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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.
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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
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2
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Abstract
The formation of membrane-bound complexes between specific coagulation factors at different cell surfaces is required for effective blood clotting. The most important of these complexes, the intrinsic Tenase and Prothrombinase complexes, are formed on the activated platelet surface during the propagation phase of coagulation. These two complexes are highly specific in their assembly mechanism and function modulated by anionic membranes, thus offering desirable targets for pharmaceutical interventions. Factor V (FV) and factor VIII (FVIII) are highly homologous non-enzymatic proteins. In their active state, FVa and FVIIIa serve as cofactors for the respective serine proteases factor Xa (FXa) and factor IXa (FIXa), significantly increasing their catalytic activity. This is achieved by forming well organized membrane-bound complexes at the phosphatidylserine rich activated platelet membrane in the presence of Ca2+ ions. The tenase (FVIIIa/FIXa) complex, catalyzes the proteolytic conversion of FX to FXa. Subsequently the prothrombinase (FVa/FXa) complex catalyzes the conversion of prothrombin to thrombin, required for efficient blood clotting. Although significant knowledge of FV and FVIII biochemistry and regulation has been achieved, the molecular mechanisms of their function are yet to be defined. Understanding the geometric assembly of the tenase and prothrombinase complexes is paramount in defining the structural basis of bleeding and thrombotic disorders. Such knowledge will enable the design of efficient pro- and anticoagulant therapies critical for regulating abnormal hemostasis. In this chapter, we will summarize the findings to date, showing our achievement in the field and outlining the future findings required to grasp the complexity of these proteins.
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Affiliation(s)
- Svetla Stoilova-McPhie
- Center for Nanoscale Systems (CNS), Laboratory For Integrated Sciences and Engineering (LISE), Faculty of Art and Sciences (FAS), Harvard University, 11 Oxford Street, Cambridge, MA, 02138, England, UK.
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Al-Azzawi A, Ouadou A, Max H, Duan Y, Tanner JJ, Cheng J. DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM. BMC Bioinformatics 2020; 21:509. [PMID: 33167860 PMCID: PMC7653784 DOI: 10.1186/s12859-020-03809-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cryo-electron microscopy (Cryo-EM) is widely used in the determination of the three-dimensional (3D) structures of macromolecules. Particle picking from 2D micrographs remains a challenging early step in the Cryo-EM pipeline due to the diversity of particle shapes and the extremely low signal-to-noise ratio of micrographs. Because of these issues, significant human intervention is often required to generate a high-quality set of particles for input to the downstream structure determination steps. RESULTS Here we propose a fully automated approach (DeepCryoPicker) for single particle picking based on deep learning. It first uses automated unsupervised learning to generate particle training datasets. Then it trains a deep neural network to classify particles automatically. Results indicate that the DeepCryoPicker compares favorably with semi-automated methods such as DeepEM, DeepPicker, and RELION, with the significant advantage of not requiring human intervention. CONCLUSIONS Our framework combing supervised deep learning classification with automated un-supervised clustering for generating training data provides an effective approach to pick particles in cryo-EM images automatically and accurately.
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Affiliation(s)
- Adil Al-Azzawi
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO 65211 USA
| | - Anes Ouadou
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO 65211 USA
| | - Highsmith Max
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO 65211 USA
| | - Ye Duan
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO 65211 USA
| | - John J. Tanner
- Departments of Biochemistry and Chemistry, University of Missouri, Columbia, MO 65211-2060 USA
| | - Jianlin Cheng
- Electrical Engineering and Computer Science Department, University of Missouri, Columbia, MO 65211 USA
- Informatics Institute, University of Missouri, Columbia, MO 65211 USA
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Szewczak‐Harris A, Wagstaff J, Löwe J. Cryo-EM structure of the MinCD copolymeric filament from Pseudomonas aeruginosa at 3.1 Å resolution. FEBS Lett 2019; 593:1915-1926. [PMID: 31166018 PMCID: PMC6771821 DOI: 10.1002/1873-3468.13471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 11/07/2022]
Abstract
Positioning of the division site in many bacterial species relies on the MinCDE system, which prevents the cytokinetic Z-ring from assembling anywhere but the mid-cell, through an oscillatory diffusion-reaction mechanism. MinD dimers bind to membranes and, via their partner MinC, inhibit the polymerization of cell division protein FtsZ into the Z-ring. MinC and MinD form polymeric assemblies in solution and on cell membranes. Here, we report the high-resolution cryo-EM structure of the copolymeric filaments of Pseudomonas aeruginosa MinCD. The filaments consist of three protofilaments made of alternating MinC and MinD dimers. The MinCD protofilaments are almost completely straight and assemble as single protofilaments on lipid membranes, which we also visualized by cryo-EM.
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Affiliation(s)
- Andrzej Szewczak‐Harris
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of CambridgeUK
| | | | - Jan Löwe
- MRC Laboratory of Molecular BiologyCambridgeUK
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5
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Zhang J, Wang Z, Chen Y, Han R, Liu Z, Sun F, Zhang F. PIXER: an automated particle-selection method based on segmentation using a deep neural network. BMC Bioinformatics 2019; 20:41. [PMID: 30658571 PMCID: PMC6339297 DOI: 10.1186/s12859-019-2614-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 01/07/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Cryo-electron microscopy (cryo-EM) has become a widely used tool for determining the structures of proteins and macromolecular complexes. To acquire the input for single-particle cryo-EM reconstruction, researchers must select hundreds of thousands of particles from micrographs. As the signal-to-noise ratio (SNR) of micrographs is extremely low, the performance of automated particle-selection methods is still unable to meet research requirements. To free researchers from this laborious work and to acquire a large number of high-quality particles, we propose an automated particle-selection method (PIXER) based on the idea of segmentation using a deep neural network. RESULTS First, to accommodate low-SNR conditions, we convert micrographs into probability density maps using a segmentation network. These probability density maps indicate the likelihood that each pixel of a micrograph is part of a particle instead of just background noise. Particles selected from density maps have a more robust signal than do those directly selected from the original noisy micrographs. Second, at present, there is no segmentation-training dataset for cryo-EM. To enable our plan, we present an automated method to generate a training dataset for segmentation using real-world data. Third, we propose a grid-based, local-maximum method to locate the particles from the probability density maps. We tested our method on simulated and real-world experimental datasets and compared PIXER with the mainstream methods RELION, DeepEM and DeepPicker to demonstrate its performance. The results indicate that, as a fully automated method, PIXER can acquire results as good as the semi-automated methods RELION and DeepEM. CONCLUSION To our knowledge, our work is the first to address the particle-selection problem using the segmentation network concept. As a fully automated particle-selection method, PIXER can free researchers from laborious particle-selection work. Based on the results of experiments, PIXER can acquire accurate results under low-SNR conditions within minutes.
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Affiliation(s)
- Jingrong Zhang
- High Performance Computer Research Center, Institute of Computing Technology Chinese Academy of Sciences, No. 6 Kexueyuan South Road, Haidian District, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zihao Wang
- High Performance Computer Research Center, Institute of Computing Technology Chinese Academy of Sciences, No. 6 Kexueyuan South Road, Haidian District, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Chen
- High Performance Computer Research Center, Institute of Computing Technology Chinese Academy of Sciences, No. 6 Kexueyuan South Road, Haidian District, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, China
| | - Renmin Han
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900 Saudi Arabia
| | - Zhiyong Liu
- High Performance Computer Research Center, Institute of Computing Technology Chinese Academy of Sciences, No. 6 Kexueyuan South Road, Haidian District, Beijing, 100190 China
| | - Fei Sun
- University of Chinese Academy of Sciences, Beijing, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101 China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101 China
| | - Fa Zhang
- High Performance Computer Research Center, Institute of Computing Technology Chinese Academy of Sciences, No. 6 Kexueyuan South Road, Haidian District, Beijing, 100190 China
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6
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Madsen JJ, Ohkubo YZ, Peters GH, Faber JH, Tajkhorshid E, Olsen OH. Membrane Interaction of the Factor VIIIa Discoidin Domains in Atomistic Detail. Biochemistry 2015; 54:6123-31. [PMID: 26346528 DOI: 10.1021/acs.biochem.5b00417] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A recently developed membrane-mimetic model was applied to study membrane interaction and binding of the two anchoring C2-like discoidin domains of human coagulation factor VIIIa (FVIIIa), the C1 and C2 domains. Both individual domains, FVIII C1 and FVIII C2, were observed to bind the phospholipid membrane by partial or full insertion of their extruding loops (the spikes). However, the two domains adopted different molecular orientations in their membrane-bound states; FVIII C2 roughly was positioned normal to the membrane plane, while FVIII C1 displayed a multitude of tilted orientations. The results indicate that FVIII C1 may be important in modulating the orientation of the FVIIIa molecule to optimize the interaction with FIXa, which is anchored to the membrane via its γ-carboxyglutamic acid-rich (Gla) domain. Additionally, a structural change was observed in FVIII C1 in the coiled main chain leading the first spike. A tight interaction with one lipid per domain, similar to what has been suggested for the homologous FVa C2, is characterized. Finally, we rationalize known FVIII antibody epitopes and the scarcity of documented hemophilic missense mutations related to improper membrane binding of FVIIIa, based on the prevalent nonspecificity of ionic interactions in the simulated membrane-bound states of FVIII C1 and FVIII C2.
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Affiliation(s)
- Jesper J Madsen
- Global Research, Novo Nordisk A/S , DK-2760 Måløv, Denmark.,Department of Chemistry, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark
| | | | - Günther H Peters
- Department of Chemistry, Technical University of Denmark , DK-2800 Kgs. Lyngby, Denmark
| | - Johan H Faber
- Global Research, Novo Nordisk A/S , DK-2760 Måløv, Denmark
| | | | - Ole H Olsen
- Global Research, Novo Nordisk A/S , DK-2760 Måløv, Denmark
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7
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Kamburova K, Radeva T, Stoilova-McPhie S, Stoylov SP. Electric polarization and size of lipid nanotubes—an electric light scattering study. Colloid Polym Sci 2015. [DOI: 10.1007/s00396-015-3688-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Dalm D, Galaz-Montoya JG, Miller JL, Grushin K, Villalobos A, Koyfman AY, Schmid MF, Stoilova-McPhie S. Dimeric Organization of Blood Coagulation Factor VIII bound to Lipid Nanotubes. Sci Rep 2015; 5:11212. [PMID: 26082135 PMCID: PMC4469981 DOI: 10.1038/srep11212] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/05/2015] [Indexed: 11/09/2022] Open
Abstract
Membrane-bound Factor VIII (FVIII) has a critical function in blood coagulation as the pro-cofactor to the serine-protease Factor IXa (FIXa) in the FVIIIa-FIXa complex assembled on the activated platelet membrane. Defects or deficiency of FVIII cause Hemophilia A, a mild to severe bleeding disorder. Despite existing crystal structures for FVIII, its membrane-bound organization has not been resolved. Here we present the dimeric FVIII membrane-bound structure when bound to lipid nanotubes, as determined by cryo-electron microscopy. By combining the structural information obtained from helical reconstruction and single particle subtomogram averaging at intermediate resolution (15-20 Å), we show unambiguously that FVIII forms dimers on lipid nanotubes. We also demonstrate that the organization of the FVIII membrane-bound domains is consistently different from the crystal structure in solution. The presented results are a critical step towards understanding the mechanism of the FVIIIa-FIXa complex assembly on the activated platelet surface in the propagation phase of blood coagulation.
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Affiliation(s)
- Daniela Dalm
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jesus G Galaz-Montoya
- 1] Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA [2] National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jaimy L Miller
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Kirill Grushin
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alex Villalobos
- School of Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alexey Y Koyfman
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Michael F Schmid
- 1] Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA [2] National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Svetla Stoilova-McPhie
- 1] Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX 77555, USA [2] Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
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9
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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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10
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Miller J, Dalm D, Koyfman AY, Grushin K, Stoilova-McPhie S. Helical organization of blood coagulation factor VIII on lipid nanotubes. J Vis Exp 2014. [PMID: 24961276 DOI: 10.3791/51254] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cryo-electron microscopy (Cryo-EM)(1) is a powerful approach to investigate the functional structure of proteins and complexes in a hydrated state and membrane environment(2). Coagulation Factor VIII (FVIII)(3) is a multi-domain blood plasma glycoprotein. Defect or deficiency of FVIII is the cause for Hemophilia type A - a severe bleeding disorder. Upon proteolytic activation, FVIII binds to the serine protease Factor IXa on the negatively charged platelet membrane, which is critical for normal blood clotting(4). Despite the pivotal role FVIII plays in coagulation, structural information for its membrane-bound state is incomplete(5). Recombinant FVIII concentrate is the most effective drug against Hemophilia type A and commercially available FVIII can be expressed as human or porcine, both forming functional complexes with human Factor IXa(6,7). In this study we present a combination of Cryo-electron microscopy (Cryo-EM), lipid nanotechnology and structure analysis applied to resolve the membrane-bound structure of two highly homologous FVIII forms: human and porcine. The methodology developed in our laboratory to helically organize the two functional recombinant FVIII forms on negatively charged lipid nanotubes (LNT) is described. The representative results demonstrate that our approach is sufficiently sensitive to define the differences in the helical organization between the two highly homologous in sequence (86% sequence identity) proteins. Detailed protocols for the helical organization, Cryo-EM and electron tomography (ET) data acquisition are given. The two-dimensional (2D) and three-dimensional (3D) structure analysis applied to obtain the 3D reconstructions of human and porcine FVIII-LNT is discussed. The presented human and porcine FVIII-LNT structures show the potential of the proposed methodology to calculate the functional, membrane-bound organization of blood coagulation Factor VIII at high resolution.
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Affiliation(s)
- Jaimy Miller
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch
| | - Daniela Dalm
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch
| | - Alexey Y Koyfman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch
| | - Kirill Grushin
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch
| | - Svetla Stoilova-McPhie
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch;
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11
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van den Ent F, Izoré T, Bharat TA, Johnson CM, Löwe J. Bacterial actin MreB forms antiparallel double filaments. eLife 2014; 3:e02634. [PMID: 24843005 PMCID: PMC4051119 DOI: 10.7554/elife.02634] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/02/2014] [Indexed: 12/30/2022] Open
Abstract
Filaments of all actin-like proteins known to date are assembled from pairs of protofilaments that are arranged in a parallel fashion, generating polarity. In this study, we show that the prokaryotic actin homologue MreB forms pairs of protofilaments that adopt an antiparallel arrangement in vitro and in vivo. We provide an atomic view of antiparallel protofilaments of Caulobacter MreB as apparent from crystal structures. We show that a protofilament doublet is essential for MreB's function in cell shape maintenance and demonstrate by in vivo site-specific cross-linking the antiparallel orientation of MreB protofilaments in E. coli. 3D cryo-EM shows that pairs of protofilaments of Caulobacter MreB tightly bind to membranes. Crystal structures of different nucleotide and polymerisation states of Caulobacter MreB reveal conserved conformational changes accompanying antiparallel filament formation. Finally, the antimicrobial agents A22/MP265 are shown to bind close to the bound nucleotide of MreB, presumably preventing nucleotide hydrolysis and destabilising double protofilaments.DOI: http://dx.doi.org/10.7554/eLife.02634.001.
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Affiliation(s)
- Fusinita van den Ent
- Structural Studies Division, Medical Research Council - Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Thierry Izoré
- Structural Studies Division, Medical Research Council - Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Tanmay Am Bharat
- Structural Studies Division, Medical Research Council - Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Christopher M Johnson
- Protein and Nucleic Acid Chemistry Division, Medical Research Council - Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Jan Löwe
- Structural Studies Division, Medical Research Council - Laboratory of Molecular Biology, Cambridge, United Kingdom
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12
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Bonazza K, Rottensteiner H, Seyfried BK, Schrenk G, Allmaier G, Turecek PL, Friedbacher G. Visualization of a protein-protein interaction at a single-molecule level by atomic force microscopy. Anal Bioanal Chem 2013; 406:1411-21. [PMID: 24363113 DOI: 10.1007/s00216-013-7563-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/02/2013] [Accepted: 12/06/2013] [Indexed: 01/24/2023]
Abstract
Atomic force microscopy is unmatched in terms of high-resolution imaging under ambient conditions. Over the years, substantial progress has been made using this technique to improve our understanding of biological systems on the nanometer scale, such as visualization of single biomolecules. For monitoring also the interaction between biomolecules, in situ high-speed imaging is making enormous progress. Here, we describe an alternative ex situ imaging method where identical molecules are recorded before and after reaction with a binding partner. Relocation of the identical molecules on the mica surface was thereby achieved by using a nanoscale scratch as marker. The method was successfully applied to study the complex formation between von Willebrand factor (VWF) and factor VIII (FVIII), two essential haemostatic components of human blood. FVIII binding was discernible by an appearance of globular domains appended to the N-terminal large globular domains of VWF. The specificity of the approach could be demonstrated by incubating VWF with FVIII in the presence of a high salt buffer which inhibits the interaction between these two proteins. The results obtained indicate that proteins can maintain their reactivity for subsequent interactions with other molecules when gently immobilized on a solid substrate and subjected to intermittent drying steps. The technique described opens up a new analytical perspective for studying protein-protein interactions as it circumvents some of the obstacles encountered by in situ imaging and other ex situ techniques.
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Affiliation(s)
- Klaus Bonazza
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164-IAC, 1060, Wien, Austria
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13
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Stoilova-McPhie S, Lynch GC, Ludtke S, Pettitt BM. Domain organization of membrane-bound factor VIII. Biopolymers 2013; 99:448-59. [PMID: 23616213 PMCID: PMC4090243 DOI: 10.1002/bip.22199] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/13/2012] [Accepted: 11/18/2012] [Indexed: 11/07/2022]
Abstract
Factor VIII (FVIII) is the blood coagulation protein which when defective or deficient causes for hemophilia A, a severe hereditary bleeding disorder. Activated FVIII (FVIIIa) is the cofactor to the serine protease factor IXa (FIXa) within the membrane-bound Tenase complex, responsible for amplifying its proteolytic activity more than 100,000 times, necessary for normal clot formation. FVIII is composed of two noncovalently linked peptide chains: a light chain (LC) holding the membrane interaction sites and a heavy chain (HC) holding the main FIXa interaction sites. The interplay between the light and heavy chains (HCs) in the membrane-bound state is critical for the biological efficiency of FVIII. Here, we present our cryo-electron microscopy (EM) and structure analysis studies of human FVIII-LC, when helically assembled onto negatively charged single lipid bilayer nanotubes. The resolved FVIII-LC membrane-bound structure supports aspects of our previously proposed FVIII structure from membrane-bound two-dimensional (2D) crystals, such as only the C2 domain interacts directly with the membrane. The LC is oriented differently in the FVIII membrane-bound helical and 2D crystal structures based on EM data, and the existing X-ray structures. This flexibility of the FVIII-LC domain organization in different states is discussed in the light of the FVIIIa-FIXa complex assembly and function.
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Affiliation(s)
- Svetla Stoilova-McPhie
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, USA.
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14
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Stoylov SP, Stoilova-McPhie S. Electro-optic properties of organic nanotubes. Adv Colloid Interface Sci 2011; 166:24-35. [PMID: 21679911 DOI: 10.1016/j.cis.2011.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Revised: 04/22/2011] [Accepted: 04/23/2011] [Indexed: 11/29/2022]
Abstract
In this review article the theoretical and experimental possibilities of applying EO-methods for estimation of the physico-chemical properties of the organic nanotubes (ONTs) are studied. The ONTs are highly organized nanostructures of strongly elongated, anysometric, and hollow cylinders with a size range of 1 nm to 10,000 nm, e.g. in aqueous solutions they could behave as colloid (disperse) particles. They have high interaction ability due to their extremely large curved, rolled-up external surfaces (bilayers of membrane walls) and unique properties because of their specific electric charge distribution and dynamics that make possible the functionalization of their surfaces. Thus they could template guestsubstances such as membrane proteins and protein complexes on the exterior surfaces and in the membrane. We performed our investigations for the case of ONT aqueous colloid suspension. Following our earlier proposition of the general expression for the electro-optic (EO) effect we derived equations for the evaluation of the electric properties of ONT particles such as mechanism of electric polarization and identification of their most important electric Dipole Moments (DM), permanent (pDM) and induced (iDMs). Further we recommend ways for the calculation of their magnitude and direction. Also we evaluated some geometrical properties such as length of the ONT particles and their polydispersity. The knowledge that we provided about the ONT properties may enable us to elucidate and predict their biological activity. Templating biological active ligands (such as membrane proteins and protein complexes) on the inner and outer surfaces as well as in the surface membrane creates their potential usefulness as carrier and deliverer of biopharmaceuticals in bio-nanodevices. The theoretical equations were compared with the experimental data for ONTs such as (lipid) LNT, Tobacco Mosaic Virus (TMV) and microtubules (MT). Comparison of EO methods with other methods used till now shows that the EO methods are faster, not invasive and do not alter the studied particles.
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Affiliation(s)
- Stoyl P Stoylov
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria.
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Dimitrov JD, Roumenina LT, Andre S, Repesse Y, Atanasov BP, Jacquemin M, Saint-Remy JM, Bayry J, Kaveri SV, Lacroix-Desmazes S. Kinetics and thermodynamics of interaction of coagulation factor VIII with a pathogenic human antibody. Mol Immunol 2009; 47:290-7. [DOI: 10.1016/j.molimm.2009.09.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 09/06/2009] [Accepted: 09/08/2009] [Indexed: 10/20/2022]
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Parmenter CDJ, Stoilova-McPhie S. Binding of recombinant human coagulation factor VIII to lipid nanotubes. FEBS Lett 2008; 582:1657-60. [PMID: 18435924 DOI: 10.1016/j.febslet.2008.04.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 04/11/2008] [Accepted: 04/14/2008] [Indexed: 10/22/2022]
Abstract
Cryo-electron microscopy has the power to visualise lipid membranes at the closest to in vivo conditions. The structure of the lipid bilayer can be well resolved and the interactions between lipid-protein and protein-protein molecules followed at the molecular level. We undertook an extended Cryo-electron microscopy study to follow the factor VIII binding to phosphatidylserine containing lipid nanotubes at different lipid composition. Obtaining well ordered tubes is required to define the factor VIII membrane-bound structure. The observed alterations in the arrangement of the protein molecules are indicative for the flexibility of the membrane-bound factor VIII. Understanding the significance of these conformational changes is essential to comprehend the function of factor VIII in coagulation and as a drug for Hemophilia A.
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