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Füllbrunn N, Nicastro R, Mari M, Griffith J, Herrmann E, Rasche R, Borchers AC, Auffarth K, Kümmel D, Reggiori F, De Virgilio C, Langemeyer L, Ungermann C. The GTPase activating protein Gyp7 regulates Rab7/Ypt7 activity on late endosomes. J Cell Biol 2024; 223:e202305038. [PMID: 38536036 PMCID: PMC10978497 DOI: 10.1083/jcb.202305038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 01/22/2024] [Accepted: 03/08/2024] [Indexed: 04/01/2024] Open
Abstract
Organelles of the endomembrane system contain Rab GTPases as identity markers. Their localization is determined by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs). It remains largely unclear how these regulators are specifically targeted to organelles and how their activity is regulated. Here, we focus on the GAP Gyp7, which acts on the Rab7-like Ypt7 protein in yeast, and surprisingly observe the protein exclusively in puncta proximal to the vacuole. Mistargeting of Gyp7 to the vacuole strongly affects vacuole morphology, suggesting that endosomal localization is needed for function. In agreement, efficient endolysosomal transport requires Gyp7. In vitro assays reveal that Gyp7 requires a distinct lipid environment for membrane binding and activity. Overexpression of Gyp7 concentrates Ypt7 in late endosomes and results in resistance to rapamycin, an inhibitor of the target of rapamycin complex 1 (TORC1), suggesting that these late endosomes are signaling endosomes. We postulate that Gyp7 is part of regulatory machinery involved in late endosome function.
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Affiliation(s)
- Nadia Füllbrunn
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
- Center of Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Raffaele Nicastro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Muriel Mari
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Janice Griffith
- Department of Cell Biology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Eric Herrmann
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - René Rasche
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Ann-Christin Borchers
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
| | - Kathrin Auffarth
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
| | - Daniel Kümmel
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Cell Biology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Lars Langemeyer
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
- Center of Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
- Center of Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
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Shvarev D, Schoppe J, König C, Perz A, Füllbrunn N, Kiontke S, Langemeyer L, Januliene D, Schnelle K, Kümmel D, Fröhlich F, Moeller A, Ungermann C. Structure of the HOPS tethering complex, a lysosomal membrane fusion machinery. eLife 2022; 11:80901. [PMID: 36098503 PMCID: PMC9592082 DOI: 10.7554/elife.80901] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Lysosomes are essential for cellular recycling, nutrient signaling, autophagy, and pathogenic bacteria and viruses invasion. Lysosomal fusion is fundamental to cell survival and requires HOPS, a conserved heterohexameric tethering complex. On the membranes to be fused, HOPS binds small membrane-associated GTPases and assembles SNAREs for fusion, but how the complex fulfills its function remained speculative. Here, we used cryo-electron microscopy to reveal the structure of HOPS. Unlike previously reported, significant flexibility of HOPS is confined to its extremities, where GTPase binding occurs. The SNARE-binding module is firmly attached to the core, therefore, ideally positioned between the membranes to catalyze fusion. Our data suggest a model for how HOPS fulfills its dual functionality of tethering and fusion and indicate why it is an essential part of the membrane fusion machinery. Our cells break down the nutrients that they receive from the body to create the building blocks needed to keep us alive. This is done by compartments called lysosomes that are filled with a cocktail of proteins called enzymes, which speed up the breakdown process. Lysosomes are surrounded by a membrane, a barrier of fatty molecules that protects the rest of the cell from being digested. When new nutrients reach the cell, they travel to the lysosome packaged in vesicles, which have their own fatty membrane. To allow the nutrients to enter the lysosome without creating a leak, the membranes of the vesicles and the lysosome must fuse. The mechanism through which these membranes fuse is not fully clear. It is known that both fusing membranes must contain proteins called SNAREs, which wind around each other when they interact. However, this alone is not enough. Other proteins are also required to tether the membranes together before they fuse. To understand how these tethers play a role, Shvarev, Schoppe, König et al. studied the structure of the HOPS complex from yeast. This assembly of six proteins is vital for lysosomal fusion and, has a composition similar to the equivalent complex in humans. Using cryo-electron microscopy, a technique that relies on freezing purified proteins to image them with an electron microscope and reveal their structure, allowed Shvarev, Schoppe, König et al. to provide a model for how HOPS interacts with SNAREs and membranes. In addition to HOPS acting as a tether to bring the membranes together, it can also bind directly to SNAREs. This creates a bridge that allows the proteins to wrap around each other, driving the membranes to fuse. HOPS is a crucial component in the cellular machinery, and mutations in the complex can cause devastating neurological defects. The complex is also targeted by viruses – such as SARS-CoV-2 – that manipulate HOPS to reduce its activity. Shvarev, Schoppe, König et al.’s findings could help researchers to develop drugs to maintain or recover the activity of HOPS. However, this will require additional information about its structure and how the complex acts in the biological environment of the cell.
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Affiliation(s)
- Dmitry Shvarev
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Jannis Schoppe
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Caroline König
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Angela Perz
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Nadia Füllbrunn
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Stephan Kiontke
- Department of Plant Physiology and Photo Biology, Philipp University of Marburg, Marburg, Germany
| | - Lars Langemeyer
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Dovile Januliene
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Kilian Schnelle
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Daniel Kümmel
- Department of Chemistry and Pharmacy, University of Münster, Münster, Germany
| | - Florian Fröhlich
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Arne Moeller
- Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
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Füllbrunn N, Li Z, Jorde L, Richter CP, Kurre R, Langemeyer L, Yu C, Meyer C, Enderlein J, Ungermann C, Piehler J, You C. Nanoscopic anatomy of dynamic multi-protein complexes at membranes resolved by graphene-induced energy transfer. eLife 2021; 10:62501. [PMID: 33513092 PMCID: PMC7847308 DOI: 10.7554/elife.62501] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/28/2020] [Indexed: 11/30/2022] Open
Abstract
Insights into the conformational organization and dynamics of proteins complexes at membranes is essential for our mechanistic understanding of numerous key biological processes. Here, we introduce graphene-induced energy transfer (GIET) to probe axial orientation of arrested macromolecules at lipid monolayers. Based on a calibrated distance-dependent efficiency within a dynamic range of 25 nm, we analyzed the conformational organization of proteins and complexes involved in tethering and fusion at the lysosome-like yeast vacuole. We observed that the membrane-anchored Rab7-like GTPase Ypt7 shows conformational reorganization upon interactions with effector proteins. Ensemble and time-resolved single-molecule GIET experiments revealed that the HOPS tethering complex, when recruited via Ypt7 to membranes, is dynamically alternating between a ‘closed’ and an ‘open’ conformation, with the latter possibly interacting with incoming vesicles. Our work highlights GIET as a unique spectroscopic ruler to reveal the axial orientation and dynamics of macromolecular complexes at biological membranes with sub-nanometer resolution. Proteins are part of the building blocks of life and are essential for structure, function and regulation of every cell, tissue and organ of the body. Proteins adopt different conformations to work efficiently within the various environments of a cell. They can also switch between shapes. One way to monitor how proteins change their shapes involves energy transfer. This approach can measure how close two proteins, or two parts of the same protein, are, by using dye labels that respond to each other when they are close together. For example, in a method called FRET, one dye label absorbs light and transfers the energy to the other label, which emits it as a different color of light. However, FRET only works over short distances (less than 10nm apart or 1/100,000th of a millimeter), so it is not useful for larger proteins. Here, Füllbrunn, Li et al. developed a method called GIET that uses graphene to analyze the dynamic structures of proteins on membrane surfaces. Graphene is a type of carbon nanomaterial that can absorb energy from dye labels and could provide a way to study protein interactions over longer distances. Graphene was deposited on a glass surface where it was coated with single layer of membrane, which could then be used to capture specific proteins. The results showed that GIET worked over longer distances (up to 30 nm) than FRET and could be used to study proteins attached to the membrane around graphene. Füllbrunn, Li et al. used it to examine a specific complex of proteins called HOPS, which is linked to multiple diseases, including Ebola, measuring distances between the head or tail of HOPS and the membrane to understand protein shapes. This revealed that HOPS adopts an upright position on membranes and alternates between open and closed shapes. The study of Füllbrunn, Li et al. highlights the ability of GIET to address unanswered questions about the function of protein complexes on membrane surfaces and sheds new light on the structural dynamics of HOPS in living cells. As it allows protein interactions to be studied over much greater distances, GIET could be a powerful new tool for cell biology research. Moreover, graphene is also useful in electron microscopy and both approaches combined could achieve a detailed structural picture of proteins in action.
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Affiliation(s)
- Nadia Füllbrunn
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Zehao Li
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany.,College of Life Sciences, Beijing University of Chemical Technology, Beijing, China
| | - Lara Jorde
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Christian P Richter
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Rainer Kurre
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Lars Langemeyer
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Changyuan Yu
- College of Life Sciences, Beijing University of Chemical Technology, Beijing, China
| | - Carola Meyer
- Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany.,Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Jörg Enderlein
- 3rd Institute of Physics - Biophysics, Georg August University, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Georg August University, Göttingen, Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Changjiang You
- Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
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Langemeyer L, Borchers AC, Herrmann E, Füllbrunn N, Han Y, Perz A, Auffarth K, Kümmel D, Ungermann C. A conserved and regulated mechanism drives endosomal Rab transition. eLife 2020; 9:56090. [PMID: 32391792 PMCID: PMC7239660 DOI: 10.7554/elife.56090] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/07/2020] [Indexed: 12/31/2022] Open
Abstract
Endosomes and lysosomes harbor Rab5 and Rab7 on their surface as key proteins involved in their identity, biogenesis, and fusion. Rab activation requires a guanine nucleotide exchange factor (GEF), which is Mon1-Ccz1 for Rab7. During endosome maturation, Rab5 is replaced by Rab7, though the underlying mechanism remains poorly understood. Here, we identify the molecular determinants for Rab conversion in vivo and in vitro, and reconstitute Rab7 activation with yeast and metazoan proteins. We show (i) that Mon1-Ccz1 is an effector of Rab5, (ii) that membrane-bound Rab5 is the key factor to directly promote Mon1-Ccz1 dependent Rab7 activation and Rab7-dependent membrane fusion, and (iii) that this process is regulated in yeast by the casein kinase Yck3, which phosphorylates Mon1 and blocks Rab5 binding. Our study thus uncovers the minimal feed-forward machinery of the endosomal Rab cascade and a novel regulatory mechanism controlling this pathway.
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Affiliation(s)
- Lars Langemeyer
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Osnabrück, Germany
| | - Ann-Christin Borchers
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Osnabrück, Germany
| | - Eric Herrmann
- University of Münster, Institute of Biochemistry, Münster, Germany
| | - Nadia Füllbrunn
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Osnabrück, Germany
| | - Yaping Han
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Osnabrück, Germany
| | - Angela Perz
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Osnabrück, Germany
| | - Kathrin Auffarth
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Osnabrück, Germany
| | - Daniel Kümmel
- University of Münster, Institute of Biochemistry, Münster, Germany
| | - Christian Ungermann
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Osnabrück, Germany.,University of Osnabrück, Center of Cellular Nanoanalytics (CellNanOs), Osnabrück, Germany
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5
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Stempel M, Chan B, Juranić Lisnić V, Krmpotić A, Hartung J, Paludan SR, Füllbrunn N, Lemmermann NA, Brinkmann MM. The herpesviral antagonist m152 reveals differential activation of STING-dependent IRF and NF-κB signaling and STING's dual role during MCMV infection. EMBO J 2019; 38:embj.2018100983. [PMID: 30696688 PMCID: PMC6396373 DOI: 10.15252/embj.2018100983] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/16/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
Cytomegaloviruses (CMVs) are master manipulators of the host immune response. Here, we reveal that the murine CMV (MCMV) protein m152 specifically targets the type I interferon (IFN) response by binding to stimulator of interferon genes (STING), thereby delaying its trafficking to the Golgi compartment from where STING initiates type I IFN signaling. Infection with an MCMV lacking m152 induced elevated type I IFN responses and this leads to reduced viral transcript levels both in vitro and in vivo. This effect is ameliorated in the absence of STING. Interestingly, while m152 inhibits STING‐mediated IRF signaling, it did not affect STING‐mediated NF‐κB signaling. Analysis of how m152 targets STING translocation reveals that STING activates NF‐κB signaling already from the ER prior to its trafficking to the Golgi. Strikingly, this response is important to promote early MCMV replication. Our results show that MCMV has evolved a mechanism to specifically antagonize the STING‐mediated antiviral IFN response, while preserving its pro‐viral NF‐κB response, providing an advantage in the establishment of an infection.
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Affiliation(s)
- Markus Stempel
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Baca Chan
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Vanda Juranić Lisnić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Astrid Krmpotić
- Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Josephine Hartung
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Søren R Paludan
- Department of Biomedicine, Aarhus Research Center for Innate Immunology, University of Aarhus, Aarhus, Denmark
| | - Nadia Füllbrunn
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Niels Aw Lemmermann
- Institute for Virology and Research Center for Immunotherapy, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Melanie M Brinkmann
- Viral Immune Modulation Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany .,Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
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Klema VJ, Sepuru KM, Füllbrunn N, Farris TR, Dunphy PS, McBride JW, Rajarathnam K, Choi KH. Ehrlichia chaffeensis TRP120 nucleomodulin binds DNA with disordered tandem repeat domain. PLoS One 2018; 13:e0194891. [PMID: 29641592 PMCID: PMC5895000 DOI: 10.1371/journal.pone.0194891] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/12/2018] [Indexed: 12/21/2022] Open
Abstract
Ehrlichia chaffeensis, the causative agent of human monocytotropic ehrlichiosis, secretes several effector proteins that bind host DNA to modulate host gene expression. The tandem repeat protein 120 (TRP120), one of the largest effector proteins, has four nearly identical tandem repeat (TR) regions that each consists of 80 amino acids. In addition to playing a role in ehrlichial binding and internalization, TRP120 translocates to the host nucleus where it is thought to function as a transcription factor that modulates gene expression. However, sequence analysis of TRP120 does not identify the presence of DNA-binding or trans-activation domains typical of classical eukaryotic transcription factors. Thus, the mechanism by which TRP120 binds DNA and modulates gene expression remains elusive. Herein, we expressed the TR regions of the TRP120 protein, and characterized its solution structure and ability to bind DNA. TRP120, expressed as either a one or two TR repeat, is a monomer in solution, and is mostly disordered as determined by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. Using NMR spectroscopy, we further show that the 1 TR construct selectively binds GC-rich DNA. Although low pH was required for TRP120 TR-DNA interaction, acidic pH alone does not induce any significant structural changes in the TR region. This suggests that TRP120 folds into an ordered structure upon forming a protein-DNA complex, and thus folding of TRP120 TR is coupled with DNA binding.
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Affiliation(s)
- Valerie J. Klema
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Krishna Mohan Sepuru
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Nadia Füllbrunn
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tierra R. Farris
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Paige S. Dunphy
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jere W. McBride
- Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kyung H. Choi
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
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