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Kelly CM, Martin JL, Coseno M, Previs MJ. Visualization of cardiac thick filament dynamics in ex vivo heart preparations. J Mol Cell Cardiol 2023; 185:88-98. [PMID: 37923195 PMCID: PMC10959293 DOI: 10.1016/j.yjmcc.2023.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
RATIONALE Cardiac muscle cells are terminally differentiated after birth and must beat continually throughout one's lifetime. This mechanical process is driven by the sliding of actin-based thin filaments along myosin-based thick filaments, organized within sarcomeres. Despite costly energetic demand, the half-life of the proteins that comprise the cardiac thick filaments is ∼10 days, with individual molecules being replaced stochastically, by unknown mechanisms. OBJECTIVES To allow for the stochastic replacement of molecules, we hypothesized that the structure of thick filaments must be highly dynamic in vivo. METHODS AND RESULTS To test this hypothesis in adult mouse hearts, we replaced a fraction of the endogenous myosin regulatory light chain (RLC), a component of thick filaments, with GFP-labeled RLC by adeno-associated viral (AAV) transduction. The RLC-GFP was properly localized to the heads of the myosin molecules within thick filaments in ex vivo heart preparations and had no effect on heart size or actin filament siding in vitro. However, the localization of the RLC-GFP molecules was highly mobile, changing its position within the sarcomere on the minute timescale, when quantified by fluorescence recovery after photobleaching (FRAP) using multiphoton microscopy. Interestingly, RLC-GFP mobility was restricted to within the boundaries of single sarcomeres. When cardiomyocytes were lysed, the RLC-GFP remained strongly bound to myosin heavy chain, and the intact myosin molecules adopted a folded, compact configuration, when disassociated from the filaments at physiological ionic conditions. CONCLUSIONS These data demonstrate that the structure of the thick filament is highly dynamic in the intact heart, with a rate of molecular exchange into and out of thick filaments that is ∼1500 times faster than that required for the replacement of molecules through protein synthesis or degradation.
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Affiliation(s)
- Colleen M Kelly
- Molecular Physiology and Biophysics Department, University of Vermont, Larner College of Medicine, Burlington, VT 05405, United States of America
| | - Jody L Martin
- Department of Pharmacology, University of California, Davis, Davis, CA 90095, United States of America
| | - Molly Coseno
- Fluidic Analytics, The Paddocks Business Centre, Cambridge CB1 8DH, United Kingdom
| | - Michael J Previs
- Molecular Physiology and Biophysics Department, University of Vermont, Larner College of Medicine, Burlington, VT 05405, United States of America.
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2
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Eskelin K, Oksanen HM. Archaeal Viruses: Production of Virus Particles and Vesicle-like Viruses and Purification Using Asymmetrical Flow Field-Flow Fractionation. Methods Mol Biol 2022; 2522:449-465. [PMID: 36125770 DOI: 10.1007/978-1-0716-2445-6_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Asymmetrical flow field-flow fractionation (AF4) is a separation method based on hydrodynamic size of the sample components. It can separate a broad size range of components (~103 to 109 Da; particle diameter from ~1 nm to ~1 μm), but is especially well suited for high molecular weight samples such as virus-sized particles and extracellular vesicles. Separation takes place in an open channel where the flows control sample elution. Separation does not involve stationary phase, allowing gentle separation and good recoveries. The method is compatible with a wide variety of buffers. Coupling to various analytical detectors enables rapid assays on the molecular weight and size and their distribution, degradation, and aggregation of the sample components giving information on the sample quality. In addition to being an advanced analytical method, AF4 can be used in a semipreparative mode for purification. Here, we summarize archaeal virus production methods and virus purification by AF4 and provide examples on the steps that need optimization for obtaining good separation with the focus on halophilic archaeal viruses. Importantly, AF4 method is suitable for a variety of viruses and extracellular vesicles regardless of their host organism.
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Affiliation(s)
- Katri Eskelin
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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3
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Reilly L, Eckhardt LL. Cardiac potassium inward rectifier Kir2: Review of structure, regulation, pharmacology, and arrhythmogenesis. Heart Rhythm 2021; 18:1423-1434. [PMID: 33857643 PMCID: PMC8328935 DOI: 10.1016/j.hrthm.2021.04.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/23/2021] [Accepted: 04/06/2021] [Indexed: 12/17/2022]
Abstract
Potassium inward rectifier channel Kir2 is an important component of terminal cardiac repolarization and resting membrane stability. This functionality is part of balanced cardiac excitability and is a defining feature of excitable cardiac membranes. “Gain-of-function” or “loss-of-function” mutations in KCNJ2, the gene encoding Kir2.1, cause genetic sudden cardiac death syndromes, and loss of the Kir2 current IK1 is a major contributing factor to arrhythmogenesis in failing human hearts. Here we provide a contemporary review of the functional structure, physiology, and pharmacology of Kir2 channels. Beyond the structure and functional relationships, we will focus on the elements of clinically used drugs that block the channel and the implications for treatment of atrial fibrillation with IK1-blocking agents. We will also review the clinical disease entities associated with KCNJ2 mutations and the growing area of research into associated arrhythmia mechanisms. Lastly, the presence of Kir2 channels has become a tipping point for electrical maturity in induced pluripotent stem cell-derived cardiomyocytes (iPS-CMs) and highlights the significance of understanding why Kir2 in iPS-CMs is important to consider for Comprehensive In Vitro Proarrhythmia Assay and drug safety testing.
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Affiliation(s)
- Louise Reilly
- Cellular and Molecular Arrhythmia Research Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin
| | - Lee L Eckhardt
- Cellular and Molecular Arrhythmia Research Program, Division of Cardiovascular Medicine, Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin.
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4
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Saponaro A, Maione V, Bonvin AMJJ, Cantini F. Understanding Docking Complexes of Macromolecules Using HADDOCK: The Synergy between Experimental Data and Computations. Bio Protoc 2020; 10:e3793. [PMID: 33659447 PMCID: PMC7842552 DOI: 10.21769/bioprotoc.3793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 08/17/2020] [Accepted: 09/01/2020] [Indexed: 11/02/2022] Open
Abstract
This protocol illustrates the modelling of a protein-peptide complex using the synergic combination of in silico analysis and experimental results. To this end, we use the integrative modelling software HADDOCK, which possesses the powerful ability to incorporate experimental data, such as NMR Chemical Shift Perturbations and biochemical protein-peptide interaction data, as restraints to guide the docking process. Based on the modelling results, a rational mutagenesis approach is used to validate the generated models. The experimental results allow to select a final structural model best representing the bona fide protein-peptide complex. The described protocol can also be applied to model protein-protein complexes. There is no size limit for the macromolecular complexes that can be characterized by HADDOCK as long as the 3D structures of the individual components are available.
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Affiliation(s)
- Andrea Saponaro
- Department of Biosciences, University of Milan, Milan, Italy
| | - Vincenzo Maione
- Department of Chemistry, University of Florence, Florence, Italy
- Magnetic Resonance Center, University of Florence, Florence, Italy
| | - Alexandre M. J. J. Bonvin
- Computational Structural Biology group, Bijvoet Center for Biomolecular Research, Faculty of Science Chemistry, Utrecht University, Utrecht, Netherland
| | - Francesca Cantini
- Department of Chemistry, University of Florence, Florence, Italy
- Magnetic Resonance Center, University of Florence, Florence, Italy
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5
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Abstract
Small-angle neutron scattering (SANS) provides structural information on biomacromolecules and their complexes in dilute solutions at the nanometer length scale. The overall dimensions, shapes, and interactions can be probed and compared to information obtained by complementary structural biology techniques such as crystallography, NMR, and EM. SANS, in combination with solvent H2O/D2O exchange and/or deuteration, is particularly well suited to probe the internal structure of RNA-protein (RNP) complexes since neutrons are more sensitive than X-rays to the difference in scattering length densities of proteins and RNA, with respect to an aqueous solvent. In this book chapter we provide a practical guide on how to carry out SANS experiments on RNP complexes, as well as possibilities of data analysis and interpretation.
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Affiliation(s)
- Audrone Lapinaite
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Teresa Carlomagno
- Centre for Biomolecular Drug Research, Leibniz University Hannover, Hannover, Germany.,Helmholtz Centre for Infection Research, Group of Structural Chemistry, Braunschweig, Germany
| | - Frank Gabel
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
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6
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Abstract
Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is sufficient for its repair functions and harbors the XPB and XPD DNA-dependent ATPase/helicase subunits, which are affected by human disease mutations. Transcription initiation additionally requires the CdK activating kinase subcomplex. Previous structural work has provided only partial insight into the architecture of TFIIH and its interactions within transcription pre-initiation complexes. Here, we present the complete structure of the human TFIIH core complex, determined by phase-plate cryo-electron microscopy at 3.7 Å resolution. The structure uncovers the molecular basis of TFIIH assembly, revealing how the recruitment of XPB by p52 depends on a pseudo-symmetric dimer of homologous domains in these two proteins. The structure also suggests a function for p62 in the regulation of XPD, and allows the mapping of previously unresolved human disease mutations.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Daniel B Toso
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyUnited States
| | - Jie Fang
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| | - Eva Nogales
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyUnited States
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7
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Jonić S. A methodology using Gaussian-based density map approximation to assess sets of cryo-electron microscopy density maps. J Struct Biol 2018; 204:344-50. [PMID: 30036578 DOI: 10.1016/j.jsb.2018.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/16/2018] [Accepted: 07/19/2018] [Indexed: 12/24/2022]
Abstract
This article presents a methodology to assess a set of density maps, as used in the Blind Assessment Phase of the 2015/2016 Map Challenge (EMDataBank Validation Challenges). The synthetic and experimental cryo-electron microscopy (cryo-EM) density maps obtained by different single particle analysis protocols and by different participants, submitted in the Challenge Phase for assessment, were analyzed with this methodology and the obtained results are presented and discussed here. The goal of using such a methodology was to blindly identify the density maps with globally similar structural information, meaning the maps with the structural information mostly "reproduced" by different protocols. To this end, the density maps are "coarsened" using Gaussian-based approximations, with the same input approximation parameters for all maps of the target biological complex. The approximated maps are then represented in a common reduced-dimension (here, 3D) space of their correlation-coefficient-based distances, in which close maps mean similar maps. The distance analysis allows identifying maps with the most "reproduced" structural information by different protocols. The obtained results are also discussed taking into account the detailed information about the protocols that has been released after the end of the Blind Assessment Phase.
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8
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Lampi M, Oksanen HM, Meier F, Moldenhauer E, Poranen MM, Bamford DH, Eskelin K. Asymmetrical flow field-flow fractionation in purification of an enveloped bacteriophage ϕ6. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1095:251-257. [PMID: 30098552 DOI: 10.1016/j.jchromb.2018.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 02/06/2023]
Abstract
Basic and applied virus research requires specimens that are purified to high homogeneity. Thus, there is much interest in the efficient production and purification of viruses and their subassemblies. Advances in the production steps have shifted the bottle neck of the process to the purification. Nonetheless, the development of purification techniques for different viruses is challenging due to the complex biological nature of the infected cell cultures as well as the biophysical and -chemical differences in the virus particles. We used bacteriophage ϕ6 as a model virus in our attempts to provide a new purification method for enveloped viruses. We compared asymmetrical flow field-flow fractionation (AF4)-based virus purification method to the well-established ultracentrifugation-based purification of ϕ6. In addition, binding of ϕ6 virions to monolithic anion exchange columns was tested to evaluate their applicability in concentrating the AF4 purified specimens. Our results show that AF4 enables one-hour purification of infectious enveloped viruses with specific infectivity of ~1 × 1013 PFU/mg of protein and ~65-95% yields. Obtained purity was comparable with that obtained using ultracentrifugation, but the yields from AF4 purification were 2-3-fold higher. Importantly, high quality virus preparations could be obtained directly from crude cell lysates. Furthermore, when used in combination with in-line light scattering detectors, AF4 purification could be coupled to simultaneous quality control of obtained virus specimen.
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Affiliation(s)
- Mirka Lampi
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9B, FI-00014 Helsinki, Finland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9B, FI-00014 Helsinki, Finland
| | - Florian Meier
- Postnova Analytics, Max-Planck-Str. 14, 86899 Landsberg, Germany
| | | | - Minna M Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9B, FI-00014 Helsinki, Finland
| | - Dennis H Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9B, FI-00014 Helsinki, Finland
| | - Katri Eskelin
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9B, FI-00014 Helsinki, Finland.
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9
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Zeng X, Leung MR, Zeev-Ben-Mordehai T, Xu M. A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation. J Struct Biol 2018; 202:150-160. [PMID: 29289599 PMCID: PMC6661905 DOI: 10.1016/j.jsb.2017.12.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 12/24/2017] [Accepted: 12/27/2017] [Indexed: 01/08/2023]
Abstract
Cellular electron cryo-tomography enables the 3D visualization of cellular organization in the near-native state and at submolecular resolution. However, the contents of cellular tomograms are often complex, making it difficult to automatically isolate different in situ cellular components. In this paper, we propose a convolutional autoencoder-based unsupervised approach to provide a coarse grouping of 3D small subvolumes extracted from tomograms. We demonstrate that the autoencoder can be used for efficient and coarse characterization of features of macromolecular complexes and surfaces, such as membranes. In addition, the autoencoder can be used to detect non-cellular features related to sample preparation and data collection, such as carbon edges from the grid and tomogram boundaries. The autoencoder is also able to detect patterns that may indicate spatial interactions between cellular components. Furthermore, we demonstrate that our autoencoder can be used for weakly supervised semantic segmentation of cellular components, requiring a very small amount of manual annotation.
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Affiliation(s)
- Xiangrui Zeng
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh 15213, USA
| | - Miguel Ricardo Leung
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Cryo-electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Tzviya Zeev-Ben-Mordehai
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Cryo-electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Min Xu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh 15213, USA.
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10
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Bard JAM, Martin A. Recombinant Expression, Unnatural Amino Acid Incorporation, and Site-Specific Labeling of 26S Proteasomal Subcomplexes. Methods Mol Biol 2018; 1844:219-36. [PMID: 30242713 DOI: 10.1007/978-1-4939-8706-1_15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The 26S proteasome is the major regulated protease in eukaryotes and is responsible for degrading ubiquitinated substrates. It consists of a barrel-shaped 20S core peptidase and one or two 19S regulatory particles, which recognize, unfold, and translocate substrates into the core. The regulatory particle can be further divided into two multi-subunit complexes: the base and the lid. Here we present protocols for expressing the Saccharomyces cerevisiae base and lid recombinantly in Escherichia coli and purifying the assembled subcomplexes using a tandem affinity purification method. The purified complexes can then be reconstituted with 20S core to form fully functional proteasomes. Furthermore, we describe a method for incorporating the unnatural amino acid p-azido-L-phenylalanine into the recombinant complexes at any residue position, allowing for non-disruptive site-specific modifications of these large assemblies. The use of recombinant proteins allows for complete mutational control over the proteasome regulatory particle, enabling detailed studies of the mechanism by which the proteasome processes its substrates. The ability to then specifically modify residues in the regulatory particle opens the door to a wide range of previously impossible biochemical and biophysical studies. The techniques described below for incorporating unnatural amino acids into the proteasomal subcomplexes should be widely transferable to other recombinant proteins, whether individually purified or in larger multi-subunit assemblies.
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11
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Heijman J, Dobrev D. Ion channels as part of macromolecular multiprotein complexes : Clinical significance. Herzschrittmacherther Elektrophysiol 2018; 29:30-5. [PMID: 29214349 DOI: 10.1007/s00399-017-0542-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/11/2017] [Indexed: 11/17/2022]
Abstract
Ion channels and Ca2+-handling proteins involved in the regulation of cardiac electrophysiology and contractility are organized in macromolecular multiprotein complexes. Recent molecular and cellular studies have significantly enhanced our understanding of the composition of these macromolecular complexes and have helped to elucidate their role in the dynamic regulation of ion channel function. Moreover, it has become clear that alterations in the composition of ion channel macromolecular complexes, for example, due to genetic mutations or acquired alterations in the expression of individual components, may lead to ion channel dysfunction and arrhythmogenesis. Here, we review novel insights into the composition of the major ion channel macromolecular complexes and discuss the potential clinical significance of alterations in these dynamic multiprotein structures.
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12
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Eden G, Archinti M, Arnaudova R, Andreotti G, Motta A, Furlan F, Citro V, Cubellis MV, Degryse B. D2A sequence of the urokinase receptor induces cell growth through αvβ3 integrin and EGFR. Cell Mol Life Sci 2018; 75:1889-907. [PMID: 29184982 DOI: 10.1007/s00018-017-2718-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 11/08/2017] [Accepted: 11/22/2017] [Indexed: 01/01/2023]
Abstract
The urokinase receptor (uPAR) stimulates cell proliferation by forming a macromolecular complex with αvβ3 integrin and the epidermal growth factor receptor (EGFR, ErbB1 or HER1) that we name the uPAR proliferasome. uPAR transactivates EGFR, which in turn mediates uPAR-initiated mitogenic signal to the cell. EGFR activation and EGFR-dependent cell growth are blocked in the absence of uPAR expression or when uPAR activity is inhibited by antibodies against either uPAR or EGFR. The mitogenic sequence of uPAR corresponds to the D2A motif present in domain 2. NMR analysis revealed that D2A synthetic peptide has a particular three-dimensional structure, which is atypical for short peptides. D2A peptide is as effective as EGF in promoting EGFR phosphorylation and cell proliferation that were inhibited by AG1478, a specific inhibitor of the tyrosine kinase activity of EGFR. Both D2A and EGF failed to induce proliferation of NR6-EGFR-K721A cells expressing a kinase-defective mutant of EGFR. Moreover, D2A peptide and EGF phosphorylate ERK demonstrating the involvement of the MAP kinase signalling pathway. Altogether, this study reveals the importance of sequence D2A of uPAR, and the interdependence of uPAR and EGFR.
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13
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Eskelin K, Lampi M, Meier F, Moldenhauer E, Bamford DH, Oksanen HM. Halophilic viruses with varying biochemical and biophysical properties are amenable to purification with asymmetrical flow field-flow fractionation. Extremophiles 2017; 21:1119-1132. [PMID: 29019077 DOI: 10.1007/s00792-017-0963-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/14/2017] [Indexed: 01/21/2023]
Abstract
Viruses come in various shapes and sizes, and a number of viruses originate from extremities, e.g. high salinity or elevated temperature. One challenge for studying extreme viruses is to find efficient purification conditions where viruses maintain their infectivity. Asymmetrical flow field-flow fractionation (AF4) is a gentle native chromatography-like technique for size-based separation. It does not have solid stationary phase and the mobile phase composition is readily adjustable according to the sample needs. Due to the high separation power of specimens up to 50 µm, AF4 is suitable for virus purification. Here, we applied AF4 for extremophilic viruses representing four morphotypes: lemon-shaped, tailed and tailless icosahedral, as well as pleomorphic enveloped. AF4 was applied to input samples of different purity: crude supernatants of infected cultures, polyethylene glycol-precipitated viruses and viruses purified by ultracentrifugation. All four virus morphotypes were successfully purified by AF4. AF4 purification of culture supernatants or polyethylene glycol-precipitated viruses yielded high recoveries, and the purities were comparable to those obtained by the multistep ultracentrifugation purification methods. In addition, we also demonstrate that AF4 is a rapid monitoring tool for virus production in slowly growing host cells living in extreme conditions.
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Affiliation(s)
- Katri Eskelin
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Mirka Lampi
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Florian Meier
- Postnova Analytics, Max-Planck-Str. 14, 86899, Landsberg, Germany
| | | | - Dennis H Bamford
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Hanna M Oksanen
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland.
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14
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Havugimana PC, Hu P, Emili A. Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks. Expert Rev Proteomics 2017; 14:845-855. [PMID: 28918672 DOI: 10.1080/14789450.2017.1374179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OVERVIEW Elucidation of the networks of physical (functional) interactions present in cells and tissues is fundamental for understanding the molecular organization of biological systems, the mechanistic basis of essential and disease-related processes, and for functional annotation of previously uncharacterized proteins (via guilt-by-association or -correlation). After a decade in the field, we felt it timely to document our own experiences in the systematic analysis of protein interaction networks. Areas covered: Researchers worldwide have contributed innovative experimental and computational approaches that have driven the rapidly evolving field of 'functional proteomics'. These include mass spectrometry-based methods to characterize macromolecular complexes on a global-scale and sophisticated data analysis tools - most notably machine learning - that allow for the generation of high-quality protein association maps. Expert commentary: Here, we recount some key lessons learned, with an emphasis on successful workflows, and challenges, arising from our own and other groups' ongoing efforts to generate, interpret and report proteome-scale interaction networks in increasingly diverse biological contexts.
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Affiliation(s)
- Pierre C Havugimana
- a Donnelly Centre for Cellular and Biomolecular Research , University of Toronto , Toronto , ON , Canada.,b Department of Molecular Genetics , University of Toronto , Toronto , ON , Canada
| | - Pingzhao Hu
- c Department of Biochemistry and Medical Genetics , University of Manitoba , Winnipeg , MB , Canada
| | - Andrew Emili
- a Donnelly Centre for Cellular and Biomolecular Research , University of Toronto , Toronto , ON , Canada.,b Department of Molecular Genetics , University of Toronto , Toronto , ON , Canada
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15
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Wang H, Wang S, Zhang K, Wang H, Lan L, Ma X, Liu X, Zhang S, Zheng J, Wei X, Yan H. Aquaporin 4 Forms a Macromolecular Complex with Glutamate Transporter 1 and Mu Opioid Receptor in Astrocytes and Participates in Morphine Dependence. J Mol Neurosci 2017; 62:17-27. [PMID: 28341892 DOI: 10.1007/s12031-017-0905-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 02/24/2017] [Indexed: 10/19/2022]
Abstract
The water channel aquaporin 4 (AQP4) is abundantly expressed in astrocytes and provides a mechanism by which water permeability of the plasma membrane can be regulated. Evidence suggests that AQP4 is associated with glutamate transporter-1 (GLT-1) for glutamate clearance and contributes to morphine dependence. Previous studies show that AQP4 deficiency changed the mu opioid receptor expression and opioid receptors' characteristics as well. In this study, we focused on whether AQP4 could form macromolecular complex with GLT-1 and mu opioid receptor (MOR) and participates in morphine dependence. By using immunofluorescence staining, fluorescence resonance energy transfer, and co-immunoprecipitation, we demonstrated that AQP4 forms protein complexes with GLT-1 and MOR in both brain tissue and primary cultured astrocytes. We then showed that the C-terminus of AQP4 containing the amino acid residues 252 to 323 is the site of interaction with GLT-1. Protein kinase C, activated by morphine, played an important role in regulating the expression of these proteins. These findings may help to reveal the mechanism that AQP4, GLT-1, and MOR form protein complex and participate in morphine dependence, and deeply understand the reason that AQP4 deficiency maintains extracellular glutamate homeostasis and attenuates morphine dependence, moreover emphasizes the function of astrocyte in morphine dependence.
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Affiliation(s)
- Hui Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Department of Biochemical Pharmacology, Beijing Institute of Pharmacology and Toxicology, 27th Taiping Road, Beijing, 100850, China
| | - Shiqi Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Department of Biochemical Pharmacology, Beijing Institute of Pharmacology and Toxicology, 27th Taiping Road, Beijing, 100850, China
| | - Kang Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Department of Biochemical Pharmacology, Beijing Institute of Pharmacology and Toxicology, 27th Taiping Road, Beijing, 100850, China
| | - Hua Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Department of Biochemical Pharmacology, Beijing Institute of Pharmacology and Toxicology, 27th Taiping Road, Beijing, 100850, China
| | - Liting Lan
- State Key Laboratory of Toxicology and Medical Countermeasures, Department of Biochemical Pharmacology, Beijing Institute of Pharmacology and Toxicology, 27th Taiping Road, Beijing, 100850, China
| | - Xiaoyun Ma
- State Key Laboratory of Toxicology and Medical Countermeasures, Department of Biochemical Pharmacology, Beijing Institute of Pharmacology and Toxicology, 27th Taiping Road, Beijing, 100850, China
| | - Xiaoyan Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, Department of Biochemical Pharmacology, Beijing Institute of Pharmacology and Toxicology, 27th Taiping Road, Beijing, 100850, China
| | - Shuzhuo Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, Department of Biochemical Pharmacology, Beijing Institute of Pharmacology and Toxicology, 27th Taiping Road, Beijing, 100850, China
| | - Jianquan Zheng
- State Key Laboratory of Toxicology and Medical Countermeasures, Department of Biochemical Pharmacology, Beijing Institute of Pharmacology and Toxicology, 27th Taiping Road, Beijing, 100850, China
| | - Xiaoli Wei
- State Key Laboratory of Toxicology and Medical Countermeasures, Department of Biochemical Pharmacology, Beijing Institute of Pharmacology and Toxicology, 27th Taiping Road, Beijing, 100850, China.
| | - Haitao Yan
- State Key Laboratory of Toxicology and Medical Countermeasures, Department of Biochemical Pharmacology, Beijing Institute of Pharmacology and Toxicology, 27th Taiping Road, Beijing, 100850, China.
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16
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Larivière D, Galindo-Murillo R, Fourmentin E, Hornus S, Lévy B, Papillon J, Ménétret JF, Lamour V. A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data. Methods Mol Biol 2017; 1624:193-210. [PMID: 28842885 DOI: 10.1007/978-1-4939-7098-8_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The structural modeling of a macromolecular machine is like a "Lego" approach that is challenged when blocks, like proteins imported from the Protein Data Bank, are to be assembled with an element adopting a serpentine shape, such as DNA templates. DNA must then be built ex nihilo, but modeling approaches are either not user-friendly or very long and fastidious. In this method chapter we show how to use GraphiteLifeExplorer, a software with a simple graphical user interface that enables the sketching of free forms of DNA, of any length, at the atomic scale, as fast as drawing a line on a sheet of paper. We took as an example the nucleoprotein complex of DNA gyrase, a bacterial topoisomerase whose structure has been determined using cryo-electron microscopy (Cryo-EM). Using GraphiteLifeExplorer, we could model in one go a 155 bp long and twisted DNA duplex that wraps around DNA gyrase in the cryo-EM map, improving the quality and interpretation of the final model compared to the initially published data.
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Affiliation(s)
- Damien Larivière
- Fourmentin-Guilbert Scientific Foundation, Noisy-le-Grand, France.
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Eric Fourmentin
- Fourmentin-Guilbert Scientific Foundation, Noisy-le-Grand, France
| | - Samuel Hornus
- Equipe Alice, Inria Nancy - Grand Est, Villers-lès-Nancy, France
| | - Bruno Lévy
- Equipe Alice, Inria Nancy - Grand Est, Villers-lès-Nancy, France
| | - Julie Papillon
- IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, Illkirch, France
| | - Jean-François Ménétret
- IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, Illkirch, France
| | - Valérie Lamour
- IGBMC, Integrated Structural Biology Department, UMR7104 CNRS, U964 Inserm, Université de Strasbourg, Illkirch, France. .,Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
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Zhang J, Li M, Zhang Z, Zhu R, Olcese R, Stefani E, Toro L. The mitochondrial BK Ca channel cardiac interactome reveals BK Ca association with the mitochondrial import receptor subunit Tom22, and the adenine nucleotide translocator. Mitochondrion 2016; 33:84-101. [PMID: 27592226 DOI: 10.1016/j.mito.2016.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/29/2016] [Accepted: 08/30/2016] [Indexed: 10/21/2022]
Abstract
Mitochondrial BKCa channel, mitoBKCa, regulates mitochondria function in the heart but information on its protein partnerships in cardiac mitochondria is missing. A directed proteomic approach discovered the novel interaction of BKCa with Tom22, a component of the mitochondrion outer membrane import system, and the adenine nucleotide translocator (ANT). The expressed protein partners co-immunoprecipitated and co-segregated into mitochondrial fractions in HEK293T cells. The BKCa 50 amino acid splice insert, DEC, facilitated BKCa interaction with ANT. Further, BKCa transmembrane domain was required for the association with both Tom22 and ANT. The results serve as a working framework to understand mitoBKCa import and functional relationships.
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Affiliation(s)
- Jin Zhang
- Department of Anesthesiology, Division of Molecular Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Molecular & Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Min Li
- Department of Anesthesiology, Division of Molecular Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zhu Zhang
- Department of Anesthesiology, Division of Molecular Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ronghui Zhu
- Department of Anesthesiology, Division of Molecular Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Riccardo Olcese
- Department of Anesthesiology, Division of Molecular Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Physiology, University of California, Los Angeles, Los Angeles, CA, USA; Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA; Cardiovascular Research Laboratory, University of California, Los Angeles, Los Angeles, CA, USA
| | - Enrico Stefani
- Department of Anesthesiology, Division of Molecular Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Physiology, University of California, Los Angeles, Los Angeles, CA, USA; Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA; Cardiovascular Research Laboratory, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ligia Toro
- Department of Anesthesiology, Division of Molecular Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Molecular & Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA; Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA; Cardiovascular Research Laboratory, University of California, Los Angeles, Los Angeles, CA, USA.
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18
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Abstract
Sodium current in the heart flows principally through the pore protein NaV1.5, which is part of a complex of interacting proteins that serve both to target and localize the complex in the membrane, and to modulate function by such post-translational modifications as phosphorylation and nitrosylation. Multiple mutations in seven different NaV1.5 interacting proteins have been associated with dysfunctional sodium current and inherited cardiac diseases, including long QT syndrome, Brugada syndrome, atrial fibrillation, and cardiomyopathy, as well as sudden infant death syndrome (SIDS). Mutations in as yet unidentified interacting proteins may account for cardiac disease for which a genetic basis has not yet been established. Characterizing the mechanisms by which these mutations cause disease may give insight into etiologies and treatments of more common acquired cardiac disease, such as ischemia and heart failure.
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Affiliation(s)
- John W Kyle
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin, Madison, Wisconsin, USA 53792
| | - Jonathan C Makielski
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin, Madison, Wisconsin, USA 53792
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Sinha C, Arora K, Moon CS, Yarlagadda S, Woodrooffe K, Naren AP. Förster resonance energy transfer - an approach to visualize the spatiotemporal regulation of macromolecular complex formation and compartmentalized cell signaling. Biochim Biophys Acta Gen Subj 2014; 1840:3067-72. [PMID: 25086255 DOI: 10.1016/j.bbagen.2014.07.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/17/2014] [Accepted: 07/21/2014] [Indexed: 01/09/2023]
Abstract
BACKGROUND Signaling messengers and effector proteins provide an orchestrated molecular machinery to relay extracellular signals to the inside of cells and thereby facilitate distinct cellular behaviors. Formations of intracellular macromolecular complexes and segregation of signaling cascades dynamically regulate the flow of a biological process. SCOPE OF REVIEW In this review, we provide an overview of the development and application of FRET technology in monitoring cyclic nucleotide-dependent signalings and protein complexes associated with these signalings in real time and space with brief mention of other important signaling messengers and effector proteins involved in compartmentalized signaling. MAJOR CONCLUSIONS The preciseness, rapidity and specificity of cellular responses indicate restricted alterations of signaling messengers, particularly in subcellular compartments rather than globally. Not only the physical confinement and selective depletion, but also the intra- and inter-molecular interactions of signaling effectors modulate the direction of signal transduction in a compartmentalized fashion. To understand the finer details of various intracellular signaling cascades and crosstalk between proteins and other effectors, it is important to visualize these processes in live cells. Förster Resonance Energy Transfer (FRET) has been established as a useful tool to do this, even with its inherent limitations. GENERAL SIGNIFICANCE FRET technology remains as an effective tool for unraveling the complex organization and distribution of various endogenous signaling proteins, as well as the spatiotemporal dynamics of second messengers inside a single cell to distinguish the heterogeneity of cell signaling under normal physiological conditions and during pathological events.
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Affiliation(s)
- Chandrima Sinha
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA; Department of Physiology, University of Tennessee Health Science Center, 426 Nash Research Building, 894 Union Avenue, Memphis, TN 38163, USA
| | - Kavisha Arora
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Chang Suk Moon
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Sunitha Yarlagadda
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Koryse Woodrooffe
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Anjaparavanda P Naren
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, MLC2120 3333 Burnet Avenue Cincinnati, OH 45229, USA; Department of Physiology, University of Tennessee Health Science Center, 426 Nash Research Building, 894 Union Avenue, Memphis, TN 38163, USA.
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Tuszynska I, Matelska D, Magnus M, Chojnowski G, Kasprzak JM, Kozlowski LP, Dunin-Horkawicz S, Bujnicki JM. Computational modeling of protein-RNA complex structures. Methods 2014; 65:310-9. [PMID: 24083976 DOI: 10.1016/j.ymeth.2013.09.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/17/2013] [Accepted: 09/19/2013] [Indexed: 12/26/2022] Open
Abstract
Protein-RNA interactions play fundamental roles in many biological processes, such as regulation of gene expression, RNA splicing, and protein synthesis. The understanding of these processes improves as new structures of protein-RNA complexes are solved and the molecular details of interactions analyzed. However, experimental determination of protein-RNA complex structures by high-resolution methods is tedious and difficult. Therefore, studies on protein-RNA recognition and complex formation present major technical challenges for macromolecular structural biology. Alternatively, protein-RNA interactions can be predicted by computational methods. Although less accurate than experimental measurements, theoretical models of macromolecular structures can be sufficiently accurate to prompt functional hypotheses and guide e.g. identification of important amino acid or nucleotide residues. In this article we present an overview of strategies and methods for computational modeling of protein-RNA complexes, including software developed in our laboratory, and illustrate it with practical examples of structural predictions.
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