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Lin MH, Chen CP, Fischer WB. Patch formation of a viral channel forming protein within a lipid membrane – Vpu of HIV-1. MOLECULAR BIOSYSTEMS 2016; 12:1118-27. [DOI: 10.1039/c5mb00798d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Dimer-first formation leads to larger assemblies with potentially relevant structures.
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Affiliation(s)
- Meng-Han Lin
- Institute of Biophotonics
- School of Biomedical Science and Engineering and Biophotonics & Molecular Imaging Research Center (BMIRC)
- National Yang-Ming University
- Taipei 112
- Taiwan
| | - Chin-Pei Chen
- Institute of Biophotonics
- School of Biomedical Science and Engineering and Biophotonics & Molecular Imaging Research Center (BMIRC)
- National Yang-Ming University
- Taipei 112
- Taiwan
| | - Wolfgang B. Fischer
- Institute of Biophotonics
- School of Biomedical Science and Engineering and Biophotonics & Molecular Imaging Research Center (BMIRC)
- National Yang-Ming University
- Taipei 112
- Taiwan
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2
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Ulmschneider JP, Ulmschneider MB. Folding Simulations of the Transmembrane Helix of Virus Protein U in an Implicit Membrane Model. J Chem Theory Comput 2015; 3:2335-46. [PMID: 26636223 DOI: 10.1021/ct700103k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vpu is an 81-amino-acid auxiliary membrane protein encoded by human immunodeficiency virus type 1 (HIV-1). One of its roles is to amplify viral release by self-assembling in homo-oligomers to form functional water-filled pores enabling the flux of ions across the membrane. Various NMR and CD studies have shown that the transmembrane domain of Vpu has a helical conformation. With a recently developed implicit membrane model and an efficient Monte Carlo (MC) algorithm using concerted backbone rotations, we simulate the folding of the transmembrane domain of Vpu at atomic resolution. The implicit membrane environment is based on the generalized Born theory and enables very long time scale events, such as folding to be observed using detailed all-atom representation of the protein. Such studies are currently computationally unfeasible with fully explicit lipid bilayer molecular dynamics simulations. The correct helical transmembrane structure of Vpu is predicted from extended conformations and remains stably inserted. Tilt and kink angles agree well with experimental estimates from NMR measurements. The experimentally observed change in tilt angle in membranes of varying hydrophobic width is accurately reproduced. The extensive simulation of a pentamer of the Vpu transmembrane domain in the implicit membrane gives results similar to the ones reported previously for fully explicit bilayer simulations.
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Affiliation(s)
- Jakob P Ulmschneider
- Department of Chemistry, University of Rome "La Sapienza", Rome, Italy, and Department of Biochemistry, University of Oxford, Oxford, U.K
| | - Martin B Ulmschneider
- Department of Chemistry, University of Rome "La Sapienza", Rome, Italy, and Department of Biochemistry, University of Oxford, Oxford, U.K
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3
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Le Noury DA, Mosebi S, Papathanasopoulos MA, Hewer R. Functional roles of HIV-1 Vpu and CD74: Details and implications of the Vpu-CD74 interaction. Cell Immunol 2015; 298:25-32. [PMID: 26321123 DOI: 10.1016/j.cellimm.2015.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 08/22/2015] [Indexed: 01/24/2023]
Abstract
HIV-1 Vpu has a variety of functions, including CD4 degradation and the downregulation of MHCII. Downregulation of the MHCII occurs through Vpu binding to the cytoplasmic domain of CD74, the chaperone for antigen presentation. The CD74 cytoplasmic domain also plays a vital role in cell signaling through the activation of an NF-κB signal cascade for the maturation, proliferation and survival of B cells as well as by binding the macrophage inhibitory factor. In view of these functions, it follows that the Vpu-CD74 interaction has multiple downstream consequences for the immune system as it not only impairs foreign antigen presentation but may also have an effect on signal transduction cascades. It is thought that Vpu specifically targets intracellular CD74 while other HIV-1 proteins cannot. Therefore, this protein-protein interaction would be a potential drug target in order to reduce viral persistence. We review the functional importance and specific binding site of Vpu and CD74.
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Affiliation(s)
- Denise A Le Noury
- Centre for Metal-based Drug Discovery, Mintek, Private Bag X3015, Randburg 2125, South Africa; Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand Medical School, Private Bag 3, WITS, 2050, South Africa.
| | - Salerwe Mosebi
- Centre for Metal-based Drug Discovery, Mintek, Private Bag X3015, Randburg 2125, South Africa.
| | - Maria A Papathanasopoulos
- Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand Medical School, Private Bag 3, WITS, 2050, South Africa.
| | - Raymond Hewer
- Centre for Metal-based Drug Discovery, Mintek, Private Bag X3015, Randburg 2125, South Africa.
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4
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Opella SJ. Relating structure and function of viral membrane-spanning miniproteins. Curr Opin Virol 2015; 12:121-5. [PMID: 26057606 DOI: 10.1016/j.coviro.2015.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 05/20/2015] [Accepted: 05/26/2015] [Indexed: 12/25/2022]
Abstract
Many viruses express small hydrophobic membrane proteins. These proteins are often referred to as viroporins because they exhibit ion channel activity. However, the channel activity has not been definitively associated with a biological function in all cases. More generally, protein-protein and protein-phospholipid interactions have been associated with specific biological activities of these proteins. As research has progressed there is a decreased emphasis on potential roles of the channel activity, and increased research on multiple other biological functions. This being the case, it may be more appropriate to refer to them as 'viral membrane-spanning miniproteins'. Structural studies are illustrated with Vpu from HIV-1 and p7 from HCV.
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Affiliation(s)
- Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0307, USA.
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Scott C, Griffin S. Viroporins: structure, function and potential as antiviral targets. J Gen Virol 2015; 96:2000-2027. [PMID: 26023149 DOI: 10.1099/vir.0.000201] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The channel-forming activity of a family of small, hydrophobic integral membrane proteins termed 'viroporins' is essential to the life cycles of an increasingly diverse range of RNA and DNA viruses, generating significant interest in targeting these proteins for antiviral development. Viroporins vary greatly in terms of their atomic structure and can perform multiple functions during the virus life cycle, including those distinct from their role as oligomeric membrane channels. Recent progress has seen an explosion in both the identification and understanding of many such proteins encoded by highly significant pathogens, yet the prototypic M2 proton channel of influenza A virus remains the only example of a viroporin with provenance as an antiviral drug target. This review attempts to summarize our current understanding of the channel-forming functions for key members of this growing family, including recent progress in structural studies and drug discovery research, as well as novel insights into the life cycles of many viruses revealed by a requirement for viroporin activity. Ultimately, given the successes of drugs targeting ion channels in other areas of medicine, unlocking the therapeutic potential of viroporins represents a valuable goal for many of the most significant viral challenges to human and animal health.
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Affiliation(s)
- Claire Scott
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
| | - Stephen Griffin
- Leeds Institute of Cancer & Pathology and Leeds CRUK Clinical Centre, Faculty of Medicine and Health, St James's University Hospital, University of Leeds, Beckett Street, Leeds LS9 7TF, UK
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Honarparvar B, Govender T, Maguire GEM, Soliman MES, Kruger HG. Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity. Chem Rev 2013; 114:493-537. [DOI: 10.1021/cr300314q] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bahareh Honarparvar
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Thavendran Govender
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Glenn E. M. Maguire
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mahmoud E. S. Soliman
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Hendrik G. Kruger
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
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7
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Jardin C, Sticht H. Identification of the Structural Features that Mediate Binding Specificity in the Recognition of STAT Proteins by Dual-Specificity Phosphatases. J Biomol Struct Dyn 2012; 29:777-92. [DOI: 10.1080/07391102.2012.10507413] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Fischer WB, Wang YT, Schindler C, Chen CP. Mechanism of function of viral channel proteins and implications for drug development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 294:259-321. [PMID: 22364876 PMCID: PMC7149447 DOI: 10.1016/b978-0-12-394305-7.00006-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Viral channel-forming proteins comprise a class of viral proteins which, similar to their host companions, are made to alter electrochemical or substrate gradients across lipid membranes. These proteins are active during all stages of the cellular life cycle of viruses. An increasing number of proteins are identified as channel proteins, but the precise role in the viral life cycle is yet unknown for the majority of them. This review presents an overview about these proteins with an emphasis on those with available structural information. A concept is introduced which aligns the transmembrane domains of viral channel proteins with those of host channels and toxins to give insights into the mechanism of function of the viral proteins from potential sequence identities. A summary of to date investigations on drugs targeting these proteins is given and discussed in respect of their mode of action in vivo.
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Affiliation(s)
- Wolfgang B. Fischer
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan
| | - Yi-Ting Wang
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan
| | - Christina Schindler
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan
| | - Chin-Pei Chen
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei 112, Taiwan
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Lv M, Wang J, Wang X, Zuo T, Zhu Y, Kong W, Yu X. Polarity changes in the transmembrane domain core of HIV-1 Vpu inhibits its anti-tetherin activity. PLoS One 2011; 6:e20890. [PMID: 21674066 PMCID: PMC3107245 DOI: 10.1371/journal.pone.0020890] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 05/12/2011] [Indexed: 11/18/2022] Open
Abstract
Tetherin (BST-2/CD317) is an interferon-inducible antiviral protein that restricts the release of enveloped viruses from infected cells. The HIV-1 accessory protein Vpu can efficiently antagonize this restriction. In this study, we analyzed mutations of the transmembrane (TM) domain of Vpu, including deletions and substitutions, to delineate amino acids important for HIV-1 viral particle release and in interactions with tetherin. The mutants had similar subcellular localization patterns with that of wild-type Vpu and were functional with respect to CD4 downregulation. We showed that the hydrophobic binding surface for tetherin lies in the core of the Vpu TM domain. Three consecutive hydrophobic isoleucine residues in the middle region of the Vpu TM domain, I15, I16 and I17, were important for stabilizing the tetherin binding interface and determining its sensitivity to tetherin. Changing the polarity of the amino acids at these positions resulted in severe impairment of Vpu-induced tetherin targeting and antagonism. Taken together, these data reveal a model of specific hydrophobic interactions between Vpu and tetherin, which can be potentially targeted in the development of novel anti-HIV-1 drugs.
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Affiliation(s)
- Mingyu Lv
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Jiawen Wang
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Xiaodan Wang
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Tao Zuo
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Yingzi Zhu
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin Province, People's Republic of China
| | - Wei Kong
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin Province, People's Republic of China
- * E-mail: (WK); (XY)
| | - Xianghui Yu
- National Engineering Laboratory For AIDS Vaccine, College of Life Science, Jilin University, Changchun, Jilin Province, People's Republic of China
- * E-mail: (WK); (XY)
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Andrew A, Strebel K. HIV-1 Vpu targets cell surface markers CD4 and BST-2 through distinct mechanisms. Mol Aspects Med 2010; 31:407-17. [PMID: 20858517 PMCID: PMC2967615 DOI: 10.1016/j.mam.2010.08.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 08/09/2010] [Indexed: 10/19/2022]
Abstract
Vpu is a small integral membrane protein encoded by HIV-1 and some SIV isolates. The protein is known to induce degradation of the viral receptor molecule CD4 and to enhance the release of newly formed virions from the cell surface. Vpu accomplishes these two functions through two distinct mechanisms. In the case of CD4, Vpu acts as a molecular adaptor to connect CD4 to an E3 ubiquitin ligase complex resulting in CD4 degradation by cellular proteasomes. This requires signals located in Vpu's cytoplasmic domain. Enhancement of virus release on the other hand involves the neutralization of a cellular host factor, BST-2 (also known as CD317, HM1.24, or tetherin) and requires Vpu's TM domain. The current review discusses recent advances on the role of Vpu in controlling degradation of CD4 and in regulating virus release.
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Affiliation(s)
- Amy Andrew
- Laboratory of Molecular Microbiology, Viral Biochemistry Section, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892-0460, USA
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Liang X, Li ZY. Ion channels as antivirus targets. Virol Sin 2010; 25:267-80. [PMID: 20960300 DOI: 10.1007/s12250-010-3136-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 05/10/2010] [Indexed: 10/19/2022] Open
Abstract
Ion channels are membrane proteins that are found in a number of viruses and which are of crucial physiological importance in the viral life cycle. They have one common feature in that their action mode involves a change of electrochemical or proton gradient across the bilayer lipid membrane which modulates viral or cellular activity. We will discuss a group of viral channel proteins that belong to the viroproin family, and which participate in a number of viral functions including promoting the release of viral particles from cells. Blocking these channel-forming proteins may be "lethal", which can be a suitable and potential therapeutic strategy. In this review we discuss seven ion channels of viruses which can lead serious infections in human beings: M2 of influenza A, NB and BM2 of influenza B, CM2 of influenza C, Vpu of HIV-1, p7 of HCV and 2B of picornaviruses.
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Affiliation(s)
- Xin Liang
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
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Chen Y, Wang M, Zhang Q, Liu J. Construction of an implicit membrane environment for the lattice Monte Carlo simulation of transmembrane protein. Biophys Chem 2009; 147:35-41. [PMID: 20079964 PMCID: PMC7117040 DOI: 10.1016/j.bpc.2009.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 12/17/2009] [Accepted: 12/18/2009] [Indexed: 02/01/2023]
Abstract
Due to the complexity of biological membrane, computer simulation of transmembrane protein's folding is challenging. In this paper, an implicit biological membrane environment has been constructed in lattice space, in which the lipid chains and water molecules were represented by the unoccupied lattice sites. The biological membrane was characterized with three features: stronger hydrogen bonding interaction, membrane lateral pressure, and lipophobicity index for the amino acid residues. In addition to the hydrocarbon core spanning region and the water solution, the lipid interface has also been represented in this implicit membrane environment, which was proved to be effective for the transmembrane protein's folding. The associated Monte Carlo simulations have been performed for SARS-CoV E protein and M2 protein segment (residues 18–60) of influenza A virus. It was found that the coil–helix transition of the transmembrane segment occurred earlier than the coil–globule transition of the two terminal domains. The folding process and final orientation of the amphipathic helical block in water solution are obviously influenced by its corresponding hydrophobicity/lipophobicity. Therefore, this implicit membrane environment, though in lattice space, can make an elaborate balance between different driving forces for the membrane protein's folding, thus offering a potential means for the simulation of transmembrane protein oligomers in feasible time.
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Affiliation(s)
- Yantao Chen
- Shenzhen Key Laboratory of Functional Polymer, College of Chemistry and Chemical Engineering, Shenzhen University, Shenzhen 518060, China.
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Wittlich M, Koenig BW, Willbold D. Structural consequences of phosphorylation of two serine residues in the cytoplasmic domain of HIV-1 VpU. J Pept Sci 2008; 14:804-10. [PMID: 18186541 DOI: 10.1002/psc.1004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) protein U (VpU) is an accessory protein responsible for enhancement of viral particle release and down regulation of the T-lymphocyte coreceptor CD4. Direct binding between the cytoplasmic domains of CD4 and VpU as well as phosphorylation of serines 53 and 57 in the cytoplasmic domain of VpU plays a central role in CD4 downregulation. We investigated structural consequences of phosphorylation of the two serines using nuclear magnetic resonance spectroscopy. A uniformly 15N and 13C stable isotope-labeled 45-residue peptide comprising the cytoplasmic domain of VpU (VpUcyt) was recombinantly produced in E .coli. The peptide forms two helices (commonly referred to as helix 2 and 3) in the presence of membrane mimicking dodecylphosphocholine (DPC) micelles, which flank a flexible region containing the two phosphorylation sites. Phosphorylation does not cause any drastic structural changes in the secondary structure of VpUcyt. However, an N-terminal elongation of helix 3 and a slightly reduced helicity at the C-terminus of helix 2 are observed upon phosphorylation based on characteristic changes of 13Calpha and 13Cbeta chemical shifts. Phosphorylation also reduces the local mobility of the protein backbone in the loop region containing the phosphorylation sites according to heteronuclear 1H--15N nuclear Overhauser enhancement (NOE) data.
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Affiliation(s)
- Marc Wittlich
- Institut für Neurowissenschaften und Biophysik, Biomolekulare NMR, Forschungszentrum Jülich, Jülich,Germany
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Affiliation(s)
- Klaus Strebel
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious, Diseases, National Institutes of Health, 4/312, Bethesda, MD 20892, USA
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