1
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Stojanovski BM, Pelc LA, Di Cera E. Thrombin has dual trypsin-like and chymotrypsin-like specificity. J Thromb Haemost 2024; 22:1009-1015. [PMID: 38160728 PMCID: PMC10960677 DOI: 10.1016/j.jtha.2023.12.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The residue at the site of activation of protein C is Arg in all species except the ray-finned fish, where it is Trp. This feature raises the question of whether thrombin is the physiological activator of protein C across vertebrates. OBJECTIVES To establish if thrombin can cleave at Trp residues. METHODS The activity of wild-type thrombin and mutant D189S was tested with a library of chromogenic substrates and toward wild-type protein C and mutants carrying substitutions at the site of cleavage. RESULTS Thrombin has trypsin-like and chymotrypsin-like specificity and cleaves substrates at Arg or Trp residues. Cleavage at Arg is preferred, but cleavage at Trp is significant and comparable with that of chymotrypsin. The D189S mutant of thrombin has broad specificity and cleaves at basic and aromatic residues without significant preference. Thrombin also cleaves natural substrates at Arg or Trp residues, showing activity toward protein C across vertebrates, including the ray-finned fish. The rate of activation of protein C in the ray-finned fish is affected by the sequence preceding Trp at the scissile bond. CONCLUSION The results provide a possible solution for the paradoxical presence of a Trp residue at the site of cleavage of protein C in ray-finned fish and support thrombin as the physiological activator of protein C in all vertebrates. The dual trypsin-like and chymotrypsin-like specificity of thrombin suggests that the spectrum of physiological substrates of this enzyme is broader currently assumed.
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Affiliation(s)
- Bosko M Stojanovski
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
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2
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Stojanovski BM, Di Cera E. Role of sequence and position of the cleavage sites in prothrombin activation. J Biol Chem 2021; 297:100955. [PMID: 34265300 PMCID: PMC8348271 DOI: 10.1016/j.jbc.2021.100955] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 11/30/2022] Open
Abstract
In the penultimate step of the coagulation cascade, the multidomain vitamin-K-dependent zymogen prothrombin is converted to thrombin by the prothrombinase complex composed of factor Xa, cofactor Va, and phospholipids. Activation of prothrombin requires cleavage at two residues, R271 and R320, along two possible pathways generating either the intermediate prethrombin-2 (following initial cleavage at R271) or meizothrombin (following initial cleavage at R320). The former pathway is preferred in the absence of and the latter in the presence of cofactor Va. Several mechanisms have been proposed to explain this preference, but the role of the sequence and position of the sites of cleavage has not been thoroughly investigated. In this study, we engineered constructs where the sequences 261DEDSDRAIEGRTATSEYQT279 and 310RELLESYIDGRIVEGSDAE328 were swapped between the R271 and R320 sites. We found that in the absence of cofactor Va, the wild-type sequence at the R271 site is cleaved preferentially regardless of its position at the R271 or R320 site, whereas in the presence of cofactor Va, the R320 site is cleaved preferentially regardless of its sequence. Additional single-molecule FRET measurements revealed that the environment of R271 changes significantly upon cleavage at R320 due to the conformational transition from the closed form of prothrombin to the open form of meizothrombin. Detailed kinetics of cleavage at the R271 site were monitored by a newly developed assay based on loss of FRET. These findings show how sequence and position of the cleavage sites at R271 and R320 dictate the preferred pathway of prothrombin activation.
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Affiliation(s)
- Bosko M Stojanovski
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, Missouri, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, Missouri, USA.
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3
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Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. Nat Commun 2021; 12:1693. [PMID: 33727531 PMCID: PMC7966775 DOI: 10.1038/s41467-021-21754-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Proteases are among the largest protein families and critical regulators of biochemical processes like apoptosis and blood coagulation. Knowledge of proteases has been expanded by the development of proteomic approaches, however, technology for multiplexed screening of proteases within native environments is currently lacking behind. Here we introduce a simple method to profile protease activity based on isolation of protease products from native lysates using a 96FASP filter, their analysis in a mass spectrometer and a custom data analysis pipeline. The method is significantly faster, cheaper, technically less demanding, easy to multiplex and produces accurate protease fingerprints. Using the blood cascade proteases as a case study, we obtain protease substrate profiles that can be used to map specificity, cleavage entropy and allosteric effects and to design protease probes. The data further show that protease substrate predictions enable the selection of potential physiological substrates for targeted validation in biochemical assays. Characterizing proteases in their native environment is still challenging. Here, the authors develop a proteomics workflow for analyzing protease-specific peptides from cell lysates in 96-well format, providing mechanistic insights into blood proteases and enabling the prediction of protease substrates.
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4
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Qi E, Wang D, Li Y, Li G, Su Z. Revealing favorable and unfavorable residues in cooperative positions in protease cleavage sites. Biochem Biophys Res Commun 2019; 519:714-720. [PMID: 31543345 DOI: 10.1016/j.bbrc.2019.09.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 09/14/2019] [Indexed: 11/17/2022]
Abstract
Proteases play critical roles in a wide variety of fundamental biological functions, and numerous protease inhibitors have been developed to treat various diseases including cancer. A wide range of experimental and computational methods have been developed to investigate the specificity and catalytic mechanisms of proteases. However, these methods only focused on the preferences of a single position around a cleavage site in a substrate, rarely on the compositionality of the subsites. We present new methods to quantify the specificity of proteases by considering the combinatorial patterns of amino acid residuals of cleavage sites in substrates. By incorporating the preference at positions, we modeled three types of favorable combinations of residues in cleavage sites. Moreover, by constructing a relationship weight matrix of residues between two positions, we can easily identify unfavorable combinations of residues at the positions. Applying these methods to a set of known cleavage sites of proteases, we revealed numerous favorable and unfavorable residues in cooperative positions in the protease cleavage sites. The results can help understand the specificity and catalytic mechanisms of proteases. To our knowledge, this is the first study that quantifies unfavorable combinations of amino acids between two sites. Furthermore, this method is not limited to the study of proteases and cleavage sites, and can be generalized to uncover the relationships of residues at meaningful sites in other proteins.
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Affiliation(s)
- Enfeng Qi
- School of Mathematics, Shandong University, Jinan, 250100, China; School of Mathematics and Statistics, Guangxi Normal University, Guilin, 541000, China
| | - Dongyu Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Yang Li
- School of Mathematics, Shandong University, Jinan, 250100, China
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, 250100, China.
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, 28223, USA.
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5
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Residues W215, E217 and E192 control the allosteric E*-E equilibrium of thrombin. Sci Rep 2019; 9:12304. [PMID: 31444378 PMCID: PMC6707225 DOI: 10.1038/s41598-019-48839-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/13/2019] [Indexed: 01/07/2023] Open
Abstract
A pre-existing, allosteric equilibrium between closed (E*) and open (E) conformations of the active site influences the level of activity in the trypsin fold and defines ligand binding according to the mechanism of conformational selection. Using the clotting protease thrombin as a model system, we investigate the molecular determinants of the E*-E equilibrium through rapid kinetics and X-ray structural biology. The equilibrium is controlled by three residues positioned around the active site. W215 on the 215-217 segment defining the west wall of the active site controls the rate of transition from E to E* through hydrophobic interaction with F227. E192 on the opposite 190-193 segment defining the east wall of the active site controls the rate of transition from E* to E through electrostatic repulsion of E217. The side chain of E217 acts as a lever that moves the entire 215-217 segment in the E*-E equilibrium. Removal of this side chain converts binding to the active site to a simple lock-and-key mechanism and freezes the conformation in a state intermediate between E* and E. These findings reveal a simple framework to understand the molecular basis of a key allosteric property of the trypsin fold.
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6
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Li B, Billur R, Maurer MC, Kohler HP, Raddatz Müller P, Alberio L, Schroeder V. Proline 36 of the Factor XIII Activation Peptide Plays a Crucial Role in Substrate Recognition and Zymogen Activation. Thromb Haemost 2018; 118:2037-2045. [PMID: 30419598 DOI: 10.1055/s-0038-1675600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The activation peptide of blood coagulation factor XIII (AP-FXIII) has important functions in stabilizing the FXIII-A2 dimer and regulating FXIII activation. Contributions of many of its 37 amino acids to these functions have been described. However, the role of proline 36, which is adjacent to the thrombin cleavage site at Arg37, has not yet been studied in detail. We approached this question when we came across a patient with congenital FXIII deficiency in whom we detected a novel Pro36Ser mutation. We expressed the mutant FXIII-A Pro36Ser protein in Chinese hamster ovary cells and found that this mutation does not influence FXIII-A expression but significantly inhibits proteolytic activation by thrombin. The enzymatic transglutaminase activity is not affected as it can be induced in the presence of high Ca2+ concentrations. We performed nuclear magnetic resonance analysis to investigate AP-FXIII-thrombin interactions, which showed that the mutant Ser36 peptide binds less well to the thrombin surface than the native Pro36 peptide. The Arg37 at the P1 position still makes strong interactions with the active site cleft but the P4-P2 residues (34VVS36) appear to be less well positioned to contact the neighbouring thrombin active site region. In conclusion, we have characterized a novel mutation in AP-FXIII representing only the fourth case of the rare FXIII-A type II deficiency. This case served as a perfect in vivo model to shed light on the crucial role of Pro36 in the proteolytic activation of FXIII-A. Our results contribute to the understanding of structure-function relationship in FXIII.
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Affiliation(s)
- Bojun Li
- Experimental Haemostasis Group, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Ramya Billur
- Department of Chemistry, University of Louisville, Louisville, Kentucky, United States
| | - Muriel C Maurer
- Department of Chemistry, University of Louisville, Louisville, Kentucky, United States
| | - Hans P Kohler
- Experimental Haemostasis Group, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Pascale Raddatz Müller
- Division of Haematology and Central Haematology Laboratory, Luzerner Kantonsspital, Lucerne, Switzerland
| | - Lorenzo Alberio
- Division of Haematology and Central Haematology Laboratory, Lausanne University Hospital, Lausanne, Switzerland.,Faculté de Biologie et Médecine, University of Lausanne, Lausanne, Switzerland
| | - Verena Schroeder
- Experimental Haemostasis Group, Department for BioMedical Research, University of Bern, Bern, Switzerland
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7
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Kretz CA, Tomberg K, Van Esbroeck A, Yee A, Ginsburg D. High throughput protease profiling comprehensively defines active site specificity for thrombin and ADAMTS13. Sci Rep 2018; 8:2788. [PMID: 29434246 PMCID: PMC5809430 DOI: 10.1038/s41598-018-21021-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/29/2018] [Indexed: 12/20/2022] Open
Abstract
We have combined random 6 amino acid substrate phage display with high throughput sequencing to comprehensively define the active site specificity of the serine protease thrombin and the metalloprotease ADAMTS13. The substrate motif for thrombin was determined by >6,700 cleaved peptides, and was highly concordant with previous studies. In contrast, ADAMTS13 cleaved only 96 peptides (out of >107 sequences), with no apparent consensus motif. However, when the hexapeptide library was substituted into the P3-P3′ interval of VWF73, an exosite-engaging substrate of ADAMTS13, 1670 unique peptides were cleaved. ADAMTS13 exhibited a general preference for aliphatic amino acids throughout the P3-P3′ interval, except at P2 where Arg was tolerated. The cleaved peptides assembled into a motif dominated by P3 Leu, and bulky aliphatic residues at P1 and P1′. Overall, the P3-P2′ amino acid sequence of von Willebrand Factor appears optimally evolved for ADAMTS13 recognition. These data confirm the critical role of exosite engagement for substrates to gain access to the active site of ADAMTS13, and define the substrate recognition motif for ADAMTS13. Combining substrate phage display with high throughput sequencing is a powerful approach for comprehensively defining the active site specificity of proteases.
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Affiliation(s)
- Colin A Kretz
- Department of Medicine, McMaster University and the Thrombosis and Atherosclerosis Research Institute, Hamilton, Ontario, Canada.
| | - Kärt Tomberg
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Alexander Van Esbroeck
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - Andrew Yee
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - David Ginsburg
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.,Howard Hughes Medical Institute and Departments of Internal Medicine and Pediatrics, University of Michigan, Ann Arbor, MI, USA
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8
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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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9
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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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10
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Manfredi MA, Antunes AA, Jesus LDOP, Juliano MA, Juliano L, Judice WADS. Specificity characterization of the α-mating factor hormone by Kex2 protease. Biochimie 2016; 131:149-158. [PMID: 27720750 DOI: 10.1016/j.biochi.2016.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/04/2016] [Accepted: 10/04/2016] [Indexed: 10/20/2022]
Abstract
Kex2 is a Ca2+-dependent serine protease from S. cerevisiae. Characterization of the substrate specificity of Kex2 is of particular interest because this protease serves as the prototype of a large family of eukaryotic subtilisin-related proprotein-processing proteases that cleave sites consisting of pairs or clusters of basic residues. Our goal was to study the prime region subsite S' of Kex2 because previous studies have only taken into account non-prime sites using AMC substrates but not the specificity of prime sites identified through structural modeling or predicted cleavage sites. Therefore, we used peptides derived from Abz-KR↓EADQ-EDDnp and Abz-YKR↓EADQ-EDDnp based on the pro-α-mating factor sequence. The specificity of Kex2 due to basic residues at P1' is affected by the type of residue in the P3 position. Some residues in P1' with large or bulky side chains yielded poor substrate specificity. The kcat/KM values for peptides with P2' substitutions containing Tyr in P3 were higher than those obtained for the peptides without Tyr. In fact, P' and P modifications mainly promoted changes in kcat and KM, respectively. The pH profile of Kex2 was fit to a double-sigmoidal pH-titration curve. The specificity results suggest that Kex2 might be involved in the processing of the putative cleavage sites in a polypeptide involved in cell elongation, hyphal formation and the processing of a toxin, which result in host cell lysis. In summary, the specificity of Kex2 is dependent on the set of interactions with prime and non-prime subsites, resulting in synergism.
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Affiliation(s)
- Marcella Araújo Manfredi
- Centro Interdisciplinar de Investigação Bioquímica, Universidade de Mogi das Cruzes - UMC, Mogi das Cruzes, SP, Brazil
| | - Alyne Alexandrino Antunes
- Centro Interdisciplinar de Investigação Bioquímica, Universidade de Mogi das Cruzes - UMC, Mogi das Cruzes, SP, Brazil
| | | | - Maria Aparecida Juliano
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP, 04044-020, Brazil
| | - Luiz Juliano
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio, 100, São Paulo, SP, 04044-020, Brazil
| | - Wagner Alves de Souza Judice
- Centro Interdisciplinar de Investigação Bioquímica, Universidade de Mogi das Cruzes - UMC, Mogi das Cruzes, SP, Brazil.
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11
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Pozzi N, Chen Z, Zapata F, Niu W, Barranco-Medina S, Pelc LA, Di Cera E. Autoactivation of thrombin precursors. J Biol Chem 2013; 288:11601-10. [PMID: 23467412 DOI: 10.1074/jbc.m113.451542] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Trypsin-like proteases are synthesized as inactive zymogens and convert to the mature form upon activation by specific enzymes, often assisted by cofactors. Central to this paradigm is that the zymogen does not convert spontaneously to the mature enzyme, which in turn does not feed back to activate its zymogen form. In the blood, the zymogens prothrombin and prethrombin-2 require the prothrombinase complex to be converted to the mature protease thrombin, which is unable to activate prothrombin or prethrombin-2. Here, we show that replacement of key residues within the activation domain causes these zymogens to spontaneously convert to thrombin. The conversion is started by the zymogen itself, which is capable of binding ligands at the active site, and is abrogated by inactivation of the catalytic residue Ser-195. The product of autoactivation is functionally and structurally equivalent to wild-type thrombin. Zymogen autoactivation is explained by conformational selection, a basic property of the trypsin fold uncovered by structural and rapid kinetics studies. Both the zymogen and protease undergo a pre-existing equilibrium between active and inactive forms. The equilibrium regulates catalytic activity in the protease and has the potential to unleash activity in the zymogen to produce autoactivation. A new strategy emerges for the facile production of enzymes through zymogen autoactivation that is broadly applicable to trypsin-like proteases of biotechnological and clinical interest.
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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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12
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PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites. PLoS One 2012; 7:e50300. [PMID: 23209700 PMCID: PMC3510211 DOI: 10.1371/journal.pone.0050300] [Citation(s) in RCA: 222] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 10/18/2012] [Indexed: 12/04/2022] Open
Abstract
The ability to catalytically cleave protein substrates after synthesis is fundamental for all forms of life. Accordingly, site-specific proteolysis is one of the most important post-translational modifications. The key to understanding the physiological role of a protease is to identify its natural substrate(s). Knowledge of the substrate specificity of a protease can dramatically improve our ability to predict its target protein substrates, but this information must be utilized in an effective manner in order to efficiently identify protein substrates by in silico approaches. To address this problem, we present PROSPER, an integrated feature-based server for in silico identification of protease substrates and their cleavage sites for twenty-four different proteases. PROSPER utilizes established specificity information for these proteases (derived from the MEROPS database) with a machine learning approach to predict protease cleavage sites by using different, but complementary sequence and structure characteristics. Features used by PROSPER include local amino acid sequence profile, predicted secondary structure, solvent accessibility and predicted native disorder. Thus, for proteases with known amino acid specificity, PROSPER provides a convenient, pre-prepared tool for use in identifying protein substrates for the enzymes. Systematic prediction analysis for the twenty-four proteases thus far included in the database revealed that the features we have included in the tool strongly improve performance in terms of cleavage site prediction, as evidenced by their contribution to performance improvement in terms of identifying known cleavage sites in substrates for these enzymes. In comparison with two state-of-the-art prediction tools, PoPS and SitePrediction, PROSPER achieves greater accuracy and coverage. To our knowledge, PROSPER is the first comprehensive server capable of predicting cleavage sites of multiple proteases within a single substrate sequence using machine learning techniques. It is freely available at http://lightning.med.monash.edu.au/PROSPER/.
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13
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Gallwitz M, Enoksson M, Thorpe M, Hellman L. The extended cleavage specificity of human thrombin. PLoS One 2012; 7:e31756. [PMID: 22384068 PMCID: PMC3288055 DOI: 10.1371/journal.pone.0031756] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 01/18/2012] [Indexed: 12/30/2022] Open
Abstract
Thrombin is one of the most extensively studied of all proteases. Its central role in the coagulation cascade as well as several other areas has been thoroughly documented. Despite this, its consensus cleavage site has never been determined in detail. Here we have determined its extended substrate recognition profile using phage-display technology. The consensus recognition sequence was identified as, P2-Pro, P1-Arg, P1'-Ser/Ala/Gly/Thr, P2'-not acidic and P3'-Arg. Our analysis also identifies an important role for a P3'-arginine in thrombin substrates lacking a P2-proline. In order to study kinetics of this cooperative or additive effect we developed a system for insertion of various pre-selected cleavable sequences in a linker region between two thioredoxin molecules. Using this system we show that mutations of P2-Pro and P3'-Arg lead to an approximate 20-fold and 14-fold reduction, respectively in the rate of cleavage. Mutating both Pro and Arg results in a drop in cleavage of 200-400 times, which highlights the importance of these two positions for maximal substrate cleavage. Interestingly, no natural substrates display the obtained consensus sequence but represent sequences that show only 1-30% of the optimal cleavage rate for thrombin. This clearly indicates that maximal cleavage, excluding the help of exosite interactions, is not always desired, which may instead cause problems with dysregulated coagulation. It is likely exosite cooperativity has a central role in determining the specificity and rate of cleavage of many of these in vivo substrates. Major effects on cleavage efficiency were also observed for residues as far away as 4 amino acids from the cleavage site. Insertion of an aspartic acid in position P4 resulted in a drop in cleavage by a factor of almost 20 times.
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Affiliation(s)
| | | | | | - Lars Hellman
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- * E-mail:
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14
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Ng NM, Pierce JD, Webb GI, Ratnikov BI, Wijeyewickrema LC, Duncan RC, Robertson AL, Bottomley SP, Boyd SE, Pike RN. Discovery of Amino Acid Motifs for Thrombin Cleavage and Validation Using a Model Substrate. Biochemistry 2011; 50:10499-507. [DOI: 10.1021/bi201333g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natasha M. Ng
- Department
of Biochemistry and
Molecular Biology, Monash University, Clayton,
Victoria 3800, Australia
| | - James D. Pierce
- Sanford-Burnham Medical Research Institute, La Jolla, California 92037-1062,
United States
| | - Geoffrey I. Webb
- Clayton School
of Information
Technology, Monash University, Clayton,
Victoria 3800, Australia
| | - Boris I. Ratnikov
- Sanford-Burnham Medical Research Institute, La Jolla, California 92037-1062,
United States
| | - Lakshmi C. Wijeyewickrema
- Department
of Biochemistry and
Molecular Biology, Monash University, Clayton,
Victoria 3800, Australia
| | - Renee C. Duncan
- Department
of Biochemistry and
Molecular Biology, Monash University, Clayton,
Victoria 3800, Australia
| | - Amy L. Robertson
- Department
of Biochemistry and
Molecular Biology, Monash University, Clayton,
Victoria 3800, Australia
| | - Stephen P. Bottomley
- Department
of Biochemistry and
Molecular Biology, Monash University, Clayton,
Victoria 3800, Australia
| | - Sarah E. Boyd
- School of Mathematical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Robert N. Pike
- Department
of Biochemistry and
Molecular Biology, Monash University, Clayton,
Victoria 3800, Australia
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15
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Koh CY, Kumar S, Kazimirova M, Nuttall PA, Radhakrishnan UP, Kim S, Jagadeeswaran P, Imamura T, Mizuguchi J, Iwanaga S, Swaminathan K, Kini RM. Crystal structure of thrombin in complex with S-variegin: insights of a novel mechanism of inhibition and design of tunable thrombin inhibitors. PLoS One 2011; 6:e26367. [PMID: 22053189 PMCID: PMC3203879 DOI: 10.1371/journal.pone.0026367] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 09/25/2011] [Indexed: 11/19/2022] Open
Abstract
The inhibition of thrombin is one of the important treatments of pathological blood clot formation. Variegin, isolated from the tropical bont tick, is a novel molecule exhibiting a unique ‘two-modes’ inhibitory property on thrombin active site (competitive before cleavage, noncompetitive after cleavage). For the better understanding of its function, we have determined the crystal structure of the human α-thrombin:synthetic-variegin complex at 2.4 Å resolution. The structure reveals a new mechanism of thrombin inhibition by disrupting the charge relay system. Based on the structure, we have designed 17 variegin variants, differing in potency, kinetics and mechanism of inhibition. The most active variant is about 70 times more potent than the FDA-approved peptidic thrombin inhibitor, hirulog-1/bivalirudin. In vivo antithrombotic effects of the variegin variants correlate well with their in vitro affinities for thrombin. Our results encourage that variegin and the variants show strong potential for the development of tunable anticoagulants.
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Affiliation(s)
- Cho Yeow Koh
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Sundramurthy Kumar
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Maria Kazimirova
- Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Uvaraj P. Radhakrishnan
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Seongcheol Kim
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Pudur Jagadeeswaran
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | | | - Jun Mizuguchi
- The Chemo-Sero-Therapeutic Research Institute, Kumamoto, Japan
| | - Sadaaki Iwanaga
- The Chemo-Sero-Therapeutic Research Institute, Kumamoto, Japan
| | - Kunchithapadam Swaminathan
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * E-mail: (RMK); (KS)
| | - R. Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Department of Biochemistry and Molecular Biophysics, Medical College of Virginia, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail: (RMK); (KS)
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16
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Song J, Tan H, Boyd SE, Shen H, Mahmood K, Webb GI, Akutsu T, Whisstock JC, Pike RN. Bioinformatic approaches for predicting substrates of proteases. J Bioinform Comput Biol 2011; 9:149-78. [PMID: 21328711 DOI: 10.1142/s0219720011005288] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 10/08/2010] [Accepted: 10/09/2010] [Indexed: 11/18/2022]
Abstract
Proteases have central roles in "life and death" processes due to their important ability to catalytically hydrolyze protein substrates, usually altering the function and/or activity of the target in the process. Knowledge of the substrate specificity of a protease should, in theory, dramatically improve the ability to predict target protein substrates. However, experimental identification and characterization of protease substrates is often difficult and time-consuming. Thus solving the "substrate identification" problem is fundamental to both understanding protease biology and the development of therapeutics that target specific protease-regulated pathways. In this context, bioinformatic prediction of protease substrates may provide useful and experimentally testable information about novel potential cleavage sites in candidate substrates. In this article, we provide an overview of recent advances in developing bioinformatic approaches for predicting protease substrate cleavage sites and identifying novel putative substrates. We discuss the advantages and drawbacks of the current methods and detail how more accurate models can be built by deriving multiple sequence and structural features of substrates. We also provide some suggestions about how future studies might further improve the accuracy of protease substrate specificity prediction.
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Affiliation(s)
- Jiangning Song
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia.
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17
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Abstract
Enzyme activation by monovalent cations is widely documented in plants and the animal world. In type II enzymes, activation entails two steps: binding of the monovalent cation to its allosteric site and transduction of this event into enhanced catalytic activity. The effect has exquisite specificity for either Na(+) or K(+), the most abundant cations present in physiological environments. Enzymes requiring K(+) such as kinases and molecular chaperones are not activated as well or at all by the larger cation Cs(+) or the smaller cations Na(+) and Li(+). Enzymes requiring Na(+) such as β-galactosidase and clotting proteases are not activated as well by Li(+), or the larger cations K(+), Rb(+), and Cs(+). Efforts to switch specificity between Na(+) and K(+) in this large class of enzymes and completely redesign the mechanism of allosteric transduction leading to enhanced catalytic activity have so far been unsuccessful. Here we show how mutagenesis of two loops defining the Na(+) binding site of thrombin, a Na(+)-activated clotting protease, generates a construct that is most active in the presence of K(+) toward synthetic and physiological substrates. The effect is the result of a higher binding affinity and more efficient allosteric transduction of binding into enhanced catalytic activity for K(+) compared to Na(+), which represents a complete reversal of the properties of wild type. In addition, the construct features altered specificity toward physiological substrates resulting in a significant anticoagulant profile. The findings are relevant to all Na(+)-activated proteases involved in blood coagulation and the complement system.
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Affiliation(s)
- Sadhna Rana
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104
| | - Nicola Pozzi
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104
| | - Leslie A. Pelc
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104
| | - Enrico Di Cera
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104
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18
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Salameh MA, Soares AS, Navaneetham D, Sinha D, Walsh PN, Radisky ES. Determinants of affinity and proteolytic stability in interactions of Kunitz family protease inhibitors with mesotrypsin. J Biol Chem 2010; 285:36884-96. [PMID: 20861008 DOI: 10.1074/jbc.m110.171348] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An important functional property of protein protease inhibitors is their stability to proteolysis. Mesotrypsin is a human trypsin that has been implicated in the proteolytic inactivation of several protein protease inhibitors. We have found that bovine pancreatic trypsin inhibitor (BPTI), a Kunitz protease inhibitor, inhibits mesotrypsin very weakly and is slowly proteolyzed, whereas, despite close sequence and structural homology, the Kunitz protease inhibitor domain of the amyloid precursor protein (APPI) binds to mesotrypsin 100 times more tightly and is cleaved 300 times more rapidly. To define features responsible for these differences, we have assessed the binding and cleavage by mesotrypsin of APPI and BPTI reciprocally mutated at two nonidentical residues that make direct contact with the enzyme. We find that Arg at P(1) (versus Lys) favors both tighter binding and more rapid cleavage, whereas Met (versus Arg) at P'(2) favors tighter binding but has minimal effect on cleavage. Surprisingly, we find that the APPI scaffold greatly enhances proteolytic cleavage rates, independently of the binding loop. We draw thermodynamic additivity cycles analyzing the interdependence of P(1) and P'(2) substitutions and scaffold differences, finding multiple instances in which the contributions of these features are nonadditive. We also report the crystal structure of the mesotrypsin·APPI complex, in which we find that the binding loop of APPI displays evidence of increased mobility compared with BPTI. Our data suggest that the enhanced vulnerability of APPI to mesotrypsin cleavage may derive from sequence differences in the scaffold that propagate increased flexibility and mobility to the binding loop.
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Affiliation(s)
- Moh'd A Salameh
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, Florida 32224, USA
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19
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Gandhi PS, Chen Z, Di Cera E. Crystal structure of thrombin bound to the uncleaved extracellular fragment of PAR1. J Biol Chem 2010; 285:15393-15398. [PMID: 20236938 DOI: 10.1074/jbc.m110.115337] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abundant structural information exists on how thrombin recognizes ligands at the active site or at exosites separate from the active site region, but remarkably little is known about how thrombin recognizes substrates that bridge both the active site and exosite I. The case of the protease-activated receptor PAR1 is particularly relevant in view of the plethora of biological effects associated with its activation by thrombin. Here, we present the 1.8 A resolution structure of thrombin S195A in complex with a 30-residue long uncleaved extracellular fragment of PAR1 that documents for the first time a productive binding mode bridging the active site and exosite I. The structure reveals two unexpected features of the thrombin-PAR1 interaction. The acidic P3 residue of PAR1, Asp(39), does not hinder binding to the active site and actually makes favorable interactions with Gly(219) of thrombin. The tethered ligand domain shows a considerable degree of disorder even when bound to thrombin. The results fill a significant gap in our understanding of the molecular mechanisms of recognition by thrombin in ways that are relevant to other physiological substrates.
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Affiliation(s)
- Prafull S Gandhi
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Zhiwei Chen
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104
| | - Enrico Di Cera
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104.
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20
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Bah A, Carrell CJ, Chen Z, Gandhi PS, Di Cera E. Stabilization of the E* form turns thrombin into an anticoagulant. J Biol Chem 2009; 284:20034-40. [PMID: 19473969 DOI: 10.1074/jbc.m109.012344] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Previous studies have shown that deletion of nine residues in the autolysis loop of thrombin produces a mutant with an anticoagulant propensity of potential clinical relevance, but the molecular origin of the effect has remained unresolved. The x-ray crystal structure of this mutant solved in the free form at 1.55 A resolution reveals an inactive conformation that is practically identical (root mean square deviation of 0.154 A) to the recently identified E* form. The side chain of Trp(215) collapses into the active site by shifting > 10 A from its position in the active E form, and the oxyanion hole is disrupted by a flip of the Glu(192)-Gly(193) peptide bond. This finding confirms the existence of the inactive form E* in essentially the same incarnation as first identified in the structure of the thrombin mutant D102N. In addition, it demonstrates that the anticoagulant profile often caused by a mutation of the thrombin scaffold finds its likely molecular origin in the stabilization of the inactive E* form that is selectively shifted to the active E form upon thrombomodulin and protein C binding.
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Affiliation(s)
- Alaji Bah
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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21
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Thermodynamic characterization of pyrazole and azaindole derivatives binding to p38 mitogen-activated protein kinase using Biacore T100 technology and van’t Hoff analysis. Anal Biochem 2008; 383:255-64. [DOI: 10.1016/j.ab.2008.08.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 08/12/2008] [Accepted: 08/14/2008] [Indexed: 12/11/2022]
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22
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Page MJ, Carrell CJ, Di Cera E. Engineering protein allostery: 1.05 A resolution structure and enzymatic properties of a Na+-activated trypsin. J Mol Biol 2008; 378:666-72. [PMID: 18377928 DOI: 10.1016/j.jmb.2008.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Revised: 02/29/2008] [Accepted: 03/04/2008] [Indexed: 11/28/2022]
Abstract
Some trypsin-like proteases are endowed with Na(+)-dependent allosteric enhancement of catalytic activity, but this important mechanism has been difficult to engineer in other members of the family. Replacement of 19 amino acids in Streptomyces griseus trypsin targeting the active site and the Na(+)-binding site were found necessary to generate efficient Na(+) activation. Remarkably, this property was linked to the acquisition of a new substrate selectivity profile similar to that of factor Xa, a Na(+)-activated protease involved in blood coagulation. The X-ray crystal structure of the mutant trypsin solved to 1.05 A resolution defines the engineered Na(+) site and active site loops in unprecedented detail. The results demonstrate that trypsin can be engineered into an efficient allosteric protease, and that Na(+) activation is interwoven with substrate selectivity in the trypsin scaffold.
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Affiliation(s)
- Michael J Page
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110, USA
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23
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Bush-Pelc LA, Marino F, Chen Z, Pineda AO, Mathews FS, Di Cera E. Important role of the cys-191 cys-220 disulfide bond in thrombin function and allostery. J Biol Chem 2007; 282:27165-27170. [PMID: 17636263 DOI: 10.1074/jbc.m703202200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Little is known on the role of disulfide bonds in the catalytic domain of serine proteases. The Cys-191-Cys-220 disulfide bond is located between the 190 strand leading to the oxyanion hole and the 220-loop that contributes to the architecture of the primary specificity pocket and the Na+ binding site in allosteric proteases. Removal of this bond in thrombin produces an approximately 100-fold loss of activity toward several chromogenic and natural substrates carrying Arg or Lys at P1. Na+ activation is compromised, and no fluorescence change can be detected in response to Na+ binding. A 1.54-A resolution structure of the C191A/C220A mutant in the free form reveals a conformation similar to the Na+-free slow form of wild type. The lack of disulfide bond exposes the side chain of Asp-189 to solvent, flips the backbone O atom of Gly-219, and generates disorder in portions of the 186 and 220 loops defining the Na+ site. This conformation, featuring perturbation of the Na+ site but with the active site accessible to substrate, offers a possible representation of the recently identified E* form of thrombin. Disorder in the 186 and 220 loops and the flip of Gly-219 are corrected by the active site inhibitor H-D-Phe-Pro-Arg-CH(2)Cl, as revealed by the 1.8-A resolution structure of the complex. We conclude that the Cys-191-Cys-220 disulfide bond confers stability to the primary specificity pocket by shielding Asp-189 from the solvent and orients the backbone O atom of Gly-219 for optimal substrate binding. In addition, the disulfide bond stabilizes the 186 and 220 loops that are critical for Na+ binding and activation.
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Affiliation(s)
- Leslie A Bush-Pelc
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Francesca Marino
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Zhiwei Chen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Agustin O Pineda
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - F Scott Mathews
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Enrico Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110.
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24
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Silva-Junior FP, Guedes HLM, Garvey LC, Aguiar AS, Bourguignon SC, Di Cera E, Giovanni-De-Simone S. BJ-48, a novel thrombin-like enzyme from the Bothrops jararacussu venom with high selectivity for Arg over Lys in P1: Role of N-glycosylation in thermostability and active site accessibility. Toxicon 2007; 50:18-31. [PMID: 17433397 DOI: 10.1016/j.toxicon.2007.02.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 02/09/2007] [Accepted: 02/19/2007] [Indexed: 10/23/2022]
Abstract
BJ-48, a serine protease from the venom of Bothrops jararacussu, was purified to homogeneity using affinity chromatography on p-aminobenzamidine-agarose followed by HPLC gel filtration. BJ-48 presented 52kDa by SDS-PAGE analysis and 48,036Da by electron spray mass spectrometry. The enzyme was shown to be highly glycosylated with 42% of N-linked carbohydrates composed of Fuc(1):GalN(4):GlcN(5):Gal(1):Man(2) and a high content of sialic acid residues (8-12%). BJ-48 had optimal esterase activity at pH 7.5 and displayed maximum catalytic rate at 50 degrees C. Its hydrolytic activity was strongly inhibited by aprotinin and dithiothreitol while N-tosyl-l-phenylalanine chloromethyl ketone, 6-aminocaproic acid, E-64 and soybean trypsin inhibitor (SBTI) were ineffective. The kinetics of BJ-48 with chromogenic substrates revealed an unprecedented selectivity (10(4)-fold) for Arg over Lys in P1. BJ-48 proved to be a thrombin-like enzyme (TLE) with a specific fibrinogen-clotting activity of 73.4NIH units/mg. The TLE rapidly digested human fibrinogen Bbeta chain, but the Aalpha chain was cleaved specifically to release fibrinopeptide A with k(cat)/K(m)=2.1 microM(-1)s(-1). The TLE showed no activity toward other thrombin substrates like protein C, protease-activated receptor-1 or inhibitors such as hirudin and antithrombin. A non-denaturing procedure using PNGase F and neuraminidase followed by hydrophobic interaction chromatography was employed to obtain active BJ-48 forms with variable carbohydrate content. Compared to the native enzyme, total or partially deglycosylated BJ-48 forms presented up to 2-fold reduction in their specific activities upon heating at 55/65 degrees C or treatment with SBTI. These results point out a role for BJ-48 glycosylation in thermostability and controlling the access of some canonical protein inhibitors to the active site.
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Affiliation(s)
- Floriano P Silva-Junior
- Laboratório de Bioquímica de Proteínas e Peptídeos, Departamento de Bioquímica e Biologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Av. Brasil 4365, 21045 900 RJ, Brazil
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25
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Abstract
Thrombin is a Na(+)-activated, allosteric serine protease that plays multiple functional roles in blood pathophysiology. Binding of Na(+) is the major driving force behind the procoagulant, prothrombotic and signaling functions of the enzyme. This review summarizes our current understanding of the molecular basis of thrombin allostery with special emphasis on the kinetic aspects of Na(+) activation. The molecular mechanism of thrombin allostery is a remarkable example of long-range communication that offers a paradigm for many other biological systems.
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Affiliation(s)
- Enrico Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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26
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Carrell CJ, Bush LA, Mathews FS, Di Cera E. High resolution crystal structures of free thrombin in the presence of K+ reveal the molecular basis of monovalent cation selectivity and an inactive slow form. Biophys Chem 2006; 121:177-84. [PMID: 16487650 DOI: 10.1016/j.bpc.2005.12.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Revised: 12/17/2005] [Accepted: 12/17/2005] [Indexed: 11/18/2022]
Abstract
Structural biology has recently advanced our understanding of the molecular mechanisms of activation and selectivity in monovalent cation activated enzymes. Here we report a 1.9 Angstrom resolution crystal structure of free thrombin, a Na(+) selective enzyme, in the presence of KCl. There are two molecules in the asymmetric unit, one with the cation site bound to K(+) and the other with this site free. The K(+)-bound form shows key differences compared with the Na(+)-bound structure that explain the different kinetics of activation. The cation-free form, on the other hand, assumes a conformation where the monovalent cation binding site is completely disordered, the S1 pocket is inaccessible to substrate and binding to exosite I is compromised by an unprecedented >20 Angstrom shift in the position of the autolysis loop. This form, named S(*), corresponds to the inactive Na(+)-free slow form identified by early kinetic studies. A simple model of thrombin allostery that incorporates the contribution of S(*) is proposed.
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Affiliation(s)
- Christopher J Carrell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110, USA
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27
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Abstract
Proteases play diverse roles in a variety of essential biological processes, both as non-specific catalysts of protein degradation and as highly specific agents that control physiologic events. Here, we review the mechanisms of substrate specificity employed by serine proteases and focus our discussion on coagulation proteases. We dissect the interplay between active site and exosite specificity and how substrate recognition is regulated allosterically by Na+ binding. We also draw attention to a functional polarity that exists in the serine protease fold, which sheds light on the structural linkages between the active site and exosites.
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Affiliation(s)
- M J Page
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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28
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Gosalia DN, Salisbury CM, Maly DJ, Ellman JA, Diamond SL. Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays. Proteomics 2005; 5:1292-8. [PMID: 15742319 DOI: 10.1002/pmic.200401011] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A novel microarray-based proteolytic profiling assay enabled the rapid determination of protease substrate specificities with minimal sample and enzyme usage. A 722-member library of fluorogenic protease substrates of the general format Ac-Ala-X-X-(Arg/Lys)-coumarin was synthesized and microarrayed, along with fluorescent calibration standards, in glycerol nanodroplets on microscope slides. The arrays were then activated by deposition of an aerosolized enzyme solution, followed by incubation and fluorometric scanning. The specificities of human blood serine proteases (human thrombin, factor Xa, plasmin, and urokinase plasminogen activator) were examined. The arrays provided complete maps of protease specificity for all of the substrates tested and allowed for detection of cooperative interactions between substrate subsites. The arrays were further utilized to explore the conservation of thrombin specificity across species by comparing the proteolytic fingerprints of human, bovine, and salmon thrombin. These enzymes share nearly identical specificity profiles despite approximately 390 million years of divergent evolution. Fluorogenic substrate microarrays provide a rapid way to determine protease substrate specificity information that can be used for the design of selective inhibitors and substrates, the study of evolutionary divergence, and potentially, for diagnostic applications.
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Affiliation(s)
- Dhaval N Gosalia
- Department of Bioengineering, Institute for Medicine and Engineering, University of Pennsylvania, PA, USA
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29
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Isetti G, Maurer MC. Probing thrombin's ability to accommodate a V34F substitution within the factor XIII activation peptide segment (28-41)*. ACTA ACUST UNITED AC 2004; 63:241-52. [PMID: 15049836 DOI: 10.1111/j.1399-3011.2004.00132.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In blood coagulation, thrombin helps to activate factor XIII (FXIII) by cleaving the activation peptide (AP) at the R37-G38 peptide bond. The common polymorphism V34L yields a FXIII that is more easily activated than the wild type enzyme. Peptides based on the FXIII (28-41) (28TVELQGVVPRGVNL41) sequence serve as an important model system to evaluate the substrate specificity of thrombin and thus how to regulate FXIII activation. Our previous kinetic and nuclear magnetic resonance (NMR) studies have suggested that the P4-P1 amino acids on this FXIII segment provide key anchors to the thrombin active site surface. Furthermore, the most effective amino acid to have at the P4 position is a leucine. In the current work, a peptide containing V34F was examined to probe the ability to accommodate an aromatic residue at this position. Kinetic parameters for thrombin-catalyzed hydrolysis of FXIII AP (28-41) V34F are comparable with that of the wild type V34. One-dimensional proton line-broadening studies reveal that the 34FVPR37 segment encompassing the P4-P1 positions makes the most contact with the thrombin surface. Two-dimensional transferred-nuclear overhauser effect spectroscopy (NOESY) studies indicate that when the peptide is bound to thrombin, the F34 aromatic ring is oriented to promote P4-P2 interactions with P36. This characteristic has been viewed as a hallmark for V34L. An ability to generate this interaction may promote the ability of FXIII AP (28-41) V34F to remain a viable substrate for thrombin.
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Affiliation(s)
- G Isetti
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, KY 40292, USA
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30
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Jacques SL, Kuliopulos A. Protease-activated receptor-4 uses dual prolines and an anionic retention motif for thrombin recognition and cleavage. Biochem J 2004; 376:733-40. [PMID: 13678420 PMCID: PMC1223816 DOI: 10.1042/bj20030954] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2003] [Revised: 09/09/2003] [Accepted: 09/18/2003] [Indexed: 11/17/2022]
Abstract
Thrombin activation of human platelets is mediated by the high-affinity PAR1 (protease-activated receptor-1) and the low-affinity PAR4 receptor. PAR1 and PAR4 exhibit markedly disparate kinetics of activation that likely reflect differences in the macromolecular association of thrombin with their respective N-terminal extracellular domains (exodomains). Here we examine the mechanism of initial thrombin binding and cleavage of the high- and low-affinity PAR exodomains using steady-state kinetic analyses. We showed that the PAR4 exodomain lacks the functional hirudin-like sequence found in PAR1 and does not bind exosite I to cause allosteric activation or inhibition of thrombin. Instead, PAR4 contains an anionic cluster, Asp(57)...Asp(59) ...Glu(62)...Asp(65) (DDED), in its exodomain, which slows the dissociation of PAR4 from the cationic thrombin. The analogous anionic residues in the PAR1 exodomain do not influence affinity for thrombin. Although PAR4 is cleaved more slowly than PAR1 on the cell surface, peptides containing the PAR4 P(4)-P(1) active-site-interacting sequence, Pro(45)-Ala-Pro-Arg (PAPR), are efficiently cleaved due to the optimal placement of dual prolines at positions P(4) and P(2). In comparison, thrombin has low affinity and slow cleavage rates for peptides that have a P(3) proline as occurs in human PAR3. Thus, to compensate for the lack of exosite I binding, PAR4 utilizes proline residues in its P(4)-P(1) sequence to provide high-affinity interactions with the active site and an anionic cluster to slow dissociation from the cationic thrombin.
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Affiliation(s)
- Suzanne L Jacques
- Molecular Cardiology Research Institute, Division of Hematology/Oncology, Tufts-New England Medical Center and Departments of Medicine and Biochemistry, Tufts University School of Medicine, Boston, MA 02111, USA
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31
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Abstract
The catalytically inactive mutant S195A was used to study the interaction of thrombin with substrates under equilibrium conditions. By monitoring changes in intrinsic fluorescence, we measured dissociation constants for a variety of synthetic substrates, PAR peptides and the inhibitor PPACK. The S195A mutant retains the Na(+)-binding properties of the wild type, and substrate binding to the mutant is enhanced by the presence of Na(+). Temperature dependence studies allowed calculation of the thermodynamic parameters of substrate binding at the active site and showed a negligible deltaC(p). Titration of synthetic substrates carrying substitutions at the P1-P3 positions revealed energetics consistent with the specificity hierarchy identified in hydrolysis by the wild type. Titration with PAR peptides, which interact with both the active site and exosite I of thrombin, also showed consistency with the results obtained with the wild type at steady state. These findings demonstrate that inactive mutants of enzymes make it possible to dissect the equilibrium components linked to substrate binding and complement information on the kinetic properties of the wild type.
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Affiliation(s)
- Maxwell M Krem
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110, USA
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32
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Magklara A, Mellati AA, Wasney GA, Little SP, Sotiropoulou G, Becker GW, Diamandis EP. Characterization of the enzymatic activity of human kallikrein 6: Autoactivation, substrate specificity, and regulation by inhibitors. Biochem Biophys Res Commun 2003; 307:948-55. [PMID: 12878203 DOI: 10.1016/s0006-291x(03)01271-3] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Human kallikrein 6 (hK6) is a trypsin-like serine protease, member of the human kallikrein gene family. Studies suggested a potential involvement of hK6 in the development and progression of Alzheimer's disease. The serum levels of hK6 might be used as a biomarker for ovarian cancer. To gain insights into the physiological role of this enzyme, we sought to determine its substrate specificity and its interactions with various inhibitors. We produced the proform of hK6 and showed that this enzyme was able to autoactivate, as well as proteolyse itself, leading to inactivation. Kinetic studies indicated that hK6 cleaved with much higher efficiency after Arg than Lys and with a preference for Ser or Pro in the P2 position. The efficient degradation of fibrinogen and collagen types I and IV by hK6 indicated that this kallikrein might play a role in tissue remodeling and/or tumor invasion and metastasis. We also demonstrated proteolysis of amyloid precursor protein by hK6 and determined the cleavage sites at the N-terminal end of the protein. Inhibition of hK6 was achieved via binding to different serpins, among which antithrombin III was the most efficient.
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Affiliation(s)
- Angeliki Magklara
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, 600 University Avenue, Toronto, Ont., Canada M5G 1X5
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33
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Abstract
Phage display substrate enables rapid determination of protease specificity by exposing vast numbers of recombinant peptides to a given protease. Peptides released through specific cleavage are amplified in an expression system. Phage display substrate has been widely exploited and developed further. The number of proteases (from various sources) characterized by this approach testifies to its power. To conserve their advantage over chemical methods, however, phage libraries must be constructed accordingly. The current phenomenal progress in genomics steadily increases the number of protease to be studied. Phage display substrate should prove a powerful method to exploit this wealth of new knowledge.
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34
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Abstract
Thrombin recognizes a number of natural substrates that are responsible for important physiologic functions. Its high specificity is controlled by residues within the active site, and by separate recognition sites located on the surface of the enzyme. A number of studies have addressed the question of how thrombin changes its specificity from fibrinogen to protein C, switching from a procoagulant to an anticoagulant enzyme. Site directed mutagenesis studies have revealed important aspects of how this switch takes place. Specifically, residues W215 and E217 have emerged as key residues in controlling the interaction with fibrinogen in that mutation of these residues compromises the procoagulant function of the enzyme up to 500-fold. The loss of fibrinogen clotting reaches 20,000-fold in the double mutant W215A/E217A, whereas protein C activation is compromised less than sevenfold. These findings demonstrate that thrombin specificity can be dissected at the molecular level using Ala-scanning mutagenesis and the procoagulant function of the enzyme can be abrogated rationally and selectively. It is now possible to extend this strategy to the study of other interactions of thrombin, as well as to related serine proteases.
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Affiliation(s)
- E Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, Box 8231, St. Louis, MO 63110, USA.
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35
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Kridel SJ, Chen E, Smith JW. A substrate phage enzyme-linked immunosorbent assay to profile panels of proteases. Anal Biochem 2001; 294:176-84. [PMID: 11444814 DOI: 10.1006/abio.2001.5167] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It is estimated that proteases comprise nearly 2% of the human genome. Given that the primary structure of all known proteases will soon be available, an important challenge is to define the structure-activity relationships that govern substrate hydrolysis. Ideally this would be accomplished on a genome-wide scale. To this end, we have developed a one-pot phage selection system that yields the substrate recognition profile of multiple proteases from a single round of selection. The system meets five key criteria: (i) multiple proteases can be analyzed simultaneously, (ii) prior knowledge of substrate preference is not required, (iii) information regarding substrate preferences on both side of the scissile bond is obtained, (iv) the system yields selective substrates that distinguish closely related proteases, and (v) semiquantitative information on substrate hydrolysis is obtained, allowing for the assignment of initial rank-order preferences. As an illustration, a phage selection with a mixture of thrombin and factor Xa (serine proteases) along with matrix-metalloproteinase-9 and atrolysin C (metalloproteinases) was performed. Peptide substrates were identified that (i) have high k(cat)/K(m) ratios, (ii) are selective for individual proteases, and (iii) match the sequences of known physiological substrates.
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Affiliation(s)
- S J Kridel
- Program on Cell Adhesion, The Burnham Institute, La Jolla, California 92037, USA
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36
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Edwards PD, Mauger RC, Cottrell KM, Morris FX, Pine KK, Sylvester MA, Scott CW, Furlong ST. Synthesis and enzymatic evaluation of a P1 arginine aminocoumarin substrate library for trypsin-like serine proteases. Bioorg Med Chem Lett 2000; 10:2291-4. [PMID: 11055341 DOI: 10.1016/s0960-894x(00)00460-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A method for the solid-phase synthesis of P1 arginine containing peptides via attachment of the arginine side-chain guanidine group is described. This procedure is applied to the preparation of a tetrapeptide, P1 arginine aminocoumarin PS-SCL. This library was validated by using it to determine the P4-P2 specificity for thrombin and comparing the results to the known thrombin subsite specificity. This is the first reported example of a PS-SCL library containing a P1 arginine.
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Affiliation(s)
- P D Edwards
- Department of Chemistry, AstraZeneca Pharmaceuticals, Wilmington, DE 19850-5437, USA.
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37
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Trumbo TA, Maurer MC. Examining thrombin hydrolysis of the factor XIII activation peptide segment leads to a proposal for explaining the cardioprotective effects observed with the factor XIII V34L mutation. J Biol Chem 2000; 275:20627-31. [PMID: 10801785 DOI: 10.1074/jbc.m000209200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the blood coagulation cascade, thrombin cleaves fibrinopeptides A and B from fibrinogen revealing sites for fibrin polymerization that lead to insoluble clot formation. Factor XIII stabilizes this clot by catalyzing the formation of intermolecular cross-links in the fibrin network. Thrombin activates the Factor XIII a(2) dimer by cleaving the Factor XIII activation peptide segment at the Arg(37)-Gly(38) peptide bond. Using a high performance liquid chromatography assay, the kinetic constants K(m), k(cat), and k(cat)/K(m) were determined for thrombin hydrolysis of fibrinogen Aalpha-(7-20), Factor XIII activation peptide-(28-41), and Factor XIII activation peptide-(28-41) with a Val(34) to Leu substitution. This Val to Leu mutation has been correlated with protection from myocardial infarction. In the absence of fibrin, the Factor XIII activation peptide-(28-41) exhibits a 10-fold lower k(cat)/K(m) value than fibrinogen Aalpha-(7-20). With the Factor XIII V34L mutation, decreases in K(m) and increases in k(cat) produce a 6-fold increase in k(cat)/K(m) relative to the wild-type Factor XIII sequence. A review of the x-ray crystal structures of known substrates and inhibitors of thrombin leads to a hypothesis that the new Leu generates a peptide with more extensive interactions with the surface of thrombin. As a result, the Factor XIII V34L is proposed to be susceptible to wasteful conversion of zymogen to activated enzyme. Premature depletion may provide cardioprotective effects.
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Affiliation(s)
- T A Trumbo
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA
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38
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Boxrud PD, Fay WP, Bock PE. Streptokinase binds to human plasmin with high affinity, perturbs the plasmin active site, and induces expression of a substrate recognition exosite for plasminogen. J Biol Chem 2000; 275:14579-89. [PMID: 10799544 DOI: 10.1074/jbc.275.19.14579] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Binding of streptokinase (SK) to plasminogen (Pg) conformationally activates the zymogen and converts both Pg and plasmin (Pm) into specific Pg activators. The interaction of SK with Pm and its relationship to the mechanism of Pg activation were evaluated in equilibrium binding studies with active site-labeled fluorescent Pm derivatives and in kinetic studies of SK-induced changes in the catalytic specificity of Pm. SK bound to fluorescein-labeled and native Pm with dissociation constants of 11 +/- 2 pm and 12 +/- 4 pm, which represented a 1,000-10,000-fold higher affinity than determined for Pg. Stoichiometric binding of SK to native Pm was followed by generation of a two-fragment form of SK cleaved at Lys(59) (SK'), which exhibited an indistinguishable affinity for labeled Pm, while a truncated, SK(55-414) species had a 120-360-fold reduced affinity. Binding of SK to native Pm was accompanied by a >50-fold enhancement in specificity for activation of Pg, which was paralleled by a surprising 2.6-10-fold loss of specificity of Pm for 8 of 11 tripeptide-pNA substrates. Further studies with Pm labeled at the active site with 2-anilinonaphthalene-6-sulfonic acid demonstrated directly that binding of SK to Pm resulted in expression of a new substrate binding exosite for Pg on the SK.Pm complex. It is concluded that SK activates Pg in part by preferential binding to the active zymogen conformation. High affinity binding of SK to Pm enhances Pg substrate specificity principally through emergence of a substrate recognition exosite.
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Affiliation(s)
- P D Boxrud
- Department of Pathology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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39
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Backes BJ, Harris JL, Leonetti F, Craik CS, Ellman JA. Synthesis of positional-scanning libraries of fluorogenic peptide substrates to define the extended substrate specificity of plasmin and thrombin. Nat Biotechnol 2000; 18:187-93. [PMID: 10657126 DOI: 10.1038/72642] [Citation(s) in RCA: 209] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have developed a strategy for the synthesis of positional-scanning synthetic combinatorial libraries (PS-SCL) that does not depend on the identity of the P1 substituent. To demonstrate the strategy, we synthesized a tetrapeptide positional library in which the P1 amino acid is held constant as a lysine and the P4-P3-P2 positions are positionally randomized. The 6,859 members of the library were synthesized on solid support with an alkane sulfonamide linker, and then displaced from the solid support by condensation with a fluorogenic 7-amino-4-methylcoumarin-derivatized lysine. This library was used to determine the extended substrate specificities of two trypsin-like enzymes, plasmin and thrombin, which are involved in the blood coagulation pathway. The optimal P4 to P2 substrate specificity for plasmin was P4-Lys/Nle (norleucine)/Val/Ile/Phe, P3-Xaa, and P2-Tyr/Phe/Trp. This cleavage sequence has recently been identified in some of plasmin's physiological substrates. The optimal P4 to P2 extended substrate sequence determined for thrombin was P4-Nle/Leu/Ile/Phe/Val, P3-Xaa, and P2-Pro, a sequence found in many of the physiological substrates of thrombin. Single-substrate kinetic analysis of plasmin and thrombin was used to validate the substrate preferences resulting from the PS-SCL. By three-dimensional structural modeling of the substrates into the active sites of plasmin and thrombin, we identified potential determinants of the defined substrate specificity. This method is amenable to the incorporation of diverse substituents at the P1 position for exploring molecular recognition elements in proteolytic enzymes.
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Affiliation(s)
- B J Backes
- Chemistry Department, University of California Berkeley, Berkeley, CA 94720, USA
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40
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Abstract
Serine proteases of the chymotrypsin family have maintained a common fold over an evolutionary span of more than one billion years. Notwithstanding modest changes in sequence, this class of enzymes has developed a wide variety of substrate specificities and important biological functions. Remarkably, the C-terminal portion of the sequence in the protease domain accounts fully for this functional diversity. This portion is often encoded by a single exon and contains most of the residues forming the contact surface in the active site for the P1-P3 residues of the substrate, as well as domains responsible for the modulation of catalytic activity. The evolution of serine proteases was therefore driven by optimization of contacts made with the unprimed subsites of the substrate and targeted a relatively short portion of the sequence toward the C-terminal end. The dominant role of the C-terminal sequence should facilitate the identification of function in newly discovered genes belonging to this class of enzymes.
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Affiliation(s)
- M M Krem
- Department of Biochemistry, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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41
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De Filippis V, Russo I, Vindigni A, Di Cera E, Salmaso S, Fontana A. Incorporation of noncoded amino acids into the N-terminal domain 1-47 of hirudin yields a highly potent and selective thrombin inhibitor. Protein Sci 1999; 8:2213-7. [PMID: 10548068 PMCID: PMC2144148 DOI: 10.1110/ps.8.10.2213] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Hirudin is an anticoagulant polypeptide isolated from a medicinal leech that inhibits thrombin with extraordinary potency (Kd = 0.2-1.0 pM) and selectivity. Hirudin is composed of a compact N-terminal region (residues 1-47, cross-linked by three disulfide bridges) that binds to the active site of thrombin, and a flexible C-terminal tail (residues 48-64) that interacts with the exosite I of the enzyme. To minimize the sequence of hirudin able to bind thrombin and also to improve its therapeutic profile, several N-terminal fragments have been prepared as potential anticoagulants. However, the practical use of these fragments has been impaired by their relatively poor affinity for the enzyme, as given by the increased value of the dissociation constant (Kd) of the corresponding thrombin complexes (Kd = 30-400 nM). The aim of the present study is to obtain a derivative of the N-terminal domain 1-47 of hirudin displaying enhanced inhibitory potency for thrombin compared to the natural product. In this view, we have synthesized an analogue of fragment 1-47 of hirudin HM2 in which Val1 has been replaced by tert-butylglycine, Ser2 by Arg, and Tyr3 by beta-naphthylalanine, to give the BugArgNal analogue. The results of chemical and conformational characterization indicate that the synthetic peptide is able to fold efficiently with the correct disulfide topology (Cys6-Cys14, Cys16-Cys28, Cys22-Cys37), while retaining the conformational properties of the natural fragment. Thrombin inhibition data indicate that the effects of amino acid replacements are perfectly additive if compared to the singly substituted analogues (De Filippis V, Quarzago D, Vindigni A, Di Cera E, Fontana A, 1998, Biochemistry 37:13507-13515), yielding a molecule that inhibits the fast or slow form of thrombin by 2,670- and 6,818-fold more effectively than the natural fragment, and that binds exclusively at the active site of the enzyme with an affinity (Kd,fast = 15.4 pM, Kd,slow = 220 pM) comparable to that of full-length hirudin (Kd,fast = 0.2 pM, Kd,slow = 5.5 pM). Moreover, BugArgNal displays absolute selectivity for thrombin over the other physiologically important serine proteases trypsin, plasmin, factor Xa, and tissue plasminogen activator, up to the highest concentration of inhibitor tested (10 microM).
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Affiliation(s)
- V De Filippis
- CRIBI Biotechnology Center and Department of Pharmaceutical Sciences, University of Padua, Italy
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42
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Chuang YJ, Gettins PG, Olson ST. Importance of the P2 glycine of antithrombin in target proteinase specificity, heparin activation, and the efficiency of proteinase trapping as revealed by a P2 Gly --> Pro mutation. J Biol Chem 1999; 274:28142-9. [PMID: 10497166 DOI: 10.1074/jbc.274.40.28142] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A sequence-specific heparin pentasaccharide activates the serpin, antithrombin, to inhibit factor Xa through an allosteric mechanism, whereas full-length heparin chains containing this sequence further activate the serpin to inhibit thrombin by an alternative bridging mechanism. To test whether the factor Xa specificity of allosterically activated antithrombin is encoded in the serpin reactive center loop, we mutated the factor Xa-preferred P2 Gly to the thrombin-preferred P2 Pro. Kinetic studies revealed that the mutation maximally enhanced the reactivity of antithrombin with thrombin 15-fold and decreased its reactivity toward factor Xa 2-fold when the serpin was activated by heparin pentasaccharide, thereby transforming antithrombin into an allosterically activated inhibitor of both factor Xa and thrombin. Surprisingly, the enhanced thrombin specificity of the mutant antithrombin was attenuated when a full-length bridging heparin was the activator, due both to a reduced rate of covalent reaction of the mutant serpin and thrombin and preferred reaction of the mutant serpin as a substrate. These results demonstrate that the reactive center loop sequence determines the specificity of allosterically activated antithrombin for factor Xa and that the conformational flexibility of the P2 Gly may be critical for optimal bridging of antithrombin and thrombin by physiologic heparin and for preventing antithrombin from reacting as a substrate in the bridging complex.
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Affiliation(s)
- Y J Chuang
- Center for Molecular Biology of Oral Diseases, College of Dentistry, University of Illinois, Chicago, Illinois 60612, USA
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43
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Grucza RA, Bradshaw JM, Fütterer K, Waksman G. SH2 domains: from structure to energetics, a dual approach to the study of structure-function relationships. Med Res Rev 1999; 19:273-93. [PMID: 10398925 DOI: 10.1002/(sici)1098-1128(199907)19:4<273::aid-med2>3.0.co;2-g] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- R A Grucza
- Washington University School of Medicine, Department of Biochemistry and Molecular Biophysics, 660 South Euclid Avenue, Saint Louis, MO 63110, USA
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44
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Abstract
Thrombin plays both procoagulant and anticoagulant roles in the blood coagulation cascade. This dual role is influenced allosterically by the binding of Na(+) near the primary specificity pocket of the enzyme. Recent findings demonstrate that it is possible to engineer recombinant thrombins that have practically lost anticoagulant activity but retain their anticoagulant properties. These anticoagulant thrombins bear substitutions in or around the Na(+) binding site, provide important clues on structure-function relations, and offer a promising alternative to current anticoagulant therapies. In addition, they demonstrate the importance of Na(+) as a coagulation factor and broaden our understanding of the function and regulation of all vitamin K-dependent clotting enzymes.
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Affiliation(s)
- E Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
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45
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Vindigni A, Di Cera E. Role of P225 and the C136-C201 disulfide bond in tissue plasminogen activator. Protein Sci 1998; 7:1728-37. [PMID: 10082369 PMCID: PMC2144078 DOI: 10.1002/pro.5560070807] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The protease domain of tissue plasminogen activator (tPA), a key fibrinolytic enzyme, was expressed in Escherichia coli with a yield of 1 mg per liter of media. The recombinant protein was titrated with the Erythrina caraffa trypsin inhibitor (ETI) and characterized in its interaction with plasminogen and the natural inhibitor plasminogen activator inhibitor-1 (PAI-1). Analysis of the catalytic properties of tPA using a library of chromogenic substrates carrying substitutions at P1, P2, and P3 reveals a strong preference for Arg over Lys at P1, unmatched by other serine proteases like thrombin or trypsin. In contrast to these proteases and plasmin, tPA shows little or no preference for Pro over Gly at P2. A specific inhibition of tPA by Cu2+ was discovered. The divalent cation presumably binds to H188 near D189 in the primary specificity pocket and inhibits substrate binding in a competitive manner with a Kd = 19 microM. In an attempt to engineer Na+ binding and enhanced catalytic activity in tPA, P225 was replaced with Tyr, the residue present in Na+-dependent allosteric serine proteases. The P225Y mutation did not result in cation binding, but caused a significant loss of specificity (up to 100-fold) toward chromogenic substrates and plasminogen and considerably reduced the inhibition by PAI-1 and ETI. Interestingly, the P225Y substitution enhanced the ability of Cu2+ to inhibit the enzyme. Elimination of the C136-C201 disulfide bond, that is absent in all Na+-dependent allosteric serine proteases, significantly enhanced the yield (5 mg per liter of media) of expression in E. coli, but caused no changes in the properties of the enzyme whether residue 225 was Pro or Tyr. These findings point out an unanticipated crucial role for residue 225 in controlling the catalytic activity of tPA, and suggest that engineering of a Na+-dependent allosteric enhancement of catalytic activity in this enzyme, must involve substantial changes in the region homologous to the Na+ binding site of allosteric serine proteases.
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Affiliation(s)
- A Vindigni
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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46
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Di Cera E. Site-Specific Thermodynamics: Understanding Cooperativity in Molecular Recognition. Chem Rev 1998; 98:1563-1592. [PMID: 11848942 DOI: 10.1021/cr960135g] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Enrico Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, Missouri 63110
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47
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di Cera E. Site-specific analysis of mutational effects in proteins. ADVANCES IN PROTEIN CHEMISTRY 1998; 51:59-119. [PMID: 9615169 DOI: 10.1016/s0065-3233(08)60651-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- E di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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48
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Katz BA, Liu B, Barnes M, Springman EB. Crystal structure of recombinant human tissue kallikrein at 2.0 A resolution. Protein Sci 1998; 7:875-85. [PMID: 9568894 PMCID: PMC2143987 DOI: 10.1002/pro.5560070405] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Human tissue kallikrein, a trypsin-like serine protease involved in blood pressure regulation and inflammation processes, was expressed in a deglycosylated form at high levels in Pichia pastoris, purified, and crystallized. The crystal structure at 2.0 A resolution is described and compared with that of porcine kallikrein and of other trypsin-like proteases. The active and S1 sites (nomenclature of Schechter I, Berger A, 1967, Biochem Biophys Res Commun 27:157-162) are similar to those of porcine kallikrein. Compared to trypsin, the S1 site is enlarged owing to the insertion of an additional residue, cis-Pro 219. The replacement Tyr 228 --> Ala further enlarges the S1 pocket. However, the replacement of Gly 226 in trypsin with Ser in human tissue kallikrein restricts accessibility of substrates and inhibitors to Asp 189 at the base of the S1 pocket; there is a hydrogen bond between O delta1Asp189 and O gammaSer226. These changes in the architecture of the S1 site perturb the binding of inhibitors or substrates from the modes determined or inferred for trypsin. The crystal structure gives insight into the structural differences responsible for changes in specificity in human tissue kallikrein compared with other trypsin-like proteases, and into the structural basis for the unusual specificity of human tissue kallikrein in cleaving both an Arg-Ser and a Met-Lys peptide bond in its natural protein substrate, kininogen. A Zn+2-dependent, small-molecule competitive inhibitor of kallikrein (Ki = 3.3 microM) has been identified and the bound structure modeled to guide drug design.
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Affiliation(s)
- B A Katz
- Arris Pharmaceutical Corporation, South San Francisco, California 94080, USA.
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49
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Kranz JK, Hall KB. RNA binding mediates the local cooperativity between the beta-sheet and the C-terminal tail of the human U1A RBD1 protein. J Mol Biol 1998; 275:465-81. [PMID: 9466924 DOI: 10.1006/jmbi.1997.1441] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Pairwise coupling theory is applied here to determine the energetic interactions between two elements of the N-terminal RNA binding domain (RBD) of the human U1A protein. The novel application of the theory to this system incorporates both measurements of protein stability and RNA binding to define thermodynamic cycles. In this first example of the application, two regions of the protein are selected for study: tyrosine 13, one of the conserved aromatic residues on the surface of the beta-sheet, and the C-terminal tail of the RBD. The six initial pairwise coupling free energies derived from this system describe the communication between these positions, both in the free and RNA-bound states of the protein. The results show that in the absence of RNA, these two elements of the protein act independently. However, when RNA is bound, there is indirect coupling between Tyr13 and the tail, mediated through the RNA. Subsequent thermodynamic cycles involving additional perturbations to the C-terminal tail further define the communication between the C terminus and the beta-sheet. This work demonstrates the general applicability of the pairwise coupling theory to protein:nucleic acid interactions, and illustrates the necessity of such analyses to describe the network of energetic interactions that comprise RNA recognition by this RBD.
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Affiliation(s)
- J K Kranz
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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