1
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Mehner C, Hockla A, Coban M, Madden B, Estrada R, Radisky DC, Radisky ES. Activity-based protein profiling reveals active serine proteases that drive malignancy of human ovarian clear cell carcinoma. J Biol Chem 2022; 298:102146. [PMID: 35716777 PMCID: PMC9304776 DOI: 10.1016/j.jbc.2022.102146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/14/2022] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is an understudied poor prognosis subtype of ovarian cancer lacking in effective targeted therapies. Efforts to define molecular drivers of OCCC malignancy may lead to new therapeutic targets and approaches. Among potential targets are secreted proteases, enzymes which in many cancers serve as key drivers of malignant progression. Here, we found that inhibitors of trypsin-like serine proteases suppressed malignant phenotypes of OCCC cell lines. To identify the proteases responsible for malignancy in OCCC, we employed activity-based protein profiling to directly analyze enzyme activity. We developed an activity-based probe featuring an arginine diphenylphosphonate warhead to detect active serine proteases of trypsin-like specificity and a biotin handle to facilitate affinity purification of labeled proteases. Using this probe, we identified active trypsin-like serine proteases within the complex proteomes secreted by OCCC cell lines, including two proteases in common, tissue plasminogen activator and urokinase-type plasminogen activator. Further interrogation of these proteases showed that both were involved in cancer cell invasion and proliferation of OCCC cells and were also detected in in vivo models of OCCC. We conclude the detection of tissue plasminogen activator and urokinase-type plasminogen activator as catalytically active proteases and significant drivers of the malignant phenotype may point to these enzymes as targets for new therapeutic strategies in OCCC. Our activity-based probe and profiling methodology will also serve as a valuable tool for detection of active trypsin-like serine proteases in models of other cancers and other diseases.
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Affiliation(s)
- Christine Mehner
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA,Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Alexandra Hockla
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Mathew Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Benjamin Madden
- Medical Genome Facility Proteomics Core, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Derek C. Radisky
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA,For correspondence: Evette S. Radisky
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2
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Modrzycka S, Kołt S, Polderdijk SGI, Adams TE, Potoczek S, Huntington JA, Kasperkiewicz P, Drąg M. Parallel imaging of coagulation pathway proteases activated protein C, thrombin, and factor Xa in human plasma. Chem Sci 2022; 13:6813-6829. [PMID: 35774156 PMCID: PMC9200056 DOI: 10.1039/d2sc01108e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022] Open
Abstract
Activated protein C (APC), thrombin, and factor (f) Xa are vitamin K-dependent serine proteases that are key factors in blood coagulation. Moreover, they play important roles in inflammation, apoptosis, fibrosis, angiogenesis, and viral infections. Abnormal activity of these coagulation factors has been related to multiple conditions, such as bleeding and thrombosis, Alzheimer's disease, sepsis, multiple sclerosis, and COVID-19. The individual activities of APC, thrombin, and fXa in coagulation and in various diseases are difficult to establish since these proteases are related and have similar substrate preferences. Therefore, the development of selective chemical tools that enable imaging and discrimination between coagulation factors in biological samples may provide better insight into their roles in various conditions and potentially aid in the establishment of novel diagnostic tests. In our study, we used a large collection of unnatural amino acids, and this enabled us to extensively explore the binding pockets of the enzymes' active sites. Based on the specificity profiles obtained, we designed highly selective substrates, inhibitors, and fluorescent activity-based probes (ABPs) that were used for fast, direct, and simultaneous detection of APC, thrombin, and fXa in human plasma. Using a collection of natural and unnatural amino acids, we synthesized a set of fluorescent activity-based probes for the fast, direct, and simultaneous detection of coagulation factors in human plasma.![]()
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Affiliation(s)
- Sylwia Modrzycka
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Sonia Kołt
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Stéphanie G I Polderdijk
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge The Keith Peters Building, Hills Road Cambridge CB2 0XY UK
| | - Ty E Adams
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge The Keith Peters Building, Hills Road Cambridge CB2 0XY UK
| | - Stanisław Potoczek
- Department of Haematology, Blood Neoplasms, and Bone Marrow Transplantation, Wrocław Medical University Pasteura 1 50-367 Wrocław Poland
| | - James A Huntington
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge The Keith Peters Building, Hills Road Cambridge CB2 0XY UK
| | - Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
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3
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Sanrattana W, Sefiane T, Smits S, van Kleef ND, Fens MH, Lenting PJ, Maas C, de Maat S. A reactive center loop-based prediction platform to enhance the design of therapeutic SERPINs. Proc Natl Acad Sci U S A 2021; 118:e2108458118. [PMID: 34740972 PMCID: PMC8609344 DOI: 10.1073/pnas.2108458118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 11/18/2022] Open
Abstract
Serine proteases are essential for many physiological processes and require tight regulation by serine protease inhibitors (SERPINs). A disturbed SERPIN-protease balance may result in disease. The reactive center loop (RCL) contains an enzymatic cleavage site between the P1 through P1' residues that controls SERPIN specificity. This RCL can be modified to improve SERPIN function; however, a lack of insight into sequence-function relationships limits SERPIN development. This is complicated by more than 25 billion mutants needed to screen the entire P4 to P4' region. Here, we developed a platform to predict the effects of RCL mutagenesis by using α1-antitrypsin as a model SERPIN. We generated variants for each of the residues in P4 to P4' region, mutating them into each of the 20 naturally occurring amino acids. Subsequently, we profiled the reactivity of the resulting 160 variants against seven proteases involved in coagulation. These profiles formed the basis of an in silico prediction platform for SERPIN inhibitory behavior with combined P4 to P4' RCL mutations, which were validated experimentally. This prediction platform accurately predicted SERPIN behavior against five out of the seven screened proteases, one of which was activated protein C (APC). Using these findings, a next-generation APC-inhibiting α1-antitrypsin variant was designed (KMPR/RIRA; / indicates the cleavage site). This variant attenuates blood loss in an in vivo hemophilia A model at a lower dosage than the previously developed variant AIKR/KIPP because of improved potency and specificity. We propose that this SERPIN-based RCL mutagenesis approach improves our understanding of SERPIN behavior and will facilitate the design of therapeutic SERPINs.
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Affiliation(s)
- Wariya Sanrattana
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht University, Utrecht 3584, The Netherlands
| | - Thibaud Sefiane
- Laboratory for Haemostasis, Inflammation and Thrombosis, INSERM, Unité Mixte de Recherche 1176, Université Paris-Saclay 94276 Le Kremlin-Bicêtre, France
| | - Simone Smits
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht University, Utrecht 3584, The Netherlands
| | - Nadine D van Kleef
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht University, Utrecht 3584, The Netherlands
| | - Marcel H Fens
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht 3584, The Netherlands
| | - Peter J Lenting
- Laboratory for Haemostasis, Inflammation and Thrombosis, INSERM, Unité Mixte de Recherche 1176, Université Paris-Saclay 94276 Le Kremlin-Bicêtre, France
| | - Coen Maas
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht University, Utrecht 3584, The Netherlands
| | - Steven de Maat
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht University, Utrecht 3584, The Netherlands;
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4
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Ponomariov M, Shabat D, Green O. Universal Access to Protease Chemiluminescent Probes through Solid-Phase Synthesis. Bioconjug Chem 2021; 32:2134-2140. [PMID: 34549945 PMCID: PMC8532118 DOI: 10.1021/acs.bioconjchem.1c00384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Indexed: 12/27/2022]
Abstract
Protease chemiluminescent probes exhibit extremely high detection sensitivity for monitoring activity of various proteolytic enzymes. However, their synthesis, performed in solution, involves multiple synthetic and purification steps, thereby generating a major limitation for rapid preparation of such probes with diverse substrate scope. To overcome this limitation, we developed a general solid-phase-synthetic approach to prepare chemiluminescent protease probes, by peptide elongation, performed on an immobilized chemiluminescent enol-ether precursor. The enol-ether precursor is immobilized on a 2-chlorotrityl-chloride resin through an acrylic acid substituent by an acid-labile ester linkage. Next, a stepwise elongation of the peptide is performed using standard Fmoc solid-phase peptide synthesis. After cleavage of the peptide-enol-ether precursor from the resin, by hexafluoro-iso-propanol, a simple oxidation of the enol-ether yields the final chemiluminescent dioxetane protease probe. To validate the applicability of the methodology, two chemiluminescent probes were efficiently prepared by solid-phase synthesis with dipeptidyl substrates designed for activation by aminopeptidase and cathepsin-B proteases. A more complex example was demonstrated by the synthesis of a chemiluminescent probe for detection of PSA, which includes a peptidyl substrate of six amino acids. We anticipate that the described methodology would be useful for rapid preparation of chemiluminescent protease probes with vast and diverse peptidyl substrates.
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Affiliation(s)
- Maria Ponomariov
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Doron Shabat
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ori Green
- School
of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
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5
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Maag A, Sharma P, Schuijt TJ, Kopatz WF, Kruijswijk D, Marquart JA, van der Poll T, Hackeng TM, Nicolaes GAF, Meijers JCM, Bos MHA, van ’t Veer C. Structure-function of anticoagulant TIX-5, the inhibitor of factor Xa-mediated FV activation. J Thromb Haemost 2021; 19:1697-1708. [PMID: 33829620 PMCID: PMC8360041 DOI: 10.1111/jth.15329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/05/2021] [Indexed: 01/30/2023]
Abstract
BACKGROUND The prothrombinase complex consists of factors Xa (FXa) and Va (FVa) on an anionic phospholipid surface and converts prothrombin into thrombin. Both coagulation factors require activation before complex assembly. We recently identified TIX-5, a unique anticoagulant tick protein that specifically inhibits FXa-mediated activation of FV. Because TIX-5 inhibited thrombin generation in blood plasma, it was concluded that FV activation by FXa contributes importantly to coagulation. OBJECTIVE We aimed to unravel the structure-function relationships of TIX-5. METHOD We used a structure model generated based on homology with the allergen Der F7. RESULTS Tick inhibitor of factor Xa toward FV was predicted to consist of a single rod formed by several beta sheets wrapped around a central C-terminal alpha helix. By mutagenesis we could show that two hydrophobic loops at one end of the rod mediate the phospholipid binding of TIX-5. On the other end of the rod an FV interaction region was identified on one side, whereas on the other side an EGK sequence was identified that could potentially form a pseudosubstrate of FXa. All three interaction sites were important for the anticoagulant properties of TIX-5 in a tissue factor-initiated thrombin generation assay as well as in the inhibition of FV activation by FXa in a purified system. CONCLUSION The structure-function properties of TIX-5 are in perfect agreement with a protein that inhibits the FXa-mediated activation on a phospholipid surface. The present elucidation of the mechanism of action of TIX-5 will aid in deciphering the processes involved in the initiation phase of blood coagulation.
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Affiliation(s)
- Anja Maag
- Amsterdam UMCUniversity of AmsterdamCenter for Experimental and Molecular MedicineAmsterdam Infection and Immunity InstituteAmsterdamThe Netherlands
- Division of Thrombosis and HemostasisLeiden University Medical CenterLeidenThe Netherlands
| | - Priyanka Sharma
- Amsterdam UMCUniversity of AmsterdamCenter for Experimental and Molecular MedicineAmsterdam Infection and Immunity InstituteAmsterdamThe Netherlands
| | - Tim J. Schuijt
- Hospital Gelderse Vallei EdeClinical Chemistry and Hematology LaboratoryEdeThe Netherlands
| | - Wil F. Kopatz
- Department of Experimental Vascular MedicineAmsterdam Cardiovascular SciencesAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
| | - Daniëlle Kruijswijk
- Amsterdam UMCUniversity of AmsterdamCenter for Experimental and Molecular MedicineAmsterdam Infection and Immunity InstituteAmsterdamThe Netherlands
| | - J. Arnoud Marquart
- Department of Molecular and Cellular HemostasisSanquin ResearchAmsterdamThe Netherlands
| | - Tom van der Poll
- Amsterdam UMCUniversity of AmsterdamCenter for Experimental and Molecular MedicineAmsterdam Infection and Immunity InstituteAmsterdamThe Netherlands
| | - Tilman M. Hackeng
- Department of BiochemistryCardiovascular Research Institute Maastricht (CARIM) Maastricht UniversityMaastrichtThe Netherlands
| | - Gerry A. F. Nicolaes
- Department of BiochemistryCardiovascular Research Institute Maastricht (CARIM) Maastricht UniversityMaastrichtThe Netherlands
| | - Joost C. M. Meijers
- Department of Experimental Vascular MedicineAmsterdam Cardiovascular SciencesAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Department of Molecular and Cellular HemostasisSanquin ResearchAmsterdamThe Netherlands
| | - Mettine H. A. Bos
- Division of Thrombosis and HemostasisLeiden University Medical CenterLeidenThe Netherlands
| | - Cornelis van ’t Veer
- Amsterdam UMCUniversity of AmsterdamCenter for Experimental and Molecular MedicineAmsterdam Infection and Immunity InstituteAmsterdamThe Netherlands
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6
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Chen S, Yim JJ, Bogyo M. Synthetic and biological approaches to map substrate specificities of proteases. Biol Chem 2020; 401:165-182. [PMID: 31639098 DOI: 10.1515/hsz-2019-0332] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023]
Abstract
Proteases are regulators of diverse biological pathways including protein catabolism, antigen processing and inflammation, as well as various disease conditions, such as malignant metastasis, viral infection and parasite invasion. The identification of substrates of a given protease is essential to understand its function and this information can also aid in the design of specific inhibitors and active site probes. However, the diversity of putative protein and peptide substrates makes connecting a protease to its downstream substrates technically difficult and time-consuming. To address this challenge in protease research, a range of methods have been developed to identify natural protein substrates as well as map the overall substrate specificity patterns of proteases. In this review, we highlight recent examples of both synthetic and biological methods that are being used to define the substrate specificity of protease so that new protease-specific tools and therapeutic agents can be developed.
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Affiliation(s)
- Shiyu Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua J Yim
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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7
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Zhao R, Ali G, Nie HG, Chang Y, Bhattarai D, Su X, Zhao X, Matthay MA, Ji HL. Plasmin improves blood-gas barrier function in oedematous lungs by cleaving epithelial sodium channels. Br J Pharmacol 2020; 177:3091-3106. [PMID: 32133621 DOI: 10.1111/bph.15038] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 02/11/2020] [Accepted: 02/25/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND AND PURPOSE Lung oedema in association with suppressed fibrinolysis is a hallmark of lung injury. Here, we have tested whether plasmin cleaves epithelial sodium channels (ENaC) to resolve lung oedema fluid. EXPERIMENTAL APPROACH Human lungs and airway acid-instilled mice were used for analysing fluid resolution. In silico prediction, mutagenesis, Xenopus oocytes, immunoblotting, voltage clamp, mass spectrometry, and protein docking were combined for identifying plasmin cleavage sites. KEY RESULTS Plasmin improved lung fluid resolution in both human lungs ex vivo and injured mice. Plasmin activated αβγENaC channels in oocytes in a time-dependent manner. Deletion of four consensus proteolysis tracts (αΔ432-444, γΔ131-138, γΔ178-193, and γΔ410-422) eliminated plasmin-induced activation significantly. Further, immunoblotting assays identified 7 cleavage sites (K126, R135, K136, R153, K168, R178, K179) for plasmin to trim both furin-cleaved C-terminal fragments and full-length human γENaC proteins. In addition, 9 new sites (R122, R137, R138, K150, K170, R172, R180, K181, K189) in synthesized peptides were found to be cleaved by plasmin. These cleavage sites were located in the finger and the thumb, particularly the GRIP domain of human ENaC 3D model composed of two proteolytic centres for plasmin. Novel uncleaved sites beyond the GRIP domain in both α and γ subunits were identified to interrupt the plasmin cleavage-induced conformational change in ENaC channel complexes. Additionally, plasmin could regulate ENaC activity via the G protein signal. CONCLUSION AND IMPLICATIONS Plasmin can cleave ENaC to improve blood-gas exchange by resolving oedema fluid and could be a potent therapy for oedematous lungs.
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Affiliation(s)
- Runzhen Zhao
- Department of Cellular and Molecular Biology, University of Texas Health Science Centre at Tyler, Tyler, Texas
| | - Gibran Ali
- Department of Cellular and Molecular Biology, University of Texas Health Science Centre at Tyler, Tyler, Texas
| | - Hong-Guang Nie
- Department of Cellular and Molecular Biology, University of Texas Health Science Centre at Tyler, Tyler, Texas.,College of Basic Medical Science, China Medical University, Shenyang, Liaoning, China
| | - Yongchang Chang
- Division of Neurobiology, Barrow Neurological Institute, Phoenix, Arizona
| | - Deepa Bhattarai
- Department of Cellular and Molecular Biology, University of Texas Health Science Centre at Tyler, Tyler, Texas
| | - Xuefeng Su
- Department of Cellular and Molecular Biology, University of Texas Health Science Centre at Tyler, Tyler, Texas
| | - Xiaoli Zhao
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, Virginia
| | - Michael A Matthay
- Department of Medicine and Anesthesia, University of California San Francisco, San Francisco, California
| | - Hong-Long Ji
- Department of Cellular and Molecular Biology, University of Texas Health Science Centre at Tyler, Tyler, Texas.,Texas Lung Injury Institute, University of Texas Health Science Centre at Tyler, Tyler, Texas
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8
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Design and characterization of α1-antitrypsin variants for treatment of contact system-driven thromboinflammation. Blood 2020; 134:1658-1669. [PMID: 31366623 DOI: 10.1182/blood.2019000481] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/22/2019] [Indexed: 01/15/2023] Open
Abstract
The contact system produces the inflammatory peptide bradykinin and contributes to experimental thrombosis. C1 esterase-inhibitor (C1INH) deficiency or gain-of-function mutations in factor XII (FXII) cause hereditary angioedema, a life-threatening tissue swelling disease. C1INH is a relatively weak contact system enzyme inhibitor. Although α1-antitrypsin (α1AT) does not naturally inhibit contact system enzymes, a human mutation (M358R; α1AT-Pittsburgh) changes it into a powerful broad-spectrum enzyme inhibitor. It blocks the contact system, but also thrombin and activated protein C (APC), making it an unattractive candidate for therapeutic contact system blockade. We adapted the reactive center loop of α1AT-Pittsburgh (AIPR/S) to overcome these obstacles. Two α1AT variants (SMTR/S and SLLR/S) strongly inhibit plasma kallikrein, activated FXII, and plasmin. α1AT-SMTR/S no longer inhibits thrombin, but residually inhibits APC. In contrast, α1AT-SLLR/S residually inhibits thrombin, but no longer APC. Additional modification at the P1' position (S→V) eliminates residual inhibition of thrombin and APC for both variants, while retaining their properties as contact system inhibitors. Both α1AT-SMTR/V and -SLLR/V are superior to C1INH in reducing bradykinin production in plasma. Owing to their capacity to selectively block contact system-driven coagulation, both variants block vascular occlusion in an in vivo model for arterial thrombosis. Furthermore, both variants block acute carrageenan-induced tissue edema in mice. Finally, α1AT-SLLR/V, our most powerful candidate, suppresses epithelial leakage of the gut in a mouse model of colitis. Our findings confirm that redesign of α1AT strongly alters its inhibitory behavior and can be used for the treatment of contact system-mediated thrombosis and inflammation.
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9
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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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10
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Maluch I, Czarna J, Drag M. Applications of Unnatural Amino Acids in Protease Probes. Chem Asian J 2019; 14:4103-4113. [PMID: 31593336 DOI: 10.1002/asia.201901152] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/01/2019] [Indexed: 12/11/2022]
Abstract
Since proteases are involved in a wide range of physiological and disease states, the development of novel tools for imaging proteolytic enzyme activity is attracting increasing interest from scientists. Peptide substrates containing proteinogenic amino acids are often the first line of defining enzyme specificity. This Minireview outlines examples of major recent advances in probing proteases using unnatural amino acid residues, which greatly expands the possibilities for designing substrate probes and inhibitory activity-based probes. This approach already yielded innovative probes that selectively target only one active protease within the group of enzymes exhibiting similar specificity both in cellular assays and in bioimaging research.
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Affiliation(s)
- Izabela Maluch
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw, University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Justyna Czarna
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw, University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw, University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
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11
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Chen D, Geis-Asteggiante L, Gomes FP, Ostrand-Rosenberg S, Fenselau C. Top-Down Proteomic Characterization of Truncated Proteoforms. J Proteome Res 2019; 18:4013-4019. [PMID: 31545043 DOI: 10.1021/acs.jproteome.9b00487] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A top-down proteomic strategy with semiautomated analysis of data sets has proven successful for the global identification of truncated proteins without the use of chemical derivatization, enzymatic manipulation, immunoprecipitation, or other enrichment. This approach provides the reliable identification of internal polypeptides formed from precursor gene products by proteolytic cleavage of both the N- and C-termini, as well as truncated proteoforms that retain one or the other termini. The strategy has been evaluated by application to the immunosuppressive extracellular vesicles released by myeloid-derived suppressor cells. More than 1000 truncated proteoforms have been identified, from which binding motifs are derived to allow characterization of the putative proteases responsible for truncation.
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Affiliation(s)
- Dapeng Chen
- Department of Chemistry and Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Lucia Geis-Asteggiante
- Department of Chemistry and Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Fabio P Gomes
- Department of Chemistry and Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Suzanne Ostrand-Rosenberg
- Department of Biological Sciences , University of Maryland Baltimore County , Baltimore , Maryland 21250 , United States
| | - Catherine Fenselau
- Department of Chemistry and Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
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12
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Li CY, de Veer SJ, Law RHP, Whisstock JC, Craik DJ, Swedberg JE. Characterising the Subsite Specificity of Urokinase-Type Plasminogen Activator and Tissue-Type Plasminogen Activator using a Sequence-Defined Peptide Aldehyde Library. Chembiochem 2018; 20:46-50. [PMID: 30225958 DOI: 10.1002/cbic.201800395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/05/2018] [Indexed: 01/08/2023]
Abstract
Urokinase-type plasminogen activator (uPA) and tissue-type plasminogen activator (tPA) are two serine proteases that contribute to initiating fibrinolysis by activating plasminogen. uPA is also an important tumour-associated protease due to its role in extracellular matrix remodelling. Overexpression of uPA has been identified in several different cancers and uPA inhibition has been reported as a promising therapeutic strategy. Although several peptide-based uPA inhibitors have been developed, the extent to which uPA tolerates different tetrapeptide sequences that span the P1-P4 positions remains to be thoroughly explored. In this study, we screened a sequence-defined peptide aldehyde library against uPA and tPA. Preferred sequences from the library screen yielded potent inhibitors for uPA, led by Ac-GTAR-H (Ki =18 nm), but not for tPA. Additionally, synthetic peptide substrates corresponding to preferred inhibitor sequences were cleaved with high catalytic efficiency by uPA but not by tPA. These findings provide new insights into the binding specificity of uPA and tPA and the relative activity of tetrapeptide inhibitors and substrates against these enzymes.
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Affiliation(s)
- Choi Yi Li
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ruby H P Law
- Department of Biochemistry and Molecular Biology, Biomedical Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Biomedical Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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13
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Evidence that cell surface localization of serine protease activity facilitates cleavage of the protease activated receptor CDCP1. Biol Chem 2018; 399:1091-1097. [DOI: 10.1515/hsz-2017-0308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/07/2018] [Indexed: 12/13/2022]
Abstract
Abstract
The cellular receptor CUB domain containing protein 1 (CDCP1) is commonly elevated and functionally important in a range of cancers. CDCP1 is cleaved by serine proteases at adjacent sites, arginine 368 (R368) and lysine 369 (K369), which induces cell migration in vitro and metastasis in vivo. We demonstrate that membrane localization of serine protease activity increases efficacy of cleavage of CDCP1, and that both secreted and membrane anchored serine proteases can have distinct preferences for cleaving at CDCP1-R368 and CDCP1-K369. Approaches that disrupt membrane localization of CDCP1 cleaving serine proteases may interfere with the cancer promoting effects of CDCP1 proteolysis.
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14
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Ivry SL, Meyer NO, Winter MB, Bohn MF, Knudsen GM, O'Donoghue AJ, Craik CS. Global substrate specificity profiling of post-translational modifying enzymes. Protein Sci 2018; 27:584-594. [PMID: 29168252 PMCID: PMC5818756 DOI: 10.1002/pro.3352] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 12/14/2022]
Abstract
Enzymes that modify the proteome, referred to as post-translational modifying (PTM) enzymes, are central regulators of cellular signaling. Determining the substrate specificity of PTM enzymes is a critical step in unraveling their biological functions both in normal physiological processes and in disease states. Advances in peptide chemistry over the last century have enabled the rapid generation of peptide libraries for querying substrate recognition by PTM enzymes. In this article, we highlight various peptide-based approaches for analysis of PTM enzyme substrate specificity. We focus on the application of these technologies to proteases and also discuss specific examples in which they have been used to uncover the substrate specificity of other types of PTM enzymes, such as kinases. In particular, we highlight our multiplex substrate profiling by mass spectrometry (MSP-MS) assay, which uses a rationally designed, physicochemically diverse library of tetradecapeptides. We show how this method has been applied to PTM enzymes to uncover biological function, and guide substrate and inhibitor design. We also briefly discuss how this technique can be combined with other methods to gain a systems-level understanding of PTM enzyme regulation and function.
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Affiliation(s)
- Sam L. Ivry
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoCalifornia
- Pharmaceutical Sciences and Pharmacogenomics Graduate ProgramUniversity of California, San FranciscoSan FranciscoCalifornia
| | - Nicole O. Meyer
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoCalifornia
| | - Michael B. Winter
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoCalifornia
| | - Markus F. Bohn
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoCalifornia
| | - Giselle M. Knudsen
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoCalifornia
| | - Anthony J. O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San DiegoLa JollaCalifornia
| | - Charles S. Craik
- Department of Pharmaceutical ChemistryUniversity of California, San FranciscoSan FranciscoCalifornia
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15
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Li W, Lucioni T, Li R, Bonin K, Cho SS, Guthold M. Stretching single fibrin fibers hampers their lysis. Acta Biomater 2017; 60:264-274. [PMID: 28754649 DOI: 10.1016/j.actbio.2017.07.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 07/23/2017] [Accepted: 07/24/2017] [Indexed: 10/19/2022]
Abstract
Blood clots, whose main structural component is a mesh of microscopic fibrin fibers, experience mechanical strain from blood flow, clot retraction and interactions with platelets and other cells. We developed a transparent, striated and highly stretchable substrate made from fugitive glue (a styrenic block copolymer) to investigate how mechanical strain affects lysis of single, suspended fibrin fibers. In this suspended fiber assay, lysis manifested itself by fiber elongation, thickening (disassembly), fraying and collapse. Stretching single fibrin fibers significantly hampered their lysis. This effect was seen in uncrosslinked and crosslinked fibers. Crosslinking (without stretching) also hampered single fiber lysis. Our data suggest that strain is a novel mechanosensitive factor that regulates blood clot dissolution (fibrinolysis) at the single fiber level. At the molecular level of single fibrin molecules, strain may distort, or hinder access to, plasmin cleavage sites and thereby hamper lysis. STATEMENT OF SIGNIFICANCE Fibrin fibers are the major structural component of a blood clot. We developed a highly stretchable substrate made from fugitive glue and a suspended fibrin fiber lysis assay to investigate the effect of stretching on single fibrin fibers lysis. The key findings from our experiments are: 1) Fibers thicken and elongate upon lysis; 2) stretching strongly reduces lysis; 3) this effect is more pronounced for uncrosslinked fibers; and 4) stretching fibers has a similar effect on reducing lysis as crosslinking fibers. At the molecular level, strain may distort plasmin cleavage sites, or restrict access to those sites. Our results suggest that strain may be a novel mechanobiological factor that regulates fibrinolysis.
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16
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Kara E, Manna D, Løset GÅ, Schneider EL, Craik CS, Kanse S. Analysis of the substrate specificity of Factor VII activating protease (FSAP) and design of specific and sensitive peptide substrates. Thromb Haemost 2017; 117:1750-1760. [PMID: 28726978 DOI: 10.1160/th17-02-0081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/11/2017] [Indexed: 01/29/2023]
Abstract
Factor VII (FVII) activating protease (FSAP) is a circulating serine protease that is likely to be involved in a number of disease conditions such as stroke, atherosclerosis, liver fibrosis, thrombosis and cancer. To date, no systematic information is available about the substrate specificity of FSAP. Applying phage display and positional scanning substrate combinatorial library (PS-SCL) approaches we have characterised the specificity of FSAP towards small peptides. Results were evaluated in the context of known protein substrates as well as molecular modelling of the peptides in the active site of FSAP. The representative FSAP-cleaved sequence obtained from the phage display method was Val-Leu-Lys-Arg-Ser (P4-P1'). The sequence X-Lys/Arg-Nle-Lys/Arg (P4-P1) was derived from the PS-SCL method. These results show a predilection for cleavage at a cluster of basic amino acids on the nonprime side. Quenched fluorescent substrate (Ala-Lys-Nle-Arg-AMC) (amino methyl coumarin) and (Ala-Leu-Lys-Arg-AMC) had a higher selectivity for FSAP compared to other proteases from the hemostasis system. These substrates could be used to measure FSAP activity in a complex biological system such as plasma. In histone-treated plasma there was a specific activation of pro-FSAP as validated by the use of an FSAP inhibitory antibody, corn trypsin inhibitor to inhibit Factor XIIa and hirudin to inhibit thrombin, which may account for some of the haemostasis-related effects of histones. These results will aid the development of further selective FSAP activity probes as well as specific inhibitors that will help to increase the understanding of the functions of FSAP in vivo.
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Affiliation(s)
| | | | | | | | | | - Sandip Kanse
- Dr. Sandip M. Kanse, Institute for Basic Medical Sciences, Oslo University Hospital and University of Oslo, Sognvannsveien 9, 0372 Oslo, Norway, E-mail:
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17
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Chinnappan R, Al Attas S, Kaman WE, Bikker FJ, Zourob M. Development of magnetic nanoparticle based calorimetric assay for the detection of bovine mastitis in cow milk. Anal Biochem 2017; 523:58-64. [PMID: 28219684 DOI: 10.1016/j.ab.2017.02.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 01/10/2023]
Abstract
Mastitis in dairy cattle is an inflammatory reaction of the udder tissue. Mastitis increases plasmin levels, leading to an increased proteolysis of milk proteins such as casein, resulting in a significant decrease in milk quality and related dairy products. Due to its key-role in mastitis, we used plasmin proteolytic activity as a biomarker for the detection of mastitis in bovine mastitic milk. Inspired by earlier studies on protease activity using mastitic milk samples, we developed a simple colorimetric assay to distinguish mastitic milk from milk derived from healthy animals. The plasmin substrate coupled to magnetic nanoparticles form a black self-assembled monolayer on a gold sensor surface. In the presence of increased levels of plasmin, the substrate is cleaved and the peptide fragment attached to the magnetic beads, will be attracted by the magnet which is present under the sensor strips revealing the golden surface. We found the area of the golden color surface proportional to plasmin activity. The sensitivity of this method was determined to be 1 ng/ml of plasmin in vitro. Next, we tested the biosensor using mastitis positive milk of which infection is confirmed by bacterial cultures. This newly developed colorimetric biosensor has high potential in applications for the diagnosis of mastitis with potential spin offs to health, food and environmental sectors.
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Affiliation(s)
- Raja Chinnappan
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia
| | - Sana Al Attas
- Department of Biological Sciences, College of Science, King abdulAziz University, Jeddah, Saudi Arabia
| | - Wendy E Kaman
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Gustav Mahlerlaan 3004, 1081 LA Amsterdam, The Netherlands; Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Wytemaweg 80, 3015 CE Rotterdam, The Netherlands
| | - Floris J Bikker
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Wytemaweg 80, 3015 CE Rotterdam, The Netherlands
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia; King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh 12713, Saudi Arabia.
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18
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Abstract
Speed and throughput are vital ingredients for discovery driven, "-omics" research. The small molecule microarray (SMM) succeeds at delivering phenomenal screening throughput and versatility. The concept at the heart of the technology is elegant, yet simple: by presenting large collections of molecules in high density on a flat surface, one is able to interrogate all possible interactions with desired targets, in just a single step. SMMs have become established as the choice platform for screening, lead discovery, and molecular characterization. This introduction describes the principles governing microarray construction and use, focusing on practical challenges faced when conducting SMM experiments. It will explain the key design considerations and lay the foundation for the chapters that follow. (An earlier version of this chapter appeared in Small Molecule Microarrays: Methods and Protocols, published in 2010.).
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Affiliation(s)
- Mahesh Uttamchandani
- Defence Medical and Environmental Research Institute, DMERI, DSO National Laboratories, #09-01, 27 Medical Drive, Singapore, Singapore, 117510. .,Department of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore, Singapore, 117543.
| | - Shao Q Yao
- Department of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore, Singapore, 117543.
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19
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Swedberg JE, Mahatmanto T, Abdul Ghani H, de Veer SJ, Schroeder CI, Harris JM, Craik DJ. Substrate-Guided Design of Selective FXIIa Inhibitors Based on the Plant-Derived Momordica cochinchinensis Trypsin Inhibitor-II (MCoTI-II) Scaffold. J Med Chem 2016; 59:7287-92. [DOI: 10.1021/acs.jmedchem.6b00557] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joakim E. Swedberg
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Tunjung Mahatmanto
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hafiza Abdul Ghani
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Simon J. de Veer
- Institute
of Health and Biomedical Innovation, Queensland University of Technology, Brisbane Queensland 4059, Australia
| | - Christina I. Schroeder
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jonathan M. Harris
- Institute
of Health and Biomedical Innovation, Queensland University of Technology, Brisbane Queensland 4059, Australia
| | - David J. Craik
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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20
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Tian T, Song Y, Wang J, Fu B, He Z, Xu X, Li A, Zhou X, Wang S, Zhou X. Small-Molecule-Triggered and Light-Controlled Reversible Regulation of Enzymatic Activity. J Am Chem Soc 2016; 138:955-61. [DOI: 10.1021/jacs.5b11532] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Tian Tian
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Yanyan Song
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Jiaqi Wang
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Boshi Fu
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Zhiyong He
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Xianqun Xu
- Zhongnan
Hospital, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Anling Li
- Zhongnan
Hospital, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Xin Zhou
- Zhongnan
Hospital, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Shaoru Wang
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Xiang Zhou
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
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21
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Berman JM, Awayda RG, Awayda MS. Effects of urine composition on epithelial Na+ channel-targeted protease activity. Physiol Rep 2015; 3:3/11/e12611. [PMID: 26564065 PMCID: PMC4673640 DOI: 10.14814/phy2.12611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We examined human urinary proteolytic activity toward the Epithelial Sodium Channel (ENaC). We focused on two sites in each of alpha and gamma ENaC that are targets of endogenous and exogenous proteases. We examined the effects of ionic strength, pH and urinary H+-buffers, metabolic intermediates, redox molecules, and large urinary proteins. Monoatomic cations caused the largest effect, with sodium inhibiting activity in the 15–515 mEq range. Multivalent cations zinc and copper inhibited urinary proteolytic activity at concentrations below 100 μmol/L. Similar to sodium, urea caused a 30% inhibition in the 0–500 mmol/L range. This was not observed with acetone and ethanol. Modulating urinary redox status modified activity with H2O2 stimulated and ascorbate inhibited activity. Minimal effects (<10%) were observed with caffeine, glucose, several TCA cycle intermediates, salicylic acid, inorganic phosphate, albumin, creatinine, and Tamm–Horsfall protein. The cumulative activity of ENaC-cleaving proteases was highest at neutral pH, however, alpha and gamma proteases exhibited an inverse dependence with alpha stimulated at acidic and gamma stimulated at alkaline pH. These data indicate that ENaC-targeting urinary proteolytic activity is sensitive to sodium, urea and pH and changes in these components can modify channel cleavage and activation status, and likely downstream sodium absorption unrelated to changes in protein or channel density.
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Affiliation(s)
- Jonathan M Berman
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York
| | - Ryan G Awayda
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York
| | - Mouhamed S Awayda
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, New York
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22
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23
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Secondary Structure Determination of Peptides and Proteins After Immobilization. Methods Mol Biol 2015; 1352:35-50. [PMID: 26490466 DOI: 10.1007/978-1-4939-3037-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The presentation of immobilized peptides and other small biomolecules attached to surfaces can be greatly affected by the attachment chemistry and linking moieties, resulting in altered activity and specificity. For this reason, it is critical to understand how the various aspects of surface immobilization-underlying substrate properties, tether structure, and site of linkage-affect the secondary and quaternary structures of the immobilized species. Here, we present methods for attaching cysteine-containing peptides to quartz surfaces and determining the secondary structure of surface-immobilized peptides. We specifically show that, even when covalently immobilized, changes in peptide conformation can still occur, with measurement occurring in real time.
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24
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Gogia S, Lo CY, Neelamegham S. Detection of Plasma Protease Activity Using Microsphere-Cytometry Assays with E. coli Derived Substrates: VWF Proteolysis by ADAMTS13. PLoS One 2015; 10:e0126556. [PMID: 25992814 PMCID: PMC4436310 DOI: 10.1371/journal.pone.0126556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 04/03/2015] [Indexed: 11/19/2022] Open
Abstract
Protease levels in human blood are often prognostic indicators of inflammatory, thrombotic or oncogenic disorders. The measurement of such enzyme activities in substrate-based assays is complicated due to the low prevalence of these enzymes and steric hindrance of the substrates by the more abundant blood proteins. To address these limitations, we developed a molecular construct that is suitable for microsphere-cytometer based assays in the milieu of human blood plasma. In this proof of principle study, we demonstrate the utility of this substrate to measure metalloprotease ADAMTS13 activity. The substrate, expressed in E. coli as a fusion protein, contains the partial A2-domain of von Willebrand factor (VWF amino acids 1594-1670) that is mutated to include a single primary amine at the N-terminus and free cysteines at the C-terminus. N-terminus fluorescence conjugation was possible using NHS (N-hydroxysuccinimide) chemistry. Maleimide-PEG(Polyethylene glycol)n-biotin coupling at the C-terminus allowed biotinylation with variable PEG spacer lengths. Once bound to streptavidin-bearing microspheres, the substrate fluorescence signal decreased in proportion with ADAMTS13 concentration. Whereas recombinant ADAMTS13 activity could be quantified using substrates with all PEG repeat-lengths, only the construct with the longer 77 PEG-unit could quantify proteolysis in blood plasma. Using this longer substrate, plasma ADAMTS13 down to 5% of normal levels could be detected within 30 min. Such measurements could also be readily performed under conditions resembling hyperbilirubinemia. Enzyme catalytic activity was tuned by varying buffer calcium, with lower divalent ion concentrations enhancing cleavage. Overall, the study highlights the substrate design features important for the creation of efficient proteolysis assays in the setting of human plasma. In particular, it emphasizes the need to introduce PEG spacers in plasma-based experiments, a design attribute commonly ignored in immobilized peptide-substrate assays.
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Affiliation(s)
- Shobhit Gogia
- Department of Chemical and Biological Engineering and NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, New York, United States of America
| | - Chi Y. Lo
- Department of Chemical and Biological Engineering and NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, New York, United States of America
| | - Sriram Neelamegham
- Department of Chemical and Biological Engineering and NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, New York, United States of America
- * E-mail:
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25
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Al-Horani RA, Desai UR. Recent advances on plasmin inhibitors for the treatment of fibrinolysis-related disorders. Med Res Rev 2014; 34:1168-1216. [PMID: 24659483 PMCID: PMC8788159 DOI: 10.1002/med.21315] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Growing evidence suggests that plasmin is involved in a number of physiological processes in addition to its key role in fibrin cleavage. Plasmin inhibition is critical in preventing adverse consequences arising from plasmin overactivity, e.g., blood loss that may follow cardiac surgery. Aprotinin was widely used as an antifibrinolytic drug before its discontinuation in 2008. Tranexamic acid and ε-aminocaproic acid, two small molecule plasmin inhibitors, are currently used in the clinic. Several molecules have been designed utilizing covalent, but reversible, chemistry relying on reactive cyclohexanones, nitrile warheads, and reactive aldehyde peptidomimetics. Other major classes of plasmin inhibitors include the cyclic peptidomimetics and polypeptides of the Kunitz and Kazal-type. Allosteric inhibitors of plasmin have also been designed including small molecule lysine analogs that bind to plasmin's kringle domain(s) and sulfated glycosaminoglycan mimetics that bind to plasmin's catalytic domain. Plasmin inhibitors have also been explored for resolving other disease states including cell metastasis, cell proliferation, angiogenesis, and embryo implantation. This review highlights functional and structural aspects of plasmin inhibitors with the goal of advancing their design.
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Affiliation(s)
- Rami A Al-Horani
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia
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26
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Stressler T, Eisele T, Kranz B, Fischer L. PepX from Lactobacillus helveticus: Automated multi-step purification and determination of kinetic parameters with original tripeptide substrates. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Bikker FJ, Koop G, Leusink NB, Nazmi K, Kaman WE, Brand HS, Veerman ECI. Tailor made plasmin substrates as potential diagnostic tool to test for mastitis. Vet Res Commun 2014; 38:271-7. [DOI: 10.1007/s11259-014-9611-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2014] [Indexed: 10/25/2022]
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28
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Salmon and human thrombin differentially regulate radicular pain, glial-induced inflammation and spinal neuronal excitability through protease-activated receptor-1. PLoS One 2013; 8:e80006. [PMID: 24278231 PMCID: PMC3835785 DOI: 10.1371/journal.pone.0080006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 10/07/2013] [Indexed: 11/22/2022] Open
Abstract
Chronic neck pain is a major problem with common causes including disc herniation and spondylosis that compress the spinal nerve roots. Cervical nerve root compression in the rat produces sustained behavioral hypersensitivity, due in part to the early upregulation of pro-inflammatory cytokines, the sustained hyperexcitability of neurons in the spinal cord and degeneration in the injured nerve root. Through its activation of the protease-activated receptor-1 (PAR1), mammalian thrombin can enhance pain and inflammation; yet at lower concentrations it is also capable of transiently attenuating pain which suggests that PAR1 activation rate may affect pain maintenance. Interestingly, salmon-derived fibrin, which contains salmon thrombin, attenuates nerve root-induced pain and inflammation, but the mechanisms of action leading to its analgesia are unknown. This study evaluates the effects of salmon thrombin on nerve root-mediated pain, axonal degeneration in the root, spinal neuronal hyperexcitability and inflammation compared to its human counterpart in the context of their enzymatic capabilities towards coagulation substrates and PAR1. Salmon thrombin significantly reduces behavioral sensitivity, preserves neuronal myelination, reduces macrophage infiltration in the injured nerve root and significantly decreases spinal neuronal hyperexcitability after painful root compression in the rat; whereas human thrombin has no effect. Unlike salmon thrombin, human thrombin upregulates the transcription of IL-1β and TNF-α and the secretion of IL-6 by cortical cultures. Salmon and human thrombins cleave human fibrinogen-derived peptides and form clots with fibrinogen with similar enzymatic activities, but salmon thrombin retains a higher enzymatic activity towards coagulation substrates in the presence of antithrombin III and hirudin compared to human thrombin. Conversely, salmon thrombin activates a PAR1-derived peptide more weakly than human thrombin. These results are the first to demonstrate that salmon thrombin has unique analgesic, neuroprotective and anti-inflammatory capabilities compared to human thrombin and that PAR1 may contribute to these actions.
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29
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Substrate phage display for protease substrate sequence characterization: bovine factor Xa as a model system. Methods Mol Biol 2013; 1088:107-24. [PMID: 24146400 DOI: 10.1007/978-1-62703-673-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Regulatory proteases modulate proteomic dynamics with a spectrum of specificities against substrate proteins. Substrate phage display is one of the key methodologies in producing substrate sequence information in vitro. Factor Xa, a key regulatory protease in the blood coagulation system, is used as a model system to demonstrate a high-throughput procedure to quantitatively characterize substrate sequences and their susceptibilities for enzymatic cleavage. This methodology can be generalized to proteases for which the active forms (not necessarily purified forms) are available for the in vitro experiments.
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30
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TMPRSS2 is an activating protease for respiratory parainfluenza viruses. J Virol 2013; 87:11930-5. [PMID: 23966399 DOI: 10.1128/jvi.01490-13] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we show that human parainfluenza viruses and Sendai virus (SeV), like other respiratory viruses, use TMPRSS2 for their activation. The membrane fusion proteins of respiratory viruses often possess serine and glutamine residues at the P2 and P3 positions, respectively, but these residues were not critical for cleavage by TMPRSS2. However, mutations of these residues affected SeV growth in specific epithelial cell lines, suggesting the importance of these residues for SeV replication in epithelia.
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31
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Rogers LD, Overall CM. Proteolytic post-translational modification of proteins: proteomic tools and methodology. Mol Cell Proteomics 2013; 12:3532-42. [PMID: 23887885 DOI: 10.1074/mcp.m113.031310] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteolytic processing is a ubiquitous and irreversible post-translational modification involving limited and highly specific hydrolysis of peptide and isopeptide bonds of a protein by a protease. Cleavage generates shorter protein chains displaying neo-N and -C termini, often with new or modified biological activities. Within the past decade, degradomics and terminomics have emerged as significant proteomics subfields dedicated to characterizing proteolysis products as well as natural protein N and C termini. Here we provide an overview of contemporary proteomics-based methods, including specific quantitation, data analysis, and curation considerations, and highlight exciting new and emerging applications within these fields enabling in vivo analysis of proteolytic events.
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Affiliation(s)
- Lindsay D Rogers
- Department of Biochemistry and Molecular Biology, Department of Oral Biological and Medical Sciences, and Centre for Blood Research, University of British Columbia, 4.401 Life Sciences Institute, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3, Canada
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32
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Abstract
The study of blood ex vivo can occur in closed or open systems, with or without flow. Microfluidic devices, which constrain fluids to a small (typically submillimeter) scale, facilitate analysis of platelet function, coagulation biology, cellular biorheology, adhesion dynamics, and pharmacology and, as a result, can be an invaluable tool for clinical diagnostics. An experimental session can accommodate hundreds to thousands of unique clotting, or thrombotic, events. Using microfluidics, thrombotic events can be studied on defined surfaces of biopolymers, matrix proteins, and tissue factor, under constant flow rate or constant pressure drop conditions. Distinct shear rates can be generated on a device using a single perfusion pump. Microfluidics facilitated both the determination of intraluminal thrombus permeability and the discovery that platelet contractility can be activated by a sudden decrease in flow. Microfluidic devices are ideal for multicolor imaging of platelets, fibrin, and phosphatidylserine and provide a human blood analog to mouse injury models. Overall, microfluidic advances offer many opportunities for research, drug testing under relevant hemodynamic conditions, and clinical diagnostics.
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Affiliation(s)
- Thomas V Colace
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
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33
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Fuchs JE, von Grafenstein S, Huber RG, Margreiter MA, Spitzer GM, Wallnoefer HG, Liedl KR. Cleavage entropy as quantitative measure of protease specificity. PLoS Comput Biol 2013; 9:e1003007. [PMID: 23637583 PMCID: PMC3630115 DOI: 10.1371/journal.pcbi.1003007] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 02/07/2013] [Indexed: 01/05/2023] Open
Abstract
A purely information theory-guided approach to quantitatively characterize protease specificity is established. We calculate an entropy value for each protease subpocket based on sequences of cleaved substrates extracted from the MEROPS database. We compare our results with known subpocket specificity profiles for individual proteases and protease groups (e.g. serine proteases, metallo proteases) and reflect them quantitatively. Summation of subpocket-wise cleavage entropy contributions yields a measure for overall protease substrate specificity. This total cleavage entropy allows ranking of different proteases with respect to their specificity, separating unspecific digestive enzymes showing high total cleavage entropy from specific proteases involved in signaling cascades. The development of a quantitative cleavage entropy score allows an unbiased comparison of subpocket-wise and overall protease specificity. Thus, it enables assessment of relative importance of physicochemical and structural descriptors in protease recognition. We present an exemplary application of cleavage entropy in tracing substrate specificity in protease evolution. This highlights the wide range of substrate promiscuity within homologue proteases and hence the heavy impact of a limited number of mutations on individual substrate specificity. Proteases show a broad range of cleavage specificities. Promiscuous proteases as digestive enzymes unspecifically degrade peptides, whereas highly specific proteases are involved in signaling cascades. As a quantitative index of substrate specificity was lacking, we introduce cleavage entropy as a measure of substrate specificity of proteases. This quantitative score allows for straight-forward rationalization of substrate recognition by a subpocket-wise assessment of substrate readout leading to specificity profiles of individual proteases as well as an estimate of overall substrate promiscuity. We present an exemplary application of the descriptor ‘cleavage entropy’ to trace substrate specificity through the evolution of different protease folds. Our score highlights the diversity of substrate specificity within evolutionary related proteases and hence the complex relationship between sequence, structure and substrate recognition. By taking into account the whole distribution of known substrates rather than simple substrate counting, cleavage entropy provides the unique opportunity to dissect the molecular origins of protease substrate specificity.
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Affiliation(s)
- Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Roland G. Huber
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Michael A. Margreiter
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Gudrun M. Spitzer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Hannes G. Wallnoefer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
- * E-mail:
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34
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Wysocka M, Lesner A, Gruba N, Korkmaz B, Gauthier F, Kitamatsu M, Łęgowska A, Rolka K. Three wavelength substrate system of neutrophil serine proteinases. Anal Chem 2012; 84:7241-8. [PMID: 22823539 DOI: 10.1021/ac301684w] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neutrophil serine proteases, including elastase, proteinase 3, and cathepsin G, are closely related enzymes stored in similar amounts in azurophil granules and released at the same time from triggered neutrophils at inflammatory sites. We have synthesized new fluorescence resonance energy transfer (FRET) substrates with different fluorescence donor-acceptor pairs that allow all three proteases to be quantified at the same time and in the same reaction mixture. This was made possible because the fluorescence emission spectra of the fluorescence donors do not overlap and because the values of the specificity constants were in the same range. Thus, similar activities of proteases can be measured with the same sensitivity. In addition, these substrates contain an N-terminal 2-(2-(2-aminoethoxy)ethoxy)acetic acid (PEG) moiety that makes them cell permeable. Using the mixture of these selected substrates, we were able to detect the neutrophil serine protease (NSP) activity on the activated neutrophil membrane and in the neutrophil lysate in a single measurement. Also, using the substrate mixture, we were in a position to efficiently determine NSP activity in human serum of healthy individuals and patients with diagnosed Wegener disease or microscopic polyangiitis.
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Affiliation(s)
- Magdalena Wysocka
- Faculty of Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk, Poland
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35
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Kong DH, Jung SH, Lee ST, Kim YM, Ha KS. Monitoring of proteolytic enzyme activity using phase transition-based peptide arrays. Biosens Bioelectron 2012; 36:147-53. [DOI: 10.1016/j.bios.2012.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 03/18/2012] [Accepted: 04/09/2012] [Indexed: 02/01/2023]
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36
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Swedberg JE, Harris JM. Natural and engineered plasmin inhibitors: applications and design strategies. Chembiochem 2012; 13:336-48. [PMID: 22238174 DOI: 10.1002/cbic.201100673] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Indexed: 12/17/2022]
Abstract
The serine protease plasmin is ubiquitously expressed throughout the human body in the form of the zymogen plasminogen. Conversion to active plasmin occurs through enzymatic cleavage by plasminogen activators. The plasminogen activator/plasmin system has a well-established function in the removal of intravascular fibrin deposition through fibrinolysis and the inhibition of plasmin activity; this has found widespread clinical use in reducing perioperative bleeding. Increasing evidence also suggests diverse, although currently less defined, roles for plasmin in a number of physiological and pathological processes relating to extracellular matrix degradation, cell migration and tissue remodelling. In particular, dysregulation of plasmin has been linked to cancer invasion/metastasis and various chronic inflammatory conditions; this has prompted efforts to develop inhibitors of this protease. Although a number of plasmin inhibitors exist, they commonly suffer from poor potency and/or specificity of inhibition that either results in reduced efficacy or prevents clinical use. Consequently, there is a need for further development of high-affinity plasmin inhibitors that maintain selectivity over other serine proteases. This review summarises clearly defined and potential applications for plasmin inhibition. The properties of naturally occurring and engineered plasmin inhibitors are discussed in the context of current knowledge regarding plasmin structure, specificity and function. This includes design strategies to obtain the potency and specificity of inhibition in addition to controlled temporal and spatial distribution tailored for the intended use.
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Affiliation(s)
- Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072 (Australia)
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37
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A comparative evaluation of microarray slides as substrates for the development of protease assay biosensors. Exp Mol Pathol 2011; 91:714-7. [DOI: 10.1016/j.yexmp.2011.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/06/2011] [Indexed: 11/20/2022]
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38
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Schilling O, dem Keller UA, Overall CM. Factor Xa subsite mapping by proteome-derived peptide libraries improved using WebPICS, a resource for proteomic identification of cleavage sites. Biol Chem 2011; 392:1031-7. [DOI: 10.1515/bc.2011.158] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Proteomic identification of protease cleavage site specificity (PICS) is a recent proteomic approach for the easy mapping of protease subsite preferences that determines both the prime- and non-prime side specificity concurrently. Here we greatly facilitate user access by providing an automated and simple web-based data-analysis resource termed WebPics (http://clipserve.clip.ubc.ca/pics/). We demonstrate the utility of WebPics analysis of PICS data by determining the substrate specificity of factor Xa from P6-P6’, an important blood coagulation protease that proteolytically generates thrombin from prothrombin. PICS confirms existing data on non-prime site specificity and refines our knowledge of factor Xa prime-site selectivity.
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39
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Swedberg JE, Harris JM. Plasmin Substrate Binding Site Cooperativity Guides the Design of Potent Peptide Aldehyde Inhibitors. Biochemistry 2011; 50:8454-62. [DOI: 10.1021/bi201203y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Joakim E. Swedberg
- Institute of Health and
Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland
4059, Australia
| | - Jonathan M. Harris
- Institute of Health and
Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland
4059, Australia
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40
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Serebryakova MV, Kordyukova LV, Semashko TA, Ksenofontov AL, Rudneva IA, Kropotkina EA, Filippova IY, Veit M, Baratova LA. Influenza virus hemagglutinin spike neck architectures and interaction with model enzymes evaluated by MALDI-TOF mass spectrometry and bioinformatics tools. Virus Res 2011; 160:294-304. [PMID: 21763731 DOI: 10.1016/j.virusres.2011.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/29/2011] [Accepted: 07/01/2011] [Indexed: 01/28/2023]
Abstract
Interactions between model enzymes and the influenza virus hemagglutinin (HA) homotrimeric spike were addressed. We digested influenza virions (naturally occurring strains and laboratory reassortants) with bromelain or subtilisin Carlsberg and analyzed by MALDI-TOF mass spectrometry the resulting HA2 C-terminal segments. All cleavage sites, together with (minor) sites detected in undigested HAs, were situated in the linker region that connects the transmembrane domain to the ectodomain. In addition to cleavage at highly favorable amino acids, various alternative enzyme preferences were found that strongly depended on the HA subtype/type. We also evaluated the surface electrostatic potentials, binding cleft topographies and spatial dimensions of stem bromelain (homologically modeled) and subtilisin Carlsberg (X-ray resolved). The results show that the enzymes (∼45Å(3)) would hardly fit into the small (∼18-20Å) linker region of the HA-spike. However, the HA membrane proximal ectodomain region was predicted to be intrinsically disordered. We propose that its motions allow steric adjustment of the enzymes' active sites to the neck of the HA spike. The subtype/type-specific architectures in this region also influenced significantly the cleavage preferences of the enzymes.
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Affiliation(s)
- Marina V Serebryakova
- Research Institute of Physical-Chemical Medicine, Federal Agency for Health Care and Social Development, Moscow, Russia
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41
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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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42
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Miller MA, Barkal L, Jeng K, Herrlich A, Griffith LG, Lauffenburger DA. Proteolytic Activity Matrix Analysis (PrAMA) for simultaneous determination of multiple protease activities. Integr Biol (Camb) 2011; 3:422-38. [PMID: 21180771 PMCID: PMC3173501 DOI: 10.1039/c0ib00083c] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Matrix metalloproteinases (MMPs) and A Disintegrin and Metalloproteinases (ADAMs) are two related protease families that play key roles in matrix remodeling and growth factor ligand shedding. Directly ascertaining the proteolytic activities of particular MMPs and ADAMs in physiological environments in a non-invasive, real-time, multiplex manner remains a challenge. This work describes Proteolytic Activity Matrix Analysis (PrAMA), an integrated experimental measurement and mathematical analysis framework for simultaneously determining the activities of particular enzymes in complex mixtures of MMPs and ADAMs. The PrAMA method interprets dynamic signals from panels of moderately specific FRET-based polypeptide protease substrates to deduce a profile of specific MMP and ADAM proteolytic activities. Deconvolution of signals from complex mixtures of proteases is accomplished using prior data on individual MMP/ADAM cleavage signatures for the substrate panel measured with purified enzymes. We first validate PrAMA inference using a compendium of roughly 4000 measurements involving known mixtures of purified enzymes and substrates, and then demonstrate application to the live-cell response of wildtype, ADAM10-/-, and ADAM17-/- fibroblasts to phorbol ester and ionomycin stimulation. Results indicate PrAMA can distinguish closely related enzymes from each other with high accuracy, even in the presence of unknown background proteolytic activity. PrAMA offers a valuable tool for applications ranging from live-cell in vitro assays to high-throughput inhibitor screening with complex enzyme mixtures. Moreover, our approach may extend to other families of proteases, such as caspases and cathepsins, that also can lack highly-specific substrates.
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Affiliation(s)
- Miles A. Miller
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Layla Barkal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Karen Jeng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Andreas Herrlich
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02139
| | - Linda G. Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139
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43
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Wu H, Ge J, Yang PY, Wang J, Uttamchandani M, Yao SQ. A peptide aldehyde microarray for high-throughput profiling of cellular events. J Am Chem Soc 2011; 133:1946-54. [PMID: 21247160 DOI: 10.1021/ja109597v] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Microarrays provide exciting opportunities in the field of large-scale proteomics. With the aim to elucidate enzymatic activity and profiles within native biological samples, we developed a microarray comprising a focused positional-scanning library of enzyme inhibitors. The library was diversified across P(1)-P(4) positions, creating 270 different inhibitor sublibraries which were immobilized onto avidin slides. The peptide aldehyde-based small-molecule microarray (SMM) specifically targeted cysteine proteases, thereby enabling large-scale functional assessment of this subgroup of proteases, within fluorescently labeled samples, including pure proteins, cellular lysates, and infected samples. The arrays were shown to elicit binding fingerprints consistent with those of model proteins, specifically caspases and purified cysteine proteases from parasites (rhodesein and cruzain). When tested against lysates from apoptotic Hela and red blood cells infected with Plasmodium falciparum, clear signatures were obtained that were readily attributable to the activity of constituent proteases within these samples. Characteristic binding profiles were further able to distinguish various stages of the parasite infection in erythrocyte lysates. By converting one of our brightest microarray hits into a probe, putative protein markers were identified and pulled down from within apoptotic Hela lysates, demonstrating the potential of target validation and discovery. Taken together, these results demonstrate the utility of targeted SMMs in dissecting cellular biology in complex proteomic samples.
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Affiliation(s)
- Hao Wu
- Department of Chemistry, 3 Science Drive 3, National University of Singapore, Singapore 117543
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44
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Wu H, Ge J, Uttamchandani M, Yao SQ. Small molecule microarrays: the first decade and beyond. Chem Commun (Camb) 2011; 47:5664-5670. [DOI: 10.1039/c1cc11464f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Molecular Bits and Chips: Profiling and discovering the next generation of small molecule ligands.
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Affiliation(s)
- Hao Wu
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Jingyan Ge
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Mahesh Uttamchandani
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Department of Biological Sciences
- National University of Singapore
| | - Shao Q. Yao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
- Department of Biological Sciences
- National University of Singapore
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45
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Liang S, Xu W, Horiuchi KY, Wang Y, Ma H. Chemical microarrays: a new tool for discovery enzyme inhibitors. Methods Mol Biol 2010; 572:149-60. [PMID: 20694690 DOI: 10.1007/978-1-60761-244-5_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Enzymes, the catalytic proteins, are playing pivotal roles in regulating basic cell functions. Drugs that inhibit enzyme activities cover varying aspects of diseases and offer potential cures. One of the major technologies used in the drug discovery industry for finding the enzyme inhibitors is high-throughput screening, which is facing a daunting challenge due to the fast-growing numbers of drug targets arising from genomic and proteomic research and the large chemical libraries generated from high-throughput synthesis. Chemical microarray, as a new technology, could be an excellent alternative for traditional well-based screening, since the technology can screen more compounds against more targets in parallel with a minimum amount of materials, reducing cost and increasing productivity. In this chapter, we have introduced the basic techniques and applications of chemical microarrays, and how to use them routinely for identifying enzyme inhibitors with functional-based assays. Sample assays for kinases, proteases, histone deacetylases, and phosphatases are demonstrated.
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46
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Kool J, de Kloe G, Denker AD, van Altena K, Smoluch M, van Iperen D, Nahar TT, Limburg RJ, Niessen WMA, Lingeman H, Leurs R, de Esch IJP, Smit AB, Irth H. Nanofractionation Spotter Technology for Rapid Contactless and High-Resolution Deposition of LC Eluent for Further Off-Line Analysis. Anal Chem 2010; 83:125-32. [DOI: 10.1021/ac102001g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeroen Kool
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Gerdien de Kloe
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Arnoud D. Denker
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Klaas van Altena
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Marek Smoluch
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Dick van Iperen
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Tariq T. Nahar
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Rob J. Limburg
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Wilfried M. A. Niessen
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Henk Lingeman
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Rob Leurs
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Iwan J. P. de Esch
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - August B. Smit
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
| | - Hubertus Irth
- BioMolecular Analysis and Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, and FMI-Bèta-VU, ELE-Bèta-VU (Mechanical and Electronic Engineering), Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands, and Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, The Netherlands
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Microarray-based enzyme profiling: Recent advances and applications (Review). Biointerphases 2010; 5:FA24-31. [DOI: 10.1116/1.3462969] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Jo YS, Rizzi SC, Ehrbar M, Weber FE, Hubbell JA, Lutolf MP. Biomimetic PEG hydrogels crosslinked with minimal plasmin-sensitive tri-amino acid peptides. J Biomed Mater Res A 2010; 93:870-7. [PMID: 19701911 DOI: 10.1002/jbm.a.32580] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Semi-synthetic, proteolytically degradable polymer hydrogels have proven effective as scaffolds to augment bone and skin regeneration in animals. However, high costs due to expensive peptide building blocks pose a significant hurdle towards broad clinical usage of these materials. Here we demonstrate that tri-amino acid peptides bearing lysine (or arginine), flanked by two cysteine residues for crosslinking, are adequate as minimal plasmin-sensitive peptides in poly(ethylene glycol)-based hydrogels formed via Michael-type addition. Substitution of lysine (or arginine) with serine rendered the matrices insensitive to the action of plasmin. This was demonstrated in vitro by performing gel degradation experiments in the presence of plasmin (0.1 U/mL), and in the in vivo situation of regeneration of critical-sized bone defects. When placed as implants into rat calvaria, gels formed from the minimal plasmin substrates showed clear signs of cell infiltration and gel remodeling that coincided with extensive bone formation.
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Affiliation(s)
- Yun Suk Jo
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
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49
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Abstract
Accurate HIV diagnostic testing continues to pose challenges, but there are also opportunities for assay performance improvements in key areas for specific intended-use settings. The genetic diversity of HIV can result in false and discordant results in assays that fail to detect new variant strains. The use of antiretroviral therapies has resulted in drug-resistant variants that require monitoring by sequencing and genotyping methods. Nucleic acid testing is the most sensitive and reliable platform for detection, but it is costly and limited to centralized testing facilities, making implementation difficult in resource-limited settings where HIV has hit the hardest. Rapid antibody tests suitable for point-of-care use are becoming more accessible in resource-limited settings, but these tests may not detect HIV during the acute infection stage. Emerging antigen/antibody combination assays are viable alternatives to nucleic acid testing for diagnosis of recent infections. Although patient monitoring (e.g., via CD4+ T-cell count and viral load determination) and infant diagnoses still rely on clinical laboratory-based testing, point-of-care options are being developed. There are other technical challenges to HIV diagnostic testing and emerging biodetection technologies that may be able to address them, but they are not yet proven.
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Affiliation(s)
- Eric Y Wong
- Laboratory of Molecular Virology, Center for Biologics Evaluation & Research, Food & Drug Administration, 8800 Rockville Pike, Building 29B, Room 4NN16, Bethesda, MD 20892, USA
| | - Indira K Hewlett
- Laboratory of Molecular Virology, Center for Biologics Evaluation & Research, Food & Drug Administration, 8800 Rockville Pike, Building 29B, Room 4NN16, Bethesda, MD 20892, USA
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50
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auf dem Keller U, Schilling O. Proteomic techniques and activity-based probes for the system-wide study of proteolysis. Biochimie 2010; 92:1705-14. [PMID: 20493233 DOI: 10.1016/j.biochi.2010.04.027] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 04/29/2010] [Indexed: 11/17/2022]
Abstract
Proteolysis constitutes a major post-translational modification but specificity and substrate selectivity of numerous proteases have remained elusive. In this review, we highlight how advanced techniques in the areas of proteomics and activity-based probes can be used to investigate i) protease active site specificity; ii) protease in vivo substrates; iii) protease contribution to proteome homeostasis and composition; and iv) detection and localization of active proteases. Peptide libraries together with genetical or biochemical selection have traditionally been used for active site profiling of proteases. These are now complemented by proteome-derived peptide libraries that simultaneously determine prime and non-prime specificity and characterize subsite cooperativity. Cell-contextual discovery of protease substrates is rendered possible by techniques that isolate and quantitate protein termini. Here, a novel approach termed Terminal Amine Isotopic Labeling of Substrates (TAILS) provides an integrated platform for substrate discovery and appropriate statistical evaluation of terminal peptide identification and quantification. Proteolytically generated carboxy-termini can now also be analyzed on a proteome-wide level. Proteolytic regulation of proteome composition is monitored by quantitative proteomic approaches employing stable isotope coding or label free quantification. Activity-based probes specifically recognize active proteases. In proteomic screens, they can be used to detect and quantitate proteolytic activity while their application in cellular histology allows to locate proteolytic activity in situ. Activity-based probes - especially in conjunction with positron emission tomography - are also promising tools to monitor proteolytic activities on an organism-wide basis with a focus on in vivo tumor imaging. Together, this array of methodological possibilities enables unveiling physiological protease substrate repertoires and defining protease function in the cellular- and organism-wide context.
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Affiliation(s)
- Ulrich auf dem Keller
- ETH Zürich Institute of Cell Biology, Schafmattstrasse 18, CH-8093 Zurich, Switzerland
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