science LaboratoryDepartment of Biological SciencesNational University of Singapore Singapore
- Singapore Eye Research Institute Singapore
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22
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Dabigatran and Argatroban Diametrically Modulate Thrombin Exosite Function. PLoS One 2016; 11:e0157471. [PMID: 27305147 PMCID: PMC4909201 DOI: 10.1371/journal.pone.0157471] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/31/2016] [Indexed: 11/23/2022] Open
Abstract
Thrombin is a highly plastic molecule whose activity and specificity are regulated by exosites 1 and 2, positively-charged domains that flank the active site. Exosite binding by substrates and cofactors regulates thrombin activity by localizing thrombin, guiding substrates, and by inducing allosteric changes at the active site. Although inter-exosite and exosite-to-active-site allostery have been demonstrated, the impact of active site ligation on exosite function has not been examined. To address this gap, we used surface plasmon resonance to determine the effects of dabigatran and argatroban, active site-directed inhibitors, on thrombin binding to immobilized γA/γA-fibrin or glycoprotein Ibα peptide via exosite 1 and 2, respectively, and thrombin binding to γA/γ′-fibrin or factor Va, which is mediated by both exosites. Whereas dabigatran attenuated binding, argatroban increased thrombin binding to γA/γA- and γA/γ′-fibrin and to factor Va. The results with immobilized fibrin were confirmed by examining the binding of radiolabeled thrombin to fibrin clots. Thus, dabigatran modestly accelerated the dissociation of thrombin from γA/γA-fibrin clots, whereas argatroban attenuated dissociation. Dabigatran had no effect on thrombin binding to glycoprotein Ibα peptide, whereas argatroban promoted binding. These findings not only highlight functional effects of thrombin allostery, but also suggest that individual active site-directed thrombin inhibitors uniquely modulate exosite function, thereby identifying potential novel mechanisms of action.
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23
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Trapaidze A, Hérault JP, Herbert JM, Bancaud A, Gué AM. Investigation of the selectivity of thrombin-binding aptamers for thrombin titration in murine plasma. Biosens Bioelectron 2015; 78:58-66. [PMID: 26594887 DOI: 10.1016/j.bios.2015.11.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/26/2015] [Accepted: 11/08/2015] [Indexed: 11/26/2022]
Abstract
Detection of thrombin in plasma raises timely challenges to enable therapeutic management of thrombosis in patients under vital threat. Thrombin binding aptamers represent promising candidates as sensing elements for the development of real-time thrombin biosensors; however implementation of such biosensor requires the clear understanding of thrombin-aptamer interaction properties in real-like environment. In this study, we used Surface Plasmon Resonance technique to answer the questions of specificity and sensitivity of thrombin detection by the thrombin-binding aptamers HD1, NU172 and HD22. We systematically characterized their properties in the presence of thrombin, as well as interfering molecular species such as the thrombin precursor prothrombin, thrombin in complex with some of its natural inhibitors, nonspecific serum proteins, and diluted plasma. Kinetic experiments show the multiple binding modes of HD1 and NU172, which both interact with multiple sites of thrombin with low nanomolar affinities and show little specificity of interaction for prothrombin vs. thrombin. HD22, on the other hand, binds specifically to thrombin exosite II and has no affinity to prothrombin at all. While thrombin in complex with some of its inhibitors could not be recognized by any aptamer, the binding of HD1 and NU172 properties is compromised by thrombin inhibitors alone, as well as with serum albumin. Finally, the complex nature of plasma was overwhelming for HD1, but we define conditions for the thrombin detection at 10nM range in 100-fold diluted plasma by HD22. Consequently HD22 showed key advantage over HD1 and NU172, and appears as the only alternative to design an aptasensor.
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Affiliation(s)
- Ana Trapaidze
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Université de Toulouse, LAAS, F-31400 Toulouse, France.
| | | | | | - Aurélien Bancaud
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Université de Toulouse, LAAS, F-31400 Toulouse, France.
| | - Anne-Marie Gué
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France; Université de Toulouse, LAAS, F-31400 Toulouse, France
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24
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Handley LD, Treuheit NA, Venkatesh VJ, Komives EA. Thrombomodulin Binding Selects the Catalytically Active Form of Thrombin. Biochemistry 2015; 54:6650-8. [PMID: 26468766 DOI: 10.1021/acs.biochem.5b00825] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human α-thrombin is a serine protease with dual functions. Thrombin acts as a procoagulant, cleaving fibrinogen to make the fibrin clot, but when bound to thrombomodulin (TM), it acts as an anticoagulant, cleaving protein C. A minimal TM fragment consisting of the fourth, fifth, and most of the sixth EGF-like domain (TM456m) that has been prepared has much improved solubility, thrombin binding capacity, and anticoagulant activity versus those of previous TM456 constructs. In this work, we compare backbone amide exchange of human α-thrombin in three states: apo, D-Phe-Pro-Arg-chloromethylketone (PPACK)-bound, and TM456m-bound. Beyond causing a decreased level of amide exchange at their binding sites, TM and PPACK both cause a decreased level of amide exchange in other regions including the γ-loop and the adjacent N-terminus of the heavy chain. The decreased level of amide exchange in the N-terminus of the heavy chain is consistent with the historic model of activation of serine proteases, which involves insertion of this region into the β-barrel promoting the correct conformation of the catalytic residues. Contrary to crystal structures of thrombin, hydrogen-deuterium exchange mass spectrometry results suggest that the conformation of apo-thrombin does not yet have the N-terminus of the heavy chain properly inserted for optimal catalytic activity, and that binding of TM allosterically promotes the catalytically active conformation.
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Affiliation(s)
- Lindsey D Handley
- Department of Chemistry and Biochemistry, University of California at San Diego , 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Nicholas A Treuheit
- Department of Medicinal Chemistry, University of Washington , Health Sciences Building H072A, 1959 Northeast Pacific Street, Seattle, Washington 98195, United States
| | - Varun J Venkatesh
- Department of Chemistry and Biochemistry, University of California at San Diego , 9500 Gilman Drive, La Jolla, California 92093-0378, United States
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California at San Diego , 9500 Gilman Drive, La Jolla, California 92093-0378, United States
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25
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Kaplan ZS, Zarpellon A, Alwis I, Yuan Y, McFadyen J, Ghasemzadeh M, Schoenwaelder SM, Ruggeri ZM, Jackson SP. Thrombin-dependent intravascular leukocyte trafficking regulated by fibrin and the platelet receptors GPIb and PAR4. Nat Commun 2015. [PMID: 26204458 DOI: 10.1038/ncomms8835] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Thrombin is a central regulator of leukocyte recruitment and inflammation at sites of vascular injury, a function thought to involve primarily endothelial PAR cleavage. Here we demonstrate the existence of a distinct leukocyte-trafficking mechanism regulated by components of the haemostatic system, including platelet PAR4, GPIbα and fibrin. Utilizing a mouse endothelial injury model we show that thrombin cleavage of platelet PAR4 promotes leukocyte recruitment to sites of vascular injury. This process is negatively regulated by GPIbα, as seen in mice with abrogated thrombin-platelet GPIbα binding (hGPIbα(D277N)). In addition, we demonstrate that fibrin limits leukocyte trafficking by forming a physical barrier to intravascular leukocyte migration. These studies demonstrate a distinct 'checkpoint' mechanism of leukocyte trafficking involving balanced thrombin interactions with PAR4, GPIbα and fibrin. Dysregulation of this checkpoint mechanism is likely to contribute to the development of thromboinflammatory disorders.
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Affiliation(s)
- Zane S Kaplan
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
| | - Alessandro Zarpellon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Imala Alwis
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia.,Heart Research Institute &Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Yuping Yuan
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
| | - James McFadyen
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
| | - Mehran Ghasemzadeh
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia.,Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Simone M Schoenwaelder
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia.,Heart Research Institute &Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Zaverio M Ruggeri
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Shaun P Jackson
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia.,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA.,Heart Research Institute &Charles Perkins Centre, The University of Sydney, Sydney, New South Wales 2006, Australia
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26
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Dutta S, Gogoi D, Mukherjee AK. Anticoagulant mechanism and platelet deaggregation property of a non-cytotoxic, acidic phospholipase A2 purified from Indian cobra (Naja naja) venom: inhibition of anticoagulant activity by low molecular weight heparin. Biochimie 2015; 110:93-106. [PMID: 25576831 DOI: 10.1016/j.biochi.2014.12.020] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 12/31/2014] [Indexed: 10/24/2022]
Abstract
In the present study, anticoagulant and platelet modulating activities of an acidic phospholipase A2 (NnPLA2-I) purified from Indian cobra Naja naja venom was investigated. The NnPLA2-I displayed a mass of 15.2 kDa and 14,186.0 Da when analyzed by SDS-PAGE and MALDI-TOF-MS, respectively. Peptide mass fingerprinting analysis of the NnPLA2-I showed its significant similarity with phospholipase A2 enzymes purified from cobra venom. BLAST analysis of one tryptic peptide sequence of NnPLA2-I demonstrated putative conserved domains of the PLA2-like superfamily. The Km and Vmax values of NnPLA2-I toward hydrolysis of its most preferred substrate-phosphotidylcholine (PC)-were determined to be 0.72 mM and 29.3 μmol min(-1) mg(-1), respectively. The anticoagulant activity of NnPLA2-I was found to be higher than the anticoagulant activity of heparin/AT-III or warfarin. The histidine modifying reagent, monovalent and polyvalent antivenom differentially inhibited the catalytic and anticoagulant activities of NnPLA2-I. Low molecular weight heparin did not inhibit the catalytic and platelet deaggregation activity of NnPLA2-I, albeit its anticoagulant activity was significantly reduced. The NnPLA2-I showed a non-enzymatic, mixed inhibition of thrombin with a Ki value of 9.3 nM. Heparin significantly decreased, with an IC50 value of 15.23 mIU, the thrombin inhibitory activity of NnPLA2-I. The NnPLA2-I uniquely increased the amidolytic activity of FXa without influencing its prothrombin activating property. NnPLA2-I showed dose-dependent deaggregation of platelet rich plasma (PRP) and inhibited the collagen and thrombin-induced aggregation of PRP. However, deaggregation of washed platelets by NnPLA2-I demonstrated in presence of PC or platelet poor plasma. Alkylation of histidine residue of NnPLA2-I resulted in 95% and 21% reduction of its platelet deaggregation and platelet binding properties, respectively. NnPLA2-I did not show cytotoxicity against human glioblastoma U87MG cells, bactericidal or hemolytic activity. The future therapeutic application of NnPLA2-I for treatment and prevention of cardiovascular disorders is therefore suggested.
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Affiliation(s)
- Sumita Dutta
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, School of Science, Tezpur University, Tezpur 784028, Assam, India
| | - Debananda Gogoi
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, School of Science, Tezpur University, Tezpur 784028, Assam, India
| | - Ashis K Mukherjee
- Microbial Biotechnology and Protein Research Laboratory, Department of Molecular Biology and Biotechnology, School of Science, Tezpur University, Tezpur 784028, Assam, India.
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27
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Hiong KC, Tan XR, Boo MV, Wong WP, Chew SF, Ip YK. Aestivation induces changes in transcription and translation of coagulation factor II and fibrinogen gamma chain in the liver of the African lungfish, Protopterus annectens. J Exp Biol 2015; 218:3717-28. [DOI: 10.1242/jeb.125260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/17/2015] [Indexed: 11/20/2022]
Abstract
This study aimed to sequence and characterize two pro-coagulant genes, coagulation factor II (f2) and fibrinogen gamma chain (fgg), from the liver of the African lungfish Protopterus annectens, and to determine their hepatic mRNA expression levels during three phases of aestivation. The protein abundances of F2 and Fgg in the liver and plasma were determined by immunoblotting. Results indicated that F2 and Fgg of P. annectens were phylogenetically closer to those of amphibians than those of teleosts. Three days of aestivation resulted in an up-regulation in the hepatic fgg mRNA expression level, while 6 days of aestivation led to a significant increase (3-fold) in the protein abundance of Fgg in the plasma. Hence, there could be an increase in the blood clotting ability in P. annectens during the induction phase of aestivation. By contrast, the blood clotting ability in P. annectens might be reduced in response to decreased blood flow and increased possibility of thrombosis during the maintenance phase of aestivation, as 6 months of aestivation led to significant decreases in mRNA expression levels of f2 and fgg in the liver. There could also be a decrease in the export of F2 and Fgg from the liver to the plasma so as to avert thrombosis. Upon 3-6 days of arousal from 6 months of aestivation, the protein abundances of F2 and Fgg recovered partially in the plasma of P. annectens, and a complete recovery of the transcription and translation of f2/F2 in the liver might occur only after refeeding.
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Affiliation(s)
- Kum C. Hiong
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Xiang R. Tan
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Mel V. Boo
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Wai P. Wong
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
| | - Shit F. Chew
- Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616, Republic of Singapore
| | - Yuen K. Ip
- Department of Biological Sciences, National University of Singapore, Kent Ridge, Singapore 117543, Republic of Singapore
- The Tropical Marine Science Institute, National University of Singapore, Kent Ridge, Singapore 119227, Republic of Singapore
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28
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Engelen M, Lombardi A, Vitale R, Lista L, Maglio O, Pavone V, Nastri F. Branched porphyrins as functional scaffolds for multisite bioconjugation. Biotechnol Appl Biochem 2014; 62:383-92. [DOI: 10.1002/bab.1280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 08/13/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Mireille Engelen
- Department of Chemical Sciences; University of Naples “Federico II,” Complesso Universitario Monte S. Angelo; Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences; University of Naples “Federico II,” Complesso Universitario Monte S. Angelo; Napoli Italy
| | - Rosa Vitale
- Department of Chemical Sciences; University of Naples “Federico II,” Complesso Universitario Monte S. Angelo; Napoli Italy
| | - Liliana Lista
- Department of Chemical Sciences; University of Naples “Federico II,” Complesso Universitario Monte S. Angelo; Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences; University of Naples “Federico II,” Complesso Universitario Monte S. Angelo; Napoli Italy
- IBB; CNR; Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences; University of Naples “Federico II,” Complesso Universitario Monte S. Angelo; Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences; University of Naples “Federico II,” Complesso Universitario Monte S. Angelo; Napoli Italy
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29
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Lim YC, Kouzani AZ, Kaynak A, Dai XJ, Littlefair G, Duan W. Theoretical modeling and experimental validation of surface stress in thrombin aptasensor. IEEE Trans Nanobioscience 2014; 13:384-91. [PMID: 25122838 DOI: 10.1109/tnb.2014.2337517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Adsorption of target molecules on the immobilized microcantilever surface produced beam displacement due to the differential surface stress generated between the immobilized and non-immobilized surface. Surface stress is caused by the intermolecular forces between the molecules. Van der Waals, electrostatic forces, hydrogen bonding, hydrophobic effect and steric hindrance are some of the intermolecular forces involved. A theoretical framework describing the adsorption-induced microcantilever displacement is derived in this paper. Experimental displacement of thrombin aptamer-thrombin interactions was carried out. The relation between the electrostatic interactions involved between adsorbates (thrombin) as well as adsorbates and substrates (thrombin aptamer) and the microcantilever beam displacement utilizing the proposed mathematical model was quantified and compared to the experimental value. This exercise is important to aid the designers in microcantilever sensing performance optimization.
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Wilson R, Bourne C, Chaudhuri RR, Gregory R, Kenny J, Cossins A. Single-step selection of bivalent aptamers validated by comparison with SELEX using high-throughput sequencing. PLoS One 2014; 9:e100572. [PMID: 24963654 PMCID: PMC4070925 DOI: 10.1371/journal.pone.0100572] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/26/2014] [Indexed: 01/23/2023] Open
Abstract
The identification of nucleic acid aptamers would be advanced if they could be obtained after fewer rounds of selection and amplification. In this paper the identification of bivalent aptamers for thrombin by SELEX and single-step selection are compared using next generation sequencing and motif finding informatics. Results show that similar aptamers are identified by both methods. This is significant because it shows that next generation sequencing and motif finding informatics have the potential to simplify the selection of aptamers by avoiding multiple rounds of enzymatic transcription and amplification.
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Affiliation(s)
- Robert Wilson
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - Christian Bourne
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - Roy R. Chaudhuri
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - Richard Gregory
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - John Kenny
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
| | - Andrew Cossins
- Centre for Genomic Research at the Institute of Integrative Biology, University Of Liverpool, Liverpool, United Kingdom
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31
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Characterization, mechanism of anticoagulant action, and assessment of therapeutic potential of a fibrinolytic serine protease (Brevithrombolase) purified from Brevibacillus brevis strain FF02B. Biochimie 2014; 103:50-60. [PMID: 24735708 DOI: 10.1016/j.biochi.2014.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 04/01/2014] [Indexed: 12/27/2022]
Abstract
In this study, biochemical and pharmacological characterization of Brevithrombolase, a fibrinolytic serine protease purified from Brevibacillus brevis strain FF02B has been reported. An assessment of its thrombolytic potency has also been made. The molecular mass of this monomeric protease was determined as 55 kDa, and 56043 Da, respectively, by SDS-PAGE and MALDI-TOF-MS. In the analytical studies, the N-terminal sequence of Brevithrombolase was found to be blocked; however, the peptide mass fingerprinting and amino acid composition analyses demonstrated the similarity of Brevithrombolase with endopeptidases in possessing serine in their catalytic triad. This finding was confirmed by the observation that the serine protease inhibitors decrease the catalytic (fibrinolytic) activity of Brevithrombolase. The secondary structure of Brevithrombolase was composed of 30.6% alpha helix and 69.4% random coil. Brevithrombolase showed the Km and Vmax values towards the chromogenic substrate for plasmin at 0.39 mM and 14.3 μmol/min, respectively. Brevithrombolase demonstrated optimum fibrinolytic activity at pH 7.4 and 37 °C, and showed marginal hydrolytic activity towards globulin, casein and fibrinogen. The anticoagulant potency of Brevithrombolase was comparable to the low molecular mass heparin/antithrombin-III and warfarin. Among the three enzymes-Brevithrombolase, plasmin and streptokinase-the fibrinolytic activity and in vitro thrombolytic potency of Brevithrombolase was found to be superior. The RP-HPLC and SDS-PAGE analyses suggested a similar pattern of fibrin degradation by Brevithrombolase and plasmin, indicating that former enzyme is a plasmin-like fibrinolytic serine protease. Brevithrombolase did not show in vitro cytotoxicity on HT29 and HeLa cells or hemolytic activity. At a dose of 10 mg/kg, Brevithrombolase did not exhibit lethality or toxicity on Wistar strain albino rats. Brevithrombolase did not inhibit factor Xa, and its mechanism of anticoagulant action was associated with the enzymatic cleavage of thrombin. The combined properties of Brevithrombolase indicate its therapeutic potential in peptide-based cardiovascular drug development.
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32
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Improved fusion tag cleavage strategies in the downstream processing of self-assembling virus-like particle vaccines. FOOD AND BIOPRODUCTS PROCESSING 2014. [DOI: 10.1016/j.fbp.2013.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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33
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Freitas SC, Maia S, Figueiredo AC, Gomes P, Pereira PJ, Barbosa MA, Martins MCL. Selective albumin-binding surfaces modified with a thrombin-inhibiting peptide. Acta Biomater 2014; 10:1227-37. [PMID: 24316365 DOI: 10.1016/j.actbio.2013.11.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/13/2013] [Accepted: 11/25/2013] [Indexed: 10/25/2022]
Abstract
Blood-contacting medical devices have been associated with severe clinical complications, such as thrombus formation, triggered by the activation of the coagulation cascade due to the adsorption of certain plasma proteins on the surface of biomaterials. Hence, the coating of such surfaces with antithrombotic agents has been used to increase biomaterial haemocompatibility. Biomaterial-induced clotting may also be decreased by albumin adsorption from blood plasma in a selective and reversible way, since this protein is not involved in the coagulation cascade. In this context, this paper reports that the immobilization of the thrombin inhibitor D-Phe-Pro-D-Arg-D-Thr-CONH2 (fPrt) onto nanostructured surfaces induces selective and reversible adsorption of albumin, delaying the clotting time when compared to peptide-free surfaces. fPrt, synthesized with two glycine residues attached to the N-terminus (GGfPrt), was covalently immobilized onto self-assembled monolayers (SAMs) having different ratios of carboxylate-hexa(ethylene glycol)- and tri(ethylene glycol)-terminated thiols (EG6-COOH/EG3) that were specifically designed to control GGfPrt orientation, exposure and density at the molecular level. In solution, GGfPrt was able to inactivate the enzymatic activity of thrombin and to delay plasma clotting time in a concentration-dependent way. After surface immobilization, and independently of its concentration, GGfPrt lost its selectivity to thrombin and its capacity to inhibit thrombin enzymatic activity against the chromogenic substrate n-p-tosyl-Gly-Pro-Arg-p-nitroanilide. Nevertheless, surfaces with low concentrations of GGfPrt could delay the capacity of adsorbed thrombin to cleave fibrinogen. In contrast, GGfPrt immobilized in high concentrations was found to induce the procoagulant activity of the adsorbed thrombin. However, all surfaces containing GGfPrt have a plasma clotting time similar to the negative control (empty polystyrene wells), showing resistance to coagulation, which is explained by its capacity to adsorb albumin in a selective and reversible way. This work opens new perspectives to the improvement of the haemocompatibility of blood-contacting medical devices.
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34
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Lim YC, Kouzani AZ, Duan W, Dai XJ, Kaynak A, Mair D. A surface-stress-based microcantilever aptasensor. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2014; 8:15-24. [PMID: 24681916 DOI: 10.1109/tbcas.2013.2286255] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Biosensors based on microcantilevers convert biological recognition events into measurable mechanical displacements. They offer advantages such as small size, low sample volume, label-free detection, ease of integration, high-throughput analysis, and low development cost. The design and development of a microcantilever-based aptasensor employing SU-8 polymer as the fabrication material is presented in this paper. Aptamers are employed as bioreceptor elements because they exhibit superior specificity compared to antibodies due to their small size and physicochemical stability. To immobilise thrombin DNA aptamer on the bare SU-8 surface of the aptasensor, a combined plasma mode treatment method is implemented which modifies the surface of the aptasensor. Label-free detection of thrombin molecules using the fabricated aptasensor is successfully demonstrated. The measured deflection is one order of magnitude higher than that of a silicon nitride microcantilever biosensor. The developed aptasensor also demonstrates high specificity.
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35
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Wendeler M, Pabst TM, Wang J, Strouse RJ, Wang X, Hunter AK. Process-scale purification and analytical characterization of highly gamma-carboxylated recombinant human prothrombin. J Chromatogr A 2014; 1325:171-8. [PMID: 24369997 DOI: 10.1016/j.chroma.2013.12.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/01/2013] [Accepted: 12/06/2013] [Indexed: 11/15/2022]
Abstract
Prothrombin (coagulation Factor II) is a complex multidomain glycoprotein that plays a central role in blood coagulation. It is the zymogen precursor to the protease thrombin that catalyzes the formation of the fibrin clot and regulates a multitude of other cellular responses related to coagulation and hemostasis. For the biological activity of prothrombin, the vitamin K dependent posttranslational modification of glutamic acid residues to gamma-carboxylglutamic acid is of crucial importance. Prothrombin can be recombinantly expressed using mammalian cell culture. However, the product is a heterogeneous mixture of variants with different degrees of carboxylation, requiring separation of closely related charge isoforms. A second challenge for purification is the need to remove traces of the product-related impurity thrombin, a protease, to extremely low levels. In this work, we describe a purification strategy that provides solutions to both challenges and results in an efficient and robust process for active recombinant prothrombin. We also describe the analytical characterization of recombinant prothrombin by HPLC, LC-MS/MS, and complementary biochemical assays.
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Affiliation(s)
- Michaela Wendeler
- MedImmune LLC, Department of Purification Process Sciences, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Timothy M Pabst
- MedImmune LLC, Department of Purification Process Sciences, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Jihong Wang
- MedImmune LLC, Department of Analytical Biotechnology, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Robert J Strouse
- MedImmune LLC, Department of Analytical Biotechnology, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Xiangyang Wang
- MedImmune LLC, Department of Purification Process Sciences, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Alan K Hunter
- MedImmune LLC, Department of Purification Process Sciences, One MedImmune Way, Gaithersburg, MD 20878, USA.
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36
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Yassin AA, Elwaseef AM, Elnashar MM, Oldenburg J, Mayer G, Pötzsch B, Müller J. Protamine-adsorbed magnetic nanoparticles for efficient isolation and concentration of hepatitis-C virus from human plasma samples. Chem Commun (Camb) 2014; 50:590-2. [DOI: 10.1039/c3cc46793g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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37
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Prima V, Serebruany VL, Svetlov A, Hayes RL, Svetlov SI. Impact of moderate blast exposures on thrombin biomarkers assessed by calibrated automated thrombography in rats. J Neurotrauma 2013; 30:1881-7. [PMID: 23805797 DOI: 10.1089/neu.2012.2758] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Severe blast exposures are frequently complicated with fatal intracranial hemorrhages. However, many more sustain low level blasts without tissue damage detectable by brain imaging. To investigate effects of nonlethal blast on thrombin-related biomarkers, rats were subjected to two different types of head-directed blast: 1) moderate "composite" blast with strong head acceleration or 2) moderate primary blast, without head acceleration. Thrombin generation (TG) ex vivo after blast was studied by calibrated automated thrombography (CAT). In the same blood samples, we assessed maximal concentration of TG (TGmax), start time, peak time, mean time, and concentrations of protein markers for vascular/hemostatic dysfunctions: integrin α/β, soluble endothelial selectin (sE-selectin), soluble intercellular cell adhesion molecule-1 (sICAM-1), and matrix metalloproteinases (MMP)-2, MMP-8, and MMP-13. Blast remarkably affected all TG indices. In animals exposed to "composite" blast, TGmax peaked at 6 h (∼4.5-fold vs. control), sustained at day 1 (∼3.8-fold increase), and declined to a 2-fold increase over control at day 7 post-blast. After primary blast, TGmax also rose to ∼4.2-fold of control at 6 h, dropped to ∼1.7-fold of control at day 1, and then exhibited a slight secondary increase at 2-fold of control at day 7. Other TG indices did not differ significantly between two types of blast exposure. The changes were also observed in other microvascular/inflammatory/hemostatic biomarkers. Integrin α/β and sICAM-1 levels were elevated after both "composite" and primary blast at 6 h, 1 day, and 7 days. sE-selectin exhibited near normal levels after "composite" blast, but increased significantly at 7 days after primary blast; MMP-2, MMP-8, and MMP-13 slightly rose after "composite" blast and significantly increased (∼2-4-fold) after primary blast. In summary, CAT may have a clinical diagnostic utility in combination with selected set of microvascular/inflammatory biomarkers in patients subjected to low/moderate level blast exposures.
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38
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Martin JA, Parekh P, Kim Y, Morey TE, Sefah K, Gravenstein N, Dennis DM, Tan W. Selection of an aptamer antidote to the anticoagulant drug bivalirudin. PLoS One 2013; 8:e57341. [PMID: 23483901 PMCID: PMC3590194 DOI: 10.1371/journal.pone.0057341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 01/21/2013] [Indexed: 11/18/2022] Open
Abstract
Adverse drug reactions, including severe patient bleeding, may occur following the administration of anticoagulant drugs. Bivalirudin is a synthetic anticoagulant drug sometimes employed as a substitute for heparin, a commonly used anticoagulant that can cause a condition called heparin-induced thrombocytopenia (HIT). Although bivalrudin has the advantage of not causing HIT, a major concern is lack of an antidote for this drug. In contrast, medical professionals can quickly reverse the effects of heparin using protamine. This report details the selection of an aptamer to bivalirudin that functions as an antidote in buffer. This was accomplished by immobilizing the drug on a monolithic column to partition binding sequences from nonbinding sequences using a low-pressure chromatography system and salt gradient elution. The elution profile of binding sequences was compared to that of a blank column (no drug), and fractions with a chromatographic difference were analyzed via real-time PCR (polymerase chain reaction) and used for further selection. Sequences were identified by 454 sequencing and demonstrated low micromolar dissociation constants through fluorescence anisotropy after only two rounds of selection. One aptamer, JPB5, displayed a dose-dependent reduction of the clotting time in buffer, with a 20 µM aptamer achieving a nearly complete antidote effect. This work is expected to result in a superior safety profile for bivalirudin, resulting in enhanced patient care.
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Affiliation(s)
- Jennifer A. Martin
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, University of Florida, Gainesville, Florida, United States of America
| | - Parag Parekh
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, University of Florida, Gainesville, Florida, United States of America
| | - Youngmi Kim
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, University of Florida, Gainesville, Florida, United States of America
| | - Timothy E. Morey
- Department of Anesthesiology and Pharmacology, University of Florida, Gainesville, Florida, United States of America
| | - Kwame Sefah
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, University of Florida, Gainesville, Florida, United States of America
| | - Nikolaus Gravenstein
- Department of Anesthesiology and Pharmacology, University of Florida, Gainesville, Florida, United States of America
| | - Donn M. Dennis
- Department of Anesthesiology and Pharmacology, University of Florida, Gainesville, Florida, United States of America
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Bio/nano Interface, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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39
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Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proc Natl Acad Sci U S A 2012. [PMID: 23197839 DOI: 10.1073/pnas.1218414109] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The serine protease α-thrombin is a dual-action protein that mediates the blood-clotting cascade. Thrombin alone is a procoagulant, cleaving fibrinogen to make the fibrin clot, but the thrombin-thrombomodulin (TM) complex initiates the anticoagulant pathway by cleaving protein C. A TM fragment consisting of only the fifth and sixth EGF-like domains (TM56) is sufficient to bind thrombin, but the presence of the fourth EGF-like domain (TM456) is critical to induce the anticoagulant activity of thrombin. Crystallography of the thrombin-TM456 complex revealed no significant structural changes in thrombin, suggesting that TM4 may only provide a scaffold for optimal alignment of protein C for its cleavage by thrombin. However, a variety of experimental data have suggested that the presence of TM4 may affect the dynamic properties of the active site loops. In the present work, we have used both conventional and accelerated molecular dynamics simulation to study the structural dynamic properties of thrombin, thrombin:TM56, and thrombin:TM456 across a broad range of time scales. Two distinct yet interrelated allosteric pathways are identified that mediate both the pro- and anticoagulant activities of thrombin. One allosteric pathway, which is present in both thrombin:TM56 and thrombin:TM456, directly links the TM5 domain to the thrombin active site. The other allosteric pathway, which is only present on slow time scales in the presence of the TM4 domain, involves an extended network of correlated motions linking the TM4 and TM5 domains and the active site loops of thrombin.
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40
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Bioengineered surfaces to improve the blood compatibility of biomaterials through direct thrombin inactivation. Acta Biomater 2012; 8:4101-10. [PMID: 22846590 DOI: 10.1016/j.actbio.2012.07.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 07/05/2012] [Accepted: 07/16/2012] [Indexed: 11/21/2022]
Abstract
Thrombus formation, due to thrombin generation, is a major problem affecting blood-contacting medical devices. This work aimed to develop a new strategy to improve the hemocompatibility of such devices by the immobilization of a naturally occurring thrombin inhibitor into a nanostructured surface. Boophilin, a direct thrombin inhibitor from the cattle tick Rhipicephalus microplus, was produced as a recombinant protein in Pichia pastoris. Boophilin was biotinylated and immobilized on biotin-terminated self-assembled monolayers (SAM) via neutravidin. In order to maintain its proteinase inhibitory capacity after surface immobilization, boophilin was biotinylated after the formation of a boophilin-thrombin complex to minimize the biotinylation of the residues involved in thrombin-boophilin interaction. The extent of boophilin biotinylation was determined using matrix-assisted laser desorption/ionization-time of flight/time of flight mass spectrometry. Boophilin immobilization and thrombin adsorption were quantified using quartz crystal microbalance with dissipation. Thrombin competitive adsorption from human serum was assessed using ¹²⁵I-thrombin. Thrombin inhibition and plasma clotting time were determined using spectrophotometric techniques. Boophilin-coated SAM were able to promote thrombin adsorption in a selective way, inhibiting most of its activity and delaying plasma coagulation in comparison with boophilin-free surfaces, demonstrating boophilin's potential to improve the hemocompatibility of biomaterials used in the production of blood-contacting devices.
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Effects of Extended-Release Dipyridamole In Vitro on Thrombin Indices Measured by Calibrated Automated Thrombography in Poststroke Survivors. Am J Ther 2012; 19:407-12. [DOI: 10.1097/mjt.0b013e318209e021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Effects of dabigatran in vitro on thrombin biomarkers by Calibrated Automated Thrombography in patients after ischemic stroke. J Thromb Thrombolysis 2012; 33:22-7. [PMID: 22065286 DOI: 10.1007/s11239-011-0654-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Randomized trials suggest superior and safe stroke prevention in patients with atrial fibrillation after anticoagulation with dabigatran (D) at a 150 mg BID as described in the RE-LY prospective randomized open-label trial when compared to warfarin. Thrombin generation (TG) is a cornerstone of coagulation cascade, and represents a critical biomarker of atherothrombosis. We, therefore, sought to define the effect of D in escalating concentrations on the time course of TG using the Calibrated Automated Thrombogram(®) (CAT) technology in patients after ischemic stroke. Serial plasma samples were obtained from 20 patients with ischemic stroke documented by neuroimaging, who were treated with aspirin for at least 30 days. The impact of 0.1, 0.23, 0.46, 0.69 mM D in platelet-poor plasma (PPP) on TG indices was assessed using fluorogenic substrate CAT device. The following integrated CAT parameters: TGmax, start time (t-start) peak time (t-peak), and mean time (t-mean) were calculated for each D dose and compared with those of the vehicle. Preincubation of PPP with D resulted in dose-dependent significant inhibition of most TG indices. The TGmax was gradually reduced from 447 ± 21 nM at baseline and reach significance for 0.46 mM D (355 ± 44 nM, P = 0.03); and decreased further at 0.69 mM D to 302 ± 27 nM (P = 0.01). The t-peak has been achieved 2-3 times later than after vehicle already at 0.23 nM D. The t-start was delayed 3-4 fold starting from 0.23 mM concentration of D (P < 0.001 for all), but not different from D 0.1 mM (1.5 vs. 1.6; P = 0.34). The t-mean was not significantly affected by D. D in vitro impacts indices of TG predominantly by dose dependent inhibition of endogenous TG, and delayed thrombin production. This preliminary evidence, while intriguing, requires confirmation in post-stroke patients receiving orally dosed D in order to determine whether these findings are clinically relevant.
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Targeting recombinant thrombomodulin fusion protein to red blood cells provides multifaceted thromboprophylaxis. Blood 2012; 119:4779-85. [PMID: 22493296 DOI: 10.1182/blood-2011-12-398149] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thrombin generates fibrin and activates platelets and endothelium, causing thrombosis and inflammation. Endothelial thrombomodulin (TM) changes thrombin's substrate specificity toward cleavage of plasma protein C into activated protein C (APC), which opposes its thrombotic and inflammatory activities. Endogenous TM activity is suppressed in pathologic conditions, and antithrombotic interventions involving soluble TM are limited by rapid blood clearance. To overcome this problem, we fused TM with a single chain fragment (scFv) of an antibody targeted to red blood cells. scFv/TM catalyzes thrombin-mediated generation of activated protein C and binds to circulating RBCs without apparent damage, thereby prolonging its circulation time and bioavailability orders of magnitude compared with soluble TM. In animal models, a single dose of scFv/TM, but not soluble TM, prevents platelet activation and vascular occlusion by clots. Thus, scFv/TM serves as a prodrug and provides thromboprophylaxis at low doses (0.15 mg/kg) via multifaceted mechanisms inhibiting platelets and coagulation.
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Bijak M, Saluk J, Ponczek MB, Nowak P. Antithrombin effect of polyphenol-rich extracts from black chokeberry and grape seeds. Phytother Res 2012; 27:71-6. [PMID: 22473647 DOI: 10.1002/ptr.4682] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 02/22/2012] [Accepted: 03/02/2012] [Indexed: 11/11/2022]
Abstract
Thrombin is a serine protease that cleaves the peptide bonds in proteins located on the carboxyl side of arginine. Thrombin plays a central role in thromboembolic diseases, which are the major cause of mortality. The aim of the study was to estimate the effects of plant extracts on proteolytic properties of thrombin. Thrombin was incubated with polyphenol-rich extracts from berries of Aronia melanocarpa or seeds of Vitis vinifera (0.5, 5, 50 µg/mL) and with polyphenols ((+)-catechin, (-)-epicatechin, gallic acid, chlorogenic acid, procyanidin B1, cyanidin, cyanidin 3-glucoside, quercetin). The in vitro experiments showed that both extracts in all used concentrations inhibited proteolytic activity of thrombin observed as inhibition of thrombin-induced fibrinogen polymerization, stabilized fibrin formation, and platelet aggregation. Moreover, thrombin amidolytic activity was inhibited by polyphenols belonging to the flavonoid class. Results presented in this study indicate that polyphenol-rich extracts from berries of A. melanocarpa and seeds of V. vinifera may become promising dietary supplements in the prevention of thrombotic states.
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Affiliation(s)
- Michał Bijak
- Department of General Biochemistry, Institute of Biochemistry, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
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Fulcher YG, Van Doren SR. Remote exosites of the catalytic domain of matrix metalloproteinase-12 enhance elastin degradation. Biochemistry 2011; 50:9488-99. [PMID: 21967233 DOI: 10.1021/bi2009807] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
How does matrix metalloproteinase-12 (MMP-12 or metalloelastase) degrade elastin with high specific activity? Nuclear magnetic resonance suggested soluble elastin covers surfaces of MMP-12 far from its active site. Two of these surfaces have been found, by mutagenesis guided by the BINDSIght approach, to affect degradation and affinity for elastin substrates but not a small peptide substrate. Main exosite 1 has been extended to Asp124 that binds calcium. Novel exosite 2 comprises residues from the II-III loop and β-strand I near the back of the catalytic domain. The high degree of exposure of these distal exosites may make them accessible to elastin made more flexible by partial hydrolysis. Importantly, the combination of one lesion each at exosites 1 and 2 and the active site decreased the catalytic competence toward soluble elastin by 13-18-fold to the level of MMP-3, homologue and poor elastase. Double-mutant cycle analysis of conservative mutations of Met156 (exosite 2) and either Asp124 (exosite 1) or Ile180 (active site) showed they had additive effects. Compared to polar substitutions observed in other MMPs, Met156 enhanced affinity and Ile180 the k(cat) for soluble elastin. Both residues detracted from the higher folding stability with polar mutations. This resembles the trend in enzymes of an inverse relationship between folding stability and activity. Restoring Asp124 from combination mutants enhanced the k(cat) for soluble elastin. In elastin degradation, exosites 1 and 2 contributed in a manner independent of each other and Ile180 at the active site, but with partial coupling to Ala182 near the active site. The concept of weak, separated interactions coalescing somewhat independently can be extended to this proteolytic digestion of a protein from fibrils.
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Affiliation(s)
- Yan G Fulcher
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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Greish K, Thiagarajan G, Herd H, Price R, Bauer H, Hubbard D, Burckle A, Sadekar S, Yu T, Anwar A, Ray A, Ghandehari H. Size and surface charge significantly influence the toxicity of silica and dendritic nanoparticles. Nanotoxicology 2011; 6:713-23. [PMID: 21793770 DOI: 10.3109/17435390.2011.604442] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The influence of size, surface charge and surface functionality of poly(amido amine) dendrimers and silica nanoparticles (SNPs) on their toxicity was studied in immunocompetent mice. After systematic characterization of nanoparticles, they were administered to CD-1 (caesarean derived-1) mice to evaluate acute toxicity. A distinct trend in nanotoxicity based on surface charge and functional group was observed with dendrimers regardless of their size. Amine-terminated dendrimers were fatal at doses >10 mg/kg causing haematological complications such as disseminated intravascular coagulation-like manifestations whereas carboxyl- and hydroxyl-terminated dendrimers of similar sizes were tolerated at 50-fold higher doses. In contrast, larger SNPs were less tolerated than smaller SNPs irrespective of their surface functionality. These findings have important implications in the use of these nanoparticles for various biomedical applications.
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Affiliation(s)
- Khaled Greish
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84108, USA
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Castro HC, Abreu PA, Geraldo RB, Martins RCA, dos Santos R, Loureiro NIV, Cabral LM, Rodrigues CR. Looking at the proteases from a simple perspective. J Mol Recognit 2011; 24:165-81. [PMID: 21360607 DOI: 10.1002/jmr.1091] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Proteases have received enormous interest from the research and medical communities because of their significant roles in several human diseases. Some examples include the involvement of thrombin in thrombosis, HIV-1 protease in Acquired Immune Deficiency Syndrome, cruzain in Trypanosoma cruzi infection, and membrane-type 1 matrix metalloproteinase in tumor invasion and metastasis. Many efforts has been undertaken to design effective inhibitors featuring potent inhibitory activity, specificity, and metabolic stability to those proteases involved in such pathologies. Protease inhibitors usually target the active site, but some of them act by other inhibitory mechanisms. The understanding of the structure-function relationships of proteases and inhibitors has an impact on new inhibitor drugs designing. In this paper, the structures of four proteases (thrombin, HIV-protease, cruzain, and a matrix metalloproteinase) are briefly reviewed, and used as examples of the importance of proteases for the development of new treatment strategies, leading to a longer and healthier life.
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Affiliation(s)
- Helena C Castro
- LABioMol, Departamento de Biologia Celular e Molecular, Instituto de Biologia, Universidade Federal Fluminense, Rio de Janeiro, 24001-970, Brazil.
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Diculescu VC, Chiorcea-Paquim AM, Eritja R, Oliveira-Brett AM. Evaluation of the structure–activity relationship of thrombin with thrombin binding aptamers by voltammetry and atomic force microscopy. J Electroanal Chem (Lausanne) 2011. [DOI: 10.1016/j.jelechem.2010.11.037] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Zhou JG, Chen YM. Research on PEGylation of porcine prothrombin for improving biostability and reducing animal immunogenicity. Bioorg Med Chem Lett 2011; 21:3268-72. [PMID: 21524910 DOI: 10.1016/j.bmcl.2011.04.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/17/2011] [Accepted: 04/08/2011] [Indexed: 11/30/2022]
Abstract
Prothrombin is a vitamin K-dependent serine protease and plays pivotal roles in both procoagulant and anticoagulant pathway of hemostasis. In this study, prothrombin purified from porcine plasma was modified through PEGylation at N-terminal residue using 40 kDa PEG-phenyl-isothiocyanate (PIT-PEG40K). The monoPEGylated prothrombin enhanced biostability and remarkably prolonged circulating half-life in mice as compared with that of the nonmodified prothrombin. Moreover, the immunogenicity of PEGylated prothrombin in mice is significantly decreased compared to nonmodified prothrombin. These studies demonstrated the feasibility of PEGylating prothrombin as a promising way for the development of new prothrombin drugs.
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Affiliation(s)
- Jian-Gang Zhou
- College of Environment and Urban Construction, Wuhan Textile University, Wuhan 430073, PR China
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50
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Pozzi N, Chen R, Chen Z, Bah A, Di Cera E. Rigidification of the autolysis loop enhances Na(+) binding to thrombin. Biophys Chem 2011; 159:6-13. [PMID: 21536369 DOI: 10.1016/j.bpc.2011.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 04/04/2011] [Accepted: 04/04/2011] [Indexed: 01/09/2023]
Abstract
Binding of Na(+) to thrombin ensures high activity toward physiological substrates and optimizes the procoagulant and prothrombotic roles of the enzyme in vivo. Under physiological conditions of pH and temperature, the binding affinity of Na(+) is weak due to large heat capacity and enthalpy changes associated with binding, and the K(d)=80 mM ensures only 64% saturation of the site at the concentration of Na(+) in the blood (140 mM). Residues controlling Na(+) binding and activation have been identified. Yet, attempts to improve the interaction of Na(+) with thrombin and possibly increase catalytic activity under physiological conditions have so far been unsuccessful. Here we report how replacement of the flexible autolysis loop of human thrombin with the homologous rigid domain of the murine enzyme results in a drastic (up to 10-fold) increase in Na(+) affinity and a significant improvement in the catalytic activity of the enzyme. Rigidification of the autolysis loop abolishes the heat capacity change associated with Na(+) binding observed in the wild-type and also increases the stability of thrombin. These findings have general relevance to protein engineering studies of clotting proteases and trypsin-like enzymes.
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Affiliation(s)
- Nicola Pozzi
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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