1
|
Madsen JJ, Ohkubo YZ. Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM. PLoS Comput Biol 2024; 20:e1011421. [PMID: 38976709 PMCID: PMC11257402 DOI: 10.1371/journal.pcbi.1011421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 07/18/2024] [Accepted: 06/19/2024] [Indexed: 07/10/2024] Open
Abstract
Membrane binding is a crucial mechanism for many proteins, but understanding the specific interactions between proteins and membranes remains a challenging endeavor. Coagulation factor Va (FVa) is a large protein whose membrane interactions are complicated due to the presence of multiple anchoring domains that individually can bind to lipid membranes. Using molecular dynamics simulations, we investigate the membrane binding of FVa and identify the key mechanisms that govern its interaction with membranes. Our results reveal that FVa can either adopt an upright or a tilted molecular orientation upon membrane binding. We further find that the domain organization of FVa deviates (sometimes significantly) from its crystallographic reference structure, and that the molecular orientation of the protein matches with domain reorganization to align the C2 domain toward its favored membrane-normal orientation. We identify specific amino acid residues that exhibit contact preference with phosphatidylserine lipids over phosphatidylcholine lipids, and we observe that mostly electrostatic effects contribute to this preference. The observed lipid-binding process and characteristics, specific to FVa or common among other membrane proteins, in concert with domain reorganization and molecular tilt, elucidate the complex membrane binding dynamics of FVa and provide important insights into the molecular mechanisms of protein-membrane interactions. An updated version of the HMMM model, termed extHMMM, is successfully employed for efficiently observing membrane bindings of systems containing the whole FVa molecule.
Collapse
Affiliation(s)
- Jesper J. Madsen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America
- Center for Global Health and Infectious Diseases Research, Global and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida, United States of America
| | - Y. Zenmei Ohkubo
- Department of Bioinformatics, School of Life and Natural Sciences, Abdullah Gül University, Kayseri, Turkey
| |
Collapse
|
2
|
Madsen JJ, Yu W. Dynamic Nature of Staphylococcus aureus Type I Signal Peptidases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576923. [PMID: 38328037 PMCID: PMC10849702 DOI: 10.1101/2024.01.23.576923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Molecular dynamics simulations are used to interrogate the dynamic nature of Staphylococcus aureus Type I signal peptidases, SpsA and SpsB, including the impact of the P29S mutation of SpsB. Fluctuations and plasticity- rigidity characteristics vary among the proteins, particularly in the extracellular domain. Intriguingly, the P29S mutation, which influences susceptibility to arylomycin antibiotics, affect the mechanically coupled motions in SpsB. The integrity of the active site is crucial for catalytic competency, and variations in sampled structural conformations among the proteins are consistent with diverse peptidase capabilities. We also explored the intricate interactions between the proteins and the model S. aureus membrane. It was observed that certain membrane-inserted residues in the loop around residue 50 (50s) and C-terminal loops, beyond the transmembrane domain, give rise to direct interactions with lipids in the bilayer membrane. Our findings are discussed in the context of functional knowledge about these signal peptidases, offering additional understanding of dynamic aspects relevant to some cellular processes with potential implications for drug targeting strategies.
Collapse
Affiliation(s)
- Jesper J. Madsen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States of America
- Center for Global Health and Infectious Diseases Research, Global and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida 33612, United States of America
| | - Wenqi Yu
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, Florida 33612, United States of America
| |
Collapse
|
3
|
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: 1.0] [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.
Collapse
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.
| |
Collapse
|
4
|
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: 2.3] [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.
Collapse
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
| |
Collapse
|
5
|
Madsen JJ, Olsen OH. Conformational Plasticity-Rigidity Axis of the Coagulation Factor VII Zymogen Elucidated by Atomistic Simulations of the N-Terminally Truncated Factor VIIa Protease Domain. Biomolecules 2021; 11:549. [PMID: 33917935 PMCID: PMC8068379 DOI: 10.3390/biom11040549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 11/22/2022] Open
Abstract
The vast majority of coagulation factor VII (FVII), a trypsin-like protease, circulates as the inactive zymogen. Activated FVII (FVIIa) is formed upon proteolytic activation of FVII, where it remains in a zymogen-like state and it is fully activated only when bound to tissue factor (TF). The catalytic domains of trypsin-like proteases adopt strikingly similar structures in their fully active forms. However, the dynamics and structures of the available corresponding zymogens reveal remarkable conformational plasticity of the protease domain prior to activation in many cases. Exactly how ligands and cofactors modulate the conformational dynamics and function of these proteases is not entirely understood. Here, we employ atomistic simulations of FVIIa (and variants hereof, including a TF-independent variant and N-terminally truncated variants) to provide fundamental insights with atomistic resolution into the plasticity-rigidity interplay of the protease domain conformations that appears to govern the functional response to proteolytic and allosteric activation. We argue that these findings are relevant to the FVII zymogen, whose structure has remained elusive despite substantial efforts. Our results shed light on the nature of FVII and demonstrate how conformational dynamics has played a crucial role in the evolutionary adaptation of regulatory mechanisms that were not present in the ancestral trypsin. Exploiting this knowledge could lead to engineering of protease variants for use as next-generation hemostatic therapeutics.
Collapse
Affiliation(s)
- Jesper J. Madsen
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Ole H. Olsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen, Denmark
| |
Collapse
|
6
|
Sorensen AB, Tuneew I, Svensson LA, Persson E, Østergaard H, Overgaard MT, Olsen OH, Gandhi PS. Beating tissue factor at its own game: Design and properties of a soluble tissue factor-independent coagulation factor VIIa. J Biol Chem 2019; 295:517-528. [PMID: 31801825 DOI: 10.1074/jbc.ra119.009183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 11/29/2019] [Indexed: 11/06/2022] Open
Abstract
Two decades of research have uncovered the mechanism by which the complex of tissue factor (TF) and the plasma serine protease factor VIIa (FVIIa) mediates the initiation of blood coagulation. Membrane-anchored TF directly interacts with substrates and induces allosteric effects in the protease domain of FVIIa. These properties are also recapitulated by the soluble ectodomain of TF (sTF). At least two interdependent allosteric activation pathways originate at the FVIIa:sTF interface are proposed to enhance FVIIa activity upon sTF binding. Here, we sought to engineer an sTF-independent FVIIa variant by stabilizing both proposed pathways, with one pathway terminating at segment 215-217 in the activation domain and the other pathway terminating at the N terminus insertion site. To stabilize segment 215-217, we replaced the flexible 170 loop of FVIIa with the more rigid 170 loop from trypsin and combined it with an L163V substitution (FVIIa-VYT). The FVIIa-VYT variant exhibited 60-fold higher amidolytic activity than FVIIa, and displayed similar FX activation and antithrombin inhibition kinetics to the FVIIa.sTF complex. The sTF-independent activity of FVIIa-VYT was partly mediated by an increase in the N terminus insertion and, as shown by X-ray crystallography, partly by Tyr-172 inserting into a cavity in the activation domain stabilizing the S1 substrate-binding pocket. The combination with L163V likely drove additional changes in a delicate hydrogen-bonding network that further stabilized S1-S3 sites. In summary, we report the first FVIIa variant that is catalytically independent of sTF and provide evidence supporting the existence of two TF-mediated allosteric activation pathways.
Collapse
Affiliation(s)
- Anders B Sorensen
- Global Research, Novo Nordisk A/S, DK-2760 Måløv, Denmark; Department of Chemistry and Bioscience, Aalborg University, DK-9220 Aalborg, Denmark.
| | - Inga Tuneew
- Global Research, Novo Nordisk A/S, DK-2760 Måløv, Denmark
| | | | - Egon Persson
- Global Research, Novo Nordisk A/S, DK-2760 Måløv, Denmark
| | | | | | - Ole H Olsen
- Global Research, Novo Nordisk A/S, DK-2760 Måløv, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen N, Denmark
| | | |
Collapse
|
7
|
Sorensen AB, Madsen JJ, Frimurer TM, Overgaard MT, Gandhi PS, Persson E, Olsen OH. Allostery in Coagulation Factor VIIa Revealed by Ensemble Refinement of Crystallographic Structures. Biophys J 2019; 116:1823-1835. [PMID: 31003762 PMCID: PMC6531671 DOI: 10.1016/j.bpj.2019.03.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/20/2019] [Accepted: 03/25/2019] [Indexed: 11/29/2022] Open
Abstract
A critical step in injury-induced initiation of blood coagulation is the formation of the complex between the trypsin-like protease coagulation factor VIIa (FVIIa) and its cofactor tissue factor (TF), which converts FVIIa from an intrinsically poor enzyme to an active protease capable of activating zymogens of downstream coagulation proteases. Unlike its constitutively active ancestor trypsin, FVIIa is allosterically activated (by TF). Here, ensemble refinement of crystallographic structures, which uses multiple copies of the entire structure as a means of representing structural flexibility, is applied to explore the impacts of inhibitor binding to trypsin and FVIIa, as well as cofactor binding to FVIIa. To assess the conformational flexibility and its role in allosteric pathways in these proteases, main-chain hydrogen bond networks are analyzed by calculating the hydrogen-bond propensity. Mapping pairwise propensity differences between relevant structures shows that binding of the inhibitor benzamidine to trypsin has a minor influence on the protease flexibility. For FVIIa, in contrast, the protease domain is "locked" into the catalytically competent trypsin-like configuration upon benzamidine binding as indicated by the stabilization of key structural features: the nonprime binding cleft and the oxyanion hole are stabilized, and the effect propagates from the active site region to the calcium-binding site and to the vicinity of the disulphide bridge connecting with the light chain. TF binding to FVIIa furthermore results in stabilization of the 170 loop, which in turn propagates an allosteric signal from the TF-binding region to the active site. Analyses of disulphide bridge energy and flexibility reflect the striking stability difference between the unregulated enzyme and the allosterically activated form after inhibitor or cofactor binding. The ensemble refinement analyses show directly, for the first time to our knowledge, whole-domain structural footprints of TF-induced allosteric networks present in x-ray crystallographic structures of FVIIa, which previously only have been hypothesized or indirectly inferred.
Collapse
Affiliation(s)
- Anders B Sorensen
- Global Research, Novo Nordisk A/S, Måløv, Denmark; Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark; Protein Research, Evaxion Biotech, Copenhagen, Denmark
| | - Jesper J Madsen
- Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida
| | - Thomas M Frimurer
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Michael T Overgaard
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Egon Persson
- Global Research, Novo Nordisk A/S, Måløv, Denmark
| | - Ole H Olsen
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
8
|
Belyanko TI, Feoktistova ES, Skrypina NA, Skamrov AV, Gurskii YG, Rutkevich NM, Dobrynina NI, Bibilashvilli RS, Savochkina LP. A Study of the Structure of Trypsin-Like Serine Proteinases. 2. A Study of Tryptophan Fluorescence in Variants of Miniplasminogen with an Altered Primary Structure. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350919030035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
9
|
Prasad R, Banerjee S, Sen P. Contribution of allosteric disulfide in the structural regulation of membrane-bound tissue factor-factor VIIa binary complex. J Biomol Struct Dyn 2018; 37:3707-3720. [PMID: 30238846 DOI: 10.1080/07391102.2018.1526118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Two distinct populations, active and cryptic forms of tissue factor (TF), reside on the cell surface. Apart from phospholipid contribution, various models have been introduced to explain decryption/encryption of TF. The proposed model, the switching of Cys186-Cys209 bond of TF, has become the matter of controversy. However, it is well accepted that this disulfide has an immense influence upon ligand factor VIIa (FVIIa) for its binding. However, molecular level understanding for this remains unveiled due to lack of detailed structural information. In this regard, we have performed the molecular dynamic study of membrane-bound TF/TF-FVIIa in both the forms (±Cys186-Cys209 allosteric disulfide bond), individually. Dynamic study depicts that disulfide bond provides structural rigidity of TF in both free and ligand-bound forms. This disulfide bond also governs the conformation of FVIIa structure as well as the binding affinity of FVIIa toward TF. Significant differences in lipid-protein interaction profiles of both the forms of TF in the complex were observed. Two forms of TF, oxidized and reduced, have different structural conformation and behave differentially toward its ligand FVIIa. This disulfide bond not only alters the conformation of GLA domain of FVIIa in the vicinity but allosterically regulates the conformation of the distantly located FVIIa protease domain. We suggest that the redox status of the disulfide bond also governs the lipid-mediated interactions with both TF and FVIIa. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ramesh Prasad
- a Department of Biological Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata , India
| | - Suparna Banerjee
- a Department of Biological Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata , India
| | - Prosenjit Sen
- a Department of Biological Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata , India
| |
Collapse
|
10
|
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: 0.2] [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
| |
Collapse
|
11
|
Madsen JJ, Persson E, Olsen OH. Evolutionary conservation of the allosteric activation of factor VIIa by tissue factor in lamprey: comment. J Thromb Haemost 2018; 16:1450-1454. [PMID: 29733494 DOI: 10.1111/jth.14142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 11/28/2022]
Affiliation(s)
- J J Madsen
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - E Persson
- Hemophilia Biology, Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
| | - O H Olsen
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
12
|
Mallik S, Prasad R, Bhattacharya A, Sen P. Synthesis of Phosphatidylserine and Its Stereoisomers: Their Role in Activation of Blood Coagulation. ACS Med Chem Lett 2018; 9:434-439. [PMID: 29795755 DOI: 10.1021/acsmedchemlett.8b00008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/12/2018] [Indexed: 11/29/2022] Open
Abstract
Natural phosphatidylserine (PS), which contains two chiral centers, enhances blood coagulation. However, the process by which PS enhanced blood coagulation is not completely understood. An efficient and flexible synthetic route has been developed to synthesize all of the possible stereoisomers of PS. In this study, we examined the role of PS chiral centers in modulating the activity of the tissue factor (TF)-factor VIIa coagulation initiation complex. Full length TF was relipidated with phosphatidylcholine, and the synthesized PS isomers were individually used to estimate the procoagulant activity of the TF-FVIIa complex via a FXa generation assay. The results revealed that the initiation complex activity was stereoselective and had increased sensitivity to the configuration of the PS glycerol backbone due to optimal protein-lipid interactions.
Collapse
Affiliation(s)
- Suman Mallik
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Ramesh Prasad
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Anindita Bhattacharya
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| | - Prosenjit Sen
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India
| |
Collapse
|
13
|
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: 3] [Impact Index Per Article: 0.5] [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.
Collapse
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
| |
Collapse
|
14
|
Ligand binding modulates the structural dynamics and activity of urokinase-type plasminogen activator: A possible mechanism of plasminogen activation. PLoS One 2018; 13:e0192661. [PMID: 29420634 PMCID: PMC5805342 DOI: 10.1371/journal.pone.0192661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 01/26/2018] [Indexed: 12/14/2022] Open
Abstract
The catalytic activity of trypsin-like serine proteases is in many cases regulated by conformational changes initiated by binding of physiological modulators to exosites located distantly from the active site. A trypsin-like serine protease of particular interest is urokinase-type plasminogen activator (uPA), which is involved in extracellular tissue remodeling processes. Herein, we used hydrogen/deuterium exchange mass spectrometry (HDXMS) to study regulation of activity in the catalytic domain of the murine version of uPA (muPA) by two muPA specific monoclonal antibodies. Using a truncated muPA variant (muPA16-243), containing the catalytic domain only, we show that the two monoclonal antibodies, despite binding to an overlapping epitope in the 37s and 70s loops of muPA16-243, stabilize distinct muPA16-243 conformations. Whereas the inhibitory antibody, mU1 was found to increase the conformational flexibility of muPA16-243, the stimulatory antibody, mU3, decreased muPA16-243 conformational flexibility. Furthermore, the HDXMS data unveil the existence of a pathway connecting the 70s loop to the active site region. Using alanine scanning mutagenesis, we further identify the 70s loop as an important exosite for the activation of the physiological uPA substrate plasminogen. Thus, the data presented here reveal important information about dynamics in uPA by demonstrating how various ligands can modulate uPA activity by mediating long-range conformational changes. Moreover, the results provide a possible mechanism of plasminogen activation.
Collapse
|
15
|
Discovery of a novel conformational equilibrium in urokinase-type plasminogen activator. Sci Rep 2017; 7:3385. [PMID: 28611361 PMCID: PMC5469797 DOI: 10.1038/s41598-017-03457-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/27/2017] [Indexed: 01/15/2023] Open
Abstract
Although trypsin-like serine proteases have flexible surface-exposed loops and are known to adopt higher and lower activity conformations, structural determinants for the different conformations have remained largely obscure. The trypsin-like serine protease, urokinase-type plasminogen activator (uPA), is central in tissue remodeling processes and also strongly implicated in tumor metastasis. We solved five X-ray crystal structures of murine uPA (muPA) in the absence and presence of allosteric molecules and/or substrate-like molecules. The structure of unbound muPA revealed an unsuspected non-chymotrypsin-like protease conformation in which two β-strands in the core of the protease domain undergoes a major antiparallel-to-parallel conformational transition. We next isolated two anti-muPA nanobodies; an active-site binding nanobody and an allosteric nanobody. Crystal structures of the muPA:nanobody complexes and hydrogen-deuterium exchange mass spectrometry revealed molecular insights about molecular factors controlling the antiparallel-to-parallel equilibrium in muPA. Together with muPA activity assays, the data provide valuable insights into regulatory mechanisms and conformational flexibility of uPA and trypsin-like serine proteases in general.
Collapse
|
16
|
Prasad R, Sen P. Molecular determinants involved in differential behaviour between soluble tissue factor and full-length tissue factor towards factor VIIa. Phys Chem Chem Phys 2017; 19:22230-22242. [DOI: 10.1039/c7cp02179h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
During blood-coagulation, the transmembrane protein tissue factor (TF) binds to its ligand, factor (F)VII, activating and allosterically modifying it to form a mature active binary complex (TF–FVIIa).
Collapse
Affiliation(s)
- Ramesh Prasad
- Department of Biological Chemistry
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Prosenjit Sen
- Department of Biological Chemistry
- Indian Association for the Cultivation of Science
- Kolkata
- India
| |
Collapse
|
17
|
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: 1.6] [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.
Collapse
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
| | | |
Collapse
|