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Dai Y, Kretz CA, Kim PY, Gross PL. A specific fluorescence resonance energy quenching-based biosensor for measuring thrombin activity in whole blood. J Thromb Haemost 2024; 22:1627-1639. [PMID: 38382740 DOI: 10.1016/j.jtha.2024.02.007] [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: 10/17/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND At sites of vessel injury, thrombin acts as the central mediator of coagulation by catalyzing fibrin clot formation and platelet activation. Thrombin generation is most frequently measured in plasma samples using small-molecule substrates; however, these have low specificity for thrombin and limited utility in whole blood. Plasma assays are limited because they ignore the hemostatic contributions of blood cells and require anticoagulation and the addition of supraphysiological concentrations of calcium. OBJECTIVES To overcome these limitations, we designed and characterized a fluorescence resonance energy quenching-based thrombin sensor (FTS) protein. METHODS The fluorescence resonance energy quenching pair of mAmetrine and tTomato, separated by a thrombin recognition sequence, was developed. The protein was expressed using Escherichia coli, and purity was assessed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The cleavage of FTS was monitored by fluorescence using excitation at 406 nm and emission at 526 nm and 581 nm. RESULTS Compared with small-molecule substrates, the FTS demonstrated high specificity for thrombin; it is not cleaved by thrombin or inhibited by α2-macroglobulin and interacts with thrombin's anion-binding exosite I. The FTS can effectively measure thrombin generation in plasma and in finger-prick whole blood, which allows it to be developed into a point-of-care test of thrombin generation. The FTS does not inhibit standard thrombin-generation assays. Lastly, FTS-based thrombin generation in nonanticoagulated finger-prick blood was delayed but enhanced compared with that in citrated plasma. CONCLUSION The FTS will broaden our understanding of thrombin generation in ways that are not attainable with current methods.
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Affiliation(s)
- Ying Dai
- Hamilton Health Sciences and Departments of Medicine and Medical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Colin A Kretz
- Hamilton Health Sciences and Departments of Medicine and Medical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Paul Y Kim
- Hamilton Health Sciences and Departments of Medicine and Medical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Peter L Gross
- Hamilton Health Sciences and Departments of Medicine and Medical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada.
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Troisi R, Balasco N, Autiero I, Vitagliano L, Sica F. Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies. Int J Mol Sci 2023; 24:16318. [PMID: 38003510 PMCID: PMC10671752 DOI: 10.3390/ijms242216318] [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: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein-aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein-aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein-aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department of Chemistry, University of Rome Sapienza, 00185 Rome, Italy;
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
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Komarevtsev SK, Evseev PV, Shneider MM, Popova EA, Tupikin AE, Stepanenko VN, Kabilov MR, Shabunin SV, Osmolovskiy AA, Miroshnikov KA. Gene Analysis, Cloning, and Heterologous Expression of Protease from a Micromycete Aspergillus ochraceus Capable of Activating Protein C of Blood Plasma. Microorganisms 2021; 9:1936. [PMID: 34576831 PMCID: PMC8471544 DOI: 10.3390/microorganisms9091936] [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: 08/06/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 12/16/2022] Open
Abstract
Micromycetes are known to secrete numerous enzymes of biotechnological and medical potential. Fibrinolytic protease-activator of protein C (PAPC) of blood plasma from micromycete Aspergillus ochraceus VKM-F4104D was obtained in recombinant form utilising the bacterial expression system. This enzyme, which belongs to the proteinase-K-like proteases, is similar to the proteases encoded in the genomes of Aspergillus fumigatus ATCC MYA-4609, A. oryzae ATCC 42149 and A. flavus 28. Mature PAPC-4104 is 282 amino acids long, preceded by the 101-amino acid propeptide necessary for proper folding and maturation. The recombinant protease was identical to the native enzyme from micromycete in terms of its biological properties, including an ability to hydrolyse substrates of activated protein C (pGlu-Pro-Arg-pNA) and factor Xa (Z-D-Arg-Gly-Arg-pNA) in conjugant reactions with human blood plasma. Therefore, recombinant PAPC-4104 can potentially be used in medicine, veterinary science, diagnostics, and other applications.
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Affiliation(s)
- Sergei K. Komarevtsev
- Biology Department, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.A.P.); (A.A.O.)
- All-Russian Scientific Research Veterinary Institute of Pathology, Pharmacology and Therapy, 394087 Voronezh, Russia; (S.V.S.); (K.A.M.)
| | - Peter V. Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (M.M.S.); (V.N.S.)
| | - Mikhail M. Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (M.M.S.); (V.N.S.)
| | - Elizaveta A. Popova
- Biology Department, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.A.P.); (A.A.O.)
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Vasiliy N. Stepanenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (M.M.S.); (V.N.S.)
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.E.T.); (M.R.K.)
| | - Sergei V. Shabunin
- All-Russian Scientific Research Veterinary Institute of Pathology, Pharmacology and Therapy, 394087 Voronezh, Russia; (S.V.S.); (K.A.M.)
| | - Alexander A. Osmolovskiy
- Biology Department, Lomonosov Moscow State University, 119234 Moscow, Russia; (E.A.P.); (A.A.O.)
- All-Russian Scientific Research Veterinary Institute of Pathology, Pharmacology and Therapy, 394087 Voronezh, Russia; (S.V.S.); (K.A.M.)
| | - Konstantin A. Miroshnikov
- All-Russian Scientific Research Veterinary Institute of Pathology, Pharmacology and Therapy, 394087 Voronezh, Russia; (S.V.S.); (K.A.M.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.V.E.); (M.M.S.); (V.N.S.)
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Gadi I, Fatima S, Elwakiel A, Nazir S, Mohanad Al-Dabet M, Rana R, Bock F, Manoharan J, Gupta D, Biemann R, Nieswandt B, Braun-Dullaeus R, Besler C, Scholz M, Geffers R, Griffin JH, Esmon CT, Kohli S, Isermann B, Shahzad K. Different DOACs Control Inflammation in Cardiac Ischemia-Reperfusion Differently. Circ Res 2020; 128:513-529. [PMID: 33353373 DOI: 10.1161/circresaha.120.317219] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RATIONALE While thrombin is the key protease in thrombus formation, other coagulation proteases, such as fXa (factor Xa) or aPC (activated protein C), independently modulate intracellular signaling via partially distinct receptors. OBJECTIVES To study the differential effects of fXa or fIIa (factor IIa) inhibition on gene expression and inflammation in myocardial ischemia-reperfusion injury. METHODS AND RESULTS Mice were treated with a direct fIIa inhibitor (fIIai) or direct fXa inhibitor (fXai) at doses that induced comparable anticoagulant effects ex vivo and in vivo (tail-bleeding assay and FeCl3-induced thrombosis). Myocardial ischemia-reperfusion injury was induced via left anterior descending ligation. We determined infarct size and in vivo aPC generation, analyzed gene expression by RNA sequencing, and performed immunoblotting and ELISA. The signaling-only 3K3A-aPC variant and inhibitory antibodies that blocked all or only the anticoagulant function of aPC were used to determine the role of aPC. Doses of fIIai and fXai that induced comparable anticoagulant effects resulted in a comparable reduction in infarct size. However, unbiased gene expression analyses revealed marked differences, including pathways related to sterile inflammation and inflammasome regulation. fXai but not fIIai inhibited sterile inflammation by reducing the expression of proinflammatory cytokines (IL [interleukin]-1β, IL-6, and TNFα [tumor necrosis factor alpha]), as well as NF-κB (nuclear factor kappa B) and inflammasome activation. This anti-inflammatory effect was associated with reduced myocardial fibrosis 28 days post-myocardial ischemia-reperfusion injury. Mechanistically, in vivo aPC generation was higher with fXai than with fIIai. Inhibition of the anticoagulant and signaling properties of aPC abolished the anti-inflammatory effect associated with fXai, while inhibiting only the anticoagulant function of aPC had no effect. Combining 3K3A-aPC with fIIai reduced the inflammatory response, mimicking the fXai-associated effect. CONCLUSIONS We showed that specific inhibition of coagulation via direct oral anticoagulants had differential effects on gene expression and inflammation, despite comparable anticoagulant effects and infarct sizes. Targeting individual coagulation proteases induces specific cellular responses unrelated to their anticoagulant effect.
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Affiliation(s)
- Ihsan Gadi
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Sameen Fatima
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Ahmed Elwakiel
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Sumra Nazir
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Moh'd Mohanad Al-Dabet
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.).,Medical Laboratories, Faculty of Health Sciences, American University of Madaba, Amman, Jordan (M.M.A.-D.)
| | - Rajiv Rana
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Fabian Bock
- Medicine, Vanderbilt University Medical Center, Nashville, TN (F.B.)
| | - Jayakumar Manoharan
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Dheerendra Gupta
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Ronald Biemann
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Bernhard Nieswandt
- Institute of Experimental Biomedicine, University Hospital and Rudolf Virchow Centre, University of Würzburg, Germany (B.N.)
| | - Ruediger Braun-Dullaeus
- Clinics of Cardiology and Angiology, Otto-von-Guericke-University, Magdeburg, Germany (R.B.-D.)
| | - Christian Besler
- Cardiology, Leipzig Heart Center (C.B.), University of Leipzig, Germany
| | - Markus Scholz
- Institute of Medical Informatics, Statistics and Epidemiology (M.S.), University of Leipzig, Germany
| | - Robert Geffers
- RG Genome Analytics, Helmholtz Center for Infection Research, Braunschweig, Germany (R.G.)
| | - John H Griffin
- Molecular Medicine, The Scripps Research Institute, La Jolla, CA (J.H.G.)
| | - Charles T Esmon
- Coagulation Biology Laboratory, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104 (C.T.E.)
| | - Shrey Kohli
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
| | - Khurrum Shahzad
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University Hospital, Leipzig, Germany (I.G., S.F., A.E., S.N., M.M.A.-D., R.R., J.M., D.G., R.B., S.K., B.I., K.S.)
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Billur R, Sabo TM, Maurer MC. Thrombin Exosite Maturation and Ligand Binding at ABE II Help Stabilize PAR-Binding Competent Conformation at ABE I. Biochemistry 2019; 58:1048-1060. [PMID: 30672691 DOI: 10.1021/acs.biochem.8b00943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Thrombin, derived from zymogen prothrombin (ProT), is a serine protease involved in procoagulation, anticoagulation, and platelet activation. Thrombin's actions are regulated through anion-binding exosites I and II (ABE I and ABE II) that undergo maturation during activation. Mature ABEs can utilize exosite-based communication to fulfill thrombin functions. However, the conformational basis behind such long-range communication and the resultant ligand binding affinities are not well understood. Protease activated receptors (PARs), involved in platelet activation and aggregation, are known to target thrombin ABE I. Unexpectedly, PAR3 (44-56) can already bind to pro-ABE I of ProT. Nuclear magnetic resonance (NMR) ligand-enzyme titrations were used to characterize how individual PAR1 (49-62) residues interact with pro-ABE I and mature ABE I. 1D proton line broadening studies demonstrated that binding affinities for native PAR1P (49-62, P54) and for the weak binding variant PAR1G (49-62, P54G) increased as ProT was converted to mature thrombin. 1H,15N-HSQC titrations revealed that PAR1G residues K51, E53, F55, D58, and E60 exhibited less affinity to pro-ABE I than comparable residues in PAR3G (44-56, P51G). Individual PAR1G residues then displayed tighter binding upon exosite maturation. Long-range communication between thrombin exosites was examined by saturating ABE II with phosphorylated GpIbα (269-282, 3Yp) and monitoring the binding of PAR1 and PAR3 peptides to ABE I. Individual PAR residues exhibited increased affinities in this dual-ligand environment supporting the presence of interexosite allostery. Exosite maturation and beneficial long-range allostery are proposed to help stabilize an ABE I conformation that can effectively bind PAR ligands.
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Affiliation(s)
- Ramya Billur
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center , University of Louisville , Louisville , Kentucky 40202 , United States
| | - Muriel C Maurer
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
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