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Boehr DD. Editorial: Allosteric functions and inhibitions: structural insights. Front Mol Biosci 2024; 11:1363100. [PMID: 38293599 PMCID: PMC10822915 DOI: 10.3389/fmolb.2024.1363100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024] Open
Affiliation(s)
- David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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2
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Wu D, Prem A, Xiao J, Salsbury FR. Thrombin - A Molecular Dynamics Perspective. Mini Rev Med Chem 2024; 24:1112-1124. [PMID: 37605420 DOI: 10.2174/1389557523666230821102655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/08/2023] [Accepted: 07/15/2023] [Indexed: 08/23/2023]
Abstract
Thrombin is a crucial enzyme involved in blood coagulation, essential for maintaining circulatory system integrity and preventing excessive bleeding. However, thrombin is also implicated in pathological conditions such as thrombosis and cancer. Despite the application of various experimental techniques, including X-ray crystallography, NMR spectroscopy, and HDXMS, none of these methods can precisely detect thrombin's dynamics and conformational ensembles at high spatial and temporal resolution. Fortunately, molecular dynamics (MD) simulation, a computational technique that allows the investigation of molecular functions and dynamics in atomic detail, can be used to explore thrombin behavior. This review summarizes recent MD simulation studies on thrombin and its interactions with other biomolecules. Specifically, the 17 studies discussed here provide insights into thrombin's switch between 'slow' and 'fast' forms, active and inactive forms, the role of Na+ binding, the effects of light chain mutation, and thrombin's interactions with other biomolecules. The findings of these studies have significant implications for developing new therapies for thrombosis and cancer. By understanding thrombin's complex behavior, researchers can design more effective drugs and treatments that target thrombin.
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Affiliation(s)
- Dizhou Wu
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
| | - Athul Prem
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
| | - Jiajie Xiao
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
- Freenome, South San Francisco, CA, 94080, USA
| | - Freddie R Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, NC, 27106, USA
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3
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Fuchs B, Birt A, Moellhoff N, Kuhlmann C, Giunta R, Wiggenhauser PS. The use of commercial fibrin glue in dermal replacement material reduces angiogenic and lymphangiogenic gene and protein expression in vitro. J Biomater Appl 2023; 37:1858-1873. [PMID: 37082911 DOI: 10.1177/08853282231171681] [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: 04/22/2023]
Abstract
BACKGROUND Commercial fibrin glue is increasingly finding its way into clinical practice in surgeries to seal anastomosis, and initiate hemostasis or tissue repair. Human biological glue is also being discussed as a possible cell carrier. To date, there are only a few studies addressing the effects of fibrin glue on the cell-molecular level. This study examines the effects of fibrin glue on angiogenesis and lymphangiogenesis, as well as adipose-derived stem cells (ASCs) with a focus on gene and protein expression in scaffolds regularly used for tissue engineering approaches. METHODS Collagen-based dermal regeneration matrices (DRM) were seeded with human umbilical vein endothelial cells (HUVEC), human dermal lymphatic endothelial cells (LECs), or adipose-derived stem cells (ASC) and fixed with or without fibrin glue according to the experimental group. Cultures were maintained for 1 and 7 days. Finally, angiogenic and lymphangiogenic gene and protein expression were measured with special regard to subtypes of vascular endothelial growth factor (VEGF) and corresponding receptors using Multiplex-qPCR and ELISA assays. In addition, the hypoxia-induced factor 1-alpha (HIF1a) mediated intracellular signaling pathways were included in assessments to analyze a hypoxic encapsulating effect of fibrin polymers. RESULTS All cell types reacted to fibrin glue application with an alteration of gene and protein expression. In particular, vascular endothelial growth factor A (VEGFA), vascular endothelial growth factor B (VEGFB), vascular endothelial growth factor C (VEGFC), vascular endothelial growth receptor 1 (VEGFR1/FLT1), vascular endothelial growth receptor 2 (VEGFR2/KDR), vascular endothelial growth receptor 3 (VEGFR3/FLT4) and Prospero Homeobox 1 (PROX1) were depressed significantly depending on fibrin glue. Especially short-term fibrin effect led to a continuous downregulation of respective gene and protein expression in HUVECs, LECs, and ASCs. CONCLUSION Our findings demonstrate the impact of fibrin glue application in dermal regeneration with special regard to angiogenesis and lymphangiogenesis. In particular, a short fibrin treatment of 24 hours led to a decrease in gene and protein levels of LECS, HUVECs, and ASCs. In contrast, the long-term application showed less effect on gene and protein expressions. Therefore, this work demonstrated the negative effects of fibrin-treated cells in tissue engineering approaches and could affect wound healing during dermal regeneration.
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Affiliation(s)
- Benedikt Fuchs
- Department of Hand, Plastic and Aesthetic Surgery, LMU, Munich, Germany
| | - Alexandra Birt
- Department of Hand, Plastic and Aesthetic Surgery, LMU, Munich, Germany
| | | | | | - Riccardo Giunta
- Department of Hand, Plastic and Aesthetic Surgery, LMU, Munich, Germany
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4
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Abdelfadiel E, Gunta R, Villuri BK, Afosah DK, Sankaranarayanan NV, Desai UR. Designing Smaller, Synthetic, Functional Mimetics of Sulfated Glycosaminoglycans as Allosteric Modulators of Coagulation Factors. J Med Chem 2023; 66:4503-4531. [PMID: 37001055 PMCID: PMC10108365 DOI: 10.1021/acs.jmedchem.3c00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Indexed: 04/03/2023]
Abstract
Natural glycosaminoglycans (GAGs) are arguably the most diverse collection of natural products. Unfortunately, this bounty of structures remains untapped. Decades of research has realized only one GAG-like synthetic, small-molecule drug, fondaparinux. This represents an abysmal output because GAGs present a frontier that few medicinal chemists, and even fewer pharmaceutical companies, dare to undertake. GAGs are heterogeneous, polymeric, polydisperse, highly water soluble, synthetically challenging, too rapidly cleared, and difficult to analyze. Additionally, GAG binding to proteins is not very selective and GAG-binding sites are shallow. This Perspective attempts to transform this negative view into a much more promising one by highlighting recent advances in GAG mimetics. The Perspective focuses on the principles used in the design/discovery of drug-like, synthetic, sulfated small molecules as allosteric modulators of coagulation factors, such as antithrombin, thrombin, and factor XIa. These principles will also aid the design/discovery of sulfated agents against cancer, inflammation, and microbial infection.
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Affiliation(s)
- Elsamani
I. Abdelfadiel
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Rama Gunta
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Bharath Kumar Villuri
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Daniel K. Afosah
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Nehru Viji Sankaranarayanan
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Umesh R. Desai
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
- Department
of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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5
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Hassan N, Efing J, Kiesel L, Bendas G, Götte M. The Tissue Factor Pathway in Cancer: Overview and Role of Heparan Sulfate Proteoglycans. Cancers (Basel) 2023; 15:1524. [PMID: 36900315 PMCID: PMC10001432 DOI: 10.3390/cancers15051524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/05/2023] Open
Abstract
Historically, the only focus on tissue factor (TF) in clinical pathophysiology has been on its function as the initiation of the extrinsic coagulation cascade. This obsolete vessel-wall TF dogma is now being challenged by the findings that TF circulates throughout the body as a soluble form, a cell-associated protein, and a binding microparticle. Furthermore, it has been observed that TF is expressed by various cell types, including T-lymphocytes and platelets, and that certain pathological situations, such as chronic and acute inflammatory states, and cancer, may increase its expression and activity. Transmembrane G protein-coupled protease-activated receptors can be proteolytically cleaved by the TF:FVIIa complex that develops when TF binds to Factor VII (PARs). The TF:FVIIa complex can activate integrins, receptor tyrosine kinases (RTKs), and PARs in addition to PARs. Cancer cells use these signaling pathways to promote cell division, angiogenesis, metastasis, and the maintenance of cancer stem-like cells. Proteoglycans play a crucial role in the biochemical and mechanical properties of the cellular extracellular matrix, where they control cellular behavior via interacting with transmembrane receptors. For TFPI.fXa complexes, heparan sulfate proteoglycans (HSPGs) may serve as the primary receptor for uptake and degradation. The regulation of TF expression, TF signaling mechanisms, their pathogenic effects, and their therapeutic targeting in cancer are all covered in detail here.
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Affiliation(s)
- Nourhan Hassan
- Department of Gynecology and Obstetrics, Münster University Hospital, Domagkstrasse 11, 48149 Münster, Germany
- Biotechnology/Biomolecular Chemistry Program, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Janes Efing
- Department of Gynecology and Obstetrics, Münster University Hospital, Domagkstrasse 11, 48149 Münster, Germany
| | - Ludwig Kiesel
- Department of Gynecology and Obstetrics, Münster University Hospital, Domagkstrasse 11, 48149 Münster, Germany
| | - Gerd Bendas
- Pharmaceutical Department, University Bonn, An der Immenburg 4, 53225 Bonn, Germany
| | - Martin Götte
- Department of Gynecology and Obstetrics, Münster University Hospital, Domagkstrasse 11, 48149 Münster, Germany
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6
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Exosite Binding in Thrombin: A Global Structural/Dynamic Overview of Complexes with Aptamers and Other Ligands. Int J Mol Sci 2021; 22:ijms221910803. [PMID: 34639143 PMCID: PMC8509272 DOI: 10.3390/ijms221910803] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/24/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Thrombin is the key enzyme of the entire hemostatic process since it is able to exert both procoagulant and anticoagulant functions; therefore, it represents an attractive target for the developments of biomolecules with therapeutic potential. Thrombin can perform its many functional activities because of its ability to recognize a wide variety of substrates, inhibitors, and cofactors. These molecules frequently are bound to positively charged regions on the surface of protein called exosites. In this review, we carried out extensive analyses of the structural determinants of thrombin partnerships by surveying literature data as well as the structural content of the Protein Data Bank (PDB). In particular, we used the information collected on functional, natural, and synthetic molecular ligands to define the anatomy of the exosites and to quantify the interface area between thrombin and exosite ligands. In this framework, we reviewed in detail the specificity of thrombin binding to aptamers, a class of compounds with intriguing pharmaceutical properties. Although these compounds anchor to protein using conservative patterns on its surface, the present analysis highlights some interesting peculiarities. Moreover, the impact of thrombin binding aptamers in the elucidation of the cross-talk between the two distant exosites is illustrated. Collectively, the data and the work here reviewed may provide insights into the design of novel thrombin inhibitors.
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7
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Shlobin NA, Har-Even M, Itsekson-Hayosh Z, Harnof S, Pick CG. Role of Thrombin in Central Nervous System Injury and Disease. Biomolecules 2021; 11:562. [PMID: 33921354 PMCID: PMC8070021 DOI: 10.3390/biom11040562] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022] Open
Abstract
Thrombin is a Na+-activated allosteric serine protease of the chymotrypsin family involved in coagulation, inflammation, cell protection, and apoptosis. Increasingly, the role of thrombin in the brain has been explored. Low concentrations of thrombin are neuroprotective, while high concentrations exert pathological effects. However, greater attention regarding the involvement of thrombin in normal and pathological processes in the central nervous system is warranted. In this review, we explore the mechanisms of thrombin action, localization, and functions in the central nervous system and describe the involvement of thrombin in stroke and intracerebral hemorrhage, neurodegenerative diseases, epilepsy, traumatic brain injury, and primary central nervous system tumors. We aim to comprehensively characterize the role of thrombin in neurological disease and injury.
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Affiliation(s)
- Nathan A. Shlobin
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Meirav Har-Even
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Sylvan Adams Sports Institute, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ze’ev Itsekson-Hayosh
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel;
- Department of Neurology and Joseph Sagol Neuroscience Center, The Chaim Sheba Medical Center, Tel HaShomer 5262000, Israel
| | - Sagi Harnof
- Department of Neurosurgery, Beilinson Hospital, Rabin Medical Center, Tel Aviv University, Petah Tikva 4941492, Israel;
| | - Chaim G. Pick
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Sylvan Adams Sports Institute, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Biology of Addictive Diseases, Tel Aviv University, Tel Aviv 6997801, Israel
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8
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Riccardi C, Napolitano E, Platella C, Musumeci D, Montesarchio D. G-quadruplex-based aptamers targeting human thrombin: Discovery, chemical modifications and antithrombotic effects. Pharmacol Ther 2020; 217:107649. [PMID: 32777331 DOI: 10.1016/j.pharmthera.2020.107649] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
First studies on thrombin-inhibiting DNA aptamers were reported in 1992, and since then a large number of anticoagulant aptamers has been discovered. TBA - also named HD1, a 15-mer G-quadruplex (G4)-forming oligonucleotide - is the best characterized thrombin binding aptamer, able to specifically recognize the protein exosite I, thus inhibiting the conversion of soluble fibrinogen into insoluble fibrin strands. Unmodified nucleic acid-based aptamers, in general, and TBA in particular, exhibit limited pharmacokinetic properties and are rapidly degraded in vivo by nucleases. In order to improve the biological performance of aptamers, a widely investigated strategy is the introduction of chemical modifications in their backbone at the level of the nucleobases, sugar moieties or phosphodiester linkages. Besides TBA, also other thrombin binding aptamers, able to adopt a well-defined G4 structure, e.g. mixed duplex/quadruplex sequences, as well as homo- and hetero-bivalent constructs, have been identified and optimized. Considering the growing need of new efficient anticoagulant agents associated with the strong therapeutic potential of these thrombin inhibitors, the research on thrombin binding aptamers is still a very hot and intriguing field. Herein, we comprehensively described the state-of-the-art knowledge on the DNA-based aptamers targeting thrombin, especially focusing on the optimized analogues obtained by chemically modifying the oligonucleotide backbone, and their biological performances in therapeutic applications.
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Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Department of Advanced Medical and Surgical Sciences, 2(nd) Division of Neurology, Center for Rare Diseases and InterUniversity Center for Research in Neurosciences, University of Campania Luigi Vanvitelli, via Sergio Pansini, 5, I-80131 Naples, Italy.
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.
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9
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Aviñó A, Jorge AF, Huertas CS, Cova TFGG, Pais A, Lechuga LM, Eritja R, Fabrega C. Aptamer-peptide conjugates as a new strategy to modulate human α-thrombin binding affinity. Biochim Biophys Acta Gen Subj 2019; 1863:1619-1630. [PMID: 31265898 DOI: 10.1016/j.bbagen.2019.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/20/2019] [Accepted: 06/27/2019] [Indexed: 12/23/2022]
Abstract
Aptamers are single-stranded RNA or DNA molecules that specifically recognize their targets and have proven valuable for functionalizing sensitive biosensors. α-thrombin is a trypsin-like serine proteinase which plays a crucial role in haemostasis and thrombosis. An abnormal activity or overexpression of this protein is associated with a variety of diseases. A great deal of attention was devoted to the construction of high-throughput biosensors for accurately detect thrombin for the early diagnosis and treatment of related diseases. Herein, we propose a new approach to modulate the interaction between α-thrombin and the aptamer TBA15. To this end, TBA15 was chemically conjugated to two peptide sequences (TBA-G3FIE-Ac and TBA-G3EIF-Ac) corresponding to a short fragment of the acidic region of the human factor V, which is known to interact directly with exosite I. Surface Plasmon Resonance (SPR) results showed enhanced analytical performances of thrombin with TBA-G3EIF-Ac than with TBA wild-type, reaching a limit of detection as low as 44.9 pM. Electrophoresis mobility shift assay (EMSA) corroborated the SPR results. Molecular dynamics (MD) simulations support experimental evidences and provided further insight into thrombin/TBA-peptide interaction. Our findings demonstrate that the combination of TBA15 with key interacting peptides offers good opportunities to produce sensitive devices for thrombin detection and potential candidates to block thrombin activity.
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Affiliation(s)
- Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Andreia F Jorge
- CQC, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - César S Huertas
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, ICN2 Building, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Tânia F G G Cova
- CQC, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Alberto Pais
- CQC, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Laura M Lechuga
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC, ICN2 Building, Campus UAB, Bellaterra, 08193 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain.
| | - Carme Fabrega
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, E-08034 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain.
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10
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Xiao J, Salsbury FR. Na +-binding modes involved in thrombin's allosteric response as revealed by molecular dynamics simulations, correlation networks and Markov modeling. Phys Chem Chem Phys 2019; 21:4320-4330. [PMID: 30724273 PMCID: PMC6993936 DOI: 10.1039/c8cp07293k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The monovalent sodium ion (Na+) is a critical modulator of thrombin. However, the mechanism of thrombin's activation by Na+ has been widely debated for more than twenty years. Details of the linkage between thrombin and Na+ remain vague due to limited temporal and spatial resolution in experiments. In this work, we combine microsecond scale atomic-detailed molecular dynamics simulations with correlation network analyses and hidden Markov modeling to probe the detailed thermodynamic and kinetic picture of Na+-binding events and their resulting allosteric responses in thrombin. We reveal that ASP189 and ALA190 comprise a stable Na+-binding site (referred as "inner" Na+-binding site) along with the previously known one (referred as "outer" Na+-binding site). The corresponding newly identified Na+-binding mode introduces significant allosteric responses in thrombin's regulatory regions by stabilizing selected torsion angles of residues responsive to Na+-binding. Our Markov model indicates that the bound Na+ prefers to transfer between the two Na+-binding sites when an unbinding event takes place. These results suggest a testable hypothesis of a substrate-driven Na+ migration (ΔG ∼ 1.7 kcal mol-1) from the "inner" Na+-binding site to the "outer" one during thrombin's catalytic activities. The binding of a Na+ ion at the "inner" Na+-binding site should be inferred as a prerequisite for thrombin's efficient recognition to the substrate, which opens a new angle for our understanding of Na+-binding's allosteric activation on thrombin and sheds light on detailed processes in thrombin's activation.
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Affiliation(s)
- Jiajie Xiao
- Department of Physics, Wake Forest University, Winston Salem, NC, USA.
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11
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Billur R, Sabo TM, Maurer MC. Thrombin Exosite Maturation and Ligand Binding at ABE II Help Stabilize PAR-Binding Competent Conformation at ABE I. Biochemistry 2019; 58:1048-1060. [PMID: 30672691 DOI: 10.1021/acs.biochem.8b00943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Thrombin, derived from zymogen prothrombin (ProT), is a serine protease involved in procoagulation, anticoagulation, and platelet activation. Thrombin's actions are regulated through anion-binding exosites I and II (ABE I and ABE II) that undergo maturation during activation. Mature ABEs can utilize exosite-based communication to fulfill thrombin functions. However, the conformational basis behind such long-range communication and the resultant ligand binding affinities are not well understood. Protease activated receptors (PARs), involved in platelet activation and aggregation, are known to target thrombin ABE I. Unexpectedly, PAR3 (44-56) can already bind to pro-ABE I of ProT. Nuclear magnetic resonance (NMR) ligand-enzyme titrations were used to characterize how individual PAR1 (49-62) residues interact with pro-ABE I and mature ABE I. 1D proton line broadening studies demonstrated that binding affinities for native PAR1P (49-62, P54) and for the weak binding variant PAR1G (49-62, P54G) increased as ProT was converted to mature thrombin. 1H,15N-HSQC titrations revealed that PAR1G residues K51, E53, F55, D58, and E60 exhibited less affinity to pro-ABE I than comparable residues in PAR3G (44-56, P51G). Individual PAR1G residues then displayed tighter binding upon exosite maturation. Long-range communication between thrombin exosites was examined by saturating ABE II with phosphorylated GpIbα (269-282, 3Yp) and monitoring the binding of PAR1 and PAR3 peptides to ABE I. Individual PAR residues exhibited increased affinities in this dual-ligand environment supporting the presence of interexosite allostery. Exosite maturation and beneficial long-range allostery are proposed to help stabilize an ABE I conformation that can effectively bind PAR ligands.
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Affiliation(s)
- Ramya Billur
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center , University of Louisville , Louisville , Kentucky 40202 , United States
| | - Muriel C Maurer
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
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12
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Abdel Aziz MH, Desai UR. Novel heparin mimetics reveal cooperativity between exosite 2 and sodium-binding site of thrombin. Thromb Res 2018; 165:61-67. [PMID: 29573721 DOI: 10.1016/j.thromres.2018.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 02/28/2018] [Accepted: 03/16/2018] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Thrombin is a primary target of most anticoagulants. Yet, thrombin's dual and opposing role in pro- as well as anti- coagulant processes imposes considerable challenges in discovering finely tuned regulators that maintain homeostasis, rather than disproportionately changing the equilibrium to one side. In this connection, we have been studying exosite 2-mediated allosteric modulation of thrombin activity using synthetic agents called low molecular weight lignins (LMWLs). Although the aromatic scaffold of LMWLs is completely different from the polysaccharidic scaffold of heparin, the presence of multiple negatively charged groups on both ligands induces binding to exosite 2 of thrombin. This work characterizes the nature of interactions between LMWLs and thrombin to understand the energetic cooperativity between exosite 2 and active site of thrombin. MATERIALS AND METHODS The thermodynamics of thrombin-LMWL complexes was studied using spectrofluorimetric titrations as a function of ionic strength and temperature of the buffer. The contributions of enthalpy and entropy to binding were evaluated using classic thermodynamic equations. Label-free surface plasmon resonance was used to assess the role of sodium ion in LMWL binding to thrombin at a fixed ionic strength. RESULTS AND CONCLUSIONS Exosite 2-induced conformational change in thrombin's active site is strongly dependent on the structure of the ligand, which has consequences with respect to regulation of thrombin. The ionic and non-ionic contributions to binding affinity and the thermodynamic signature were highly ligand specific. Interestingly, LMWLs display preference for the sodium-bound form of thrombin, which supports the existence of an energetic coupling between exosite 2 and sodium-binding site of thrombin.
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Affiliation(s)
- May H Abdel Aziz
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, United States
| | - Umesh R Desai
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, United States; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 23219, United States.
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13
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Billur R, Ban D, Sabo TM, Maurer MC. Deciphering Conformational Changes Associated with the Maturation of Thrombin Anion Binding Exosite I. Biochemistry 2017; 56:6343-6354. [PMID: 29111672 DOI: 10.1021/acs.biochem.7b00970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Thrombin participates in procoagulation, anticoagulation, and platelet activation. This enzyme contains anion binding exosites, ABE I and ABE II, which attract regulatory biomolecules. As prothrombin is activated to thrombin, pro-ABE I is converted into mature ABE I. Unexpectedly, certain ligands can bind to pro-ABE I specifically. Moreover, knowledge of changes in conformation and affinity that occur at the individual residue level as pro-ABE I is converted to ABE I is lacking. Such changes are transient and were not captured by crystallography. Therefore, we employed nuclear magnetic resonance (NMR) titrations to monitor development of ABE I using peptides based on protease-activated receptor 3 (PAR3). Proton line broadening NMR revealed that PAR3 (44-56) and more weakly binding PAR3G (44-56) could already interact with pro-ABE I on prothrombin. 1H-15N heteronuclear single-quantum coherence NMR titrations were then used to probe binding of individual 15N-labeled PAR3G residues (F47, E48, L52, and D54). PAR3G E48 and D54 could interact electrostatically with prothrombin and tightened upon thrombin maturation. The higher affinity for PAR3G D54 suggests the region surrounding thrombin R77a is better oriented to bind D54 than the interaction between PAR3G E48 and thrombin R75. Aromatic PAR3G F47 and aliphatic L52 both reported on significant changes in the chemical environment upon conversion of prothrombin to thrombin. The ABE I region surrounding the 30s loop was more affected than the hydrophobic pocket (F34, L65, and I82). Our NMR titrations demonstrate that PAR3 residues document structural rearrangements occurring during exosite maturation that are missed by reported X-ray crystal structures.
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Affiliation(s)
- Ramya Billur
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville , Louisville, Kentucky 40202, United States
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville , Louisville, Kentucky 40202, United States
| | - Muriel C Maurer
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40292, United States
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Al-Horani RA, Karuturi R, Lee M, Afosah DK, Desai UR. Allosteric Inhibition of Factor XIIIa. Non-Saccharide Glycosaminoglycan Mimetics, but Not Glycosaminoglycans, Exhibit Promising Inhibition Profile. PLoS One 2016; 11:e0160189. [PMID: 27467511 PMCID: PMC4965010 DOI: 10.1371/journal.pone.0160189] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/14/2016] [Indexed: 12/13/2022] Open
Abstract
Factor XIIIa (FXIIIa) is a transglutaminase that catalyzes the last step in the coagulation process. Orthostery is the only approach that has been exploited to design FXIIIa inhibitors. Yet, allosteric inhibition of FXIIIa is a paradigm that may offer a key advantage of controlled inhibition over orthosteric inhibition. Such an approach is likely to lead to novel FXIIIa inhibitors that do not carry bleeding risks. We reasoned that targeting a collection of basic amino acid residues distant from FXIIIa’s active site by using sulfated glycosaminoglycans (GAGs) or non-saccharide GAG mimetics (NSGMs) would lead to the discovery of the first allosteric FXIIIa inhibitors. We tested a library of 22 variably sulfated GAGs and NSGMs against human FXIIIa to discover promising hits. Interestingly, although some GAGs bound to FXIIIa better than NSGMs, no GAG displayed any inhibition. An undecasulfated quercetin analog was found to inhibit FXIIIa with reasonable potency (efficacy of 98%). Michaelis-Menten kinetic studies revealed an allosteric mechanism of inhibition. Fluorescence studies confirmed close correspondence between binding affinity and inhibition potency, as expected for an allosteric process. The inhibitor was reversible and at least 9-fold- and 26-fold selective over two GAG-binding proteins factor Xa (efficacy of 71%) and thrombin, respectively, and at least 27-fold selective over a cysteine protease papain. The inhibitor also inhibited the FXIIIa-mediated polymerization of fibrin in vitro. Overall, our work presents the proof-of-principle that FXIIIa can be allosterically modulated by sulfated non-saccharide agents much smaller than GAGs, which should enable the design of selective and safe anticoagulants.
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Affiliation(s)
- Rami A. Al-Horani
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Rajesh Karuturi
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Michael Lee
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Daniel K. Afosah
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Umesh R. Desai
- Department of Medicinal Chemistry & Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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15
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Gao YS, Zhu XF, Xu JK, Lu LM, Wang WM, Yang TT, Xing HK, Yu YF. Label-free electrochemical immunosensor based on Nile blue A-reduced graphene oxide nanocomposites for carcinoembryonic antigen detection. Anal Biochem 2016; 500:80-7. [DOI: 10.1016/j.ab.2016.02.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/05/2015] [Accepted: 02/09/2016] [Indexed: 11/29/2022]
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16
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Kurisaki I, Takayanagi M, Nagaoka M. Toward understanding allosteric activation of thrombin: a conjecture for important roles of unbound Na(+) molecules around thrombin. J Phys Chem B 2015; 119:3635-42. [PMID: 25654267 DOI: 10.1021/jp510657n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We shed light on important roles of unbound Na(+) molecules in enzymatic activation of thrombin. Molecular mechanism of Na(+)-activation of thrombin has been discussed in the context of allostery. However, the recent challenge to redesign K(+)-activated thrombin revealed that the allosteric interaction is insufficient to explain the mechanism. Under these circumstances, we have examined the roles of unbound Na(+) molecule in maximization of thrombin-substrate association reaction rate. We performed all-atomic molecular dynamics (MD) simulations of thrombin in the presence of three different cations; Li(+), Na(+), and Cs(+). Although these cations are commonly observed in the vicinity of the S1-pocket of thrombin, smaller cations are distributed more densely and extensively than larger ones. This suggests the two observation rules: (i) thrombin surrounded by Na(+) is at an advantage in the initial step of association reaction, namely, the formation of an encounter complex ensemble, and (ii) the presence of Na(+) molecules does not necessarily have an advantage in the final step of association reaction, namely, the formation of the stereospecific complex. In conclusion, we propose a conjecture that unbound Na(+) molecules also affect the maximization of rate constant of thrombin-substrate association reaction through optimally forming an encounter complex ensemble.
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Affiliation(s)
- Ikuo Kurisaki
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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17
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Arutyunova E, Panwar P, Skiba PM, Gale N, Mak MW, Lemieux MJ. Allosteric regulation of rhomboid intramembrane proteolysis. EMBO J 2014; 33:1869-81. [PMID: 25009246 DOI: 10.15252/embj.201488149] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Proteolysis within the lipid bilayer is poorly understood, in particular the regulation of substrate cleavage. Rhomboids are a family of ubiquitous intramembrane serine proteases that harbour a buried active site and are known to cleave transmembrane substrates with broad specificity. In vitro gel and Förster resonance energy transfer (FRET)-based kinetic assays were developed to analyse cleavage of the transmembrane substrate psTatA (TatA from Providencia stuartii). We demonstrate significant differences in catalytic efficiency (kcat/K0.5) values for transmembrane substrate psTatA (TatA from Providencia stuartii) cleavage for three rhomboids: AarA from P. stuartii, ecGlpG from Escherichia coli and hiGlpG from Haemophilus influenzae demonstrating that rhomboids specifically recognize this substrate. Furthermore, binding of psTatA occurs with positive cooperativity. Competitive binding studies reveal an exosite-mediated mode of substrate binding, indicating allostery plays a role in substrate catalysis. We reveal that exosite formation is dependent on the oligomeric state of rhomboids, and when dimers are dissociated, allosteric substrate activation is not observed. We present a novel mechanism for specific substrate cleavage involving several dynamic processes including positive cooperativity and homotropic allostery for this interesting class of intramembrane proteases.
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Affiliation(s)
- Elena Arutyunova
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Pankaj Panwar
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Pauline M Skiba
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Nicola Gale
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - Michelle W Mak
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine & Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton, AB, Canada
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18
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Mehta AY, Thakkar JN, Mohammed BM, Martin EJ, Brophy DF, Kishimoto T, Desai UR. Targeting the GPIbα binding site of thrombin to simultaneously induce dual anticoagulant and antiplatelet effects. J Med Chem 2014; 57:3030-9. [PMID: 24635452 PMCID: PMC4203406 DOI: 10.1021/jm4020026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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Exosite 2 of human thrombin contributes
to two opposing pathways, the anticoagulant pathway and the platelet
aggregation pathway. We reasoned that an exosite 2 directed allosteric
thrombin inhibitor should simultaneously induce anticoagulant and
antiplatelet effects. To assess this, we synthesized SbO4L based on
the sulfated tyrosine-containing sequence of GPIbα. SbO4L was
synthesized in three simple steps in high yield and found to be a
highly selective, direct inhibitor of thrombin. Michelis–Menten
kinetic studies indicated a noncompetitive mechanism of inhibition.
Competitive inhibition studies suggested ideal competition with heparin
and glycoprotein Ibα, as predicted. Studies with site-directed
mutants of thrombin indicated that SbO4L binds to Arg233, Lys235,
and Lys236 of exosite 2. SbO4L prevented thrombin-mediated platelet
activation and aggregation as expected on the basis of competition
with GPIbα. SbO4L presents a novel paradigm of simultaneous
dual anticoagulant and antiplatelet effects achieved through the GPIbα
binding site of thrombin.
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Affiliation(s)
- Akul Y Mehta
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University , Richmond, Virginia 23219, United States
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19
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Gadwal S, Korotkov KV, Delarosa JR, Hol WGJ, Sandkvist M. Functional and structural characterization of Vibrio cholerae extracellular serine protease B, VesB. J Biol Chem 2014; 289:8288-98. [PMID: 24459146 PMCID: PMC3961656 DOI: 10.1074/jbc.m113.525261] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 01/22/2014] [Indexed: 11/06/2022] Open
Abstract
The chymotrypsin subfamily A of serine proteases consists primarily of eukaryotic proteases, including only a few proteases of bacterial origin. VesB, a newly identified serine protease that is secreted by the type II secretion system in Vibrio cholerae, belongs to this subfamily. VesB is likely produced as a zymogen because sequence alignment with trypsinogen identified a putative cleavage site for activation and a catalytic triad, His-Asp-Ser. Using synthetic peptides, VesB efficiently cleaved a trypsin substrate, but not chymotrypsin and elastase substrates. The reversible serine protease inhibitor, benzamidine, inhibited VesB and served as an immobilized ligand for VesB affinity purification, further indicating its relationship with trypsin-like enzymes. Consistent with this family of serine proteases, N-terminal sequencing implied that the propeptide is removed in the secreted form of VesB. Separate mutagenesis of the activation site and catalytic serine rendered VesB inactive, confirming the importance of these features for activity, but not for secretion. Similar to trypsin but, in contrast to thrombin and other coagulation factors, Na(+) did not stimulate the activity of VesB, despite containing the Tyr(250) signature. The crystal structure of catalytically inactive pro-VesB revealed that the protease domain is structurally similar to trypsinogen. The C-terminal domain of VesB was found to adopt an immunoglobulin (Ig)-fold that is structurally homologous to Ig-folds of other extracellular Vibrio proteins. Possible roles of the Ig-fold domain in stability, substrate specificity, cell surface association, and type II secretion of VesB, the first bacterial multidomain trypsin-like protease with known structure, are discussed.
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Affiliation(s)
- Shilpa Gadwal
- From the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109 and
| | - Konstantin V. Korotkov
- the Department of Biochemistry and Biomolecular Structure Center, University of Washington, Seattle, Washington 98195
| | - Jaclyn R. Delarosa
- the Department of Biochemistry and Biomolecular Structure Center, University of Washington, Seattle, Washington 98195
| | - Wim G. J. Hol
- the Department of Biochemistry and Biomolecular Structure Center, University of Washington, Seattle, Washington 98195
| | - Maria Sandkvist
- From the Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109 and
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20
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Forneris F, Burnley BT, Gros P. Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:733-43. [PMID: 24598742 PMCID: PMC3949522 DOI: 10.1107/s1399004713032549] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/29/2013] [Indexed: 11/16/2022]
Abstract
Human factor D (FD) is a self-inhibited thrombin-like serine proteinase that is critical for amplification of the complement immune response. FD is activated by its substrate through interactions outside the active site. The substrate-binding, or `exosite', region displays a well defined and rigid conformation in FD. In contrast, remarkable flexibility is observed in thrombin and related proteinases, in which Na(+) and ligand binding is implied in allosteric regulation of enzymatic activity through protein dynamics. Here, ensemble refinement (ER) of FD and thrombin crystal structures is used to evaluate structure and dynamics simultaneously. A comparison with previously published NMR data for thrombin supports the ER analysis. The R202A FD variant has enhanced activity towards artificial peptides and simultaneously displays active and inactive conformations of the active site. ER revealed pronounced disorder in the exosite loops for this FD variant, reminiscent of thrombin in the absence of the stabilizing Na(+) ion. These data indicate that FD exhibits conformational dynamics like thrombin, but unlike in thrombin a mechanism has evolved in FD that locks the unbound native state into an ordered inactive conformation via the self-inhibitory loop. Thus, ensemble refinement of X-ray crystal structures may represent an approach alternative to spectroscopy to explore protein dynamics in atomic detail.
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Affiliation(s)
- Federico Forneris
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - B. Tom Burnley
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Piet Gros
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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21
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Mehta AY, Jin Y, Desai UR. An update on recent patents on thrombin inhibitors (2010 – 2013). Expert Opin Ther Pat 2013; 24:47-67. [DOI: 10.1517/13543776.2014.845169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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22
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Abstract
Thrombin is the central protease in the blood coagulation network. It has multiple substrates and cofactors, and it appears that four serpins are responsible for inhibiting the thrombin produced in haemostasis and thrombosis. Structural studies conducted over the last 10 years have resolved how thrombin recognises these serpins with the aid of cofactors. Although antithrombin (AT), protein C inhibitor (PCI), heparin cofactor II (HCII) and protease nexin-1 (PN1) all share a common fold and mechanism of protease inhibition, they have evolved radically different mechanisms for cofactor-assisted thrombin recognition. This is likely to be due to the varied environments in which thrombin is found. In this review, I discuss the unusual structural features of thrombin that are involved in substrate and cofactor recognition, the serpin mechanism of protease inhibition and the fate of thrombin in the complex, and how the four thrombin-specific serpins exploit the special features of thrombin to accelerate complex formation.
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Affiliation(s)
- J A Huntington
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, UK.
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23
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Berezovsky IN. Thermodynamics of allostery paves a way to allosteric drugs. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:830-5. [PMID: 23376182 DOI: 10.1016/j.bbapap.2013.01.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 01/16/2013] [Accepted: 01/21/2013] [Indexed: 12/30/2022]
Abstract
We overview here our recent work on the thermodynamic view of allosteric regulation and communication. Starting from the geometry-based prediction of regulatory binding sites in a static structure, we move on to exploring a connection between ligand binding and the intrinsic dynamics of the protein molecule. We describe here two recently introduced measures, binding leverage and leverage coupling, which allow one to analyze the molecular basis of allosteric regulation. We discuss the advantages of these measures and show that they work universally in proteins of different sizes, oligomeric states, and functions. We also point the problems that have to be solved before completing an atomic level description of allostery, and briefly discuss ideas for computational design of allosteric drugs. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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Affiliation(s)
- Igor N Berezovsky
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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24
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Borbone N, Bucci M, Oliviero G, Morelli E, Amato J, D'Atri V, D'Errico S, Vellecco V, Cirino G, Piccialli G, Fattorusso C, Varra M, Mayol L, Persico M, Scuotto M. Investigating the role of T7 and T12 residues on the biological properties of thrombin-binding aptamer: enhancement of anticoagulant activity by a single nucleobase modification. J Med Chem 2012; 55:10716-28. [PMID: 23126678 DOI: 10.1021/jm301414f] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An acyclic pyrimidine analogue, containing a five-member cycle fused on the pyrimidine ring, was synthesized and introduced at position 7 or 12 of the 15-mer oligodeoxynucleotide GGTTGGTGTGGTTGG, known as thrombin-binding aptamer (TBA). Characterization by 1H NMR and CD spectroscopies of the resulting aptamers, TBA-T7b and TBA-T12b, showed their ability to fold into the typical antiparallel chairlike G-quadruplex structure formed by TBA. The apparent CD melting temperatures indicated that the introduction of the acyclic residue, mainly at position 7, improves the thermal stability of resulting G-quadruplexes with respect to TBA. The anticoagulant activity of the new molecules was then valued in PT assay, and it resulted that TBA-T7b is more potent than TBA in prolonging clotting time. On the other hand, in purified fibrinogen assay the thrombin inhibitory activity of both modified sequences was lower than that of TBA using human enzyme, whereas the potency trend was again reversed using bovine enzyme. Obtained structure-activity relationships were investigated by structural and computational studies. Taken together, these results reveal the active role of TBA residues T7 and T12 and the relevance of some amino acids located in the anion binding exosite I of the protein in aptamer-thrombin interaction.
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Affiliation(s)
- Nicola Borbone
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
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25
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Bradford HN, Krishnaswamy S. Meizothrombin is an unexpectedly zymogen-like variant of thrombin. J Biol Chem 2012; 287:30414-25. [PMID: 22815477 DOI: 10.1074/jbc.m112.394809] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Thrombin is produced by the ordered action of prothrombinase on two cleavage sites in prothrombin. Meizothrombin, a proteinase precursor of thrombin, is a singly cleaved species that accumulates abundantly as an intermediate. We now show that covalent linkage of the N-terminal propiece with the proteinase domain in meizothrombin imbues it with exceptionally zymogen-like character. Meizothrombin exists in a slowly reversible equilibrium between two equally populated states, differing by as much as 140-fold in their affinity for active site-directed ligands. The distribution between the two forms, designated zymogen-like and proteinase-like, is affected by Na(+), thrombomodulin binding, or active site ligation. In rapid kinetic measurements with prothrombinase, we also show that the zymogen-like form is produced following the initial cleavage reaction and slowly equilibrates with the proteinase-like form in a previously unanticipated rate-limiting step before it can be further cleaved to thrombin. The reversible equilibration of meizothrombin between zymogen- and proteinase-like states provides new insights into its ability to selectively exhibit the anticoagulant function of thrombin and the mechanistic basis for its accumulation during prothrombin activation. Our findings also provide unexpected insights into the regulation of proteinase function and how the formation of meizothrombin may yield a long lived intermediate with an important regulatory role in coagulation.
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Affiliation(s)
- Harlan N Bradford
- Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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26
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Mitternacht S, Berezovsky IN. Coherent conformational degrees of freedom as a structural basis for allosteric communication. PLoS Comput Biol 2011; 7:e1002301. [PMID: 22174669 PMCID: PMC3234217 DOI: 10.1371/journal.pcbi.1002301] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 10/29/2011] [Indexed: 01/10/2023] Open
Abstract
Conformational changes in allosteric regulation can to a large extent be described as motion along one or a few coherent degrees of freedom. The states involved are inherent to the protein, in the sense that they are visited by the protein also in the absence of effector ligands. Previously, we developed the measure binding leverage to find sites where ligand binding can shift the conformational equilibrium of a protein. Binding leverage is calculated for a set of motion vectors representing independent conformational degrees of freedom. In this paper, to analyze allosteric communication between binding sites, we introduce the concept of leverage coupling, based on the assumption that only pairs of sites that couple to the same conformational degrees of freedom can be allosterically connected. We demonstrate how leverage coupling can be used to analyze allosteric communication in a range of enzymes (regulated by both ligand binding and post-translational modifications) and huge molecular machines such as chaperones. Leverage coupling can be calculated for any protein structure to analyze both biological and latent catalytic and regulatory sites. What are the molecular mechanisms of allosteric communication in proteins? We base our analysis on the hypothesis that a folded protein has a number of conformational degrees of freedom, which describe fluctuations around the native conformation and switching from/to functional states. Transitions between the protein states involved in function and its regulation are based on coherent conformational degrees of freedom. Motion of one part of a protein along such a degree of freedom, implies a correlated motion in other parts of the protein. By determining which binding sites are simultaneously affected by the same motion we find sites that are allosterically coupled, i.e. where binding at one site can cause a change in ligand-affinity at another. Leverage coupling, the quantity introduced to measure this type of connection, reflects allosteric communication between different binding sites. We show how it can be used to understand allostery in enzymes of different sizes as well as in large protein complexes such as chaperones. Analysis of leverage coupling provides guidance in targeting native and latent regulatory sites.
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Affiliation(s)
- Simon Mitternacht
- Computational Biology Unit/Uni Research, University of Bergen, Bergen, Norway
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Igor N. Berezovsky
- Computational Biology Unit/Uni Research, University of Bergen, Bergen, Norway
- * E-mail:
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28
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Di Cera E. Thrombin as an Anticoagulant. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 99:145-84. [DOI: 10.1016/b978-0-12-385504-6.00004-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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29
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Niu W, Chen Z, Bush-Pelc LA, Bah A, Gandhi PS, Di Cera E. Mutant N143P reveals how Na+ activates thrombin. J Biol Chem 2009; 284:36175-36185. [PMID: 19846563 PMCID: PMC2794733 DOI: 10.1074/jbc.m109.069500] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 10/12/2009] [Indexed: 01/09/2023] Open
Abstract
The molecular mechanism of thrombin activation by Na(+) remains elusive. Its kinetic formulation requires extension of the classical Botts-Morales theory for the action of a modifier on an enzyme to correctly account for the contribution of the E*, E, and E:Na(+) forms. The extended scheme establishes that analysis of k(cat) unequivocally identifies allosteric transduction of Na(+) binding into enhanced catalytic activity. The thrombin mutant N143P features no Na(+)-dependent enhancement of k(cat) yet binds Na(+) with an affinity comparable to that of wild type. Crystal structures of the mutant in the presence and absence of Na(+) confirm that Pro(143) abrogates the important H-bond between the backbone N atom of residue 143 and the carbonyl O atom of Glu(192), which in turn controls the orientation of the Glu(192)-Gly(193) peptide bond and the correct architecture of the oxyanion hole. We conclude that Na(+) activates thrombin by securing the correct orientation of the Glu(192)-Gly(193) peptide bond, which is likely flipped in the absence of cation. Absolute conservation of the 143-192 H-bond in trypsin-like proteases and the importance of the oxyanion hole in protease function suggest that this mechanism of Na(+) activation is present in all Na(+)-activated trypsin-like proteases.
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Affiliation(s)
- Weiling Niu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Zhiwei Chen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Leslie A Bush-Pelc
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Alaji Bah
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Prafull S Gandhi
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Enrico Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110.
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30
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Thrombin allosteric modulation revisited: a molecular dynamics study. J Mol Model 2009; 16:725-35. [DOI: 10.1007/s00894-009-0590-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 09/02/2009] [Indexed: 10/20/2022]
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Demerdash ONA, Daily MD, Mitchell JC. Structure-based predictive models for allosteric hot spots. PLoS Comput Biol 2009; 5:e1000531. [PMID: 19816556 PMCID: PMC2748687 DOI: 10.1371/journal.pcbi.1000531] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 09/09/2009] [Indexed: 12/12/2022] Open
Abstract
In allostery, a binding event at one site in a protein modulates the behavior of a distant site. Identifying residues that relay the signal between sites remains a challenge. We have developed predictive models using support-vector machines, a widely used machine-learning method. The training data set consisted of residues classified as either hotspots or non-hotspots based on experimental characterization of point mutations from a diverse set of allosteric proteins. Each residue had an associated set of calculated features. Two sets of features were used, one consisting of dynamical, structural, network, and informatic measures, and another of structural measures defined by Daily and Gray [1]. The resulting models performed well on an independent data set consisting of hotspots and non-hotspots from five allosteric proteins. For the independent data set, our top 10 models using Feature Set 1 recalled 68–81% of known hotspots, and among total hotspot predictions, 58–67% were actual hotspots. Hence, these models have precision P = 58–67% and recall R = 68–81%. The corresponding models for Feature Set 2 had P = 55–59% and R = 81–92%. We combined the features from each set that produced models with optimal predictive performance. The top 10 models using this hybrid feature set had R = 73–81% and P = 64–71%, the best overall performance of any of the sets of models. Our methods identified hotspots in structural regions of known allosteric significance. Moreover, our predicted hotspots form a network of contiguous residues in the interior of the structures, in agreement with previous work. In conclusion, we have developed models that discriminate between known allosteric hotspots and non-hotspots with high accuracy and sensitivity. Moreover, the pattern of predicted hotspots corresponds to known functional motifs implicated in allostery, and is consistent with previous work describing sparse networks of allosterically important residues. Allostery is the process whereby a molecule binds to one site in a protein and alters the function of a distant site. This phenomenon is ubiquitous, as proteins frequently must adapt their behavior to changes in the cellular milieu. The mechanism(s) underlying allostery remains incompletely understood. In particular, predictive models are needed that distinguish amino-acid residues that are critical to allostery, or “hotspots”, from non-hotspots. Here we have used data-mining approaches to infer rules that distinguish hotspots from non-hotspots. Starting with a data set of known hotspot and non-hotspot residues from a diverse set of allosteric proteins, the training data set, we applied machine learning to this data to “learn” models, or sets of rules, for distinguishing hotspots and non-hotspots by inferring associations between the classification (hotspot or non-hotspot) and an associated set of calculated attributes. Many models that showed the highest predictive power on the training data also exhibited high accuracy and sensitivity when applied to an independent data set. Moreover, the pattern of predicted hotspots in the proteins we studied was consistent with known structure/function relationships and previous work suggesting that a network of essential residues mediates the allosteric transition.
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Affiliation(s)
- Omar N. A. Demerdash
- Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Medical Scientist Training Program, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael D. Daily
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Julie C. Mitchell
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Mathematics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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32
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Denisov IG, Frank DJ, Sligar SG. Cooperative properties of cytochromes P450. Pharmacol Ther 2009; 124:151-67. [PMID: 19555717 DOI: 10.1016/j.pharmthera.2009.05.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 05/28/2009] [Indexed: 02/07/2023]
Abstract
Cytochromes P450 form a large and important class of heme monooxygenases with a broad spectrum of substrates and corresponding functions, from steroid hormone biosynthesis to the metabolism of xenobiotics. Despite decades of study, the molecular mechanisms responsible for the complex non-Michaelis behavior observed with many members of this superfamily during metabolism, often termed 'cooperativity', remain to be fully elucidated. Although there is evidence that oligomerization may play an important role in defining the observed cooperativity, some monomeric cytochromes P450, particularly those involved in xenobiotic metabolism, also display this behavior due to their ability to simultaneously bind several substrate molecules. As a result, formation of distinct enzyme-substrate complexes with different stoichiometry and functional properties can give rise to homotropic and heterotropic cooperative behavior. This review aims to summarize the current understanding of cooperativity in cytochromes P450, with a focus on the nature of cooperative effects in monomeric enzymes.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States of America
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Abstract
Meizothrombin is the physiologically active intermediate generated by a single cleavage of prothrombin at R320 to separate the A and B chains. Recent evidence has suggested that meizothrombin, like thrombin, is a Na(+)-activated enzyme. In this study we present the first X-ray crystal structure of human meizothrombin desF1 solved in the presence of the active site inhibitor PPACK at 2.1 A resolution. The structure reveals a Na(+) binding site whose architecture is practically identical to that of human thrombin. Stopped-flow measurements of Na(+) binding to meizothrombin desF1 document a slow phase of fluorescence change with a k(obs) decreasing hyperbolically with increasing [Na(+)], consistent with the existence of three conformations in equilibrium, E*, E and E:Na(+), as for human thrombin. Evidence that meizothrombin exists in multiple conformations provides valuable new information for studies of the mechanism of prothrombin activation.
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Affiliation(s)
- M. E. Papaconstantinou
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110 USA
| | - P. S. Gandhi
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110 USA
| | - Z. Chen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110 USA
| | - A. Bah
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110 USA
| | - E. Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110 USA
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Sun W, Parry S, Panico M, Morris HR, Kjellberg M, Engström A, Dell A, Schedin-Weiss S. N-glycans and the N terminus of protein C inhibitor affect the cofactor-enhanced rates of thrombin inhibition. J Biol Chem 2008; 283:18601-11. [PMID: 18467335 DOI: 10.1074/jbc.m800608200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein C inhibitor (PCI) is a serine protease inhibitor, displaying broad protease specificity, found in blood and other tissues. In blood, it is capable of inhibiting both procoagulant and anticoagulant proteases. Mechanisms that provide specificity to PCI remain largely unrevealed. In this study we have for the first time provided a full explanation for the marked size heterogeneity of blood-derived PCI and identified functional differences between naturally occurring PCI variants. The heterogeneity was caused by differences in N-glycan structures, N-glycosylation occupancy, and the presence of a Delta6-N-cleaved form. Bi-, tri-, and tetra-antennary complex N-glycans were identified. Fucose residues were identified both on the core GlcNAc and as parts of sialyl-Le(a/x) epitopes. Moreover, a glycan with a composition that implied a di-sialyl antenna was observed. PCI was N-glycosylated at all three potential N-glycosylation sites, Asn-230, Asn-243, and Asn-319, but a small fraction of PCI lacked the N-glycan at Asn-243. The overall removal of N-glycans affected the maximal heparin- and thrombomodulin-enhanced rates of thrombin inhibition differently in different solution conditions. In contrast, the Delta6-N-region increased both the heparin- and the thrombomodulin-enhanced rates of thrombin inhibition at all conditions examined. These results thus demonstrate that the N-linked glycans and the N-terminal region of blood-derived PCI in different ways affect the cofactor-enhanced rates of thrombin inhibition and provide information on the mechanisms by which this may be achieved. The findings are medically important, in view of the documented association of PCI with atherosclerotic plaques and the promising effect of PCI on reducing hypercoagulability states.
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Affiliation(s)
- Wei Sun
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Uppsala SE-751 23, Sweden
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Page MJ, Carrell CJ, Di Cera E. Engineering protein allostery: 1.05 A resolution structure and enzymatic properties of a Na+-activated trypsin. J Mol Biol 2008; 378:666-72. [PMID: 18377928 DOI: 10.1016/j.jmb.2008.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Revised: 02/29/2008] [Accepted: 03/04/2008] [Indexed: 11/28/2022]
Abstract
Some trypsin-like proteases are endowed with Na(+)-dependent allosteric enhancement of catalytic activity, but this important mechanism has been difficult to engineer in other members of the family. Replacement of 19 amino acids in Streptomyces griseus trypsin targeting the active site and the Na(+)-binding site were found necessary to generate efficient Na(+) activation. Remarkably, this property was linked to the acquisition of a new substrate selectivity profile similar to that of factor Xa, a Na(+)-activated protease involved in blood coagulation. The X-ray crystal structure of the mutant trypsin solved to 1.05 A resolution defines the engineered Na(+) site and active site loops in unprecedented detail. The results demonstrate that trypsin can be engineered into an efficient allosteric protease, and that Na(+) activation is interwoven with substrate selectivity in the trypsin scaffold.
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Affiliation(s)
- Michael J Page
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110, USA
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36
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Structural identification of the pathway of long-range communication in an allosteric enzyme. Proc Natl Acad Sci U S A 2008; 105:1832-7. [PMID: 18250335 DOI: 10.1073/pnas.0710894105] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Allostery is a common mechanism of regulation of enzyme activity and specificity, and its signatures are readily identified from functional studies. For many allosteric systems, structural evidence exists of long-range communication among protein domains, but rarely has this communication been traced to a detailed pathway. The thrombin mutant D102N is stabilized in a self-inhibited conformation where access to the active site is occluded by a collapse of the entire 215-219 beta-strand. Binding of a fragment of the protease activated receptor PAR1 to exosite I, 30-A away from the active site region, causes a large conformational change that corrects the position of the 215-219 beta-strand and restores access to the active site. The crystal structure of the thrombin-PAR1 complex, solved at 2.2-A resolution, reveals the details of this long-range allosteric communication in terms of a network of polar interactions.
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Abstract
Thrombin is a Na+-activated, allosteric serine protease that plays opposing functional roles in blood coagulation. Binding of Na+ is the major driving force behind the procoagulant, prothrombotic and signaling functions of the enzyme, but is dispensable for cleavage of the anticoagulant protein C. The anticoagulant function of thrombin is under the allosteric control of the cofactor thrombomodulin. Much has been learned on the mechanism of Na+ binding and recognition of natural substrates by thrombin. Recent structural advances have shed light on the remarkable molecular plasticity of this enzyme and the molecular underpinnings of thrombin allostery mediated by binding to exosite I and the Na+ site. This review summarizes our current understanding of the molecular basis of thrombin function and allosteric regulation. The basic information emerging from recent structural, mutagenesis and kinetic investigation of this important enzyme is that thrombin exists in three forms, E*, E and E:Na+, that interconvert under the influence of ligand binding to distinct domains. The transition between the Na+ -free slow from E and the Na+ -bound fast form E:Na+ involves the structure of the enzyme as a whole, and so does the interconversion between the two Na+ -free forms E* and E. E* is most likely an inactive form of thrombin, unable to interact with Na + and substrate. The complexity of thrombin function and regulation has gained this enzyme pre-eminence as the prototypic allosteric serine protease. Thrombin is now looked upon as a model system for the quantitative analysis of biologically important enzymes.
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Affiliation(s)
- Enrico Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, MO 63110, United States.
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Berny MA, White TC, Tucker EI, Bush-Pelc LA, Di Cera E, Gruber A, McCarty OJ. Thrombin Mutant W215A/E217A Acts as a Platelet GPIb Antagonist. Arterioscler Thromb Vasc Biol 2008; 28:329-34. [DOI: 10.1161/atvbaha.107.156273] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Michelle A. Berny
- From the Departments of Biomedical Engineering (M.A.B., T.C.W., E.I.T., A.G., O.J.T.M.) and Cell and Developmental Biology (O.J.T.M.), Oregon Health and Science University, Portland; and Biochemistry and Molecular Biophysics (L.A.B.-P., E.D.C.), Washington University, St. Louis, Mo
| | - Tara C. White
- From the Departments of Biomedical Engineering (M.A.B., T.C.W., E.I.T., A.G., O.J.T.M.) and Cell and Developmental Biology (O.J.T.M.), Oregon Health and Science University, Portland; and Biochemistry and Molecular Biophysics (L.A.B.-P., E.D.C.), Washington University, St. Louis, Mo
| | - Erik I. Tucker
- From the Departments of Biomedical Engineering (M.A.B., T.C.W., E.I.T., A.G., O.J.T.M.) and Cell and Developmental Biology (O.J.T.M.), Oregon Health and Science University, Portland; and Biochemistry and Molecular Biophysics (L.A.B.-P., E.D.C.), Washington University, St. Louis, Mo
| | - Leslie A. Bush-Pelc
- From the Departments of Biomedical Engineering (M.A.B., T.C.W., E.I.T., A.G., O.J.T.M.) and Cell and Developmental Biology (O.J.T.M.), Oregon Health and Science University, Portland; and Biochemistry and Molecular Biophysics (L.A.B.-P., E.D.C.), Washington University, St. Louis, Mo
| | - Enrico Di Cera
- From the Departments of Biomedical Engineering (M.A.B., T.C.W., E.I.T., A.G., O.J.T.M.) and Cell and Developmental Biology (O.J.T.M.), Oregon Health and Science University, Portland; and Biochemistry and Molecular Biophysics (L.A.B.-P., E.D.C.), Washington University, St. Louis, Mo
| | - András Gruber
- From the Departments of Biomedical Engineering (M.A.B., T.C.W., E.I.T., A.G., O.J.T.M.) and Cell and Developmental Biology (O.J.T.M.), Oregon Health and Science University, Portland; and Biochemistry and Molecular Biophysics (L.A.B.-P., E.D.C.), Washington University, St. Louis, Mo
| | - Owen J.T. McCarty
- From the Departments of Biomedical Engineering (M.A.B., T.C.W., E.I.T., A.G., O.J.T.M.) and Cell and Developmental Biology (O.J.T.M.), Oregon Health and Science University, Portland; and Biochemistry and Molecular Biophysics (L.A.B.-P., E.D.C.), Washington University, St. Louis, Mo
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39
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Gianni S, Ivarsson Y, Bah A, Bush-Pelc LA, Di Cera E. Mechanism of Na(+) binding to thrombin resolved by ultra-rapid kinetics. Biophys Chem 2007; 131:111-4. [PMID: 17935858 DOI: 10.1016/j.bpc.2007.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 09/24/2007] [Accepted: 09/24/2007] [Indexed: 11/19/2022]
Abstract
The interaction of Na(+) and K(+) with proteins is at the basis of numerous processes of biological importance. However, measurement of the kinetic components of the interaction has eluded experimentalists for decades because the rate constants are too fast to resolve with conventional stopped-flow methods. Using a continuous-flow apparatus with a dead time of 50 micro s we have been able to resolve the kinetic rate constants and entire mechanism of Na(+) binding to thrombin, an interaction that is at the basis of the procoagulant and prothrombotic roles of the enzyme in the blood.
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Affiliation(s)
- Stefano Gianni
- Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche, Universita' di Roma La Sapienza, Rome, Italy.
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40
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Bush-Pelc LA, Marino F, Chen Z, Pineda AO, Mathews FS, Di Cera E. Important role of the cys-191 cys-220 disulfide bond in thrombin function and allostery. J Biol Chem 2007; 282:27165-27170. [PMID: 17636263 DOI: 10.1074/jbc.m703202200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Little is known on the role of disulfide bonds in the catalytic domain of serine proteases. The Cys-191-Cys-220 disulfide bond is located between the 190 strand leading to the oxyanion hole and the 220-loop that contributes to the architecture of the primary specificity pocket and the Na+ binding site in allosteric proteases. Removal of this bond in thrombin produces an approximately 100-fold loss of activity toward several chromogenic and natural substrates carrying Arg or Lys at P1. Na+ activation is compromised, and no fluorescence change can be detected in response to Na+ binding. A 1.54-A resolution structure of the C191A/C220A mutant in the free form reveals a conformation similar to the Na+-free slow form of wild type. The lack of disulfide bond exposes the side chain of Asp-189 to solvent, flips the backbone O atom of Gly-219, and generates disorder in portions of the 186 and 220 loops defining the Na+ site. This conformation, featuring perturbation of the Na+ site but with the active site accessible to substrate, offers a possible representation of the recently identified E* form of thrombin. Disorder in the 186 and 220 loops and the flip of Gly-219 are corrected by the active site inhibitor H-D-Phe-Pro-Arg-CH(2)Cl, as revealed by the 1.8-A resolution structure of the complex. We conclude that the Cys-191-Cys-220 disulfide bond confers stability to the primary specificity pocket by shielding Asp-189 from the solvent and orients the backbone O atom of Gly-219 for optimal substrate binding. In addition, the disulfide bond stabilizes the 186 and 220 loops that are critical for Na+ binding and activation.
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Affiliation(s)
- Leslie A Bush-Pelc
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Francesca Marino
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Zhiwei Chen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Agustin O Pineda
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - F Scott Mathews
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Enrico Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110.
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41
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Bah A, Chen Z, Bush-Pelc LA, Mathews FS, Di Cera E. Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4. Proc Natl Acad Sci U S A 2007; 104:11603-8. [PMID: 17606903 PMCID: PMC1913866 DOI: 10.1073/pnas.0704409104] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Indexed: 11/18/2022] Open
Abstract
It has been proposed that the cleaved form of protease-activated receptor 3 (PAR3) acts as a cofactor for thrombin cleavage and activation of PAR4 on murine platelets, but the molecular basis of this physiologically important effect remains elusive. X-ray crystal structures of murine thrombin bound to extracellular fragments of the murine receptors PAR3 ((38)SFNGGPQNTFEEFPLSDIE(56)) and PAR4 ((51)KSSDKPNPR downward arrow GYPGKFCANDSDTLELPASSQA(81), downward arrow = site of cleavage) have been solved at 2.0 and 3.5 A resolution, respectively. The cleaved form of PAR3, traced in the electron density maps from Gln-44 to Glu-56, makes extensive hydrophobic and electrostatic contacts with exosite I of thrombin through the fragment (47)FEEFPLSDIE(56). Occupancy of exosite I by PAR3 allosterically changes the conformation of the 60-loop and shifts the position of Trp-60d approximately 10 A with a resulting widening of the access to the active site. The PAR4 fragment, traced entirely in the electron density maps except for five C-terminal residues, clamps Trp-60d, Tyr-60a, and the aryl-binding site of thrombin with Pro-56 and Pro-58 at the P2 and P4 positions and engages the primary specificity pocket with Arg-59. The fragment then leaves the active site with Gly-60 and folds into a short helical turn that directs the backbone away from exosite I and over the autolysis loop. The structures demonstrate that thrombin activation of PAR4 may occur with exosite I available to bind cofactor molecules, like the cleaved form of PAR3, whose function is to promote substrate diffusion into the active site by allosterically changing the conformation of the 60-loop.
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Affiliation(s)
- Alaji Bah
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110
| | - Zhiwei Chen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110
| | - Leslie A. Bush-Pelc
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110
| | - F. Scott Mathews
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110
| | - Enrico Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110
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Abstract
Thrombin is a Na(+)-activated, allosteric serine protease that plays opposing functional roles in blood coagulation. Binding of Na(+) is the major driving force behind the procoagulant, prothrombotic and signaling functions of the enzyme, but is dispensable for cleavage of the anticoagulant protein C. This basic regulatory feature of thrombin has fostered the rational engineering of mutants with selectively compromised fibrinogen and PAR1 cleavage. The discovery of the Na(+) effect on thrombin interaction with substrates and the mapping of functional epitopes by Ala scanning mutagenesis have provided a rational and effective strategy for dissociating the procoagulant and anticoagulant activities of the enzyme. Thrombin mutants with selectively compromised activity toward fibrinogen and PAR1 are effective in vivo as anticoagulant and antithrombotic agents.
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Affiliation(s)
- E Di Cera
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St Louis, MO 63110, USA.
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43
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Marino F, Chen ZW, Ergenekan CE, Bush-Pelc LA, Mathews FS, Di Cera E. Structural basis of Na+ activation mimicry in murine thrombin. J Biol Chem 2007; 282:16355-61. [PMID: 17428793 DOI: 10.1074/jbc.m701323200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Unlike human thrombin, murine thrombin lacks Na+ activation due to the charge reversal substitution D222K in the Na+ binding loop. However, the enzyme is functionally stabilized in a Na+-bound form and is highly active toward physiologic substrates. The structural basis of this peculiar property is unknown. Here, we present the 2.2 A resolution x-ray crystal structure of murine thrombin in the absence of inhibitors and salts. The enzyme assumes an active conformation, with Ser-195, Glu-192, and Asp-189 oriented as in the Na+-bound fast form of human thrombin. Lys-222 completely occludes the pore of entry to the Na+ binding site and positions its side chain inside the pore, with the Nzeta atom H-bonded to the backbone oxygen atoms of Lys-185, Asp-186b, and Lys-186d. The same architecture is observed in the 1.75 A resolution structure of a thrombin chimera in which the human enzyme carries all residues defining the Na+ pore in the murine enzyme. These findings demonstrate that Na+ activation in thrombin is linked to the architecture of the Na+ pore. The molecular strategy of Na+ activation mimicry unraveled for murine thrombin is relevant to serine proteases and enzymes activated by monovalent cations in general.
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Affiliation(s)
- Francesca Marino
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri 63110, USA
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