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Denisov IG, Sligar SG. Nanodiscs for the study of membrane proteins. Curr Opin Struct Biol 2024; 87:102844. [PMID: 38795563 PMCID: PMC11283964 DOI: 10.1016/j.sbi.2024.102844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 05/28/2024]
Abstract
Nanodiscs represent a versatile tool for studies of membrane proteins and protein-membrane interactions under native-like conditions. Multiple variations of the Nanodisc platform, as well as new experimental methods, have been recently developed to understand various aspects of structure, dynamics and functional properties of systems involved in signaling, transport, blood coagulation and many other critically important processes. In this mini-review, we focus on some of these exciting recent developments that utilize the Nanodisc platform.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.
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Chang HW, Lee IO, Kang H, Won YJ, Lim YS. Coagulation Effect of Sugammadex as Determined by Thromboelastography in a Randomized Controlled Study of Surgical Patients. Int J Med Sci 2021; 18:1318-1324. [PMID: 33628086 PMCID: PMC7893551 DOI: 10.7150/ijms.42563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/05/2021] [Indexed: 11/18/2022] Open
Abstract
Introduction: Sugammadex has been shown to be associated with prolongation of prothrombin time and activated partial thromboplastin time. However, it is not known whether it could be associated with enhancing postoperative hypocoagulation. The objective of this study was to analyze the effect of 4 mg/kg of sugammadex on thromboelastography (TEG) parameters in surgical patients. Methods: After Institutional Review Board approval, a prospective double-blinded randomized controlled study was conducted between September 2016 and April 2017. Sixty adult patients scheduled for laparoscopic abdominal surgery were randomly allocated to receive either sugammadex 4 mg/kg (sugammadex group) or pyridostigmine 0.15 mg/kg in combination with glycopyrrolate 0.4 mg (control group) to reverse rocuronium-induced neuromuscular blockade at the completion of surgery. Blood samples were collected three time points; After the final suture of surgery (baseline) (T1), and at 10 min (T2) and 1 h (T3) after administration of the study drug. Whole blood was analyzed by TEG using TEG 5000 (Hemonetics Corp, Braintree, MA, USA). The primary endpoints were comparison of coagulation time (K, time to 20 mm clot amplitude), R (reaction time), alpha angle, and maximal amplitude (MA) between two groups. Results: Coagulation time was significantly prolonged in sugammadex group after 10 min of the study drug administration compared to control group (mean value 1.3 ± 0.4 vs. 1.5 ± 0.4, P = 0.03). However, R, alpha angle and MA value were not different between two groups. Conclusions: Sugammadex 4 mg/kg showed an increase in coagulation time in surgical patients. Physician should aware the potential enhancement of hypocoagulation by sugammadex in the setting of high risk of postoperative bleeding.
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Affiliation(s)
- Hae Wone Chang
- Department of Anesthesiology and Pain Medicine, Eulji University Hospital, Seoul, Korea
| | - Il Ok Lee
- Department of Anesthesiology and Pain Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Hyoseok Kang
- Department of Anesthesiology and Pain Medicine, Eulji University Hospital, Seoul, Korea
| | - Young Ju Won
- Department of Anesthesiology and Pain Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Young-Seob Lim
- Department of Anesthesiology and Pain Medicine, Eulji University Hospital, Seoul, Korea
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Sligar SG, Denisov IG. Nanodiscs: A toolkit for membrane protein science. Protein Sci 2020; 30:297-315. [PMID: 33165998 DOI: 10.1002/pro.3994] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022]
Abstract
Membrane proteins are involved in numerous vital biological processes, including transport, signal transduction and the enzymes in a variety of metabolic pathways. Integral membrane proteins account for up to 30% of the human proteome and they make up more than half of all currently marketed therapeutic targets. Unfortunately, membrane proteins are inherently recalcitrant to study using the normal toolkit available to scientists, and one is most often left with the challenge of finding inhibitors, activators and specific antibodies using a denatured or detergent solubilized aggregate. The Nanodisc platform circumvents these challenges by providing a self-assembled system that renders typically insoluble, yet biologically and pharmacologically significant, targets such as receptors, transporters, enzymes, and viral antigens soluble in aqueous media in a native-like bilayer environment that maintain a target's functional activity. By providing a bilayer surface of defined composition and structure, Nanodiscs have found great utility in the study of cellular signaling complexes that assemble on a membrane surface. Nanodiscs provide a nanometer scale vehicle for the in vivo delivery of amphipathic drugs, therapeutic lipids, tethered nucleic acids, imaging agents and active protein complexes. This means for generating nanoscale lipid bilayers has spawned the successful use of numerous other polymer and peptide amphipathic systems. This review, in celebration of the Anfinsen Award, summarizes some recent results and provides an inroad into the current and historical literature.
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Affiliation(s)
- Stephen G Sligar
- Departments of Biochemistry Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Ilia G Denisov
- Departments of Biochemistry Chemistry, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
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Abstract
The interactions between lipids and proteins are one of the most fundamental processes in living organisms, responsible for critical cellular events ranging from replication, cell division, signaling, and movement. Enabling the central coupling responsible for maintaining the functionality of the breadth of proteins, receptors, and enzymes that find their natural home in biological membranes, the fundamental mechanisms of recognition of protein for lipid, and vice versa, have been a focal point of biochemical and biophysical investigations for many decades. Complexes of lipids and proteins, such as the various lipoprotein factions, play central roles in the trafficking of important proteins, small molecules and metabolites and are often implicated in disease states. Recently an engineered lipoprotein particle, termed the nanodisc, a modified form of the human high density lipoprotein fraction, has served as a membrane mimetic for the investigation of membrane proteins and studies of lipid-protein interactions. In this review, we summarize the current knowledge regarding this self-assembling lipid-protein complex and provide examples for its utility in the investigation of a large number of biological systems.
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McLean MA, Gregory MC, Sligar SG. Nanodiscs: A Controlled Bilayer Surface for the Study of Membrane Proteins. Annu Rev Biophys 2018; 47:107-124. [PMID: 29494254 DOI: 10.1146/annurev-biophys-070816-033620] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The study of membrane proteins and receptors presents many challenges to researchers wishing to perform biophysical measurements to determine the structure, function, and mechanism of action of such components. In most cases, to be fully functional, proteins and receptors require the presence of a native phospholipid bilayer. In addition, many complex multiprotein assemblies involved in cellular communication require an integral membrane protein as well as a membrane surface for assembly and information transfer to soluble partners in a signaling cascade. Incorporation of membrane proteins into Nanodiscs renders the target soluble and provides a native bilayer environment with precisely controlled composition of lipids, cholesterol, and other components. Likewise, Nanodiscs provide a surface of defined area useful in revealing lipid specificity and affinities for the assembly of signaling complexes. In this review, we highlight several biophysical techniques made possible through the use of Nanodiscs.
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Affiliation(s)
- Mark A McLean
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA; , ,
| | - Michael C Gregory
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA; , ,
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA; , ,
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Abstract
Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
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Tsunaka M, Arai R, Ohashi A, Koyama T. Cell-based laboratory evaluation of coagulation activation by antineoplastic drugs for the treatment of lymphoid tumors. SAGE Open Med 2016; 4:2050312116660936. [PMID: 27504186 PMCID: PMC4963813 DOI: 10.1177/2050312116660936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/28/2016] [Indexed: 01/19/2023] Open
Abstract
Objectives: Combining vorinostat, L-asparaginase, and doxorubicin (Dox) led to improved response rates in the treatment of lymphoid tumors. However, deep-vein thrombosis has been noted as one of the most serious side effects with these drugs, and how these regimens cause deep-vein thrombosis is unclear. Methods: We investigated the procoagulant effects of vorinostat, L-asparaginase, and doxorubicin in lymphoid tumors, focusing on tissue factor, phosphatidylserine, and antithrombin. The human vascular endothelial cell line EAhy926 as well as the lymphoid neoplastic cell lines HUT78 (cutaneous T-cell lymphoma), Molt4 (acute T-lymphoblastic leukemia), and Ramos (Burkitt lymphoma) were employed to investigate these procoagulant effects. Results: Vorinostat, L-asparaginase, and doxorubicin induced exposure of phosphatidylserine and procoagulant activity on the surface of lymphoid tumor cells. Vorinostat and doxorubicin also induced phosphatidylserine exposure and increased procoagulant activity on EAhy926 cells. Expression of tissue factor antigen was induced by doxorubicin on the surface of each type of cells, whereas expression of tissue factor mRNA was unchanged. Secretion of antithrombin from HepG2 cells was reduced only by L-asparaginase. Conclusion: These data suggest that vorinostat and doxorubicin may induce procoagulant activity in vessels through apoptosis of tumor cells and through phosphatidylserine exposure and/or tissue factor expression on vascular endothelial cells. L-asparaginase may induce a thrombophilic state by reducing the secretion of anticoagulant proteins such as antithrombin. The laboratory methods described here could be useful to evaluate the procoagulant effects of antineoplastic drugs.
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Affiliation(s)
- Misae Tsunaka
- Laboratory Molecular Genetics of Hematology, Field of Applied Laboratory Science, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Reina Arai
- Laboratory Molecular Genetics of Hematology, Field of Applied Laboratory Science, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ayaka Ohashi
- Laboratory Molecular Genetics of Hematology, Field of Applied Laboratory Science, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takatoshi Koyama
- Laboratory Molecular Genetics of Hematology, Field of Applied Laboratory Science, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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Csencsits-Smith K, Grushin K, Stoilova-McPhie S. Binding of Factor VIII to Lipid Nanodiscs Increases its Clotting Function in a Mouse Model of Hemophilia A. ACTA ACUST UNITED AC 2015; 6:325. [PMID: 28936365 PMCID: PMC5603210 DOI: 10.4172/2155-9864.1000325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Background Hemophilia A is a congenital bleeding disorder caused by defective or deficient factor VIII (FVIII). The active form of FVIII is the co-factor for the serine protease factor IXa (FIXa) in the membrane-bound intrinsic tenase (FVIIIa-FIXa) complex. The assembly of the FVIIIa-FIXa complex on the activated platelet surface is critical for successful blood clotting. Objectives To characterize the role of lipid nanodiscs (ND) for on FVIII function in vivo and test the lipid ND as a delivery system for FVIII. To evaluate the potential of binding recombinant FVIII to ND as improved treatment for Hemophilia A. Methods Recombinant porcine FVIII (rpFVIII) was expressed and characterized in solution, and when bound to ND. The rpFVIII, ND and rpFVIII-ND complexes were characterized via transmission electron microscopy. Functional studies were carried out using aPTT tests and time resolved tail snip studies of hemophilic mice. Results Functional rpFVIII was successfully assembled on lipid ND. When injected in hemophilic mice, the rpFVIII-ND complexes showed a pronounced pro-coagulant effect, which was stronger than that of rpFVIII alone. While injection of the ND alone showed a pro-coagulant effect this effect was not additive, implying that the rpFVIII-ND complexes have a synergistic effect on the clotting process in hemophilic mice. Conclusions Binding of rpFVIII to ND prior to its injection in hemophilic mice significantly improves the therapeutic function of the protein. This represents a meaningful step towards a new approach to modulate blood coagulation at the membrane-bound FVIII level and the assembly of the intrinsic tenase complex.
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Affiliation(s)
- Keri Csencsits-Smith
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center, Houston, TX-77030, USA
| | - Krill Grushin
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX-77555, USA
| | - Svetla Stoilova-McPhie
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX-77555, USA
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Stoilova-McPhie S, Grushin K, Dalm D, Miller J. Lipid nanotechnologies for structural studies of membrane-associated proteins. Proteins 2014; 82:2902-9. [PMID: 24957666 PMCID: PMC5292012 DOI: 10.1002/prot.24631] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 06/04/2014] [Accepted: 06/08/2014] [Indexed: 11/09/2022]
Abstract
We present a methodology of lipid nanotubes (LNT) and nanodisks technologies optimized in our laboratory for structural studies of membrane-associated proteins at close to physiological conditions. The application of these lipid nanotechnologies for structure determination by cryo-electron microscopy (cryo-EM) is fundamental for understanding and modulating their function. The LNTs in our studies are single bilayer galactosylceramide based nanotubes of ∼20 nm inner diameter and a few microns in length, that self-assemble in aqueous solutions. The lipid nanodisks (NDs) are self-assembled discoid lipid bilayers of ∼10 nm diameter, which are stabilized in aqueous solutions by a belt of amphipathic helical scaffold proteins. By combining LNT and ND technologies, we can examine structurally how the membrane curvature and lipid composition modulates the function of the membrane-associated proteins. As proof of principle, we have engineered these lipid nanotechnologies to mimic the activated platelet's phosphtaidylserine rich membrane and have successfully assembled functional membrane-bound coagulation factor VIII in vitro for structure determination by cryo-EM. The macromolecular organization of the proteins bound to ND and LNT are further defined by fitting the known atomic structures within the calculated three-dimensional maps. The combination of LNT and ND technologies offers a means to control the design and assembly of a wide range of functional membrane-associated proteins and complexes for structural studies by cryo-EM. The presented results confirm the suitability of the developed methodology for studying the functional structure of membrane-associated proteins, such as the coagulation factors, at a close to physiological environment.
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Affiliation(s)
- Svetla Stoilova-McPhie
- Department of Neuroscience and Cell Biology, The University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, 301 University Blvd, Galveston, Texas, 77555
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Smith E, Vekaria R, Brown KA, Longstaff C. Kinetic regulation of the binding of prothrombin to phospholipid membranes. Mol Cell Biochem 2013; 382:193-201. [PMID: 23812842 PMCID: PMC3771376 DOI: 10.1007/s11010-013-1735-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/14/2013] [Indexed: 11/25/2022]
Abstract
A wide range of equilibrium and kinetic constants exist for the interaction of prothrombin and other coagulation factors with various model membranes from a variety of techniques. We have investigated the interaction of prothrombin with pure dioleoylphosphatidylcholine (DOPC) membranes and dioleoylphosphatidlyserine (DOPS)-containing membranes (DOPC:DOPS, 3:1) using surface plasmon resonance (SPR, with four different model membrane presentations) in addition to isotheral titration calorimetry (ITC, with suspensions of phospholipid vesicles) and ELISA methods. Using ITC, we found a simple low-affinity interaction with DOPC:DOPS membranes with a K(D) = 5.1 μM. However, ELISA methods using phospholipid bound to microtitre plates indicated a complex interaction with both DOPC:DOPS and DOPC membranes with K(D) values of 20 and 58 nM, respectively. An explanation for these discrepant results was developed from SPR studies. Using SPR with low levels of immobilised DOPC:DOPS, a high-affinity interaction with a K(D) of 18 nM was obtained. However, as phospholipid and prothrombin concentrations were increased, two distinct interactions could be discerned: (i) a kinetically slow, high-affinity interaction with K(D) in the 10(-8) M range and (ii) a kinetically rapid, low-affinity interaction with K(D) in the 10(-6 )M range. This low affinity, rapidly equilibrating, interaction dominated in the presence of DOPS. Detailed SPR studies supported a heterogeneous binding model in agreement with ELISA data. The binding of prothrombin with phospholipid membranes is complex and the techniques used to measure binding will report K D values reflecting the mixture of complexes detected. Existing data suggest that the weaker rapid interaction between prothrombin and membranes is the most important in vivo when considering the activation of prothrombin at the cell surface.
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Affiliation(s)
- Emma Smith
- Division of Cardiovascular and Diabetes Research, The LIGHT Laboratories, University of Leeds, Leeds, UK
| | | | - Katherine A. Brown
- Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712 USA
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE UK
| | - Colin Longstaff
- Biotherapeutics Section, National Institute for Biological Standards and Control, South Mimms, Hertfordshire EN6 3QG UK
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Activation of coagulation by lenalidomide-based regimens for the treatment of multiple myeloma. PLoS One 2013; 8:e64369. [PMID: 23696885 PMCID: PMC3655994 DOI: 10.1371/journal.pone.0064369] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 04/11/2013] [Indexed: 11/22/2022] Open
Abstract
We investigated the procoagulant effects of lenalidomide (Len)-based regimens in vitro focusing on tissue factor (TF) and phosphatidylserine (PS). We examined the effects of a pharmacological concentration of Len with or without the corticosteroid dexamethasone (Dex) and the proteasome inhibitor bortezomib (Bor) using the human vascular endothelial cell line EAhy926 and the monocytic cell lines THP-1 and U937. Cell-surface procoagulant activity (PCA) was induced by Dex-containing regimens in all lines. Expression of TF antigen on the cell surface and of TF mRNA was markedly increased by Dex-containing regimens. PS exposure was increased modestly by a Len-based regimen. PS exposure was increased modestly in EAhy926 cells, and markedly increased in THP-1 and U937 cells by Bor-containing treatment. An anti-TF monoclonal antibody almost completely blocked the induced PCA. When Len is given in combination with Dex, PCA may be induced on endothelial cells and monocytes through TF expression and PS exposure.
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Abstract
Nanodiscs are self-assembled discoidal fragments of lipid bilayers 8-16 nm in diameter, stabilized in solution by two amphipathic helical scaffold proteins. As stable and highly soluble membrane mimetics with controlled lipid composition and ability to add affinity tags to the scaffold protein, nanodiscs represent an attractive model system for solubilization, isolation, purification, and biophysical and biochemical studies of membrane proteins. In this chapter we overview various approaches to structural and functional studies of different classes of integral membrane proteins such as ion channels, transporters, GPCR and other receptors, membrane enzymes, and blood coagulation cascade proteins which have been incorporated into nanodiscs. We outline the advantages provided by homogeneity, ability to control oligomerization state of the target protein and lipid composition of the bilayer. Special attention is paid to the opportunities afforded by nanodisc system for the detailed studies of the role of different lipid properties and protein-lipid interactions in the functional behavior of membrane proteins.
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Affiliation(s)
- Mary A. Schuler
- Department of Biochemistry, University of Illinois, Urbana, IL 61801 USA
- Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801 USA
| | - Ilia G. Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL 61801 USA
| | - Stephen G. Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL 61801 USA
- Department of Chemistry, University of Illinois, Urbana, IL 61801 USA
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Tanner DE, Phillips JC, Schulten K. GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations. J Chem Theory Comput 2012; 8:2521-2530. [PMID: 23049488 PMCID: PMC3464051 DOI: 10.1021/ct3003089] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Molecular dynamics methodologies comprise a vital research tool for structural biology. Molecular dynamics has benefited from technological advances in computing, such as multi-core CPUs and graphics processing units (GPUs), but harnessing the full power of hybrid GPU/CPU computers remains difficult. The generalized Born/solvent-accessible surface area implicit solvent model (GB/SA) stands to benefit from hybrid GPU/CPU computers, employing the GPU for the GB calculation and the CPU for the SA calculation. Here, we explore the computational challenges facing GB/SA calculations on hybrid GPU/CPU computers and demonstrate how NAMD, a parallel molecular dynamics program, is able to efficiently utilize GPUs and CPUs simultaneously for fast GB/SA simulations. The hybrid computation principles demonstrated here are generally applicable to parallel applications employing hybrid GPU/CPU calculations.
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Affiliation(s)
- David E. Tanner
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
- Beckman Institute, University of Illinois at Urbana-Champaign
| | | | - Klaus Schulten
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
- Beckman Institute, University of Illinois at Urbana-Champaign
- Department of Physics, University of Illinois at Urbana-Champaign
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Bravo MC, Orfeo T, Mann KG, Everse SJ. Modeling of human factor Va inactivation by activated protein C. BMC SYSTEMS BIOLOGY 2012; 6:45. [PMID: 22607732 PMCID: PMC3403913 DOI: 10.1186/1752-0509-6-45] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 05/20/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND Because understanding of the inventory, connectivity and dynamics of the components characterizing the process of coagulation is relatively mature, it has become an attractive target for physiochemical modeling. Such models can potentially improve the design of therapeutics. The prothrombinase complex (composed of the protease factor (F)Xa and its cofactor FVa) plays a central role in this network as the main producer of thrombin, which catalyses both the activation of platelets and the conversion of fibrinogen to fibrin, the main substances of a clot. A key negative feedback loop that prevents clot propagation beyond the site of injury is the thrombin-dependent generation of activated protein C (APC), an enzyme that inactivates FVa, thus neutralizing the prothrombinase complex. APC inactivation of FVa is complex, involving the production of partially active intermediates and "protection" of FVa from APC by both FXa and prothrombin. An empirically validated mathematical model of this process would be useful in advancing the predictive capacity of comprehensive models of coagulation. RESULTS A model of human APC inactivation of prothrombinase was constructed in a stepwise fashion by analyzing time courses of FVa inactivation in empirical reaction systems with increasing number of interacting components and generating corresponding model constructs of each reaction system. Reaction mechanisms, rate constants and equilibrium constants informing these model constructs were initially derived from various research groups reporting on APC inactivation of FVa in isolation, or in the presence of FXa or prothrombin. Model predictions were assessed against empirical data measuring the appearance and disappearance of multiple FVa degradation intermediates as well as prothrombinase activity changes, with plasma proteins derived from multiple preparations. Our work integrates previously published findings and through the cooperative analysis of in vitro experiments and mathematical constructs we are able to produce a final validated model that includes 24 chemical reactions and interactions with 14 unique rate constants which describe the flux in concentrations of 24 species. CONCLUSION This study highlights the complexity of the inactivation process and provides a module of equations describing the Protein C pathway that can be integrated into existing comprehensive mathematical models describing tissue factor initiated coagulation.
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Affiliation(s)
- Maria Cristina Bravo
- Cell and Molecular Biology Program, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405, USA
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Osterud B. Tissue factor/TFPI and blood cells. Thromb Res 2011; 129:274-8. [PMID: 22197177 DOI: 10.1016/j.thromres.2011.11.049] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 11/21/2011] [Accepted: 11/22/2011] [Indexed: 10/14/2022]
Abstract
Vascular injury-induced access of blood to tissue factor (TF) leads to the formation of a TF-FVII/FVIIa complex and the triggering of blood coagulation. The activated TF-dependent pathway is regulated by Tissue Factor Pathway Inhibitor (TFPI), which binds and inhibits FXa, but more importantly forms an inactive quaternary complex with TF-FVIIa-FXa, effectively shutting off the TF activity. The old view of TF residing in extravascular sites exclusively has recently been challenged by several reports on TF expression in various blood cells. The latter arena has unfortunately been marred by many contradictions, apparently related to inferior tools and/or study design, notably the widespread use of antibodies with inferior and misleading specificity and TF activity assays of low sensitivity/specificity. Our own studies along with many other reports, compels the conclusion that in blood of healthy individuals TF is exclusively associated with and expressed in circulating monocytes. In this short review the distribution of TF and TFPI in blood is discussed.
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Affiliation(s)
- Bjarne Osterud
- HERG, Department of Medical Biology, Faculty of Health Sciences and MabCent SFI, University of Tromsø, 9037 Tromsø, Norway.
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Abstract
Combining thalidomide (Thal) with chemotherapeutic agents or steroid preparations led to improved response rates in the treatment of multiple myeloma. However, deep vein thrombosis (DVT) is one of the most serious side-effects noted with this regimen, and how a Thal-based regimen causes DVT is unclear. We investigated the procoagulant effects of Thal when combined with chemotherapeutic agents in vitro, focusing on tissue factor (TF) and phosphatidylserine. We examined the effects of the chemotherapeutic doxorubicin hydrochloride (Dox) and the steroid dexamethasone (Dex), with or without Thal. Our study used the human vascular endothelial, monocytic, and myeloma cell lines, EAhy926, THP-1, and RPMI8226, respectively. In EAhy926 and THP-1, Dex treatment increased expression of TF, which may induce procoagulant activity (PCA). Upregulation of TF mRNA correlated with activation of the Egr-1 pathway. In Thal and Dex treatments, the increase of PCA induction from phosphatidylserine exposure was modest. In contrast, Dox and Thal-Dox increased phosphatidylserine exposure in both cell types. In THP-1 cells, cell surface phosphatidylserine exposure correlated with increased PCA by Dox. Thal alone showed a modest increase in phosphatidylserine exposure in endothelial cells and monocytes. When Thal is given in combination with chemotherapies or Dex, endothelial cell and monocyte PCA may be induced through phosphatidylserine exposure, or TF expression. Induction may be protracted by Thal, which has an antiangiogenic activity. Therefore, prophylactic anticoagulant strategies should be considered in Thal-based combination regimens.
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Boettcher JM, Davis-Harrison RL, Clay MC, Nieuwkoop AJ, Ohkubo YZ, Tajkhorshid E, Morrissey JH, Rienstra CM. Atomic view of calcium-induced clustering of phosphatidylserine in mixed lipid bilayers. Biochemistry 2011; 50:2264-73. [PMID: 21294564 PMCID: PMC3069658 DOI: 10.1021/bi1013694] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membranes play key regulatory roles in biological processes, with bilayer composition exerting marked effects on binding affinities and catalytic activities of a number of membrane-associated proteins. In particular, proteins involved in diverse processes such as vesicle fusion, intracellular signaling cascades, and blood coagulation interact specifically with anionic lipids such as phosphatidylserine (PS) in the presence of Ca(2+) ions. While Ca(2+) is suspected to induce PS clustering in mixed phospholipid bilayers, the detailed structural effects of this ion on anionic lipids are not established. In this study, combining magic angle spinning (MAS) solid-state NMR (SSNMR) measurements of isotopically labeled serine headgroups in mixed lipid bilayers with molecular dynamics (MD) simulations of PS lipid bilayers in the presence of different counterions, we provide site-resolved insights into the effects of Ca(2+) on the structure and dynamics of lipid bilayers. Ca(2+)-induced conformational changes of PS in mixed bilayers are observed in both liposomes and Nanodiscs, a nanoscale membrane mimetic of bilayer patches. Site-resolved multidimensional correlation SSNMR spectra of bilayers containing (13)C,(15)N-labeled PS demonstrate that Ca(2+) ions promote two major PS headgroup conformations, which are well resolved in two-dimensional (13)C-(13)C, (15)N-(13)C, and (31)P-(13)C spectra. The results of MD simulations performed on PS lipid bilayers in the presence or absence of Ca(2+) provide an atomic view of the conformational effects underlying the observed spectra.
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Affiliation(s)
- John M. Boettcher
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | | | - Mary C. Clay
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Andrew J. Nieuwkoop
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Y. Zenmei Ohkubo
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - James H. Morrissey
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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Abstract
PURPOSE OF REVIEW Venous thromboembolism (VTE) is a frequent cause of morbidity and mortality in cancer patients. A significant proportion of cancer-associated VTE occurs in the ambulatory setting and is associated with poorer outcomes and reduced survival. Risk for VTE is influenced by patient, cancer and treatment-specific factors. RECENT FINDINGS Recent studies have identified biomarkers associated with increased VTE risk in malignancy, including leukocyte and platelet counts, tissue factor, prothrombin split products, D-dimer, P-selectin, factor VIII and C-reactive protein. Recent and ongoing clinical trials have focused on VTE prophylaxis with low-molecular weight heparins in high-risk cancer outpatients, particularly those with pancreatic cancer. These studies have yielded encouraging preliminary results but whether thromboprophylaxis provides significant benefit to unselected cancer outpatients remains unclear. SUMMARY A risk stratification model incorporating known risk factors and biomarkers can identify those patients at highest risk. This review focuses on emerging data regarding risk assessment and benefit of thromboprophylaxis in patients with cancer.
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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: 2.4] [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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Rand JH, Wu XX, Quinn AS, Taatjes DJ. The annexin A5-mediated pathogenic mechanism in the antiphospholipid syndrome: role in pregnancy losses and thrombosis. Lupus 2010; 19:460-9. [PMID: 20353989 DOI: 10.1177/0961203310361485] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Annexin A5 (AnxA5) binds to phospholipid bilayers, forming two-dimensional crystals that block the phospholipids from availability for coagulation enzyme reactions. Antiphospholipid (aPL) antibodies cause gaps in the ordered crystallization of AnxA5 which expose phospholipids and thereby accelerate blood coagulation reactions. The aPL antibody-mediated disruption of AnxA5 crystallization has been confirmed on artificial phospholipid bilayers and on cell membranes including endothelial cells, placental trophoblasts and platelets. Recently, we reported that hydroxychloroquine, a synthetic antimalarial drug, can reverse this antibody-mediated process through two mechanisms: (1) by inhibiting the formation of aPL IgG-β2glycoprotein I complexes; and (2) by promoting the formation of a second layer of AnxA5 crystal ‘patches’ over areas where the immune complexes had disrupted AnxA5 crystallization. In another translational application, we have developed a mechanistic assay that reports resistance to AnxA5 anticoagulant activity in plasmas of patients with aPL antibodies. AnxA5 resistance may identify a subset of aPL syndrome patients for whom this is a mechanism for pregnancy losses and thrombosis. The elucidation of aPL-mediated mechanisms for thrombosis and pregnancy complications may open new paths towards addressing this disorder with targeted treatments and mechanistic assays.
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Affiliation(s)
- JH Rand
- Department of Pathology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - X-X. Wu
- Department of Pathology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - AS Quinn
- Department of Pathology and Microscopy Imaging Center, College of Medicine, University of Vermont, Burlington, VT, USA
| | - DJ Taatjes
- Department of Pathology and Microscopy Imaging Center, College of Medicine, University of Vermont, Burlington, VT, USA
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