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Madsen JJ, Persson E, Olsen OH. The intricate allostery in factor VIIa: triggering the trigger. J Thromb Haemost 2024:S1538-7836(24)00551-8. [PMID: 39332529 DOI: 10.1016/j.jtha.2024.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 08/13/2024] [Accepted: 08/22/2024] [Indexed: 09/29/2024]
Abstract
In the last couple of decades, numerous investigations have shed considerable light on how precisely factor (F)VIIa mediates the initiation of blood coagulation upon association with its cofactor, tissue factor (TF). The role of the cofactor in this process is indispensable under physiological conditions, serving as a membrane-tethering allosteric activator of FVIIa also interacting with substrates (eg, FX). Available evidence reveals the induction and manifestation of complex allostery within FVIIa when stimulated by TF, involving at least 2 connected pathways spanning the interactive interface of the FVIIa-TF complex and the functional segments of FVIIa. Carefully designed FVIIa variants demonstrate corresponding modulations of their properties and response to TF-triggered allostery and activation. In addition, antibodies can stimulate FVIIa activity in both similar and distinctly different ways compared to that employed by TF. The mechanistic insights obtained through basic biochemical investigations have been validated through select engineered FVIIa constructs which, even in vivo, demonstrate beneficial, proof-of-concept effects. Altogether, we have recently gained unprecedented knowledge about and control over FVIIa allostery, enabling us to influence FVIIa activity in advanced manners and in a desired direction. Here, we summarize our current understanding of the allosteric activation of FVIIa ending up with some prospects of future investigations.
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Affiliation(s)
- Jesper J Madsen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Center for Global Health and Infectious Diseases Research, Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA.
| | | | - Ole H Olsen
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
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2
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Sorensen AB, Greisen PJ, Madsen JJ, Lund J, Andersen G, Wulff-Larsen PG, Pedersen AA, Gandhi PS, Overgaard MT, Østergaard H, Olsen OH. A systematic approach for evaluating the role of surface-exposed loops in trypsin-like serine proteases applied to the 170 loop in coagulation factor VIIa. Sci Rep 2022; 12:3747. [PMID: 35260627 PMCID: PMC8904457 DOI: 10.1038/s41598-022-07620-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/14/2022] [Indexed: 12/27/2022] Open
Abstract
Proteases play a major role in many vital physiological processes. Trypsin-like serine proteases (TLPs), in particular, are paramount in proteolytic cascade systems such as blood coagulation and complement activation. The structural topology of TLPs is highly conserved, with the trypsin fold comprising two β-barrels connected by a number of variable surface-exposed loops that provide a surprising capacity for functional diversity and substrate specificity. To expand our understanding of the roles these loops play in substrate and co-factor interactions, we employ a systematic methodology akin to the natural truncations and insertions observed through evolution of TLPs. The approach explores a larger deletion space than classical random or directed mutagenesis. Using FVIIa as a model system, deletions of 1–7 amino acids through the surface exposed 170 loop, a vital allosteric regulator, was introduced. All variants were extensively evaluated by established functional assays and computational loop modelling with Rosetta. The approach revealed detailed structural and functional insights recapitulation and expanding on the main findings in relation to 170 loop functions elucidated over several decades using more cumbersome crystallization and single deletion/mutation methodologies. The larger deletion space was key in capturing the most active variant, which unexpectedly had a six-amino acid truncation. This variant would have remained undiscovered if only 2–3 deletions were considered, supporting the usefulness of the methodology in general protease engineering approaches. Our findings shed further light on the complex role that surface-exposed loops play in TLP function and supports the important role of loop length in the regulation and fine-tunning of enzymatic function throughout evolution.
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Affiliation(s)
- Anders B Sorensen
- Global Research, Novo Nordisk A/S, 2760, Måløv, Denmark.,Department of Chemistry and Bioscience, Aalborg University, 9220, Ålborg, Denmark
| | | | - Jesper J Madsen
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL, 33612, USA.,Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Jacob Lund
- Global Research, Novo Nordisk A/S, 2760, Måløv, Denmark
| | - Gorm Andersen
- Global Research, Novo Nordisk A/S, 2760, Måløv, Denmark
| | | | | | | | - Michael T Overgaard
- Department of Chemistry and Bioscience, Aalborg University, 9220, Ålborg, Denmark
| | | | - Ole H Olsen
- Global Research, Novo Nordisk A/S, 2760, Måløv, Denmark. .,Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen, Denmark.
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Ohkubo YZ, Madsen JJ. Uncovering Membrane-Bound Models of Coagulation Factors by Combined Experimental and Computational Approaches. Thromb Haemost 2021; 121:1122-1137. [PMID: 34214998 PMCID: PMC8432591 DOI: 10.1055/s-0040-1722187] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In the life sciences, including hemostasis and thrombosis, methods of structural biology have become indispensable tools for shedding light on underlying mechanisms that govern complex biological processes. Advancements of the relatively young field of computational biology have matured to a point where it is increasingly recognized as trustworthy and useful, in part due to their high space–time resolution that is unparalleled by most experimental techniques to date. In concert with biochemical and biophysical approaches, computational studies have therefore proven time and again in recent years to be key assets in building or suggesting structural models for membrane-bound forms of coagulation factors and their supramolecular complexes on membrane surfaces where they are activated. Such endeavors and the proposed models arising from them are of fundamental importance in describing and understanding the molecular basis of hemostasis under both health and disease conditions. We summarize the body of work done in this important area of research to drive forward both experimental and computational studies toward new discoveries and potential future therapeutic strategies.
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Affiliation(s)
- Y Zenmei Ohkubo
- Department of Bioinformatics, School of Life and Natural Sciences, Abdullah Gül University, Kayseri, Turkey
| | - Jesper J Madsen
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida, United States
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Beeler DL, Aird WC, Grant MA. Evolutionary conservation of the allosteric activation of factor VIIa by tissue factor in lamprey: reply. J Thromb Haemost 2018; 16:1454-1456. [PMID: 29734527 DOI: 10.1111/jth.14141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Indexed: 11/27/2022]
Affiliation(s)
- D L Beeler
- Center for Vascular Biology Research and Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - W C Aird
- Center for Vascular Biology Research and Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
- Mount Dessert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - M A Grant
- Center for Vascular Biology Research and Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA
- Mount Dessert Island Biological Laboratory, Salisbury Cove, ME, USA
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Beeler DL, Aird WC, Grant MA. Evolutionary conservation of the allosteric activation of factor VIIa by tissue factor in lamprey. J Thromb Haemost 2018; 16:734-748. [PMID: 29418058 PMCID: PMC5893411 DOI: 10.1111/jth.13968] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Indexed: 11/28/2022]
Abstract
Essentials Tissue factor (TF) enhances factor VIIa (FVIIa) activity through structural and dynamic changes. We analyzed conservation of TF-activated FVIIa allosteric networks in extant vertebrate lamprey. Lamprey Tf/FVIIa molecular dynamics show conserved Tf-induced structural/dynamic FVIIa changes. Lamprey Tf activation of FVIIa allosteric networks follows molecular pathways similar to human. SUMMARY Background Previous studies have provided insight into the molecular basis of human tissue factor (TF) activation of activated factor VII (FVIIa). TF-induced allosteric networks of FVIIa activation have been rationalized through analysis of the dynamic changes and residue connectivities in the human soluble TF (sTF)/FVIIa complex structure during molecular dynamics (MD) simulation. Evolutionary conservation of the molecular mechanisms for TF-induced allosteric FVIIa activation between humans and extant vertebrate jawless fish (lampreys), where blood coagulation emerged more than 500 million years ago, is unknown and of considerable interest. Objective To model the sTf/FVIIa complex from cloned Petromyzon marinus lamprey sequences, and with comparisons to human sTF/FVlla investigate conservation of allosteric mechanisms of FVIIa activity enhancement by soluble TF using MD simulations. Methods Full-length cDNAs of lamprey tf and f7 were cloned and characterized. Comparative models of lamprey sTf/FVIIa complex and free FVIIa were determined based on constructed human sTF/FVIIa complex and free FVIIa models, used in full-atomic MD simulations, and characterized using dynamic network analysis approaches. Results Allosteric paths of correlated motion from Tf contact points in lamprey sTf/FVIIa to the FVIIa active site were determined and quantified, and were found to encompass residue-residue interactions along significantly similar paths compared with human. Conclusions Despite low conservation of residues between lamprey and human proteins, 30% TF and 39% FVII, the structural and protein dynamic effects of TF activation of FVIIa appear conserved and, moreover, present in extant vertebrate proteins from 500 million years ago when TF/FVIIa-initiated extrinsic pathway blood coagulation emerged.
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Affiliation(s)
- D L Beeler
- Center for Vascular Biology Research and Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - W C Aird
- Center for Vascular Biology Research and Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
| | - M A Grant
- Center for Vascular Biology Research and Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, USA
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Abstract
Coagulation factor VIIa (FVIIa) is an intrinsically poor serine protease that requires assistance from its cofactor tissue factor (TF) to trigger the extrinsic pathway of blood coagulation. TF stimulates FVIIa through allosteric maturation of its active site and by facilitating substrate recognition. The surface dependence of the latter property allowed us to design a potent membrane-triggered activity switch in FVIIa by engineering a disulfide cross-link between an allosterically silent FVIIa variant and soluble TF. These results show that optimization of substrate recognition remote from the active site represents a promising new route to simultaneously enhance and localize the procoagulant activity of FVIIa for therapeutic purposes. Recombinant factor VIIa (FVIIa) variants with increased activity offer the promise to improve the treatment of bleeding episodes in patients with inhibitor-complicated hemophilia. Here, an approach was adopted to enhance the activity of FVIIa by selectively optimizing substrate turnover at the membrane surface. Under physiological conditions, endogenous FVIIa engages its cell-localized cofactor tissue factor (TF), which stimulates activity through membrane-dependent substrate recognition and allosteric effects. To exploit these properties of TF, a covalent complex between FVIIa and the soluble ectodomain of TF (sTF) was engineered by introduction of a nonperturbing cystine bridge (FVIIa Q64C-sTF G109C) in the interface. Upon coexpression, FVIIa Q64C and sTF G109C spontaneously assembled into a covalent complex with functional properties similar to the noncovalent wild-type complex. Additional introduction of a FVIIa-M306D mutation to uncouple the sTF-mediated allosteric stimulation of FVIIa provided a final complex with FVIIa-like activity in solution, while exhibiting a two to three orders-of-magnitude increase in activity relative to FVIIa upon exposure to a procoagulant membrane. In a mouse model of hemophilia A, the complex normalized hemostasis upon vascular injury at a dose of 0.3 nmol/kg compared with 300 nmol/kg for FVIIa.
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Prasad R, Sen P. Structural modulation of factor VIIa by full-length tissue factor (TF 1-263): implication of novel interactions between EGF2 domain and TF. J Biomol Struct Dyn 2017; 36:621-633. [PMID: 28150568 DOI: 10.1080/07391102.2017.1289125] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Tissue factor (TF)-mediated factor VII (FVII) activation and a subsequent proteolytic TF-FVIIa binary complex formation is the key step initiating the coagulation cascade, with implications in various homeostatic and pathologic scenarios. TF binding allosterically modifies zymogen-like free FVIIa to its highly catalytically active form. As a result of unresolved crystal structure of the full-length TF1-263-FVIIa binary complex and free FVIIa, allosteric alterations in FVIIa following its binding to full-length TF and the consequences of these on function are not entirely clear. The present study aims to map and identify structural alterations in FVIIa and TF resulting from full-length TF binding to FVIIa and the key events responsible for enhanced FVIIa activity in coagulation. We constructed the full-length TF1-263-FVIIa membrane bound complex using computational modeling and subjected it to molecular dynamics (MD) simulations. MD simulations showed that TF alters the structure of each domain of FVIIa and these combined alterations contribute to enhanced TF-FVIIa activity. Detailed, domain-wise investigation revealed several new non-covalent interactions between TF and FVIIa that were not found in the truncated soluble TF-FVIIa crystal structure. The structural modulation of each FVIIa domain imparted by TF indicated that both inter and intra-domain communication is crucial for allosteric modulation of FVIIa. Our results suggest that these newly formed interactions can provide additional stability to the protease domain and regulate its activity profile by governing catalytic triad (CT) orientation and localization. The unexplored newly formed interactions between EGF2 and TF provides a possible explanation for TF-induced allosteric activation of FVIIa.
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Affiliation(s)
- Ramesh Prasad
- a Department of Biological Chemistry , Indian Association for the Cultivation of Science , 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032 , India
| | - Prosenjit Sen
- a Department of Biological Chemistry , Indian Association for the Cultivation of Science , 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032 , India
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Sorensen AB, Madsen JJ, Svensson LA, Pedersen AA, Østergaard H, Overgaard MT, Olsen OH, Gandhi PS. Molecular Basis of Enhanced Activity in Factor VIIa-Trypsin Variants Conveys Insights into Tissue Factor-mediated Allosteric Regulation of Factor VIIa Activity. J Biol Chem 2015; 291:4671-83. [PMID: 26694616 DOI: 10.1074/jbc.m115.698613] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Indexed: 11/06/2022] Open
Abstract
The complex of coagulation factor VIIa (FVIIa), a trypsin-like serine protease, and membrane-bound tissue factor (TF) initiates blood coagulation upon vascular injury. Binding of TF to FVIIa promotes allosteric conformational changes in the FVIIa protease domain and improves its catalytic properties. Extensive studies have revealed two putative pathways for this allosteric communication. Here we provide further details of this allosteric communication by investigating FVIIa loop swap variants containing the 170 loop of trypsin that display TF-independent enhanced activity. Using x-ray crystallography, we show that the introduced 170 loop from trypsin directly interacts with the FVIIa active site, stabilizing segment 215-217 and activation loop 3, leading to enhanced activity. Molecular dynamics simulations and novel fluorescence quenching studies support that segment 215-217 conformation is pivotal to the enhanced activity of the FVIIa variants. We speculate that the allosteric regulation of FVIIa activity by TF binding follows a similar path in conjunction with protease domain N terminus insertion, suggesting a more complete molecular basis of TF-mediated allosteric enhancement of FVIIa activity.
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Affiliation(s)
- Anders B Sorensen
- From Global Research, Novo Nordisk A/S, 2760 Måløv, Denmark, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark, and
| | - Jesper J Madsen
- From Global Research, Novo Nordisk A/S, 2760 Måløv, Denmark, Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | | | | | - Michael T Overgaard
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark, and
| | - Ole H Olsen
- From Global Research, Novo Nordisk A/S, 2760 Måløv, Denmark
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Gajsiewicz JM, Morrissey JH. Structure-Function Relationship of the Interaction between Tissue Factor and Factor VIIa. Semin Thromb Hemost 2015; 41:682-90. [PMID: 26408924 DOI: 10.1055/s-0035-1564044] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interactions between tissue factor and factor VIIa are the primary initiators of coagulation in hemostasis and certain thrombotic diseases. Tissue factor, an integral membrane protein expressed extensively outside of the vasculature, is the regulatory protein cofactor for coagulation factor VIIa. Factor VIIa, a trypsin-like serine protease homologous with other blood coagulation proteases, is weakly active when free in solution and must bind its membrane-bound cofactor for physiologically relevant activity. Tissue factor allosterically activates factor VIIa by several mechanisms such as active site positioning, spatial stabilization, and direct interactions with the substrate. Protein-membrane interactions between tissue factor, factor VIIa, and substrates all play critical roles in modulating the activity of this enzyme complex. Additionally, divalent cations such as Ca(2+) and Mg(2+) are critical for correct protein folding, as well as protein-membrane and protein-protein interactions. The contributions of these factors toward tissue factor-factor VIIa activity are discussed in this review.
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Affiliation(s)
| | - James H Morrissey
- Department of Biochemistry, University of Illinois, Urbana, Illinois
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Madsen JJ, Persson E, Olsen OH. Tissue factor activates allosteric networks in factor VIIa through structural and dynamic changes. J Thromb Haemost 2015; 13:262-7. [PMID: 25403348 DOI: 10.1111/jth.12791] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/10/2014] [Indexed: 11/30/2022]
Abstract
BACKGROUND Tissue factor (TF) promotes colocalization of enzyme (factor VIIa) and substrate (FX or FIX), and stabilizes the active conformation of FVIIa. Details on how TF induces structural and dynamic changes in the catalytic domain of FVIIa to enhance its efficiency remain elusive. OBJECTIVE To elucidate the activation of allosteric networks in the catalytic domain of the FVIIa protease it is when bound to TF. METHODS Long-timescale molecular dynamics simulations of FVIIa, free and in complex with TF, were executed and analyzed by dynamic network analysis. RESULTS Allosteric paths of correlated motion from the TF contact point, Met306, in FVIIa to the active site triad can be described and quantified. In particular, the shortest paths from Met306 to Ser344 and His193 are 16% and 8% longer in free FVIIa than in TF-FVIIa, and they encompass previously undiscovered residue-residue interactions that are not likely to be inferred from mutagenesis studies. Furthermore, paths from Met306 to Ile153 (N-terminus) and Trp364, both representing hallmark residues of allostery, are 7% and 37% longer, respectively, in free FVIIa. Thus, there is significantly weaker coupling between the TF contact point and key residues in the catalytic domain of FVIIa, causing the active site triad to disintegrate in the simulation when TF is not present. CONCLUSIONS These findings complement our current understanding of how the protease FVIIa is stimulated by TF. We demonstrate allosteric networks in the catalytic domain that are activated by TF and help to make FVIIa an efficient catalyst of FIX and FX activation.
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Affiliation(s)
- J J Madsen
- Haemophilia Biochemistry, Novo Nordisk A/S, Måløv, Denmark; DTU Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
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Song H, Olsen OH, Persson E, Rand KD. Sites involved in intra- and interdomain allostery associated with the activation of factor VIIa pinpointed by hydrogen-deuterium exchange and electron transfer dissociation mass spectrometry. J Biol Chem 2014; 289:35388-96. [PMID: 25344622 DOI: 10.1074/jbc.m114.614297] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Factor VIIa (FVIIa) is a trypsin-like protease that plays an important role in initiating blood coagulation. Very limited structural information is available for the free, inactive form of FVIIa that circulates in the blood prior to vascular injury and the molecular details of its activity enhancement remain elusive. Here we have applied hydrogen/deuterium exchange mass spectrometry coupled to electron transfer dissociation to pinpoint individual residues in the heavy chain of FVIIa whose conformation and/or local interaction pattern changes when the enzyme transitions to the active form, as induced either by its cofactor tissue factor or a covalent active site inhibitor. Identified regulatory residues are situated at key sites across one continuous surface of the protease domain spanning the TF-binding helix across the activation pocket to the calcium binding site and are embedded in elements of secondary structure and at the base of flexible loops. Thus these residues are optimally positioned to mediate crosstalk between functional sites in FVIIa, particularly the cofactor binding site and the active site. Our results unambiguously show that the conformational allosteric activation signal extends to the EGF1 domain in the light chain of FVIIa, underscoring a remarkable intra- and interdomain allosteric regulation of this trypsin-like protease.
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Affiliation(s)
- Hongjian Song
- From the Department of Pharmacy, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark and
| | - Ole H Olsen
- Haemostasis Biology, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - Egon Persson
- Haemostasis Biology, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - Kasper D Rand
- From the Department of Pharmacy, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark and
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Pan J, Borchers CH. Top-down mass spectrometry and hydrogen/deuterium exchange for comprehensive structural characterization of interferons: Implications for biosimilars. Proteomics 2014; 14:1249-58. [DOI: 10.1002/pmic.201300341] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 11/14/2013] [Accepted: 02/24/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Jingxi Pan
- University of Victoria - Genome BC Proteomics Centre; University of Victoria; Victoria BC Canada
| | - Christoph H. Borchers
- University of Victoria - Genome BC Proteomics Centre; University of Victoria; Victoria BC Canada
- Department of Biochemistry and Microbiology; University of Victoria; Victoria BC Canada
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13
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Emerging computational approaches for the study of protein allostery. Arch Biochem Biophys 2013; 538:6-15. [DOI: 10.1016/j.abb.2013.07.025] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/23/2013] [Accepted: 07/30/2013] [Indexed: 12/12/2022]
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Ben-Hadj-Khalifa S, Lakhal B, Nsiri B, Mahjoub T, Almawi WY. Factor VII levels, R353Q and -323P0/10 Factor VII variants, and the risk of acute coronary syndrome among Arab-African Tunisians. Mol Biol Rep 2013; 40:3793-8. [PMID: 23275237 DOI: 10.1007/s11033-012-2456-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 12/18/2012] [Indexed: 11/29/2022]
Abstract
The importance of the extrinsic haemostatic system, of which factor VII/VIIa (FVII/FVIIa) is a key constituent, in acute coronary syndrome (ACS) is well recognized. The contribution of FVII gene variants R353Q and -323P0/10, and altered FVII plasma levels to the risk of ACS was investigated in a North African Tunisian Arab cohort consisting of 308 ACS cases and 312 age-, gender- and ethnically-matched control subjects; FVII antigen levels were determined by ELISA. Regression analysis was used in assessing the association of FVII variants and changes in FVII levels to the overall risk of ACS. Significantly higher FVII antigen levels were seen in ACS patients (P < 0.001), and were associated with ACS and with ACS severity, and this association was confirmed by multivariate regression analysis, after adjusting for a number of confounders (BMI, smoking, systolic blood pressure, hypertension, diabetes, and glucose, cholesterol, and triglycerides levels). While the carriage of 353Q allele, was associated with significant reduction in FVII plasma levels, the distribution of the R353Q genotypes was comparable between cases and control subjects, thereby indicating that altered FVII levels, independent of R353 variant, were associated with increased risk of ACS. In contrast, the -323Ins variant, while not associated with altered FVII plasma levels, was associated with ACS, following adjustment for BMI, smoking, systolic blood pressure, hypertension, diabetes, and glucose, cholesterol, triglycerides and FVII levels. In summary, elevated FVII levels, and the -323P0/10 but not R353Q polymorphism, constitute risk factors for ACS.
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Affiliation(s)
- Sonia Ben-Hadj-Khalifa
- Faculty of Pahrmacy, Research Unit of Biology and Genetics of Hematologic and Autoimmune Diseases, Monastir, Tunisia
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15
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Andersen LM, Andreasen PA, Svendsen I, Keemink J, Østergaard H, Persson E. Antibody-induced enhancement of factor VIIa activity through distinct allosteric pathways. J Biol Chem 2012; 287:8994-9001. [PMID: 22275370 DOI: 10.1074/jbc.m111.312330] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the absence of its cofactor tissue factor (TF), coagulation factor VIIa (FVIIa) predominantly exists in a zymogen-like, catalytically incompetent state. Here we demonstrate that conformation-specific monoclonal antibodies (mAbs) can be used to characterize structural features determining the activity of FVIIa. We isolated two classes of mAbs, which both increased the catalytic efficiency of FVIIa more than 150-fold. The effects of the antibodies were retained with a FVIIa variant, which has been shown to be inert to allosteric activation by the natural activator TF, suggesting that the antibodies and TF employ distinct mechanisms of activation. The antibodies could be classified into two groups based on their patterns of affinities for different conformations of FVIIa. Whereas one class of antibodies affected both the K(m) and k(cat), the other class mainly affected the K(m). The antibody-induced activity enhancement could be traced to maturation of the S1 substrate binding pocket and the oxyanion hole, evident by an increased affinity for p-aminobenzamidine, an increased rate of antithrombin inhibition, an increased rate of incorporation of diisopropylfluorophosphate, and an enhanced fraction of molecules with a buried N terminus of the catalytic domain in the presence of antibodies. As demonstrated by site-directed mutagenesis, the two groups of antibodies appear to have overlapping, although clearly different, epitopes in the 170-loop. Our findings suggest that binding of ligands to specific residues in the 170-loop or its spatial vicinity may stabilize the S1 pocket and the oxyanion hole, and they may have general implications for the molecular understanding of FVIIa regulatory mechanisms.
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Gaso-Sokac D, Kovac S, Clifton J, Josic D. Therapeutic plasma proteins--application of proteomics in process optimization, validation, and analysis of the final product. Electrophoresis 2011; 32:1104-17. [PMID: 21544836 DOI: 10.1002/elps.201000641] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An overview is given on the application of proteomic technology in the monitoring of different steps during the production of therapeutic proteins from human plasma. Recent advances in this technology enable the use of proteomics as an advantageous tool for the validation of already existing processes, the development and fine tuning of new production steps, the characterization and quality control of final products, the detection of both harmful impurities and modifications of the therapeutic protein and the auditing of batch-to-batch variations. Further, use of proteomics for preclinical testing of new products, which can be either recombinant or plasma-derived, is also discussed.
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Affiliation(s)
- Dajana Gaso-Sokac
- Department of Chemistry, J. J. Strossmayer Univeristy, Osijek, Croatia
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Clearance of rFVIIa and NN1731 after intravenous administration to Beagle dogs. Eur J Pharm Sci 2011; 42:578-83. [DOI: 10.1016/j.ejps.2011.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 01/20/2011] [Accepted: 02/24/2011] [Indexed: 11/20/2022]
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Houde D, Berkowitz SA, Engen JR. The utility of hydrogen/deuterium exchange mass spectrometry in biopharmaceutical comparability studies. J Pharm Sci 2010; 100:2071-86. [PMID: 21491437 DOI: 10.1002/jps.22432] [Citation(s) in RCA: 286] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/23/2010] [Accepted: 11/15/2010] [Indexed: 12/13/2022]
Abstract
The function, efficacy, and safety of protein biopharmaceuticals are tied to their three-dimensional structure. The analysis and verification of this higher-order structure are critical in demonstrating manufacturing consistency and in establishing the absence of structural changes in response to changes in production. It is, therefore, essential to have reliable, high-resolution and high sensitivity biophysical tools capable of interrogating protein structure and conformation. Here, we demonstrate the use of hydrogen/deuterium exchange mass spectrometry (H/DX-MS) in biopharmaceutical comparability studies. H/DX-MS measurements can be conducted with good precision, consume only picomoles of protein, interrogate nearly the entire molecule with peptide level resolution, and can be completed in a few days. Structural comparability or lack of comparability was monitored for different preparations of interferon-β-1a. We present specific graphical formats for the display of H/DX-MS data that aid in rapidly making both the qualitative (visual) and quantitative assessment of comparability. H/DX-MS is capable of making significant contributions in biopharmaceutical characterization by providing more informative and confidant comparability assessments of protein higher-order structures than are currently available within the biopharmaceutical industry.
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Affiliation(s)
- Damian Houde
- Biogen Idec, Inc, Cambridge, Massachusetts 02142, USA
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Mosbaek CR, Nolan D, Persson E, Svergun DI, Bukrinsky JT, Vestergaard B. Extensive small-angle X-ray scattering studies of blood coagulation factor VIIa reveal interdomain flexibility. Biochemistry 2010; 49:9739-45. [PMID: 20873866 DOI: 10.1021/bi1011207] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Blood coagulation factor VIIa (FVIIa) is used in the treatment of replacement therapy resistant hemophilia patients, and FVIIa is normally activated upon complex formation with tissue factor (TF), potentially in context with structural rearrangements. The solution behavior of uncomplexed FVIIa is important for understanding the mechanism of activation and for the stability and activity of the pharmaceutical product. However, crystal structures of FVIIa in complex with TF and of truncated free FVIIa reveal different overall conformations while previous small-angle scattering studies suggest FVIIa always to be fully extended in solution. Here, small-angle X-ray scattering analysis of multiple forms of FVIIa and TF under several experimental conditions elaborate extensively on the understanding of the solution behavior of FVIIa. We reveal significant FVIIa domain flexibility in solution, whereas TF has a well-defined conformation. Unspecific formation of dimers of FVIIa is also observed and varies with experimental conditions. In particular, active site-inhibited FVIIa displays a distinct solution behavior different from that of uninhibited FVIIa, which may reflect structural rearrangements causing resistance to activation, thereby emphasizing the connection between the distribution of different conformations of FVII and the mechanism of activation.
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Affiliation(s)
- Charlotte Rode Mosbaek
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.
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Li CZ, Koter M, Ye X, Zhou SF, Chou W, Luo R, Gershon PD. Widespread but Small-Scale Changes in the Structural and Dynamic Properties of Vaccinia Virus Poly(A) Polymerase upon Association with Its Processivity Factor in Solution. Biochemistry 2010; 49:6247-62. [DOI: 10.1021/bi100166x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C.-Z. Li
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
| | - M. Koter
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
| | - X. Ye
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
| | - S.-F. Zhou
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
| | - W. Chou
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
| | - R. Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
| | - P. D. Gershon
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
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21
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Ohkubo YZ, Morrissey JH, Tajkhorshid E. Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factor. J Thromb Haemost 2010; 8:1044-53. [PMID: 20180816 PMCID: PMC2890040 DOI: 10.1111/j.1538-7836.2010.03826.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
SUMMARY BACKGROUND The molecular mechanism of enhancement of the enzymatic activity of factor VIIa by tissue factor (TF) is not fully understood, primarily because of the lack of atomic models for the membrane-bound form of the TF-FVIIa complex. OBJECTIVES To construct the first membrane-bound model of the TF-FVIIa complex, and to investigate the dynamics of the complex in solution and on the surface of anionic membranes by using large-scale molecular dynamics (MD) simulations in full atomic detail. METHODS Membrane-bound models of the TF-FVIIa complex and the individual factors were constructed and subjected to MD simulations, in order to characterize protein-protein and protein-lipid interactions, and to investigate the dynamics of TF and FVIIa. RESULTS The MD trajectories reveal that isolated FVIIa undergoes large structural fluctuation, primarily due to the hinge motions between its domains, whereas soluble TF (sTF) is structurally stable. Upon complex formation, sTF restricts the motion of FVIIa significantly. The results also show that, in the membrane-bound form, sTF directly interacts with the lipid headgroups, even in the absence of FVIIa. CONCLUSION The first atomic models of membrane-bound sTF-FVIIa, FVIIa and sTF are presented, revealing that sTF forms direct contacts with the lipids, both in the isolated form and in complex with FVIIa. The main effect of sTF binding to FVIIa is spatial stabilization of the catalytic site of FVIIa, which ensures optimal interaction with the substrate, FX.
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Affiliation(s)
- Y Z Ohkubo
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, IL, USA
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23
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Persson E, Olsen OH. Activation loop 3 and the 170 loop interact in the active conformation of coagulation factor VIIa. FEBS J 2009; 276:3099-109. [PMID: 19490111 DOI: 10.1111/j.1742-4658.2009.07028.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The initiation of blood coagulation involves tissue factor (TF)-induced allosteric activation of factor VIIa (FVIIa), which circulates in a zymogen-like state. In addition, the (most) active conformation of FVIIa presumably relies on a number of intramolecular interactions. We have characterized the role of Gly372(223) in FVIIa, which is the sole residue in activation loop 3 that is capable of forming backbone hydrogen bonds with the unusually long 170 loop and with activation loop 2, by studying the effects of replacement with Ala [G372(223)A]. G372A-FVIIa, both in the free and TF-bound form, exhibited reduced cleavage of factor X (FX) and of peptidyl substrates, and had increased K(m) values compared with wild-type FVIIa. Inhibition of G372A-FVIIa.sTF by p-aminobenzamidine was characterized by a seven-fold higher K(i) than obtained with FVIIa.sTF. Crystallographic and modelling data suggest that the most active conformation of FVIIa depends on the backbone hydrogen bond between Gly372(223) and Arg315(170C) in the 170 loop. Despite the reduced activity and inhibitor susceptibility, native and active site-inhibited G372A-FVIIa bound sTF with the same affinity as the corresponding forms of FVIIa, and burial of the N-terminus of the protease domain increased similarly upon sTF binding to G372A-FVIIa and FVIIa. Thus Gly372(223) in FVIIa appears to play a critical role in maturation of the S1 pocket and adjacent subsites, but does not appear to be of importance for TF binding and the ensuing allostery.
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Affiliation(s)
- Egon Persson
- Haemostasis Biochemistry, Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark.
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Suchanova B, Tuma R. Folding and assembly of large macromolecular complexes monitored by hydrogen-deuterium exchange and mass spectrometry. Microb Cell Fact 2008; 7:12. [PMID: 18394161 PMCID: PMC2365927 DOI: 10.1186/1475-2859-7-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2008] [Accepted: 04/04/2008] [Indexed: 11/26/2022] Open
Abstract
Recent advances in protein mass spectrometry (MS) have enabled determinations of hydrogen deuterium exchange (HDX) in large macromolecular complexes. HDX-MS became a valuable tool to follow protein folding, assembly and aggregation. The methodology has a wide range of applications in biotechnology ranging from quality control for over-expressed proteins and their complexes to screening of potential ligands and inhibitors. This review provides an introduction to protein folding and assembly followed by the principles of HDX and MS detection, and concludes with selected examples of applications that might be of interest to the biotechnology community.
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Rand KD, Andersen MD, Olsen OH, Jørgensen TJD, Ostergaard H, Jensen ON, Stennicke HR, Persson E. The origins of enhanced activity in factor VIIa analogs and the interplay between key allosteric sites revealed by hydrogen exchange mass spectrometry. J Biol Chem 2008; 283:13378-87. [PMID: 18343822 DOI: 10.1074/jbc.m709716200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Factor VIIa (FVIIa) circulates in the blood in a zymogen-like state. Only upon association with membrane-bound tissue factor (TF) at the site of vascular injury does FVIIa become active and able to initiate blood coagulation. Here we used hydrogen exchange monitored by mass spectrometry to investigate the conformational effects of site-directed mutagenesis at key positions in FVIIa and the origins of enhanced intrinsic activity of FVIIa analogs. The differences in hydrogen exchange of two highly active variants, FVIIa(DVQ) and FVIIa(VEAY), imply that enhanced catalytic efficiency was attained by two different mechanisms. Regions protected from exchange in FVIIa(DVQ) include the N-terminal tail and the activation pocket, which is a subset of the regions of FVIIa protected from exchange upon TF binding. FVIIa(DVQ) appeared to adopt an intermediate conformation between the free (zymogen-like) and TF-bound (active) form of FVIIa and to attain enhanced activity by partial mimicry of TF-induced activation. In contrast, exchange-protected regions in FVIIa(VEAY) were confined to the vicinity of the active site of FVIIa. Thus, the changes in FVIIa(VEAY) appeared to optimize the active site region rather than imitate the TF-induced effect. Hydrogen exchange analysis of the FVIIa(M306D) variant, which was unresponsive to stimulation by TF, correlated widespread reductions in exchange to the single mutation in the TF-binding region. These results reveal the delicate interplay between key allosteric sites necessary to achieve the transition of FVIIa into the active form.
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Affiliation(s)
- Kasper D Rand
- Department of Haemostasis Biochemistry, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark.
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