1
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Poddar S, Roy R, Kar P. The conformational dynamics of Hepatitis C Virus E2 glycoprotein with the increasing number of N-glycosylation unraveled by molecular dynamics simulations. J Biomol Struct Dyn 2024:1-16. [PMID: 38393644 DOI: 10.1080/07391102.2024.2319679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/12/2024] [Indexed: 02/25/2024]
Abstract
The Hepatitis C Virus (HCV), responsible for causing hepatitis and a significant contributor to liver disorders, presents a challenge for treatment due to its high genetic variability. Despite efforts, there is still no effective medication available for this virus. One of the promising targets for drug development involves targeting glycoprotein E2. However, our understanding of the dynamic behavior of E2 and its associated glycans remains limited. In this study, we investigated the dynamic characteristics of E2 with varying degrees of glycosylation using all-atom molecular dynamics simulations. We also explored glycan's interactions with the protein and among themselves. An overall increase in correlation between the vital protein regions was observed with an increase in glycan number. The protein dynamics is followed by the analysis of glycan dynamics, where the flexibility of the individual glycans was analyzed in their free and bound state, which revealed a decrease in their fluctuation in some cases. Furthermore, we generated the free energy landscape of individual N-glycan linkages in both free and bound states and observed both increases and decreases in flexibility, which can be attributed to the formation and breakage of hydrogen bonds with amino acids. Finally, we found that for a high glycosylation system, glycans interact with glycoprotein and form hydrogen bonds among themselves. Moreover, the hydrogen bond profiles of a given glycan can vary when influenced by other glycans. In summary, our study provides valuable insights into the dynamics of the core region of HCV E2 glycoprotein and its associated glycans.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sayan Poddar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Rajarshi Roy
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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2
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Induction of cross-neutralizing antibodies by a permuted hepatitis C virus glycoprotein nanoparticle vaccine candidate. Nat Commun 2022; 13:7271. [PMID: 36434005 PMCID: PMC9700739 DOI: 10.1038/s41467-022-34961-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022] Open
Abstract
Hepatitis C virus (HCV) infection affects approximately 58 million people and causes ~300,000 deaths yearly. The only target for HCV neutralizing antibodies is the highly sequence diverse E1E2 glycoprotein. Eliciting broadly neutralizing antibodies that recognize conserved cross-neutralizing epitopes is important for an effective HCV vaccine. However, most recombinant HCV glycoprotein vaccines, which usually include only E2, induce only weak neutralizing antibody responses. Here, we describe recombinant soluble E1E2 immunogens that were generated by permutation of the E1 and E2 subunits. We displayed the E2E1 immunogens on two-component nanoparticles and these nanoparticles induce significantly more potent neutralizing antibody responses than E2. Next, we generated mosaic nanoparticles co-displaying six different E2E1 immunogens. These mosaic E2E1 nanoparticles elicit significantly improved neutralization compared to monovalent E2E1 nanoparticles. These results provide a roadmap for the generation of an HCV vaccine that induces potent and broad neutralization.
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3
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de la Peña AT, Sliepen K, Eshun-Wilson L, Newby ML, Allen JD, Zon I, Koekkoek S, Chumbe A, Crispin M, Schinkel J, Lander GC, Sanders RW, Ward AB. Structure of the hepatitis C virus E1E2 glycoprotein complex. Science 2022; 378:263-269. [PMID: 36264808 PMCID: PMC10512783 DOI: 10.1126/science.abn9884] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Hepatitis C virus (HCV) infection is a leading cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma in humans and afflicts more than 58 million people worldwide. The HCV envelope E1 and E2 glycoproteins are essential for viral entry and comprise the primary antigenic target for neutralizing antibody responses. The molecular mechanisms of E1E2 assembly, as well as how the E1E2 heterodimer binds broadly neutralizing antibodies, remain elusive. Here, we present the cryo-electron microscopy structure of the membrane-extracted full-length E1E2 heterodimer in complex with three broadly neutralizing antibodies-AR4A, AT1209, and IGH505-at ~3.5-angstrom resolution. We resolve the interface between the E1 and E2 ectodomains and deliver a blueprint for the rational design of vaccine immunogens and antiviral drugs.
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Affiliation(s)
- Alba Torrents de la Peña
- Department of Integrative Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kwinten Sliepen
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Lisa Eshun-Wilson
- Department of Integrative Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maddy L. Newby
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Joel D. Allen
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Ian Zon
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Sylvie Koekkoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Ana Chumbe
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Janke Schinkel
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
| | - Gabriel C. Lander
- Department of Integrative Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, Netherlands
- Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Andrew B. Ward
- Department of Integrative Structural Biology and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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4
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Donnison T, McGregor J, Chinnakannan S, Hutchings C, Center RJ, Poumbourios P, Klenerman P, Drummer HE, Barnes E. A pan-genotype hepatitis C virus viral vector vaccine generates T cells and neutralizing antibodies in mice. Hepatology 2022; 76:1190-1202. [PMID: 35313015 PMCID: PMC9790311 DOI: 10.1002/hep.32470] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS A prophylactic vaccine targeting multiple HCV genotypes (gt) is urgently required to meet World Health Organization elimination targets. Neutralizing antibodies (nAbs) and CD4+ and CD8+ T cells are associated with spontaneous clearance of HCV, and each may contribute to protective immunity. However, current vaccine candidates generate either nAbs or T cells targeting genetically variable epitopes and have failed to show efficacy in human trials. We have previously shown that a simian adenovirus vector (ChAdOx1) encoding conserved sequences across gt1-6 (ChAd-Gt1-6), and separately gt-1a E2 protein with variable regions deleted (E2Δ123HMW ), generates pan-genotypic T cells and nAbs, respectively. We now aim to develop a vaccine to generate both viral-specific B- and T-cell responses concurrently. APPROACH AND RESULTS We show that vaccinating with ChAd-Gt1-6 and E2Δ123HMW sequentially in mice generates T-cell and antibody (Ab) responses comparable to either vaccine given alone. We encoded E2Δ123 in ChAdOx1 (ChAd-E2Δ123) and show that this, given with an E2Δ123HMW protein boost, induces greater CD81-E2 inhibitory and HCV-pseudoparticle nAb titers compared to the E2Δ123HMW prime boost. We developed bivalent viral vector vaccines (ChAdOx1 and modified vaccinia Ankara [MVA]) encoding both Gt1-6 and E2Δ123 immunogens (Gt1-6-E2Δ123) generating polyfunctional CD4+ and CD8+ T cells and nAb titers in prime/boost strategies. This approach generated nAb responses comparable to monovalent E2Δ123 ChAd/MVA vaccines and superior to three doses of recombinant E2Δ123HMW protein, while also generating high-magnitude T-cell responses. CONCLUSIONS These data are an important step forward for the development of a pan-genotype HCV vaccine to elicit T cells and nAbs for future assessment in humans.
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Affiliation(s)
- Timothy Donnison
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Joey McGregor
- Burnet Institute, Melbourne, Victoria, Australia.,Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Senthil Chinnakannan
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Claire Hutchings
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Rob J Center
- Burnet Institute, Melbourne, Victoria, Australia.,Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Pantelis Poumbourios
- Burnet Institute, Melbourne, Victoria, Australia.,Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Paul Klenerman
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Heidi E Drummer
- Burnet Institute, Melbourne, Victoria, Australia.,Department of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.,Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Eleanor Barnes
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, Jenner Institute, University of Oxford, Oxford, UK
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5
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Kalemera MD, Capella-Pujol J, Chumbe A, Underwood A, Bull RA, Schinkel J, Sliepen K, Grove J. Optimized cell systems for the investigation of hepatitis C virus E1E2 glycoproteins. J Gen Virol 2021; 102. [PMID: 33147126 PMCID: PMC8116788 DOI: 10.1099/jgv.0.001512] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Great strides have been made in understanding and treating hepatitis C virus (HCV) thanks to the development of various experimental systems including cell-culture-proficient HCV, the HCV pseudoparticle system and soluble envelope glycoproteins. The HCV pseudoparticle (HCVpp) system is a platform used extensively in studies of cell entry, screening of novel entry inhibitors, assessing the phenotypes of clinically observed E1 and E2 glycoproteins and, most pertinently, in characterizing neutralizing antibody breadth induced upon vaccination and natural infection in patients. Nonetheless, some patient-derived clones produce pseudoparticles that are either non-infectious or exhibit infectivity too low for meaningful phenotyping. The mechanisms governing whether any particular clone produces infectious pseudoparticles are poorly understood. Here we show that endogenous expression of CD81, an HCV receptor and a cognate-binding partner of E2, in producer HEK 293T cells is detrimental to the infectivity of recovered HCVpp for most strains. Many HCVpp clones exhibited increased infectivity or had their infectivity rescued when they were produced in 293T cells CRISPR/Cas9 engineered to ablate CD81 expression (293TCD81KO). Clones made in 293TCD81KO cells were antigenically very similar to their matched counterparts made parental cells and appear to honour the accepted HCV entry pathway. Deletion of CD81 did not appreciably increase the recovered titres of soluble E2 (sE2). However, we did, unexpectedly, find that monomeric sE2 made in 293T cells and Freestyle 293-F (293-F) cells exhibit important differences. We found that 293-F-produced sE2 harbours mostly complex-type glycans whilst 293T-produced sE2 displays a heterogeneous mixture of both complex-type glycans and high-mannose or hybrid-type glycans. Moreover, sE2 produced in 293T cells is antigenically superior; exhibiting increased binding to conformational antibodies and the large extracellular loop of CD81. In summary, this work describes an optimal cell line for the production of HCVpp and reveals that sE2 made in 293T and 293-F cells are not antigenic equals. Our findings have implications for functional studies of E1E2 and the production of candidate immunogens.
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Affiliation(s)
- Mphatso D Kalemera
- Institute of Immunity and Transplantation, Division of Infection and Immunity, The Royal Free Hospital, University College London, London, UK
| | - Joan Capella-Pujol
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Ana Chumbe
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Alexander Underwood
- Viral Immunology Systems Program, The Kirby Institute, School of Medical Sciences, Faculty of Medicine, The University of New South Wales, Sydney, Australia
| | - Rowena A Bull
- Viral Immunology Systems Program, The Kirby Institute, School of Medical Sciences, Faculty of Medicine, The University of New South Wales, Sydney, Australia
| | - Janke Schinkel
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
| | - Joe Grove
- Institute of Immunity and Transplantation, Division of Infection and Immunity, The Royal Free Hospital, University College London, London, UK
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6
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Structure-Based and Rational Design of a Hepatitis C Virus Vaccine. Viruses 2021; 13:v13050837. [PMID: 34063143 PMCID: PMC8148096 DOI: 10.3390/v13050837] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/27/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022] Open
Abstract
A hepatitis C virus (HCV) vaccine is a critical yet unfulfilled step in addressing the global disease burden of HCV. While decades of research have led to numerous clinical and pre-clinical vaccine candidates, these efforts have been hindered by factors including HCV antigenic variability and immune evasion. Structure-based and rational vaccine design approaches have capitalized on insights regarding the immune response to HCV and the structures of antibody-bound envelope glycoproteins. Despite successes with other viruses, designing an immunogen based on HCV glycoproteins that can elicit broadly protective immunity against HCV infection is an ongoing challenge. Here, we describe HCV vaccine design approaches where immunogens were selected and optimized through analysis of available structures, identification of conserved epitopes targeted by neutralizing antibodies, or both. Several designs have elicited immune responses against HCV in vivo, revealing correlates of HCV antigen immunogenicity and breadth of induced responses. Recent studies have elucidated the functional, dynamic and immunological features of key regions of the viral envelope glycoproteins, which can inform next-generation immunogen design efforts. These insights and design strategies represent promising pathways to HCV vaccine development, which can be further informed by successful immunogen designs generated for other viruses.
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7
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Guest JD, Wang R, Elkholy KH, Chagas A, Chao KL, Cleveland TE, Kim YC, Keck ZY, Marin A, Yunus AS, Mariuzza RA, Andrianov AK, Toth EA, Foung SKH, Pierce BG, Fuerst TR. Design of a native-like secreted form of the hepatitis C virus E1E2 heterodimer. Proc Natl Acad Sci U S A 2021; 118:e2015149118. [PMID: 33431677 PMCID: PMC7826332 DOI: 10.1073/pnas.2015149118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Hepatitis C virus (HCV) is a major worldwide health burden, and a preventive vaccine is needed for global control or eradication of this virus. A substantial hurdle to an effective HCV vaccine is the high variability of the virus, leading to immune escape. The E1E2 glycoprotein complex contains conserved epitopes and elicits neutralizing antibody responses, making it a primary target for HCV vaccine development. However, the E1E2 transmembrane domains that are critical for native assembly make it challenging to produce this complex in a homogenous soluble form that is reflective of its state on the viral envelope. To enable rational design of an E1E2 vaccine, as well as structural characterization efforts, we have designed a soluble, secreted form of E1E2 (sE1E2). As with soluble glycoprotein designs for other viruses, it incorporates a scaffold to enforce assembly in the absence of the transmembrane domains, along with a furin cleavage site to permit native-like heterodimerization. This sE1E2 was found to assemble into a form closer to its expected size than full-length E1E2. Preservation of native structural elements was confirmed by high-affinity binding to a panel of conformationally specific monoclonal antibodies, including two neutralizing antibodies specific to native E1E2 and to its primary receptor, CD81. Finally, sE1E2 was found to elicit robust neutralizing antibodies in vivo. This designed sE1E2 can both provide insights into the determinants of native E1E2 assembly and serve as a platform for production of E1E2 for future structural and vaccine studies, enabling rational optimization of an E1E2-based antigen.
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Affiliation(s)
- Johnathan D Guest
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Ruixue Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Khadija H Elkholy
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Molecular Biology Department, Genetic Engineering and Biotechnology Division, National Research Centre, Cairo 12622, Egypt
| | - Andrezza Chagas
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Kinlin L Chao
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Thomas E Cleveland
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Young Chang Kim
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Zhen-Yong Keck
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Alexander Marin
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Abdul S Yunus
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Roy A Mariuzza
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Alexander K Andrianov
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Eric A Toth
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850
| | - Steven K H Foung
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Brian G Pierce
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850;
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Thomas R Fuerst
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850;
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
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