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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.
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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
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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: 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.
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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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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.
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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
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Abstract
Ca2+ binding proteins (CBP) are of key importance for calcium to play its role as a pivotal second messenger. CBP bind Ca2+ in specific domains, contributing to the regulation of its concentration at the cytosol and intracellular stores. They also participate in numerous cellular functions by acting as Ca2+ transporters across cell membranes or as Ca2+-modulated sensors, i.e. decoding Ca2+ signals. Since CBP are integral to normal physiological processes, possible roles for them in a variety of diseases has attracted growing interest in recent years. In addition, research on CBP has been reinforced with advances in the structural characterization of new CBP family members. In this chapter we have updated a previous review on CBP, covering in more depth potential participation in physiopathological processes and candidacy for pharmacological targets in many diseases. We review intracellular CBP that contain the structural EF-hand domain: parvalbumin, calmodulin, S100 proteins, calcineurin and neuronal Ca2+ sensor proteins (NCS). We also address intracellular CBP lacking the EF-hand domain: annexins, CBP within intracellular Ca2+ stores (paying special attention to calreticulin and calsequestrin), proteins that contain a C2 domain (such as protein kinase C (PKC) or synaptotagmin) and other proteins of interest, such as regucalcin or proprotein convertase subtisilin kexins (PCSK). Finally, we summarise the latest findings on extracellular CBP, classified according to their Ca2+ binding structures: (i) EF-hand domains; (ii) EGF-like domains; (iii) ɣ-carboxyl glutamic acid (GLA)-rich domains; (iv) cadherin domains; (v) Ca2+-dependent (C)-type lectin-like domains; (vi) Ca2+-binding pockets of family C G-protein-coupled receptors.
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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.
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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.
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Plautz WE, Sekhar Pilli VS, Cooley BC, Chattopadhyay R, Westmark PR, Getz T, Paul D, Bergmeier W, Sheehan JP, Majumder R. Anticoagulant Protein S Targets the Factor IXa Heparin-Binding Exosite to Prevent Thrombosis. Arterioscler Thromb Vasc Biol 2018; 38:816-828. [PMID: 29419409 DOI: 10.1161/atvbaha.117.310588] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/16/2018] [Indexed: 01/20/2023]
Abstract
OBJECTIVE PS (protein S) is a plasma protein that directly inhibits the coagulation FIXa (factor IXa) in vitro. Because elevated FIXa is associated with increased risk of venous thromboembolism, it is important to establish how PS inhibits FIXa function in vivo. The goal of this study is to confirm direct binding of PS with FIXa in vivo, identify FIXa amino acid residues required for binding PS in vivo, and use an enzymatically active FIXa mutant that is unable to bind PS to measure the significance of PS-FIXa interaction in hemostasis. APPROACH AND RESULTS We demonstrate that PS inhibits FIXa in vivo by associating with the FIXa heparin-binding exosite. We used fluorescence tagging, immunohistochemistry, and protein-protein crosslinking to show in vivo interaction between FIXa and PS. Importantly, platelet colocalization required a direct interaction between the 2 proteins. FIXa and PS also coimmunoprecipitated from plasma, substantiating their interaction in a physiological milieu. PS binding to FIXa and PS inhibition of the intrinsic Xase complex required residues K132, K126, and R170 in the FIXa heparin-binding exosite. A double mutant, K132A/R170A, retained full activity but could not bind to PS. Crucially, Hemophilia B mice infused with FIXa K132A/R170A displayed an accelerated rate of fibrin clot formation compared with wild-type FIXa. CONCLUSIONS Our findings establish PS as an important in vivo inhibitor of FIXa. Disruption of the interaction between PS and FIXa causes an increased rate of thrombus formation in mice. This newly discovered function of PS implies an unexploited target for antithrombotic therapeutics.
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Affiliation(s)
- William E Plautz
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Vijaya Satish Sekhar Pilli
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Brian C Cooley
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Rima Chattopadhyay
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Pamela R Westmark
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Todd Getz
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - David Paul
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Wolfgang Bergmeier
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - John P Sheehan
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.)
| | - Rinku Majumder
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans (W.E.P., V.S.S.P., R.C., R.M.); Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill (B.C.C., T.G., D.P., W.B.); and Department of Medicine/Hematology-Oncology, University of Wisconsin School of Medicine and Public Health, Madison (P.R.W., J.P.S.).
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