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De Filippis V, Acquasaliente L, Pontarollo G, Peterle D. Noncoded amino acids in protein engineering: Structure-activity relationship studies of hirudin-thrombin interaction. Biotechnol Appl Biochem 2018; 65:69-80. [DOI: 10.1002/bab.1632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 12/06/2017] [Indexed: 11/12/2022]
Affiliation(s)
- Vincenzo De Filippis
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Laura Acquasaliente
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Giulia Pontarollo
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
| | - Daniele Peterle
- Laboratory of Protein Chemistry; Department of Pharmaceutical & Pharmacological Sciences; University of Padua; Padua Italy
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52
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Shabanova EM, Drozdov AS, Fakhardo AF, Dudanov IP, Kovalchuk MS, Vinogradov VV. Thrombin@Fe 3O 4 nanoparticles for use as a hemostatic agent in internal bleeding. Sci Rep 2018; 8:233. [PMID: 29321571 PMCID: PMC5762673 DOI: 10.1038/s41598-017-18665-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/05/2017] [Indexed: 12/21/2022] Open
Abstract
Bleeding remains one of the main causes of premature mortality at present, with internal bleeding being the most dangerous case. In this paper, magnetic hemostatic nanoparticles are shown for the first time to assist in minimally invasive treatment of internal bleeding, implying the introduction directly into the circulatory system followed by localization in the bleeding zone due to the application of an external magnetic field. Nanoparticles were produced by entrapping human thrombin (THR) into a sol-gel derived magnetite matrix followed by grinding to sizes below 200 nm and subsequent colloidization. Prepared colloids show protrombotic activity and cause plasma coagulation in in vitro experiments. We also show here using a model blood vessel that the THR@ferria composite does not cause systematic thrombosis due to low activity, but being concentrated by an external magnetic field with simultaneous fibrinogen injection accelerates local hemostasis and stops the bleeding. For instance, a model vessel system with circulating blood at the puncture of the vessel wall and the application of a permanent magnetic field yielded a hemostasis time by a factor of 6.5 shorter than that observed for the control sample. Biocompatibility of composites was tested on HELF and HeLa cells and revealed no toxic effects.
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Affiliation(s)
- Emiliya M Shabanova
- ITMO University, Laboratory of Solution Chemistry of Advanced Materials and Technologies, Lomonosova St. 9, 191002, St. Petersburg, Russian Federation
| | - Andrey S Drozdov
- ITMO University, Laboratory of Solution Chemistry of Advanced Materials and Technologies, Lomonosova St. 9, 191002, St. Petersburg, Russian Federation.
| | - Anna F Fakhardo
- ITMO University, Laboratory of Solution Chemistry of Advanced Materials and Technologies, Lomonosova St. 9, 191002, St. Petersburg, Russian Federation
| | - Ivan P Dudanov
- ITMO University, Laboratory of Solution Chemistry of Advanced Materials and Technologies, Lomonosova St. 9, 191002, St. Petersburg, Russian Federation
- Mariinsky Hospital, Regional Cardiovascular Center, Liteyny Ave. 56, 191054, St. Petersburg, Russian Federation
| | - Marina S Kovalchuk
- Mariinsky Hospital, Regional Cardiovascular Center, Liteyny Ave. 56, 191054, St. Petersburg, Russian Federation
| | - Vladimir V Vinogradov
- ITMO University, Laboratory of Solution Chemistry of Advanced Materials and Technologies, Lomonosova St. 9, 191002, St. Petersburg, Russian Federation.
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53
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Billur R, Ban D, Sabo TM, Maurer MC. Deciphering Conformational Changes Associated with the Maturation of Thrombin Anion Binding Exosite I. Biochemistry 2017; 56:6343-6354. [PMID: 29111672 DOI: 10.1021/acs.biochem.7b00970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Thrombin participates in procoagulation, anticoagulation, and platelet activation. This enzyme contains anion binding exosites, ABE I and ABE II, which attract regulatory biomolecules. As prothrombin is activated to thrombin, pro-ABE I is converted into mature ABE I. Unexpectedly, certain ligands can bind to pro-ABE I specifically. Moreover, knowledge of changes in conformation and affinity that occur at the individual residue level as pro-ABE I is converted to ABE I is lacking. Such changes are transient and were not captured by crystallography. Therefore, we employed nuclear magnetic resonance (NMR) titrations to monitor development of ABE I using peptides based on protease-activated receptor 3 (PAR3). Proton line broadening NMR revealed that PAR3 (44-56) and more weakly binding PAR3G (44-56) could already interact with pro-ABE I on prothrombin. 1H-15N heteronuclear single-quantum coherence NMR titrations were then used to probe binding of individual 15N-labeled PAR3G residues (F47, E48, L52, and D54). PAR3G E48 and D54 could interact electrostatically with prothrombin and tightened upon thrombin maturation. The higher affinity for PAR3G D54 suggests the region surrounding thrombin R77a is better oriented to bind D54 than the interaction between PAR3G E48 and thrombin R75. Aromatic PAR3G F47 and aliphatic L52 both reported on significant changes in the chemical environment upon conversion of prothrombin to thrombin. The ABE I region surrounding the 30s loop was more affected than the hydrophobic pocket (F34, L65, and I82). Our NMR titrations demonstrate that PAR3 residues document structural rearrangements occurring during exosite maturation that are missed by reported X-ray crystal structures.
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Affiliation(s)
- Ramya Billur
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville , Louisville, Kentucky 40202, 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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54
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Jadhav MA, Goldsberry WN, Zink SE, Lamb KN, Simmons KE, Riposo CM, Anokhin BA, Maurer MC. Screening cleavage of Factor XIII V34X Activation Peptides by thrombin mutants: A strategy for controlling fibrin architecture. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1246-1254. [PMID: 28687225 DOI: 10.1016/j.bbapap.2017.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 06/26/2017] [Accepted: 07/02/2017] [Indexed: 10/19/2022]
Abstract
In blood coagulation, thrombin converts fibrinogen into fibrin monomers that polymerize into a clot network. Thrombin also activates Factor XIII by cleaving the R37-G38 peptide bond of the Activation Peptide (AP) segment. The resultant transglutaminase introduces covalent crosslinks into the fibrin clot. A strategy to modify clot architecture would be to design FXIII AP sequences that are easier or more difficult to be thrombin-cleaved thus controlling initiation of crosslinking. To aid in this design process, FXIII V34X (28-41) Activation Peptides were kinetically ranked for cleavage by wild-type thrombin and several anticoagulant mutants. Thrombin-catalyzed hydrolysis of aromatic FXIII F34, W34, and Y34 APs was compared with V34 and L34. Cardioprotective FXIII L34 remained the variant most readily cleaved by wild-type thrombin. The potent anticoagulant thrombins W215A and W215A/E217A (missing a key substrate platform for binding fibrinogen) were best able to hydrolyze FXIII F34 and W34 APs. Thrombin I174A and L99A could effectively accommodate FXIII W34 and Y34 APs yielding kinetic parameters comparable to FXIII AP L34 with wild-type thrombin. None of the aromatic FXIII V34X APs could be hydrolyzed by thrombin Y60aA. FXIII F34 and W34 are promising candidates for FXIII - anticoagulant thrombin systems that could permit FXIII-catalyzed crosslinking in the presence of reduced fibrin formation. By contrast, FXIII Y34 with thrombin (Y60aA or W215A/E217A) could help assure that both fibrin clot formation and protein crosslinking are hindered. Regulating the activation of FXIII is predicted to be a strategy for helping to control fibrin clot architecture and its neighboring environments.
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Affiliation(s)
- Madhavi A Jadhav
- Chemistry Department, University of Louisville, 2320 South Brook Street, Louisville, KY 40292, USA
| | - Whitney N Goldsberry
- Chemistry Department, University of Louisville, 2320 South Brook Street, Louisville, KY 40292, USA
| | - Sara E Zink
- Chemistry Department, University of Louisville, 2320 South Brook Street, Louisville, KY 40292, USA
| | - Kelsey N Lamb
- Chemistry Department, University of Louisville, 2320 South Brook Street, Louisville, KY 40292, USA
| | - Katelyn E Simmons
- Chemistry Department, University of Louisville, 2320 South Brook Street, Louisville, KY 40292, USA
| | - Carmela M Riposo
- Chemistry Department, University of Louisville, 2320 South Brook Street, Louisville, KY 40292, USA
| | - Boris A Anokhin
- Chemistry Department, University of Louisville, 2320 South Brook Street, Louisville, KY 40292, USA
| | - Muriel C Maurer
- Chemistry Department, University of Louisville, 2320 South Brook Street, Louisville, KY 40292, USA.
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55
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Pontarollo G, Acquasaliente L, Peterle D, Frasson R, Artusi I, De Filippis V. Non-canonical proteolytic activation of human prothrombin by subtilisin from Bacillus subtilis may shift the procoagulant-anticoagulant equilibrium toward thrombosis. J Biol Chem 2017; 292:15161-15179. [PMID: 28684417 DOI: 10.1074/jbc.m117.795245] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 06/28/2017] [Indexed: 12/26/2022] Open
Abstract
Blood coagulation is a finely regulated physiological process culminating with the factor Xa (FXa)-mediated conversion of the prothrombin (ProT) zymogen to active α-thrombin (αT). In the prothrombinase complex on the platelet surface, FXa cleaves ProT at Arg-271, generating the inactive precursor prethrombin-2 (Pre2), which is further attacked at Arg-320-Ile-321 to yield mature αT. Whereas the mechanism of physiological ProT activation has been elucidated in great detail, little is known about the role of bacterial proteases, possibly released in the bloodstream during infection, in inducing blood coagulation by direct proteolytic ProT activation. This knowledge gap is particularly concerning, as bacterial infections are frequently complicated by severe coagulopathies. Here, we show that addition of subtilisin (50 nm to 2 μm), a serine protease secreted by the non-pathogenic bacterium Bacillus subtilis, induces plasma clotting by proteolytically converting ProT into active σPre2, a nicked Pre2 derivative with a single cleaved Ala-470-Asn-471 bond. Notably, we found that this non-canonical cleavage at Ala-470-Asn-471 is instrumental for the onset of catalysis in σPre2, which was, however, reduced about 100-200-fold compared with αT. Of note, σPre2 could generate fibrin clots from fibrinogen, either in solution or in blood plasma, and could aggregate human platelets, either isolated or in whole blood. Our findings demonstrate that alternative cleavage of ProT by proteases, even by those secreted by non-virulent bacteria such as B. subtilis, can shift the delicate procoagulant-anticoagulant equilibrium toward thrombosis.
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Affiliation(s)
- Giulia Pontarollo
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Laura Acquasaliente
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Daniele Peterle
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Roberta Frasson
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Ilaria Artusi
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
| | - Vincenzo De Filippis
- From the Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo 5, Padua 35131, Italy
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56
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Takayama K, Mori K, Tanaka A, Nomura E, Sohma Y, Mori M, Taguchi A, Taniguchi A, Sakane T, Yamamoto A, Minamino N, Miyazato M, Kangawa K, Hayashi Y. Discovery of a Human Neuromedin U Receptor 1-Selective Hexapeptide Agonist with Enhanced Serum Stability. J Med Chem 2017; 60:5228-5234. [PMID: 28548497 DOI: 10.1021/acs.jmedchem.7b00694] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Neuromedin U (NMU) activates two NMU receptors (NMUR1 and NMUR2) and is a useful antiobesity drug lead. We report discovery of a hexapeptide agonist, 2-thienylacetyl-Trp1-Phe(4-F)2-Arg3-Pro4-Arg5-Asn6-NH2 (4). However, the NMUR1 selectivity and serum stability of this agonist were unsatisfactory. Through a structure-activity relationship study focused on residue 2 of agonist 4, serum stability, and pharmacokinetic properties, we report here the discovery of a novel NMUR1 selective hexapeptide agonist 7b that suppresses body weight gain in mice.
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Affiliation(s)
- Kentaro Takayama
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences , 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Kenji Mori
- Department of Biochemistry, National Cerebral and Cardiovascular Center Research Institute , 5-7-1 Fujishirodai, Suita, Osaka 565-8565, Japan
| | - Akiko Tanaka
- Department of Biopharmaceutics, Kyoto Pharmaceutical University , 5 Misasaginakauchi-cho, Yamashina, Kyoto 607-8414, Japan
| | - Erina Nomura
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences , 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yuko Sohma
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences , 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Miwa Mori
- Department of Biochemistry, National Cerebral and Cardiovascular Center Research Institute , 5-7-1 Fujishirodai, Suita, Osaka 565-8565, Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences , 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences , 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Toshiyasu Sakane
- Laboratory of Pharmaceutical Technology, Kobe Pharmaceutical University , 4-19-1 Motoyamakitamachi, Higashinada, Kobe, Hyogo 658-8558, Japan
| | - Akira Yamamoto
- Department of Biopharmaceutics, Kyoto Pharmaceutical University , 5 Misasaginakauchi-cho, Yamashina, Kyoto 607-8414, Japan
| | - Naoto Minamino
- Omics Research Center, National Cerebral and Cardiovascular Center , 5-7-1 Fujishirodai, Suita, Osaka 565-8565, Japan
| | - Mikiya Miyazato
- Department of Biochemistry, National Cerebral and Cardiovascular Center Research Institute , 5-7-1 Fujishirodai, Suita, Osaka 565-8565, Japan
| | - Kenji Kangawa
- Department of Biochemistry, National Cerebral and Cardiovascular Center Research Institute , 5-7-1 Fujishirodai, Suita, Osaka 565-8565, Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences , 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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57
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A cluster of aspartic residues in the extracellular loop II of PAR 4 is important for thrombin interaction and activation of platelets. Thromb Res 2017; 154:84-92. [DOI: 10.1016/j.thromres.2017.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/29/2017] [Accepted: 04/10/2017] [Indexed: 12/25/2022]
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58
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Abstract
Conformational selection (CS) and induced fit (IF) are two widely used interpretations of binding of a ligand to biological macromolecules. Both mechanisms envision a two-step reaction in which a conformational transition either precedes (CS) or follows (IF) the binding step. Under pseudo-first-order conditions where the ligand is in excess compared to the macromolecule, both mechanisms produce two relaxations. A fast one eventually increases linearly with ligand concentration and reflects the binding interaction. A slow one saturates to a constant value after decreasing or increasing hyperbolically with ligand concentration. This relaxation is the one most often accessible to experimental measurements and is potentially diagnostic of the mechanism involved. A relaxation that decreases unequivocally identifies CS, but a hyperbolic increase is compatible with both CS and IF. The potential ambiguity between the two mechanisms is more than qualitative. Here we show that the entire kinetic repertoire of IF is nothing but a mathematical special case of CS as revealed by a simple transformation of the rate constants, which emphasizes the need for independent support of either mechanism from additional experimental evidence. We discuss a simple strategy for distinguishing between IF and CS under the most common conditions encountered in practice, i.e., when the ligand is in excess compared to the macromolecule and a single relaxation is accessible to experimental measurements.
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Affiliation(s)
- Pradipta Chakraborty
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , St. Louis, Missouri 63104, United States
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , St. Louis, Missouri 63104, United States
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59
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Pereira RCC, Lourenço AL, Terra L, Abreu PA, Laneuville Teixeira V, Castro HC. Marine Diterpenes: Molecular Modeling of Thrombin Inhibitors with Potential Biotechnological Application as an Antithrombotic. Mar Drugs 2017; 15:E79. [PMID: 28335516 PMCID: PMC5367036 DOI: 10.3390/md15030079] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/10/2017] [Accepted: 03/14/2017] [Indexed: 12/18/2022] Open
Abstract
Thrombosis related diseases are among the main causes of death and incapacity in the world. Despite the existence of antithrombotic agents available for therapy, they still present adverse effects like hemorrhagic risks which justify the search for new options. Recently, pachydictyol A, isopachydictyol A, and dichotomanol, three diterpenes isolated from Brazilian marine brown alga Dictyota menstrualis were identified as potent antithrombotic molecules through inhibition of thrombin, a key enzyme of coagulation cascade and a platelet agonist. Due to the biotechnological potential of these marine metabolites, in this work we evaluated their binding mode to thrombin in silico and identified structural features related to the activity in order to characterize their molecular mechanism. According to our theoretical studies including structure-activity relationship and molecular docking analysis, the highest dipole moment, polar surface area, and lowest electronic density of dichotomanol are probably involved in its higher inhibition percentage towards thrombin catalytic activity compared to pachydictyol A and isopachydictyol A. Interestingly, the molecular docking studies also revealed a good shape complementarity of pachydictyol A and isopachydictyol A and interactions with important residues and regions (e.g., H57, S195, W215, G216, and loop-60), which probably justify their thrombin inhibitor effects demonstrated in vitro. Finally, this study explored the structural features and binding mode of these three diterpenes in thrombin which reinforced their potential to be further explored and may help in the design of new antithrombotic agents.
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Affiliation(s)
- Rebeca Cristina Costa Pereira
- Programa de Pós-Graduação em Ciências e Biotecnologia (PPBI), Instituto de Biologia, Universidade Federal Fluminense, Niterói 24210-130, RJ, Brazil.
| | - André Luiz Lourenço
- Laboratório de Trombose e Câncer, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21944-970, RJ, Brazil.
- Programa de Pós-Graduação em Patologia, Hospital Universitário Antonio Pedro, Universidade Federal Fluminense, Niterói 24210-130, RJ, Brazil.
| | - Luciana Terra
- Programa de Pós-Graduação em Ciências e Biotecnologia (PPBI), Instituto de Biologia, Universidade Federal Fluminense, Niterói 24210-130, RJ, Brazil.
| | - Paula Alvarez Abreu
- Laboratório de Modelagem Molecular e Pesquisa em Ciências Farmacêuticas-LAMCIFAR, NUPEM, Universidade Federal do Rio de Janeiro, Campus Macaé, Rio de Janeiro27965-045, RJ, Brazil.
| | - Valéria Laneuville Teixeira
- Programa de Pós-Graduação em Ciências e Biotecnologia (PPBI), Instituto de Biologia, Universidade Federal Fluminense, Niterói 24210-130, RJ, Brazil.
| | - Helena Carla Castro
- Programa de Pós-Graduação em Ciências e Biotecnologia (PPBI), Instituto de Biologia, Universidade Federal Fluminense, Niterói 24210-130, RJ, Brazil.
- Programa de Pós-Graduação em Patologia, Hospital Universitário Antonio Pedro, Universidade Federal Fluminense, Niterói 24210-130, RJ, Brazil.
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60
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Gvozdenov M, Pruner I, Tomic B, Kovac M, Radojkovic D, Djordjevic V. The effect of FII c.1787G>A (prothrombin Belgrade) mutation on prothrombin gene expression in vitro. Mol Biol 2017. [DOI: 10.1134/s0026893316060078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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61
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Ito K, Hongo K, Date T, Ikegami M, Hano H, Owada M, Morimoto S, Kashiwagi Y, Katoh D, Yoshino T, Yoshii A, Kimura H, Nagoshi T, Kajimura I, Kusakari Y, Akaike T, Minamisawa S, Ogawa K, Minai K, Ogawa T, Kawai M, Yajima J, Matsuo S, Yamane T, Taniguchi I, Morimoto S, Yoshimura M. Tissue thrombin is associated with the pathogenesis of dilated cardiomyopathy. Int J Cardiol 2016; 228:821-827. [PMID: 27888761 DOI: 10.1016/j.ijcard.2016.11.176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/06/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Thrombin is a serine protease known to be the final product of the coagulation cascade. However, thrombin plays other physiological roles in processes such as gastric contractions and vessel wound healing, and a state of coagulability is increased in patients with dilated cardiomyopathy (DCM). In this study, we investigate the role of thrombin in the pathogenesis of DCM. The purpose of this study is to clarify the role of thrombin in the pathogenesis of DCM and investigate the possibility of treatment against DCM by thrombin inhibition. METHODS We investigated the expression of thrombin in the left ventricles of five patients with DCM who underwent the Batista operation and four patients without heart disease. Furthermore, we investigated the involvement of thrombin in the development of DCM using knock-in mice with a deletion mutation of cardiac troponin T that causes human DCM (∆K210 knock-in mouse) (B6;129-Tnnt2tm2Mmto) and assessed the effects of a direct thrombin inhibitor, dabigatran on ∆K210 knock-in mice using echocardiographic examinations, the Kaplan-Meier method and Western blotting. RESULTS The immunohistochemical analysis showed a strong thrombin expression in the DCM patients compared to the patients without heart disease. In immunohistochemical analysis, a strong thrombin expression was observed in the heart tissues analysis in the ∆K210 knock-in mice. Dabigatran administration significantly improved fractional shortening according to the echocardiographic examination and the survival outcomes in ∆K210 knock-in mice. CONCLUSION Tissue thrombin is involved in the pathogenesis of DCM and thrombin inhibition can be beneficial for the treatment of DCM.
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Affiliation(s)
- Keiichi Ito
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan.
| | - Kenichi Hongo
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Taro Date
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Masahiro Ikegami
- Department of Pathology, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Hiroshi Hano
- Department of Pathology, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Mamiko Owada
- Department of Pathology, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Satoshi Morimoto
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Yusuke Kashiwagi
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Daisuke Katoh
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Takuya Yoshino
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Akira Yoshii
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Haruka Kimura
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Tomohisa Nagoshi
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Ichige Kajimura
- Department of Cell Physiology, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Yoichiro Kusakari
- Department of Cell Physiology, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Toru Akaike
- Department of Cell Physiology, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Susumu Minamisawa
- Department of Cell Physiology, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Kazuo Ogawa
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Kosuke Minai
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Takayuki Ogawa
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Makoto Kawai
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Junji Yajima
- Department of Cardiovascular Medicine, The Cardiovascular Institute, 3-2-19, Nishiazabu, Minato-ku, Tokyo 106-0031, Japan
| | - Seiichiro Matsuo
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Teiichi Yamane
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Ikuo Taniguchi
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Sachio Morimoto
- Department of Clinical Pharmacology, Kyushu University Graduate School of Medicine, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Michihiro Yoshimura
- Division of Cardiology, Department of Internal Medicine, The Jikei University School of Medicine, 3-25-8, Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
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Molecular mapping of α-thrombin (αT)/β2-glycoprotein I (β2GpI) interaction reveals how β2GpI affects αT functions. Biochem J 2016; 473:4629-4650. [PMID: 27760842 DOI: 10.1042/bcj20160603] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/07/2016] [Accepted: 10/14/2016] [Indexed: 01/15/2023]
Abstract
β2-Glycoprotein I (β2GpI) is the major autoantigen in the antiphospholipid syndrome, a thrombotic autoimmune disease. Nonetheless, the physiological role of β2GpI is still unclear. In a recent work, we have shown that β2GpI selectively inhibits the procoagulant functions of human α-thrombin (αT; i.e. prolongs fibrin clotting time, tc, and inhibits αT-induced platelet aggregation) without affecting the unique anticoagulant activity of the protease, i.e. the proteolytic generation of the anticoagulant protein C (PC) from the PC zymogen, which interacts with αT exclusively at the protease catalytic site. Here, we used several different biochemical/biophysical techniques and molecular probes for mapping the binding sites in the αT-β2GpI complex. Our results indicate that αT exploits the highly electropositive exosite-II, which is also responsible for anchoring αT on the platelet GpIbα (platelet receptor glycoprotein Ibα) receptor, for binding to a continuous negative region on β2GpI structure, spanning domain IV and (part of) domain V, whereas the protease active site and exosite-I (i.e. the fibrinogen-binding site) remain accessible for substrate/ligand binding. Furthermore, we provided evidence that the apparent increase in tc, previously observed with β2GpI, is more likely caused by alteration in the ensuing fibrin structure rather than by the inhibition of fibrinogen hydrolysis. Finally, we produced a theoretical docking model of αT-β2GpI interaction, which was in agreement with the experimental results. Altogether, these findings help to understand how β2GpI affects αT interactions and suggest that β2GpI may function as a scavenger of αT for binding to the GpIbα receptor, thus impairing platelet aggregation while enabling normal cleavage of fibrinogen and PC.
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Takayama K, Taguchi A, Yakushiji F, Hayashi Y. Identification of a degrading enzyme in human serum that hydrolyzes a C-terminal core sequence of neuromedin U. Biopolymers 2016; 106:440-5. [DOI: 10.1002/bip.22770] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/12/2015] [Accepted: 11/02/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Kentaro Takayama
- Department of Medicinal Chemistry; Tokyo University of Pharmacy and Life Sciences; Horinouchi, Hachioji Tokyo 192-0392 Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry; Tokyo University of Pharmacy and Life Sciences; Horinouchi, Hachioji Tokyo 192-0392 Japan
| | - Fumika Yakushiji
- Department of Medicinal Chemistry; Tokyo University of Pharmacy and Life Sciences; Horinouchi, Hachioji Tokyo 192-0392 Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry; Tokyo University of Pharmacy and Life Sciences; Horinouchi, Hachioji Tokyo 192-0392 Japan
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64
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Pozzi N, Bystranowska D, Zuo X, Di Cera E. Structural Architecture of Prothrombin in Solution Revealed by Single Molecule Spectroscopy. J Biol Chem 2016; 291:18107-16. [PMID: 27435675 DOI: 10.1074/jbc.m116.738310] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Indexed: 01/29/2023] Open
Abstract
The coagulation factor prothrombin has a complex spatial organization of its modular assembly that comprises the N-terminal Gla domain, kringle-1, kringle-2, and the C-terminal protease domain connected by three intervening linkers. Here we use single molecule Förster resonance energy transfer to access the conformational landscape of prothrombin in solution and uncover structural features of functional significance that extend recent x-ray crystallographic analysis. Prothrombin exists in equilibrium between two alternative conformations, open and closed. The closed conformation predominates (70%) and features an unanticipated intramolecular collapse of Tyr(93) in kringle-1 onto Trp(547) in the protease domain that obliterates access to the active site and protects the zymogen from autoproteolytic conversion to thrombin. The open conformation (30%) is more susceptible to chymotrypsin digestion and autoactivation, and features a shape consistent with recent x-ray crystal structures. Small angle x-ray scattering measurements of prothrombin wild type stabilized 70% in the closed conformation and of the mutant Y93A stabilized 80% in the open conformation directly document two envelopes that differ 50 Å in length. These findings reveal important new details on the conformational plasticity of prothrombin in solution and the drastic structural difference between its alternative conformations. Prothrombin uses the intramolecular collapse of kringle-1 onto the active site in the closed form to prevent autoactivation. The open-closed equilibrium also defines a new structural framework for the mechanism of activation of prothrombin by prothrombinase.
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Affiliation(s)
- Nicola Pozzi
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104 and
| | - Dominika Bystranowska
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104 and
| | - Xiaobing Zuo
- the X-Ray Science Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104 and
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65
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Bowerman S, Wereszczynski J. Detecting Allosteric Networks Using Molecular Dynamics Simulation. Methods Enzymol 2016; 578:429-47. [PMID: 27497176 DOI: 10.1016/bs.mie.2016.05.027] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules.
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Affiliation(s)
- S Bowerman
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States
| | - J Wereszczynski
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States.
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66
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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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67
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Patel NR, Patel DV, Murumkar PR, Yadav MR. Contemporary developments in the discovery of selective factor Xa inhibitors: A review. Eur J Med Chem 2016; 121:671-698. [PMID: 27322757 DOI: 10.1016/j.ejmech.2016.05.039] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/25/2016] [Accepted: 05/19/2016] [Indexed: 11/25/2022]
Abstract
Thrombosis is a leading cause of death in cardiovascular diseases such as myocardial infarction (MI), unstable angina and acute coronary syndrome (ACS) in the industrialized world. Venous thromboembolism is observed in about 1 million people every year in United States causing significant morbidity and mortality. Conventional antithrombotic therapy has been reported to have several disadvantages and limitations like inconvenience in oral administration, bleeding risks (heparin analogs), narrow therapeutic window and undesirable interactions with food and drugs (vitamin K antagonist-warfarin). The unmet medical demand for orally active safe anticoagulants has generated widespread interest among the medicinal chemists engaged in this field. To modulate blood coagulation, various enzymes involved in the coagulation process have received great attention as potential targets by various research groups for the development of oral anticoagulants. Among these enzymes, factor Xa (FXa) has remained the centre of attention in the last decade. Intensive research efforts have been made by various research groups for the development of small, safe and orally bioavailable FXa inhibitors. This review is an attempt to compile the research work of various researchers in the direction of development of FXa inhibitors reported since 2010 onward.
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Affiliation(s)
- Nirav R Patel
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India
| | - Dushyant V Patel
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India
| | - Prashant R Murumkar
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India
| | - Mange Ram Yadav
- Faculty of Pharmacy, Kalabhavan Campus, The Maharaja Sayajirao University of Baroda, Vadodara 390001, Gujarat, India.
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Bulato C, Radu CM, Campello E, Gavasso S, Spiezia L, Tormene D, Simioni P. New Prothrombin Mutation (Arg596Trp, Prothrombin Padua 2) Associated With Venous Thromboembolism. Arterioscler Thromb Vasc Biol 2016; 36:1022-9. [DOI: 10.1161/atvbaha.115.306914] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 03/14/2016] [Indexed: 11/16/2022]
Abstract
Objective—
Two different prothrombin variants, p.Arg596Leu and p.Arg596Gln, conferring antithrombin resistance to patients with venous thromboembolism have been recently reported. Here, we describe a novel substitution affecting Arg596 of prothrombin molecule (Arginine596 to Tryptophan or p.Arg596Trp or Arg221aTrp in the chymotrypsinogen numbering system or prothrombin Padua 2) in 2 Italian families with venous thromboembolism.
Approach and Results—
Prothrombin Padua 2 has been characterized either in plasma of carriers or using Arg596Trp recombinant prothrombin. Routine coagulation tests, thrombin generation, and antithrombin resistance tests were performed, as well as measurement of the levels of thrombin–antithrombin complexes. All carriers were heterozygotes and presented with a mild reduction of the prothrombin activity. Thrombin generation in carriers showed only a markedly prolonged decay. This finding was confirmed in plasma reconstituted with Arg596Trp recombinant prothrombin mimicking a homozygous condition, which showed longer decay and higher endogenous thrombin potential in thrombin generation than wild-type recombinant prothrombin reconstituted plasma. Patient’s plasma as well as Arg596Trp recombinant prothrombin showed a clear thrombin resistance to antithrombin inactivation. These findings were supported by the assessment of thrombin–antithrombin complexes formation, which was strongly reduced for Arg596Trp recombinant prothrombin as compared with wild-type recombinant prothrombin. In a series of 400 unrelated consecutive patients with venous thromboembolism, 2 carriers of prothrombin Padua 2 were found (estimated prevalence of 0.5%).
Conclusions—
Our study showed that prothrombin Padua 2 induces antithrombin resistance and is associated with an increased risk of venous thromboembolism. Codon 596 (CGG) of prothrombin is a hot spot for mutations, which constitute a new and relatively frequent cause of inherited thrombophilia.
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Affiliation(s)
- Cristiana Bulato
- From the Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Hemophilia and Thrombophilia Center, University of Padua Medical School, Padua, Italy
| | - Claudia Maria Radu
- From the Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Hemophilia and Thrombophilia Center, University of Padua Medical School, Padua, Italy
| | - Elena Campello
- From the Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Hemophilia and Thrombophilia Center, University of Padua Medical School, Padua, Italy
| | - Sabrina Gavasso
- From the Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Hemophilia and Thrombophilia Center, University of Padua Medical School, Padua, Italy
| | - Luca Spiezia
- From the Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Hemophilia and Thrombophilia Center, University of Padua Medical School, Padua, Italy
| | - Daniela Tormene
- From the Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Hemophilia and Thrombophilia Center, University of Padua Medical School, Padua, Italy
| | - Paolo Simioni
- From the Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Veneto Region Hemophilia and Thrombophilia Center, University of Padua Medical School, Padua, Italy
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69
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Sokolov AV, Acquasaliente L, Kostevich VA, Frasson R, Zakharova ET, Pontarollo G, Vasilyev VB, De Filippis V. Thrombin inhibits the anti-myeloperoxidase and ferroxidase functions of ceruloplasmin: relevance in rheumatoid arthritis. Free Radic Biol Med 2015; 86:279-94. [PMID: 26001728 DOI: 10.1016/j.freeradbiomed.2015.05.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 04/24/2015] [Accepted: 05/12/2015] [Indexed: 01/29/2023]
Abstract
Human ceruloplasmin (CP) is a multifunctional copper-binding protein produced in the liver. CP oxidizes Fe(2+) to Fe(3+), decreasing the concentration of Fe(2+) available for generating harmful oxidant species. CP is also a potent inhibitor of leukocyte myeloperoxidase (MPO) (Kd=130nM), a major source of oxidants in vivo. Rheumatoid arthritis (RA) is an inflammatory autoimmune disease affecting flexible joints and characterized by activation of both inflammatory and coagulation processes. Indeed, the levels of CP, MPO, and thrombin are markedly increased in the synovial fluid of RA patients. Here we show that thrombin cleaves CP in vitro at (481)Arg-Ser(482) and (887)Lys-Val(888) bonds, generating a nicked species that retains the native-like fold and the ferroxidase activity of the intact protein, whereas the MPO inhibitory function of CP is abrogated. Analysis of the synovial fluid of 24 RA patients reveals that CP is proteolytically degraded to a variable extent, with a fragmentation pattern similar to that observed with thrombin in vitro, and that proteolysis is blocked by hirudin, a highly potent and specific thrombin inhibitor. Using independent biophysical techniques, we show that thrombin has intrinsic affinity for CP (Kd=60-270nM), independent of proteolysis, and inhibits CP ferroxidase activity (KI=220±20nM). Mapping of thrombin binding sites with specific exosite-directed ligands (i.e., hirugen, fibrinogen γ'-peptide) and thrombin analogues having the exosites variably compromised (i.e., prothrombin, prethrombin-2, βT-thrombin) reveals that the positively charged exosite-II of thrombin binds to the negatively charged upper region of CP, while the protease active site and exosite-I remain accessible. These results suggest that thrombin can exacerbate inflammation in RA by impairing the MPO inhibitory function of CP via proteolysis and by competitively inhibiting CP ferroxidase activity. Notably, local administration of hirudin, a highly potent and specifc thrombin inhibitor, reduces the concentration of active MPO in the synovial fluid of RA patients and has a beneficial effect on the clinical symptoms of the disease.
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Affiliation(s)
- Alexej V Sokolov
- Institute for Experimental Medicine, Pavlov str., 12, Saint Petersburg, 197376 Russia; State University of Saint Petersburg, University Embankment, 4-7, Saint Petersburg, 199034 Russia
| | - Laura Acquasaliente
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo, 5, Padua, 35131 Italy
| | - Valeria A Kostevich
- Institute for Experimental Medicine, Pavlov str., 12, Saint Petersburg, 197376 Russia
| | - Roberta Frasson
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo, 5, Padua, 35131 Italy
| | - Elena T Zakharova
- Institute for Experimental Medicine, Pavlov str., 12, Saint Petersburg, 197376 Russia
| | - Giulia Pontarollo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo, 5, Padua, 35131 Italy
| | - Vadim B Vasilyev
- Institute for Experimental Medicine, Pavlov str., 12, Saint Petersburg, 197376 Russia; State University of Saint Petersburg, University Embankment, 4-7, Saint Petersburg, 199034 Russia
| | - Vincenzo De Filippis
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, via Marzolo, 5, Padua, 35131 Italy.
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70
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Vogt AD, Chakraborty P, Di Cera E. Kinetic dissection of the pre-existing conformational equilibrium in the trypsin fold. J Biol Chem 2015. [PMID: 26216877 DOI: 10.1074/jbc.m115.675538] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structural biology has recently documented the conformational plasticity of the trypsin fold for both the protease and zymogen in terms of a pre-existing equilibrium between closed (E*) and open (E) forms of the active site region. How such plasticity is manifested in solution and affects ligand recognition by the protease and zymogen is poorly understood in quantitative terms. Here we dissect the E*-E equilibrium with stopped-flow kinetics in the presence of excess ligand or macromolecule. Using the clotting protease thrombin and its zymogen precursor prethrombin-2 as relevant models we resolve the relative distribution of the E* and E forms and the underlying kinetic rates for their interconversion. In the case of thrombin, the E* and E forms are distributed in a 1:4 ratio and interconvert on a time scale of 45 ms. In the case of prethrombin-2, the equilibrium is shifted strongly (10:1 ratio) in favor of the closed E* form and unfolds over a faster time scale of 4.5 ms. The distribution of E* and E forms observed for thrombin and prethrombin-2 indicates that zymogen activation is linked to a significant shift in the pre-existing equilibrium between closed and open conformations that facilitates ligand binding to the active site. These findings broaden our mechanistic understanding of how conformational transitions control ligand recognition by thrombin and its zymogen precursor prethrombin-2 and have direct relevance to other members of the trypsin fold.
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Affiliation(s)
- Austin D Vogt
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Pradipta Chakraborty
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Enrico Di Cera
- From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
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71
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Müller A, König B. Vesicular aptasensor for the detection of thrombin. Chem Commun (Camb) 2015; 50:12665-8. [PMID: 25205174 DOI: 10.1039/c4cc05221h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Self-assembled phospholipid vesicles are functionalized with thrombin-binding aptamers using a thiol-click reaction. The resulting aptasensors signal the binding of the analyte to the vesicle surface by changes of the emission properties of membrane co-embedded reporter dyes.
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Affiliation(s)
- Andreas Müller
- Institut für Organische Chemie, Universität Regensburg, 93040 Regensburg, Germany.
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72
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The structure–function relationship of thrombin-like enzymes from the green pit viper (Trimeresurus albolabris). Toxicon 2015; 100:53-9. [DOI: 10.1016/j.toxicon.2015.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 04/06/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
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73
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Pelc LA, Chen Z, Gohara DW, Vogt AD, Pozzi N, Di Cera E. Why Ser and not Thr brokers catalysis in the trypsin fold. Biochemistry 2015; 54:1457-64. [PMID: 25664608 DOI: 10.1021/acs.biochem.5b00014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although Thr is equally represented as Ser in the human genome and as a nucleophile is as good as Ser, it is never found in the active site of the large family of trypsin-like proteases that utilize the Asp/His/Ser triad. The molecular basis of the preference of Ser over Thr in the trypsin fold was investigated with X-ray structures of the thrombin mutant S195T free and bound to an irreversible active site inhibitor. In the free form, the methyl group of T195 is oriented toward the incoming substrate in a conformation seemingly incompatible with productive binding. In the bound form, the side chain of T195 is reoriented for efficient substrate acylation without causing steric clash within the active site. Rapid kinetics prove that this change is due to selection of an active conformation from a preexisting ensemble of reactive and unreactive rotamers whose relative distribution determines the level of activity of the protease. Consistent with these observations, the S195T substitution is associated with a weak yet finite activity that allows identification of an unanticipated important role for S195 as the end point of allosteric transduction in the trypsin fold. The S195T mutation abrogates the Na(+)-dependent enhancement of catalytic activity in thrombin, activated protein C, and factor Xa and significantly weakens the physiologically important allosteric effects of thrombomodulin on thrombin and of cofactor Va on factor Xa. The evolutionary selection of Ser over Thr in trypsin-like proteases was therefore driven by the need for high catalytic activity and efficient allosteric regulation.
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Affiliation(s)
- Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , St. Louis, Missouri 63104, United States
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74
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Fernandes LG, de Morais ZM, Vasconcellos SA, Nascimento ALTO. Leptospira interrogans reduces fibrin clot formation by modulating human thrombin activity via exosite I. Pathog Dis 2015; 73:ftv001. [PMID: 25834144 DOI: 10.1093/femspd/ftv001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2014] [Indexed: 01/08/2023] Open
Abstract
Pathogenic bacteria of the genus Leptospira are the etiological agents of leptospirosis, a disease that affects humans and animals worldwide. Although there are an increasing number of studies on the biology of Leptospira, the mechanisms of pathogenesis are not yet understood. We report in this work that Leptospira interrogans FIOCRUZ L1-130 virulent, M20 culture attenuated and the saprophyte L. biflexa Patoc 1 strains do not bind prothrombin. Leptospiral binding to thrombin was detected with the virulent, followed by culture-attenuated M20, and practically none was observed with the saprophyte strain. The interaction of Leptospira with thrombin mostly occurs via exosite I, with a minor participation of catalytic site, as determined by employing the thrombin inhibitors hirugen, hirudin and argatroban. Leptospira interrogans binding to thrombin inhibits its catalytic activity reducing fibrin clot formation in thrombin-catalyzed reaction of fibrinogen. This inhibition was more efficient with the virulent FIOCRUZ L1-130 than with the M20 culture attenuated, while none was seen with the saprophyte strain, suggesting that this binding might be important for bacterial virulence. This is the first study reporting the binding of pathogenic Leptospira to thrombin promoting a decrease in fibrin clotting that could lead to hemorrhage, helping bacteria dissemination.
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Affiliation(s)
- Luis G Fernandes
- Centro de Biotecnologia, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, SP 05503-900, Brazil Programa de Pós-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, USP, São Paulo 05508-900, Brazil
| | - Zenaide M de Morais
- Laboratório de Zoonoses Bacterianas do VPS, Faculdade de MedicinaVeterinária e Zootecnia da Universidade de São Paulo, São Paulo 05508-270, Brazil
| | - Silvio A Vasconcellos
- Laboratório de Zoonoses Bacterianas do VPS, Faculdade de MedicinaVeterinária e Zootecnia da Universidade de São Paulo, São Paulo 05508-270, Brazil
| | - Ana L T O Nascimento
- Centro de Biotecnologia, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, SP 05503-900, Brazil Programa de Pós-Graduação Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, USP, São Paulo 05508-900, Brazil
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75
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Chen J, Vemuri C, Palekar RU, Gaut JP, Goette M, Hu L, Cui G, Zhang H, Wickline SA. Antithrombin nanoparticles improve kidney reperfusion and protect kidney function after ischemia-reperfusion injury. Am J Physiol Renal Physiol 2015; 308:F765-73. [PMID: 25651565 DOI: 10.1152/ajprenal.00457.2014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 01/20/2015] [Indexed: 01/24/2023] Open
Abstract
In the extension phase of acute kidney injury, microvascular thrombosis, inflammation, vasoconstriction, and vascular endothelial cell dysfunction promote progressive damage to renal parenchyma after reperfusion. In this study, we hypothesized that direct targeting and pharmaceutical knockdown of activated thrombin at the sites of injury with a selective nanoparticle (NP)-based thrombin inhibitor, PPACK (phenylalanine-proline-arginine-chloromethylketone), would improve kidney reperfusion and protect renal function after transient warm ischemia in rodent models. Saline- or plain NP-treated animals were employed as controls. In vivo 19F magnetic resonance imaging revealed that kidney nonreperfusion was evident within 3 h after global kidney reperfusion at 34 ± 13% area in the saline group and 43 ± 12% area in the plain NP group and substantially reduced to 17 ± 4% (∼50% decrease, P < 0.05) in the PPACK NP pretreatment group. PPACK NP pretreatment prevented an increase in serum creatinine concentration within 24 h after ischemia-reperfusion, reflecting preserved renal function. Histologic analysis illustrated substantially reduced intrarenal thrombin accumulation within 24 h after reperfusion for PPACK NP-treated kidneys (0.11% ± 0.06%) compared with saline-treated kidneys (0.58 ± 0.37%). These results suggest a direct role for thrombin in the pathophysiology of AKI and a nanomedicine-based preventative strategy for improving kidney reperfusion after transient warm ischemia.
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Affiliation(s)
- Junjie Chen
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Chandu Vemuri
- Department of Medicine, Washington University, St. Louis, Missouri; Department of Surgery, Washington University, St. Louis, Missouri
| | - Rohun U Palekar
- Department of Medicine, Washington University, St. Louis, Missouri; Department of Biomedical Engineering, Washington University, St. Louis, Missouri; and
| | - Joseph P Gaut
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri
| | - Matthew Goette
- Department of Medicine, Washington University, St. Louis, Missouri; Department of Biomedical Engineering, Washington University, St. Louis, Missouri; and
| | - Lingzhi Hu
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Grace Cui
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Huiying Zhang
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Samuel A Wickline
- Department of Medicine, Washington University, St. Louis, Missouri; Department of Biomedical Engineering, Washington University, St. Louis, Missouri; and
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76
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Macazo F, Karpel RL, White RJ. Monitoring cooperative binding using electrochemical DNA-based sensors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:868-75. [PMID: 25517392 PMCID: PMC4303326 DOI: 10.1021/la504083c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/15/2014] [Indexed: 05/20/2023]
Abstract
Electrochemical DNA-based (E-DNA) sensors are utilized to detect a variety of targets including complementary DNA, small molecules, and proteins. These sensors typically employ surface-bound single-stranded oligonucleotides that are modified with a redox-active molecule on the distal 3' terminus. Target-induced flexibility changes of the DNA probe alter the efficiency of electron transfer between the redox active methylene blue and the electrode surface, allowing for quantitative detection of target concentration. While numerous studies have utilized the specific and sensitive abilities of E-DNA sensors to quantify target concentration, no studies to date have demonstrated the ability of this class of collision-based sensors to elucidate biochemical-binding mechanisms such as cooperativity. In this study, we demonstrate that E-DNA sensors fabricated with various lengths of surface-bound oligodeoxythymidylate [(dT)n] sensing probes are able to quantitatively distinguish between cooperative and noncooperative binding of a single-stranded DNA-binding protein. Specifically, we demonstrate that oligo(dT) E-DNA sensors are able to quantitatively detect nM levels (50 nM-4 μM) of gene 32 protein (g32p). Furthermore, the sensors exhibit signal that is able to distinguish between the cooperative binding of the full-length g32p and the noncooperative binding of the core domain (*III) fragment to single-stranded DNA. Finally, we demonstrate that this binding is both probe-length- and ionic-strength-dependent. This study illustrates a new quantitative property of this powerful class of biosensor and represents a rapid and simple methodology for understanding protein-DNA binding mechanisms.
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Affiliation(s)
- Florika
C. Macazo
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
| | - Richard L. Karpel
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
| | - Ryan J. White
- Department
of Chemistry and Biochemistry, University
of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, United
States
- E-mail:
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77
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Multiple inhibitory kinetics reveal an allosteric interplay among thrombin functional sites. Thromb Res 2015; 135:212-6. [DOI: 10.1016/j.thromres.2014.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/20/2014] [Accepted: 11/10/2014] [Indexed: 11/19/2022]
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78
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Skala W, Utzschneider DT, Magdolen V, Debela M, Guo S, Craik CS, Brandstetter H, Goettig P. Structure-function analyses of human kallikrein-related peptidase 2 establish the 99-loop as master regulator of activity. J Biol Chem 2014; 289:34267-83. [PMID: 25326387 PMCID: PMC4256358 DOI: 10.1074/jbc.m114.598201] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Human kallikrein-related peptidase 2 (KLK2) is a tryptic serine protease predominantly expressed in prostatic tissue and secreted into prostatic fluid, a major component of seminal fluid. Most likely it activates and complements chymotryptic KLK3 (prostate-specific antigen) in cleaving seminal clotting proteins, resulting in sperm liquefaction. KLK2 belongs to the “classical” KLKs 1–3, which share an extended 99- or kallikrein loop near their non-primed substrate binding site. Here, we report the 1.9 Å crystal structures of two KLK2-small molecule inhibitor complexes. In both structures discontinuous electron density for the 99-loop indicates that this loop is largely disordered. We provide evidence that the 99-loop is responsible for two biochemical peculiarities of KLK2, i.e. reversible inhibition by micromolar Zn2+ concentrations and permanent inactivation by autocatalytic cleavage. Indeed, several 99-loop mutants of KLK2 displayed an altered susceptibility to Zn2+, which located the Zn2+ binding site at the 99-loop/active site interface. In addition, we identified an autolysis site between residues 95e and 95f in the 99-loop, whose elimination prevented the mature enzyme from limited autolysis and irreversible inactivation. An exhaustive comparison of KLK2 with related structures revealed that in the KLK family the 99-, 148-, and 220-loop exist in open and closed conformations, allowing or preventing substrate access, which extends the concept of conformational selection in trypsin-related proteases. Taken together, our novel biochemical and structural data on KLK2 identify its 99-loop as a key player in activity regulation.
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Affiliation(s)
- Wolfgang Skala
- From the Division of Structural Biology, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Daniel T Utzschneider
- Klinische Forschergruppe der Frauenklinik, Klinikum rechts der Isar der TU München, D-81675 Munich, Germany
| | - Viktor Magdolen
- Klinische Forschergruppe der Frauenklinik, Klinikum rechts der Isar der TU München, D-81675 Munich, Germany
| | - Mekdes Debela
- Max-Planck-Institut for Biochemistry, Proteinase Research Group, D-82152 Martinsried, Germany, and
| | - Shihui Guo
- From the Division of Structural Biology, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Hans Brandstetter
- From the Division of Structural Biology, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria
| | - Peter Goettig
- From the Division of Structural Biology, Department of Molecular Biology, University of Salzburg, A-5020 Salzburg, Austria,
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79
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Antithrombin-resistant prothrombin Yukuhashi mutation also causes thrombomodulin resistance in fibrinogen clotting but not in protein C activation. Thromb Res 2014; 134:914-7. [DOI: 10.1016/j.thromres.2014.07.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 06/16/2014] [Accepted: 07/28/2014] [Indexed: 11/21/2022]
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80
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Boechi L, Pierce L, Komives EA, McCammon JA. Trypsinogen activation as observed in accelerated molecular dynamics simulations. Protein Sci 2014; 23:1550-8. [PMID: 25131668 DOI: 10.1002/pro.2532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Revised: 06/17/2014] [Accepted: 08/03/2014] [Indexed: 11/07/2022]
Abstract
Serine proteases are involved in many fundamental physiological processes, and control of their activity mainly results from the fact that they are synthetized in an inactive form that becomes active upon cleavage. Three decades ago Martin Karplus's group performed the first molecular dynamics simulations of trypsin, the most studied member of the serine protease family, to address the transition from the zymogen to its active form. Based on the computational power available at the time, only high frequency fluctuations, but not the transition steps, could be observed. By performing accelerated molecular dynamics (aMD) simulations, an interesting approach that increases the configurational sampling of atomistic simulations, we were able to observe the N-terminal tail insertion, a crucial step of the transition mechanism. Our results also support the hypothesis that the hydrophobic effect is the main force guiding the insertion step, although substantial enthalpic contributions are important in the activation mechanism. As the N-terminal tail insertion is a conserved step in the activation of serine proteases, these results afford new perspective on the underlying thermodynamics of the transition from the zymogen to the active enzyme.
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Affiliation(s)
- Leonardo Boechi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
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81
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Factor X M402T: a homozygous missense mutation identified as the cause of cross-reacting material-reduced deficiency. Int J Hematol 2014; 100:345-52. [PMID: 25064371 DOI: 10.1007/s12185-014-1643-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 07/10/2014] [Accepted: 07/11/2014] [Indexed: 10/25/2022]
Abstract
We investigated a mildly hemorrhagic patient with factor X (FX) deficiency to identify the nature of his defect by comprehensive analyses. A 42-year-old Japanese man was admitted to our hospital for uncontrolled gingival hemorrhage. His FX activity based on prothrombin time (PT) and activated partial thromboplastin time (aPTT) and FX antigen were <1, 6.5 and 11 %, respectively. A homozygous M402T missense mutation (c.1205 t>c; p.Met402Thr) was identified in the FX gene (F10) from both the patient and his brother. The mutation was not detected in the F10 of 82 unrelated normal Japanese individuals. We studied the functional consequences of this mutation by expressing mutant FX-M402T protein in HEK293 cells. This analysis revealed that the antigen of the FX-M402T mutants was approximately 26 % that of the wild-type FX in conditioned media. The FX-specific activity of FX-M402T mutants measured by a one-stage clotting assay based upon PT and aPTT, and a chromogenic assay using Russell's viper venom in the concentrated media was 7.7, 31.7, and 41.2 % of wild type, respectively. The results suggest that the mutation FX-M402T may cause a secretion defect and a molecular abnormality in FX.
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82
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A new peptide (Ruviprase) purified from the venom of Daboia russelii russelii shows potent anticoagulant activity via non-enzymatic inhibition of thrombin and factor Xa. Biochimie 2014; 105:149-58. [PMID: 25038567 DOI: 10.1016/j.biochi.2014.07.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/07/2014] [Indexed: 12/24/2022]
Abstract
Compounds showing dual inhibition of thrombin and factor Xa (FXa) are the subject of great interest owing to their broader specificity for effective anticoagulation therapy against cardiovascular disorders. This is the first report on the functional characterization and assessment of therapeutic potential of a 4423.6 Da inhibitory peptide (Ruviprase) purified from Daboia russelii russelii venom. The secondary structure of Ruviprase is composed of α-helices (61.9%) and random coils (38.1%). The partial N-terminal sequence (E(1)-V(2)-X(3)-W(4)-W(5)-W(6)-A(7)-Q(8)-L(9)-S(10)) of Ruviprase demonstrated significant similarity (80.0%) with an internal sequence of apoptosis-stimulating protein reported from the venom of Ophiophagus hannah and Python bivittatus; albeit Ruviprase did not show sequence similarity with existing thrombin/FXa inhibitors, suggesting its uniqueness. Ruviprase demonstrated a potent in vitro anticoagulant property and inhibited both thrombin and FXa following slow binding kinetics. Ruviprase inhibited thrombin by binding to its active site via an uncompetitive mechanism with a Ki value and dissociation constant (KD) of 0.42 μM and 0.46 μM, respectively. Conversely, Ruviprase demonstrated mixed inhibition (Ki = 0.16 μM) of FXa towards its physiological substrate prothrombin. Furthermore, the biological properties of Ruviprase could not be neutralized by commercial polyvalent or monovalent antivenom. Ruviprase at a dose of 2.0 mg/kg was non-toxic and showed potent in vivo anticoagulant activity after 6 h of intraperitoneal treatment in mice. Because of the potent anticoagulant property as well as non-toxic nature of Ruviprase, the possible application of the peptide as an antithrombotic agent for combating thrombosis-associated ailments appears promising.
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83
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Sheffield WP, Lambourne MD, Eltringham-Smith LJ, Bhakta V, Arnold DM, Crowther MA. γT -S195A thrombin reduces the anticoagulant effects of dabigatran in vitro and in vivo. J Thromb Haemost 2014; 12:1110-5. [PMID: 24815541 DOI: 10.1111/jth.12601] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 05/05/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Dabigatran etexilate (DE) is an oral direct thrombin inhibitor used to prevent strokes in patients with atrial fibrillation. No licensed DE antidote is currently available. We hypothesized that active site-mutated S195A thrombin (S195A-IIa) and/or its trypsinized derivative (γT -S195A-IIa) would sequester dabigatran, the active form of DE, and reduce its anticoagulant effects. OBJECTIVE To assess active site-mutated S195A or γT -S195A-IIa as dabigatran reversal agents in vitro and in vivo. METHODS Diluted thrombin time (dTT) assays were performed using human or murine plasma containing dabigatran, combined with S195A-IIa, γT -S195A-IIa or FPR-chloromethyl ketone-treated thrombin (FPR-IIa). Bleeding times were determined in anesthetized DE-treated mice also receiving γT -S195A-IIa or vehicle 15 min prior to tail transection. The time to occlusion of carotid arteries of DE-treated mice also receiving S195A-IIa, γT -S195A-IIa, prothrombin complex concentrate (PCC) or vehicle, 15 min prior to topical FeCl3 , was determined using Doppler ultrasound. RESULTS γT-S195A-IIa reduced dTT values of dabigatran-containing human and murine plasma more effectively than S195-IIa; FPR-IIa had no effect. A dose of 13 mg kg(-1) DE abrogated occlusive thrombus formation in the carotid arteries of FeCl3 -treated mice; γT -S195A-IIa (6 mg kg(-1) ) or PCC (14.3 IU kg(-1) ), but not saline vehicle or S195A-IIa (6 mg kg(-1) ), was equally effective in restoring thrombus formation. Bleeding times of mice treated with 60 mg kg(-1) DE and γT -S195A-IIa (6 mg kg(-1) ) or saline vehicle did not differ. CONCLUSIONS Our data suggest that γT -S195A-IIa decreases the anticoagulant effects of dabigatran in vitro and is partially effective at restoring hemostasis-related thrombus formation in DE-treated mice in vivo.
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Affiliation(s)
- W P Sheffield
- Canadian Blood Services, Centre for Innovation, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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84
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Alberelli MA, De Candia E. Functional role of protease activated receptors in vascular biology. Vascul Pharmacol 2014; 62:72-81. [PMID: 24924409 DOI: 10.1016/j.vph.2014.06.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/30/2014] [Accepted: 06/01/2014] [Indexed: 01/22/2023]
Abstract
Protease activated receptors (PARs) are a small family of G protein-coupled receptors (GPCR) mediating the cellular effects of some proteases of the coagulation system, such as thrombin, or other proteases, such as trypsin or metalloproteinase 1. As the prototype of PARs, PAR1 is a seven transmembrane GPCR that, upon cleavage by thrombin, unmasks a new amino-terminus able to bind intramolecularly to PAR1 itself thus inducing signaling. In the vascular system, thrombin and other proteases of the coagulation-fibrinolysis system, such as plasmin, factor VIIa and factor Xa, activated protein C, are considered physiologically relevant agonists, and PARs appear to largely account for the cellular effects of these enzymes. In the vasculature, PARs are expressed on platelets, endothelial cells (ECs) and vascular smooth muscle cells (VSMCs). In the vessel wall, under physiological conditions, PARs are mainly expressed in ECs and participate in the regulation of vascular tone, by inducing endothelium-dependent relaxation. PAR activation on ECs promotes conversion of these cells into a proinflammatory phenotype, causes increase of vascular permeability, and the exposure/secretion of proteins and cytokines mediating the local accumulation of platelets and leukocytes. These effects contribute to the vascular consequences of sepsis and of diseases such as acute lung injury and acute respiratory distress syndrome. In normal arteries PARs are to a much lesser amount expressed on VSMCs. However, in conditions associated with endothelial dysfunction, PARs mediate contraction, proliferation, migration, hypertrophy of VSMCs and their production of extracellular matrix, thereby contributing to the pathophysiology of atherosclerosis and hypertension. Inhibition of protease-PAR interaction might thus become a potential therapeutic target in various vascular diseases.
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Affiliation(s)
- Maria Adele Alberelli
- Hemostasis and Thrombosis Unit, Department of Internal Medicine, Agostino Gemelli Hospital School of Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Erica De Candia
- Hemostasis and Thrombosis Unit, Department of Internal Medicine, Agostino Gemelli Hospital School of Medicine, Università Cattolica del Sacro Cuore, Rome, Italy.
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85
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Nair DG, Narayanan SP, Chittalakkottu S. Interactions of some commonly used drugs with human α-thrombin. J Biomol Struct Dyn 2014; 33:1008-15. [PMID: 24819365 DOI: 10.1080/07391102.2014.923329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Adverse side effects of drugs are often caused by the interaction of drug molecules to targets other than the intended ones. In this study, we investigated the off-target interactions of some commercially available drugs with human α-thrombin. The drugs used in the study were selected from Super Drug Database based on the structural similarity to a known thrombin inhibitor argatroban. Interactions of these drugs with thrombin were initially checked by in silico docking studies and then confirmed by thrombin inhibition assay using a fluorescence microplate-based method. Results show that the three commonly used drugs piperacillin (anti-bacterial), azlocillin (anti-bacterial), and metolazone (anti-hypertensive and diuretic) have thrombin inhibitory activity almost similar to that of argatroban. The Ki values of piperacillin, azlocillin, and metolazone with thrombin are .55, .95, and .62 nM, respectively. The IC50 values of piperacillin, azlocillin, and metolazone with thrombin are 1.7, 2.9, and 1.92 nM, respectively. This thrombin inhibitory activity might be a reason for the observed side effects of these drugs related to blood coagulation and other thrombin activities. Furthermore, these compounds (drugs) may be used as anti-coagulants as such or with structural modifications.
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Affiliation(s)
- Divya Gopalakrishnan Nair
- a Department of Biotechnology and Microbiology , Kannur University , Thalassery Campus, Palayad P.O., Kannur , Kerala 670661 , India
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86
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Gray K, Elghadban S, Thongyoo P, Owen KA, Szabo R, Bugge TH, Tate EW, Leatherbarrow RJ, Ellis V. Potent and specific inhibition of the biological activity of the type-II transmembrane serine protease matriptase by the cyclic microprotein MCoTI-II. Thromb Haemost 2014; 112:402-11. [PMID: 24696092 DOI: 10.1160/th13-11-0895] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 03/10/2014] [Indexed: 12/14/2022]
Abstract
Matriptase is a type-II transmembrane serine protease involved in epithelial homeostasis in both health and disease, and is implicated in the development and progression of a variety of cancers. Matriptase mediates its biological effects both via as yet undefined substrates and pathways, and also by proteolytic cleavage of a variety of well-defined protein substrates, several of which it shares with the closely-related protease hepsin. Development of targeted therapeutic strategies will require discrimination between these proteases. Here we have investigated cyclic microproteins of the squash Momordica cochinchinensis trypsin-inhibitor family (generated by total chemical synthesis) and found MCoTI-II to be a high-affinity (Ki 9 nM) and highly selective (> 1,000-fold) inhibitor of matriptase. MCoTI-II efficiently inhibited the proteolytic activation of pro-hepatocyte growth factor (HGF) by matriptase but not by hepsin, in both purified and cell-based systems, and inhibited HGF-dependent cell scattering. MCoTI-II also selectively inhibited the invasion of matriptase-expressing prostate cancer cells. Using a model of epithelial cell tight junction assembly, we also found that MCoTI-II could effectively inhibit the re-establishment of tight junctions and epithelial barrier function in MDCK-I cells after disruption, consistent with the role of matriptase in regulating epithelial integrity. Surprisingly, MCoTI-II was unable to inhibit matriptase-dependent proteolytic activation of prostasin, a GPI-anchored serine protease also implicated in epithelial homeostasis. These observations suggest that the unusually high selectivity afforded by MCoTI-II and its biological effectiveness might represent a useful starting point for the development of therapeutic inhibitors, and further highlight the role of matriptase in epithelial maintenance.
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Affiliation(s)
| | | | | | | | | | | | | | | | - V Ellis
- Vincent Ellis, PhD, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK, Tel.: +44 1603 592570, E-mail:
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87
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Menegatti M, Vangone A, Palla R, Milano G, Cavallo L, Oliva R, De Cristofaro R, Peyvandi F. A recurrent Gly43Asp substitution in coagulation Factor X rigidifies its catalytic pocket and impairs catalytic activity and intracellular trafficking. Thromb Res 2014; 133:481-7. [DOI: 10.1016/j.thromres.2013.12.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 11/28/2013] [Accepted: 12/16/2013] [Indexed: 11/30/2022]
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88
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Huntington JA. Natural inhibitors of thrombin. Thromb Haemost 2014; 111:583-9. [PMID: 24477356 DOI: 10.1160/th13-10-0811] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/31/2013] [Indexed: 11/05/2022]
Abstract
The serine protease thrombin is the effector enzyme of blood coagulation. It has many activities critical for the formation of stable clots, including cleavage of fibrinogen to fibrin, activation of platelets and conversion of procofactors to active cofactors. Thrombin carries-out its multiple functions by utilising three special features: a deep active site cleft and two anion binding exosites (exosite I and II). Similarly, thrombin inhibitors have evolved to exploit the unique features of thrombin to achieve rapid and specific inactivation of thrombin. Exogenous thrombin inhibitors come from several different protein families and are generally found in the saliva of haematophagous animals (blood suckers) as part of an anticoagulant cocktail that allows them to feed. Crystal structures of several of these inhibitors reveal how peptides and proteins can be targeted to thrombin in different and interesting ways. Thrombin activity must also be regulated by endogenous inhibitors so that thrombi do not occlude blood flow and cause thrombosis. A single protein family, the serpins, provides all four of the endogenous thrombin inhibitors found in man. The crystal structures of these serpins bound to thrombin have been solved, revealing a similar exosite-dependence on complex formation. In addition to forming the recognition complex, serpins destroy the structure of thrombin, allowing them to be released from cofactors and substrates for clearance. This review examines how the special features of thrombin have been exploited by evolution to achieve inhibition of the ultimate coagulation protease.
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Affiliation(s)
- James A Huntington
- James A. Huntington, Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK, Tel.: +44 1223 763230, Fax: +44 1223 336827, E-mail:
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89
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Kumar Y, Vadivel K, Schmidt AE, Ogueli GI, Ponnuraj SM, Rannulu N, Loo JA, Bajaj M, Bajaj SP. Decoy plasminogen receptor containing a selective Kunitz-inhibitory domain. Biochemistry 2014; 53:505-17. [PMID: 24383758 PMCID: PMC3985851 DOI: 10.1021/bi401584b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/31/2013] [Indexed: 11/29/2022]
Abstract
Kunitz domain 1 (KD1) of tissue factor pathway inhibitor-2 in which P2' residue Leu17 (bovine pancreatic trypsin inhibitor numbering) is mutated to Arg selectively inhibits the active site of plasmin with ∼5-fold improved affinity. Thrombin cleavage (24 h extended incubation at a 1:50 enzyme-to-substrate ratio) of the KD1 mutant (Leu17Arg) yielded a smaller molecule containing the intact Kunitz domain with no detectable change in the active-site inhibitory function. The N-terminal sequencing and MALDI-TOF/ESI data revealed that the starting molecule has a C-terminal valine (KD1L17R-VT), whereas the smaller molecule has a C-terminal lysine (KD1L17R-KT). Because KD1L17R-KT has C-terminal lysine, we examined whether it could serve as a decoy receptor for plasminogen/plasmin. Such a molecule might inhibit plasminogen activation as well as the active site of generated plasmin. In surface plasmon resonance experiments, tissue plasminogen activator (tPA) and Glu-plasminogen bound to KD1L17R-KT (Kd ∼ 0.2 to 0.3 μM) but not to KD1L17R-VT. Furthermore, KD1L17R-KT inhibited tPA-induced plasma clot fibrinolysis more efficiently than KD1L17R-VT. Additionally, compared to ε-aminocaproic acid KD1L17R-KT was more effective in reducing blood loss in a mouse liver-laceration injury model, where the fibrinolytic system is activated. In further experiments, the micro(μ)-plasmin-KD1L17R-KT complex inhibited urokinase-induced plasminogen activation on phorbol-12-myristate-13-acetate-stimulated U937 monocyte-like cells, whereas the μ-plasmin-KD1L17R-VT complex failed to inhibit this process. In conclusion, KD1L17R-KT inhibits the active site of plasmin as well as acts as a decoy receptor for the kringle domain(s) of plasminogen/plasmin; hence, it limits both plasmin generation and activity. With its dual function, KD1L17R-KT could serve as a preferred agent for controlling plasminogen activation in pathological processes.
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Affiliation(s)
- Yogesh Kumar
- Department
of Orthopaedic Surgery, UCLA School of Medicine, Los Angeles, California 90095, United States
| | - Kanagasabai Vadivel
- Department
of Orthopaedic Surgery, UCLA School of Medicine, Los Angeles, California 90095, United States
| | - Amy E. Schmidt
- Department
of Pathology and Laboratory Medicine, Indiana
University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Godwin I. Ogueli
- Department
of Orthopaedic Surgery, UCLA School of Medicine, Los Angeles, California 90095, United States
| | - Sathya M. Ponnuraj
- Department
of Orthopaedic Surgery, UCLA School of Medicine, Los Angeles, California 90095, United States
| | - Nalaka Rannulu
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Joseph A. Loo
- Department
of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- Molecular
Biology Institute, UCLA, Los Angeles, California 90095, United States
| | - Madhu
S. Bajaj
- Department
of Medicine, Division of Pulmonary, and Critical Care Medicine, David
Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States
| | - S. Paul Bajaj
- Department
of Orthopaedic Surgery, UCLA School of Medicine, Los Angeles, California 90095, United States
- Molecular
Biology Institute, UCLA, Los Angeles, California 90095, United States
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90
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Low anticoagulant heparin blocks thrombin-induced endothelial permeability in a PAR-dependent manner. Vascul Pharmacol 2014; 62:63-71. [PMID: 24469066 DOI: 10.1016/j.vph.2014.01.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 01/12/2014] [Accepted: 01/19/2014] [Indexed: 11/23/2022]
Abstract
Acute lung injury and acute respiratory distress syndrome are accompanied by thrombin activation and fibrin deposition that enhance lung inflammation, activate endothelial cells and disrupt lung paracellular permeability. Heparin possesses anti-inflammatory properties but its clinical use is limited by hemorrhage and heparin induced thrombocytopenia. We studied the effects of heparin and low anticoagulant 2-O, 3-O desulfated heparin (ODSH) on thrombin-induced increases in paracellular permeability of cultured human pulmonary endothelial cells (ECs). Pretreatment with heparin or ODSH blocked thrombin-induced decrease in the EC transendothelial electrical resistance (TER), attenuated thrombin-stimulated paracellular gap formation and actin cytoskeletal rearrangement. Our data demonstrated that heparin and ODSH had inhibitory effects on thrombin-induced RhoA activation and intracellular calcium elevation. Thrombin-stimulated phosphorylation of the cytoskeletal regulatory proteins, myosin light chain and ezrin/radixin/moesin was also reduced. In these effects, low anticoagulant ODSH was more potent than heparin. Heparin or ODSH alone produced decreases in the EC TER that were abolished by siRNA-mediated depletion of the thrombin receptor, PAR-1. We also demonstrated that, in contrast to heparin, ODSH did not possess thrombin-binding activity. Results suggest that heparin and low anticoagulant ODSH can interfere with thrombin-activated signaling.
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91
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Doneux T, De Rache A, Triffaux E, Meunier A, Steichen M, Buess-Herman C. Optimization of the Probe Coverage in DNA Biosensors by a One-Step Coadsorption Procedure. ChemElectroChem 2013. [DOI: 10.1002/celc.201300145] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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92
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Pol-Fachin L, Verli H. Structural glycobiology of heparin dynamics on the exosite 2 of coagulation cascade proteases: Implications for glycosaminoglycans antithrombotic activity. Glycobiology 2013; 24:97-105. [PMID: 24201825 DOI: 10.1093/glycob/cwt095] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
fIIa and fXa are two of the main targets of antithrombin, a serine proteases inhibitor that plays a major role in the regulation of blood clotting. The formation of ternary complexes between such molecules and glycosaminoglycans, as heparin, is the main path for inhibiting those enzymes, which may occur through two distinct mechanisms of action. While these serine proteases present distinct susceptibilities to these paths, in which fIIa demands an interaction with heparin, neither the molecular basis of this differential inhibition nor the role of fIIa glycosylation on this process is fully understood. Thus, the present work evaluated through molecular dynamics simulations the effects of glycosylation on fIIa and the consequences of heparin binding to both proteases function and dynamics. Based on the obtained data, fIIa N-linked glycan promoted an increase in the active site pocket size by stabilizing regions that encircle it, while heparin binding was observed to reverse such an effect. Additionally, heparin orientation observed on the surface of fIIa, but not fXa, allows a linear long-chain heparin binding to antithrombin in ternary complexes. Finally, the enzymes catalytic triad organization was disrupted due to a strong glycosaminoglycan binding to the proteases exosite 2. Such data support an atomic-level explanation for the higher inhibition constant of the antithrombin-heparin complex over fIIa than fXa, as well as for the different susceptibilities of those enzymes for antithrombin mechanisms of action.
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Affiliation(s)
- Laercio Pol-Fachin
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil
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93
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94
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Djordjevic V, Kovac M, Miljic P, Murata M, Takagi A, Pruner I, Francuski D, Kojima T, Radojkovic D. A novel prothrombin mutation in two families with prominent thrombophilia--the first cases of antithrombin resistance in a Caucasian population. J Thromb Haemost 2013; 11:1936-9. [PMID: 23927452 DOI: 10.1111/jth.12367] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Indexed: 11/29/2022]
Affiliation(s)
- V Djordjevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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95
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Turk D. MAIN software for density averaging, model building, structure refinement and validation. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1342-57. [PMID: 23897458 PMCID: PMC3727325 DOI: 10.1107/s0907444913008408] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/26/2013] [Indexed: 11/11/2022]
Abstract
MAIN is software that has been designed to interactively perform the complex tasks of macromolecular crystal structure determination and validation. Using MAIN, it is possible to perform density modification, manual and semi-automated or automated model building and rebuilding, real- and reciprocal-space structure optimization and refinement, map calculations and various types of molecular structure validation. The prompt availability of various analytical tools and the immediate visualization of molecular and map objects allow a user to efficiently progress towards the completed refined structure. The extraordinary depth perception of molecular objects in three dimensions that is provided by MAIN is achieved by the clarity and contrast of colours and the smooth rotation of the displayed objects. MAIN allows simultaneous work on several molecular models and various crystal forms. The strength of MAIN lies in its manipulation of averaged density maps and molecular models when noncrystallographic symmetry (NCS) is present. Using MAIN, it is possible to optimize NCS parameters and envelopes and to refine the structure in single or multiple crystal forms.
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Affiliation(s)
- Dušan Turk
- Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, Ljubljana, Slovenia.
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96
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Lou X, Zhang Y. Mechanism studies on nanoPCR and applications of gold nanoparticles in genetic analysis. ACS APPLIED MATERIALS & INTERFACES 2013; 5:6276-84. [PMID: 23734951 DOI: 10.1021/am4013209] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Recently, the applications of nanomaterial-assisted polymerase chain reaction (nanoPCR) have received considerable attention. Several potential mechanisms have been proposed, but mainly according to the results of PCR assays under specific conditions and lacking direct and general evidence. The mechanism of nanoPCR has not been elucidated yet. Here, taking gold nanoparticles (AuNPs) as an example, we report the three general effects of AuNPs: (1) AuNPs adsorb polymerase and modulate the amount of active polymerase in PCR, which was directly demonstrated by a simple and straightforward colorimetric assay and the dynamic light scattering measurements. (2) AuNPs adsorb primers and decrease the melting temperatures (Tm) of the duplexes formed with perfectly matched and mismatched primers and increase the Tm difference between them. (3) AuNPs adsorb PCR products and facilitate the dissociation of them in the denaturing step. All these effects were confirmed by addition of a rationally selected surface adsorbent, bovine thrombin, to highly efficiently modulate the surface adsorption of PCR components. These findings suggested that AuNPs should have multiple effects on PCR: (1) to regulate PCR in a case-by-case way via modulating the amount of active polymerase in PCR; (2) to improve PCR specificity in the annealing step via increasing the Tm difference between the perfectly matched and mismatched primers; (3) to improve PCR efficiency via speeding up the dissociation of the PCR products in the denaturing step. Taken together, we proposed the mechanism of nanoPCR is that the surface interaction of PCR components (polymerase, primers, and products) with AuNPs regulates nanoPCR. We further demonstrated that the applications of these findings improve the PCR of the amelogenin genes and Hepatitis B virus gene for genetic analysis. These findings could also provide helpful insight for the applications of other nanomaterials in nanoPCR.
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Affiliation(s)
- Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, China.
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97
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Pozzi N, Chen Z, Gohara DW, Niu W, Heyduk T, Di Cera E. Crystal structure of prothrombin reveals conformational flexibility and mechanism of activation. J Biol Chem 2013; 288:22734-44. [PMID: 23775088 DOI: 10.1074/jbc.m113.466946] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The zymogen prothrombin is composed of fragment 1 containing a Gla domain and kringle-1, fragment 2 containing kringle-2, and a protease domain containing A and B chains. The prothrombinase complex assembled on the surface of platelets converts prothrombin to thrombin by cleaving at Arg-271 and Arg-320. The three-dimensional architecture of prothrombin and the molecular basis of its activation remain elusive. Here we report the first x-ray crystal structure of prothrombin as a Gla-domainless construct carrying an Ala replacement of the catalytic Ser-525. Prothrombin features a conformation 80 Å long, with fragment 1 positioned at a 36° angle relative to the main axis of fragment 2 coaxial to the protease domain. High flexibility of the linker connecting the two kringles suggests multiple arrangements for kringle-1 relative to the rest of the prothrombin molecule. Luminescence resonance energy transfer measurements detect two distinct conformations of prothrombin in solution, in a 3:2 ratio, with the distance between the two kringles either fully extended (54 ± 2 Å) or partially collapsed (≤34 Å) as seen in the crystal structure. A molecular mechanism of prothrombin activation emerges from the structure. Of the two sites of cleavage, Arg-271 is located in a disordered region connecting kringle-2 to the A chain, but Arg-320 is well defined within the activation domain and is not accessible to proteolysis in solution. Burial of Arg-320 prevents prothrombin autoactivation and directs prothrombinase to cleave at Arg-271 first. Reversal of the local electrostatic potential then redirects prothrombinase toward Arg-320, leading to thrombin generation via the prethrombin-2 intermediate.
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Affiliation(s)
- Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, USA
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98
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Pozzi N, Acquasaliente L, Frasson R, Cristiani A, Moro S, Banzato A, Pengo V, Scaglione GL, Arcovito A, De Cristofaro R, De Filippis V. β2 -Glycoprotein I binds to thrombin and selectively inhibits the enzyme procoagulant functions. J Thromb Haemost 2013; 11:1093-102. [PMID: 23578283 DOI: 10.1111/jth.12238] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Indexed: 08/31/2023]
Abstract
BACKGROUND This work was aimed at characterizing the interaction of β(2)-glycoprotein I (β(2)GPI), an abundant plasma protein of unknown function, with human thrombin, the final effector protease in the coagulation cascade. METHODS The β(2)GPI-thrombin interaction was studied by surface plasmon resonance (SPR), fluorescence, and molecular modeling. The effect of β(2)GPI on the procoagulant (fibrin generation and platelet aggregation) and anticoagulant (protein C activation) functions of thrombin were investigated with turbidimetric, immunocytofluorimetric and enzymatic assays. RESULTS SPR and fluorescence data indicated that β(2)GPI tightly bound thrombin (K(d) = 34 nM) by interacting with both protease exosites, while leaving the active site accessible. This picture is fully consistent with the theoretical model of the β(2)GPI-thrombin complex. In particular, blockage of thrombin exosites with binders specific for exosite-1 (hirugen and HD1 aptamer) or exosite-2 (fibrinogen γ'-peptide and HD22 aptamer) impaired the β2 GPI-thrombin interaction. Identical results were obtained with thrombin mutants having one of the two exosites selectively compromised by mutation (Arg73Ala and Arg101Ala). Fluorescence measurements indicated that β(2)GPI did not affect the affinity of the enzyme for active site inhibitors, such as p-aminobenzamidine and the hirudin(1-47) domain, in agreement with the structural model. β(2)GPI dose-dependently prolonged the thrombin clotting time and ecarin clotting time in β(2)GPI-deficient plasma. β(2)GPI inhibited thrombin-induced platelet aggregation (IC50 = 0.36 μM) by impairing thrombin cleavage of protease-activated receptor 1 (PAR1) (IC50 = 0.32 μM), both on gel-filtered platelets and in whole blood. Strikingly, β(2) GPI did not affect thrombin-mediated generation of the anticoagulant protein C. CONCLUSIONS β(2) GPI functions as a physiologic anticoagulant by inhibiting the key procoagulant activities of thrombin without affecting its unique anticoagulant function.
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Affiliation(s)
- N Pozzi
- Laboratory of Protein Chemistry, School of Medicine, University of Padua, Padova, Italy
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99
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Yamada T, Kurihara K, Ohnishi Y, Tamada T, Tomoyori K, Masumi K, Tanaka I, Kuroki R, Niimura N. Neutron and X-ray crystallographic analysis of the human α-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1532-8. [PMID: 23712263 DOI: 10.1016/j.bbapap.2013.05.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 05/16/2013] [Accepted: 05/17/2013] [Indexed: 11/26/2022]
Abstract
The protonation states and hydration structures of the α-thrombin-bivalirudin complex were studied by joint XN refinement of the single crystal X-ray and neutron diffraction data at resolutions of 1.6 and 2.8Å, respectively. The atomic distances were estimated by carrying out X-ray crystallographic analysis at 1.25Å resolution. The complex represents a model of the enzyme-product (EP) complex of α-thrombin. The neutron scattering length maps around the active site suggest that the side chain of H57/H was deuterated. The joint XN refinement showed that occupancies for Dδ1 and Dε2 of H57/H were 1.0 and 0.7, respectively. However, no significant neutron scattering length density was observed around the hydroxyl oxygen Oγ of S195/H, which was close to the carboxylic carbon atom of dFPR-COOH. These observations suggest that the Oγ atom of S195/H is deprotonated and maintains its nucleophilicity in the EP complex. In addition to the active site, the hydration structures of the S1 subsite and the Exosite I, which are involved in the recognition of bivalirudin, are presented.
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100
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Oroval M, Climent E, Coll C, Eritja R, Aviñó A, Marcos MD, Sancenón F, Martínez-Máñez R, Amorós P. An aptamer-gated silica mesoporous material for thrombin detection. Chem Commun (Camb) 2013; 49:5480-2. [PMID: 23660687 DOI: 10.1039/c3cc42157k] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An aptamer-capped mesoporous material for the selective and sensitive detection of α-thrombin in human plasma and serum has been prepared and characterised.
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Affiliation(s)
- Mar Oroval
- Centro de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Unidad Mixta Universidad Politécnica de Valencia - Universidad de Valencia, Spain
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