1
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Guo J, Li S, Bai L, Zhao H, Shang W, Zhong Z, Maimaiti T, Gao X, Ji N, Chao Y, Li Z, Du D. Structural transition of GP64 triggered by a pH-sensitive multi-histidine switch. Nat Commun 2024; 15:7668. [PMID: 39227374 PMCID: PMC11372198 DOI: 10.1038/s41467-024-51799-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/16/2024] [Indexed: 09/05/2024] Open
Abstract
The fusion of viruses with cellular membranes is a critical step in the life cycle of enveloped viruses. This process is facilitated by viral fusion proteins, many of which are conformationally pH-sensitive. The specifics of how changes in pH initiate this fusion have remained largely elusive. This study presents the cryo-electron microscopy (cryo-EM) structures of a prototype class III fusion protein, GP64, in its prefusion and early intermediate states, revealing the structural intermediates accompanying the membrane fusion process. The structures identify the involvement of a pH-sensitive switch, comprising H23, H245, and H304, in sensing the low pH that triggers the initial step of membrane fusion. The pH sensing role of this switch is corroborated by assays of cell-cell syncytium formation and dual dye-labeling. The findings demonstrate that coordination between multiple histidine residues acts as a pH sensor and activator. The involvement of a multi-histidine switch in viral fusion is applicable to fusogens of human-infecting thogotoviruses and other viruses, which could lead to strategies for developing anti-viral therapies and vaccines.
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Affiliation(s)
- Jinliang Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shangrong Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Lisha Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Huimin Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wenyu Shang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhaojun Zhong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | | | - Xueyan Gao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ning Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yanjie Chao
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Zhaofei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Dijun Du
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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2
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Dehinwal R, Gopinath T, Smith RD, Ernst RK, Schifferli DM, Waldor MK, Marassi FM. A pH-sensitive motif in an outer membrane protein activates bacterial membrane vesicle production. Nat Commun 2024; 15:6958. [PMID: 39138228 PMCID: PMC11322160 DOI: 10.1038/s41467-024-51364-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
Outer membrane vesicles (OMVs) produced by Gram-negative bacteria have key roles in cell envelope homeostasis, secretion, interbacterial communication, and pathogenesis. The facultative intracellular pathogen Salmonella Typhimurium increases OMV production inside the acidic vacuoles of host cells by changing expression of its outer membrane proteins and modifying the composition of lipid A. However, the molecular mechanisms that translate pH changes into OMV production are not completely understood. Here, we show that the outer membrane protein PagC promotes OMV production through pH-dependent interactions between its extracellular loops and surrounding lipopolysaccharide (LPS). Structural comparisons and mutational studies indicate that a pH-responsive amino acid motif in PagC extracellular loops, containing PagC-specific histidine residues, is crucial for OMV formation. Molecular dynamics simulations suggest that protonation of histidine residues leads to changes in the structure and flexibility of PagC extracellular loops and their interactions with the surrounding LPS, altering membrane curvature. Consistent with that hypothesis, mimicking acidic pH by mutating those histidine residues to lysine increases OMV production. Thus, our findings reveal a mechanism for sensing and responding to environmental pH and for control of membrane dynamics by outer membrane proteins.
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Affiliation(s)
- Ruchika Dehinwal
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, USA
- Department of Microbiology, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, USA
| | - Tata Gopinath
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Richard D Smith
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA
| | - Dieter M Schifferli
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, USA.
- Department of Microbiology, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, USA.
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3
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Kao CF, Liu CY, Hsieh CL, Carillo KJD, Tzou DLM, Wang HC, Chang W. Structural and functional analyses of viral H2 protein of the vaccinia virus entry fusion complex. J Virol 2023; 97:e0134323. [PMID: 37975688 PMCID: PMC10734489 DOI: 10.1128/jvi.01343-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/02/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Vaccinia virus infection requires virus-cell membrane fusion to complete entry during endocytosis; however, it contains a large viral fusion protein complex of 11 viral proteins that share no structure or sequence homology to all the known viral fusion proteins, including type I, II, and III fusion proteins. It is thus very challenging to investigate how the vaccinia fusion complex works to trigger membrane fusion with host cells. In this study, we crystallized the ectodomain of vaccinia H2 protein, one component of the viral fusion complex. Furthermore, we performed a series of mutational, biochemical, and molecular analyses and identified two surface loops containing 170LGYSG174 and 125RRGTGDAW132 as the A28-binding region. We also showed that residues in the N-terminal helical region (amino acids 51-90) are also important for H2 function.
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Affiliation(s)
- Chi-Fei Kao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chang-Yi Liu
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Chia-Lin Hsieh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | | | - Hao-Ching Wang
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Wen Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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4
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Jain A, Govindan R, Berkman AR, Luban J, Díaz-Salinas MA, Durham ND, Munro JB. Regulation of Ebola GP conformation and membrane binding by the chemical environment of the late endosome. PLoS Pathog 2023; 19:e1011848. [PMID: 38055723 PMCID: PMC10727438 DOI: 10.1371/journal.ppat.1011848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/18/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023] Open
Abstract
Interaction between the Ebola virus envelope glycoprotein (GP) and the endosomal membrane is an essential step during virus entry into the cell. Acidic pH and Ca2+ have been implicated in mediating the GP-membrane interaction. However, the molecular mechanism by which these environmental factors regulate the conformational changes that enable engagement of GP with the target membrane is unknown. Here, we apply fluorescence correlation spectroscopy (FCS) and single-molecule Förster resonance energy transfer (smFRET) imaging to elucidate how the acidic pH, Ca2+ and anionic phospholipids in the late endosome promote GP-membrane interaction, thereby facilitating virus entry. We find that bis(monoacylglycero)phosphate (BMP), which is specific to the late endosome, is especially critical in determining the Ca2+-dependence of the GP-membrane interaction. Molecular dynamics (MD) simulations suggested residues in GP that sense pH and induce conformational changes that make the fusion loop available for insertion into the membrane. We similarly confirm residues in the fusion loop that mediate GP's interaction with Ca2+, which likely promotes local conformational changes in the fusion loop and mediates electrostatic interactions with the anionic phospholipids. Collectively, our results provide a mechanistic understanding of how the environment of the late endosome regulates the timing and efficiency of virus entry.
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Affiliation(s)
- Aastha Jain
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Ramesh Govindan
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
- Medical Scientist Training Program, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Alex R. Berkman
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Jeremy Luban
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Marco A. Díaz-Salinas
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - Natasha D. Durham
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
| | - James B. Munro
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, Worcester, Massachusetts, United States of America
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, Massachusetts, United States of America
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5
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Chathuranga WAG, Nikapitiya C, Kim JH, Chathuranga K, Weerawardhana A, Dodantenna N, Kim DJ, Poo H, Jung JU, Lee CH, Lee JS. Gadd45β is critical for regulation of type I interferon signaling by facilitating G3BP-mediated stress granule formation. Cell Rep 2023; 42:113358. [PMID: 37917584 DOI: 10.1016/j.celrep.2023.113358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/04/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
Stress granules (SGs) constitute a signaling hub that plays a critical role in type I interferon responses. Here, we report that growth arrest and DNA damage-inducible beta (Gadd45β) act as a positive regulator of SG-mediated interferon signaling by targeting G3BP upon RNA virus infection. Gadd45β deficiency markedly impairs SG formation and SG-mediated activation of interferon signaling in vitro. Gadd45β knockout mice are highly susceptible to RNA virus infection, and their ability to produce interferon and cytokines is severely impaired. Specifically, Gadd45β interacts with the RNA-binding domain of G3BP, leading to conformational expansion of G3BP1 via dissolution of its autoinhibitory electrostatic intramolecular interaction. The acidic loop 1- and RNA-binding properties of Gadd45β markedly increase the conformational expansion and RNA-binding affinity of the G3BP1-Gadd45β complex, thereby promoting assembly of SGs. These findings suggest a role for Gadd45β as a component and critical regulator of G3BP1-mediated SG formation, which facilitates RLR-mediated interferon signaling.
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Affiliation(s)
- W A Gayan Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Chamilani Nikapitiya
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Jae-Hoon Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea; Livestock Products Analysis Division, Division of Animal Health, Daejeon Metropolitan City Institute of Health and Environment, Daejeon 34146, Republic of Korea
| | - Kiramage Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Asela Weerawardhana
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Niranjan Dodantenna
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Doo-Jin Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Haryoung Poo
- Department of Biomedical Science and Engineering, Konkuk Institute of Technology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jae U Jung
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRRIB), Daejeon 34141, Republic of Korea.
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea.
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6
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Jain A, Govindan R, Berkman A, Luban J, Durham ND, Munro J. Regulation of Ebola GP conformation and membrane binding by the chemical environment of the late endosome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524651. [PMID: 36711925 PMCID: PMC9882366 DOI: 10.1101/2023.01.18.524651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Interaction between the Ebola virus envelope glycoprotein (GP) and the endosomal membrane is an essential step during virus entry into the cell. Acidic pH and Ca2+ have been implicated in mediating the GP-membrane interaction. However, the molecular mechanism by which these environmental factors regulate the conformational changes that enable engagement of GP with the target membrane is unknown. Here, we apply fluorescence correlation spectroscopy (FCS) and single-molecule Forster resonance energy transfer (smFRET) imaging to elucidate how the acidic pH, Ca2+ and anionic phospholipids in the late endosome promote GP-membrane interaction, thereby facilitating virus entry. We find that bis(monoacylglycero)phosphate (BMP), which is specific to the late endosome, is especially critical in determining the Ca2+-dependence of the GP-membrane interaction. Molecular dynamics (MD) simulations suggested residues in GP that sense pH and induce conformational changes that make the fusion loop available for insertion into the membrane. We similarly confirm residues in the fusion loop that mediate GPs interaction with Ca2+, which likely promotes local conformational changes in the fusion loop and mediates electrostatic interactions with the anionic phospholipids. Collectively, our results provide a mechanistic understanding of how the environment of the late endosome regulates the timing and efficiency of virus entry.
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7
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Asrorov AM, Wang H, Zhang M, Wang Y, He Y, Sharipov M, Yili A, Huang Y. Cell penetrating peptides: Highlighting points in cancer therapy. Drug Dev Res 2023; 84:1037-1071. [PMID: 37195405 DOI: 10.1002/ddr.22076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/29/2023] [Indexed: 05/18/2023]
Abstract
Cell-penetrating peptides (CPPs), first identified in HIV a few decades ago, deserved great attention in the last two decades; especially to support the penetration of anticancer drug means. In the drug delivery discipline, they have been involved in various approaches from mixing with hydrophobic drugs to the use of genetically conjugated proteins. The early classification as cationic and amphipathic CPPs has been extended to a few more classes such as hydrophobic and cyclic CPPs so far. Developing potential sequences utilized almost all methods of modern science: choosing high-efficiency peptides from natural protein sequences, sequence-based comparison, amino acid substitution, obtaining chemical and/or genetic conjugations, in silico approaches, in vitro analysis, animal experiments, etc. The bottleneck effect in this discipline reveals the complications that modern science faces in drug delivery research. Most CPP-based drug delivery systems (DDSs) efficiently inhibited tumor volume and weight in mice, but only in rare cases reduced their levels and continued further processes. The integration of chemical synthesis into the development of CPPs made a significant contribution and even reached the clinical stage as a diagnostic tool. But constrained efforts still face serious problems in overcoming biobarriers to reach further achievements. In this work, we reviewed the roles of CPPs in anticancer drug delivery, focusing on their amino acid composition and sequences. As the most suitable point, we relied on significant changes in tumor volume in mice resulting from CPPs. We provide a review of individual CPPs and/or their derivatives in a separate subsection.
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Affiliation(s)
- Akmal M Asrorov
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Institute of Bioorganic Chemistry, AS of Uzbekistan, Tashkent, Uzbekistan
- Department of Natural Substances Chemistry, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Huiyuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Meng Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yonghui Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yang He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Mirkomil Sharipov
- Institute of Bioorganic Chemistry, AS of Uzbekistan, Tashkent, Uzbekistan
| | - Abulimiti Yili
- The Key Laboratory of Plant Resources and Chemistry of Arid Zone, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, Xinjiang, China
| | - Yongzhuo Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Zhongshan Institute for Drug Discovery, Institutes of Drug Discovery and Development, Chinese Academy of Sciences, Zhongshan, China
- NMPA Key Laboratory for Quality Research and Evaluation of Pharmaceutical Excipients, Shanghai, China
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8
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Histidine network regulates the structure-stability features of T7 endolysin native and partially folded conformations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Amara U, Rashid S, Mahmood K, Nawaz MH, Hayat A, Hassan M. Insight into prognostics, diagnostics, and management strategies for SARS CoV-2. RSC Adv 2022; 12:8059-8094. [PMID: 35424750 PMCID: PMC8982343 DOI: 10.1039/d1ra07988c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 02/04/2022] [Indexed: 01/08/2023] Open
Abstract
The foremost challenge in countering infectious diseases is the shortage of effective therapeutics. The emergence of coronavirus disease (COVID-19) outbreak has posed a great menace to the public health system globally, prompting unprecedented endeavors to contain the virus. Many countries have organized research programs for therapeutics and management development. However, the longstanding process has forced authorities to implement widespread infrastructures for detailed prognostic and diagnostics study of severe acute respiratory syndrome (SARS CoV-2). This review discussed nearly all the globally developed diagnostic methodologies reported for SARS CoV-2 detection. We have highlighted in detail the approaches for evaluating COVID-19 biomarkers along with the most employed nucleic acid- and protein-based detection methodologies and the causes of their severe downfall and rejection. As the variable variants of SARS CoV-2 came into the picture, we captured the breadth of newly integrated digital sensing prototypes comprised of plasmonic and field-effect transistor-based sensors along with commercially available food and drug administration (FDA) approved detection kits. However, more efforts are required to exploit the available resources to manufacture cheap and robust diagnostic methodologies. Likewise, the visualization and characterization tools along with the current challenges associated with waste-water surveillance, food security, contact tracing, and their role during this intense period of the pandemic have also been discussed. We expect that the integrated data will be supportive and aid in the evaluation of sensing technologies not only in current but also future pandemics.
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Affiliation(s)
- Umay Amara
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 608000 Pakistan
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Sidra Rashid
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Khalid Mahmood
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 608000 Pakistan
| | - Mian Hasnain Nawaz
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Akhtar Hayat
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad Lahore Campus 54000 Pakistan
| | - Maria Hassan
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan 608000 Pakistan
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10
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Batishchev OV. Physico-Chemical Mechanisms of the Functioning of Membrane-Active Proteins of Enveloped Viruses. BIOCHEMISTRY (MOSCOW) SUPPLEMENT. SERIES A, MEMBRANE AND CELL BIOLOGY 2022; 16:247-260. [PMCID: PMC9734521 DOI: 10.1134/s1990747822050038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/14/2022]
Abstract
Over the past few years, the attention of the whole world has been riveted to the emergence of new dangerous strains of viruses, among which a special place is occupied by coronaviruses that have overcome the interspecies barrier in the past 20 years: SARS viruses (SARS), Middle East respiratory syndrome (MERS), as well as a new coronavirus infection (SARS-CoV-2), which caused the largest pandemic since the Spanish flu in 1918. Coronaviruses are members of a class of enveloped viruses that have a lipoprotein envelope. This class also includes such serious pathogens as human immunodeficiency virus (HIV), hepatitis, Ebola virus, influenza, etc. Despite significant differences in the clinical picture of the course of disease caused by enveloped viruses, they themselves have a number of characteristic features, which determine their commonality. Regardless of the way of penetration into the cell—by endocytosis or direct fusion with the cell membrane—enveloped viruses are characterized by the following stages of interaction with the target cell: binding to receptors on the cell surface, interaction of the surface glycoproteins of the virus with the membrane structures of the infected cell, fusion of the lipid envelope of the virion with plasma or endosomal membrane, destruction of the protein capsid and its dissociation from the viral nucleoprotein. Subsequently, within the infected cell, the newly synthesized viral proteins must self-assemble on various membrane structures to form a progeny virion. Thus, both the initial stages of viral infection and the assembly and release of new viral particles are associated with the activity of viral proteins in relation to the cell membrane and its organelles. This review is devoted to the analysis of physicochemical mechanisms of functioning of the main structural proteins of a number of enveloped viruses in order to identify possible strategies for the membrane activity of such proteins at various stages of viral infection of the cell.
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Affiliation(s)
- O. V. Batishchev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071 Moscow, Russia
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11
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du Preez HN, Aldous C, Hayden MR, Kruger HG, Lin J. Pathogenesis of COVID-19 described through the lens of an undersulfated and degraded epithelial and endothelial glycocalyx. FASEB J 2021; 36:e22052. [PMID: 34862979 DOI: 10.1096/fj.202101100rr] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022]
Abstract
The glycocalyx surrounds every eukaryotic cell and is a complex mesh of proteins and carbohydrates. It consists of proteoglycans with glycosaminoglycan side chains, which are highly sulfated under normal physiological conditions. The degree of sulfation and the position of the sulfate groups mainly determine biological function. The intact highly sulfated glycocalyx of the epithelium may repel severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) through electrostatic forces. However, if the glycocalyx is undersulfated and 3-O-sulfotransferase 3B (3OST-3B) is overexpressed, as is the case during chronic inflammatory conditions, SARS-CoV-2 entry may be facilitated by the glycocalyx. The degree of sulfation and position of the sulfate groups will also affect functions such as immune modulation, the inflammatory response, vascular permeability and tone, coagulation, mediation of sheer stress, and protection against oxidative stress. The rate-limiting factor to sulfation is the availability of inorganic sulfate. Various genetic and epigenetic factors will affect sulfur metabolism and inorganic sulfate availability, such as various dietary factors, and exposure to drugs, environmental toxins, and biotoxins, which will deplete inorganic sulfate. The role that undersulfation plays in the various comorbid conditions that predispose to coronavirus disease 2019 (COVID-19), is also considered. The undersulfated glycocalyx may not only increase susceptibility to SARS-CoV-2 infection, but would also result in a hyperinflammatory response, vascular permeability, and shedding of the glycocalyx components, giving rise to a procoagulant and antifibrinolytic state and eventual multiple organ failure. These symptoms relate to a diagnosis of systemic septic shock seen in almost all COVID-19 deaths. The focus of prevention and treatment protocols proposed is the preservation of epithelial and endothelial glycocalyx integrity.
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Affiliation(s)
- Heidi N du Preez
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Colleen Aldous
- College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Melvin R Hayden
- Division of Endocrinology Diabetes and Metabolism, Department of Internal Medicine, University of Missouri-Columbia School of Medicine, Columbia, Missouri, USA.,Diabetes and Cardiovascular Disease Center, University of Missouri-Columbia School of Medicine, Columbia, Missouri, USA
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Johnson Lin
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
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12
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Kudlacek ST, Metz S, Thiono D, Payne AM, Phan TTN, Tian S, Forsberg LJ, Maguire J, Seim I, Zhang S, Tripathy A, Harrison J, Nicely NI, Soman S, McCracken MK, Gromowski GD, Jarman RG, Premkumar L, de Silva AM, Kuhlman B. Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies. SCIENCE ADVANCES 2021; 7:eabg4084. [PMID: 34652943 PMCID: PMC8519570 DOI: 10.1126/sciadv.abg4084] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 08/25/2021] [Indexed: 05/30/2023]
Abstract
Dengue virus (DENV) is a worldwide health burden, and a safe vaccine is needed. Neutralizing antibodies bind to quaternary epitopes on DENV envelope (E) protein homodimers. However, recombinantly expressed soluble E proteins are monomers under vaccination conditions and do not present these quaternary epitopes, partly explaining their limited success as vaccine antigens. Using molecular modeling, we found DENV2 E protein mutations that induce dimerization at low concentrations (<100 pM) and enhance production yield by more than 50-fold. Cross-dimer epitope antibodies bind to the stabilized dimers, and a crystal structure resembles the wild-type (WT) E protein bound to a dimer epitope antibody. Mice immunized with the stabilized dimers developed antibodies that bind to E dimers and not monomers and elicited higher levels of DENV2-neutralizing antibodies compared to mice immunized with WT E antigen. Our findings demonstrate the feasibility of using structure-based design to produce subunit vaccines for dengue and other flaviviruses.
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Affiliation(s)
- Stephan T. Kudlacek
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Stefan Metz
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Devina Thiono
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Alexander M. Payne
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Thanh T. N. Phan
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Shaomin Tian
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Lawrence J. Forsberg
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Jack Maguire
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Ian Seim
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27514, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC 27514, USA
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Shu Zhang
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Joseph Harrison
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Nathan I. Nicely
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Sandrine Soman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Michael K. McCracken
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Gregory D. Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Richard G. Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Aravinda M. de Silva
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27514, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC 27514, USA
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13
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Alias M, Hamzah S, Saidin J, Yatim NI, Che Harun MH, Wan Mohamad WAF, Hairom NHH, Ali A, Ali N. Integration of hydroxyapatite from fish scales and polyethersulfone membrane for protease separation from Bacillus subtilis. SEP SCI TECHNOL 2021. [DOI: 10.1080/01496395.2021.1948866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Maslinda Alias
- Faculty of Ocean Engineering Technology and Informatics, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Sofiah Hamzah
- Faculty of Ocean Engineering Technology and Informatics, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Jasnizat Saidin
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Norhafiza Ilyana Yatim
- Higher Institution Centre of Excellence (Hicoe), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Mohammad Hakim Che Harun
- Faculty of Ocean Engineering Technology and Informatics, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | | | - Nur Hanis Hayati Hairom
- Microelectronics and Nanotechnology-Shamsuddin Research Center, Institute for Integrated Engineering, Universiti Tun Hussein Onn Malaysia, Batu Pahat, Malaysia
- Faculty of Engineering Technology, Universiti Tun Hussein Onn Malaysia, Muar, Malaysia
| | - Asmadi Ali
- Faculty of Ocean Engineering Technology and Informatics, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Nora’aini Ali
- Faculty of Ocean Engineering Technology and Informatics, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
- Higher Institution Centre of Excellence (Hicoe), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
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14
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Balogh RK, Németh E, Jones NC, Hoffmann SV, Jancsó A, Gyurcsik B. A study on the secondary structure of the metalloregulatory protein CueR: effect of pH, metal ions and DNA. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:491-500. [PMID: 33907862 DOI: 10.1007/s00249-021-01539-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/13/2021] [Accepted: 04/14/2021] [Indexed: 11/30/2022]
Abstract
The response of CueR towards environmental changes in solution was investigated. CueR is a bacterial metal ion selective transcriptional metalloregulator protein, which controls the concentration of copper ions in the cell. Although several articles have been devoted to the discussion of the structural and functional features of this protein, CueR has not previously been extensively characterized in solution. Here, we studied the effect of change in pH, temperature, and the presence of specific or non-specific binding partners on the secondary structure of CueR with circular dichroism (CD) spectroscopy. A rather peculiar reversible pH-dependent secondary structure transformation was observed, elucidated and supplemented with pKa estimation by PROPKA and CpHMD simulations suggesting an important role of His(76) and His(94) in this process. CD experiments revealed that the presence of DNA prevents this structural switch, suggesting that DNA locks CueR in the α-helical-rich form. In contrast to the non-cognate metal ions HgII, CdII and ZnII, the presence of the cognate AgI ion affects the secondary structure of CueR, most probably by stabilizing the metal ion and DNA-binding domains of the protein.
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Affiliation(s)
- Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary.,Institute of Enzymology, Genome Stability Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest, 1117, Hungary
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary.
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15
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Identification of critical amino acid residues in the regulatory N-terminal domain of PMEL. Sci Rep 2021; 11:7730. [PMID: 33833328 PMCID: PMC8032716 DOI: 10.1038/s41598-021-87259-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/26/2021] [Indexed: 01/22/2023] Open
Abstract
The pigment cell-specific protein PMEL forms a functional amyloid matrix in melanosomes onto which the pigment melanin is deposited. The amyloid core consists of a short proteolytic fragment, which we have termed the core-amyloid fragment (CAF) and perhaps additional parts of the protein, such as the PKD domain. A highly O-glycosylated repeat (RPT) domain also derived from PMEL proteolysis associates with the amyloid and is necessary to establish the sheet-like morphology of the assemblies. Excluded from the aggregate is the regulatory N-terminus, which nevertheless must be linked in cis to the CAF in order to drive amyloid formation. The domain is then likely cleaved away immediately before, during, or immediately after the incorporation of a new CAF subunit into the nascent amyloid. We had previously identified a 21 amino acid long region, which mediates the regulatory activity of the N-terminus towards the CAF. However, many mutations in the respective segment caused misfolding and/or blocked PMEL export from the endoplasmic reticulum, leaving their phenotype hard to interpret. Here, we employ a saturating mutagenesis approach targeting the motif at single amino acid resolution. Our results confirm the critical nature of the PMEL N-terminal region and identify several residues essential for PMEL amyloidogenesis.
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16
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Shevel E. Conditions Favoring Increased COVID-19 Morbidity and Mortality: Their Common Denominator and its Early Treatment. MISSOURI MEDICINE 2021; 118:113-115. [PMID: 33840847 PMCID: PMC8029622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The factors contributing to increased morbidity and mortality in SARS-CoV-2 infection are diverse, and include diabetes, obesity, Chronic Obstructive Pulmonary Disease (COPD), advanced age, and male sex. Although there is no obvious connection between these, they do have one common denominator-they all have a tendency towards lower urine pH, which may indicate a lower-than-normal tissue pH. Furthermore, it has been shown that lower pH has two important negative influences: 1) it enhances viral fusion via the endosomal route, thereby facilitating viral multiplication; and 2) it facilitates increased production of inflammatory cytokines, thereby exacerbating the cytokine storm. This paper discusses published literature on lower tissue/interstitial pH in those diseases/co-morbidities that are known risk factors of severe COVID-19, and hypothesize that small doses of baking soda could be a simple, cost-effective, and rapid method of reducing both morbidity and mortality in COVID-19 patients.
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Affiliation(s)
- Eliot Shevel
- Head of the South African Headache Society, the South African affiliate of the International Headache Society. He is founder and practices at The Headache Clinic in Johannesburg, South Africa
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17
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Santoro AM, Zimbone S, Magrì A, La Mendola D, Grasso G. The Role of Copper (II) on Kininogen Binding to Tropomyosin in the Presence of a Histidine-Proline-Rich Peptide. Int J Mol Sci 2020; 21:ijms21249343. [PMID: 33302425 PMCID: PMC7762548 DOI: 10.3390/ijms21249343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022] Open
Abstract
The antiangiogenic activity of the H/P domain of histidine-proline-rich glycoprotein is mediated by its binding with tropomyosin, a protein exposed on endothelial cell-surface during the angiogenic switch, in presence of zinc ions. Although it is known that copper ion serum concentration is significantly increased in cancer patients, its role in the interaction of H/P domain with tropomyosin, has not yet been studied. In this paper, by using ELISA assay, we determined the modulating effect of TetraHPRG peptide, a sequence of 20 aa belonging to H/P domain, on the binding of Kininogen (HKa) with tropomyosin, both in absence and presence of copper and zinc ions. A potentiometric study was carried out to characterize the binding mode adopted by metal ions with TetraHPRG, showing the formation of complex species involving imidazole amide nitrogen atoms in metal binding. Moreover, circular dichroism showed a conformational modification of ternary systems formed by TetraHPRG, HKa and copper or zinc. Interestingly, slight pH variation influenced the HKa-TetraHPRG-tropomyosin binding. All these results indicate that both metal ions are crucial in the interaction between TetraHPRG, tropomyosin and HKa.
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Affiliation(s)
- Anna Maria Santoro
- CNR Istituto di Cristallografia Sede Secondaria di Catania, Via Gaifami 18, 95126 Catania, Italy; (A.M.S.); (S.Z.); (A.M.)
| | - Stefania Zimbone
- CNR Istituto di Cristallografia Sede Secondaria di Catania, Via Gaifami 18, 95126 Catania, Italy; (A.M.S.); (S.Z.); (A.M.)
| | - Antonio Magrì
- CNR Istituto di Cristallografia Sede Secondaria di Catania, Via Gaifami 18, 95126 Catania, Italy; (A.M.S.); (S.Z.); (A.M.)
| | - Diego La Mendola
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy
- Correspondence: (D.L.M.); (G.G.)
| | - Giulia Grasso
- CNR Istituto di Cristallografia Sede Secondaria di Catania, Via Gaifami 18, 95126 Catania, Italy; (A.M.S.); (S.Z.); (A.M.)
- Correspondence: (D.L.M.); (G.G.)
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18
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Unravelling the mechanism of pH-regulation in dinoflagellate luciferase. Int J Biol Macromol 2020; 164:2671-2680. [PMID: 32822730 DOI: 10.1016/j.ijbiomac.2020.08.071] [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: 06/26/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 10/23/2022]
Abstract
Dinoflagellates are the dominant source of bioluminescence in coastal waters. The luminescence reaction involves the oxidation of luciferin by a luciferase enzyme, which only takes place at low pH. The pH-dependence has previously been linked to four conserved histidines. It has been suggested that their protonation might induce a conformational change in the enzyme, thereby allowing substrate access to the binding pocket. Yet, the precise mechanism of luciferase activation has remained elusive. Here, we use computational tools to predict the open structure of the luciferase in Lingulodinium polyedra and to decipher the nature of the opening mechanism. Through accelerated molecular dynamics simulations, we demonstrate that the closed-open conformational change likely takes place via a tilt of the pH-regulatory helix-loop-helix domain. Moreover, we propose that the molecular basis for the transition is electrostatic repulsion between histidine-cation pairs, which destabilizes the closed conformation at low pH. Finally, by simulating truncated mutants, we show that eliminating the C-terminus alters the shape of the active site, effectively inactivating the luciferase.
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19
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Bhalla N, Pan Y, Yang Z, Payam AF. Opportunities and Challenges for Biosensors and Nanoscale Analytical Tools for Pandemics: COVID-19. ACS NANO 2020; 14:7783-7807. [PMID: 32551559 PMCID: PMC7319134 DOI: 10.1021/acsnano.0c04421] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/18/2020] [Indexed: 05/05/2023]
Abstract
Biosensors and nanoscale analytical tools have shown huge growth in literature in the past 20 years, with a large number of reports on the topic of 'ultrasensitive', 'cost-effective', and 'early detection' tools with a potential of 'mass-production' cited on the web of science. Yet none of these tools are commercially available in the market or practically viable for mass production and use in pandemic diseases such as coronavirus disease 2019 (COVID-19). In this context, we review the technological challenges and opportunities of current bio/chemical sensors and analytical tools by critically analyzing the bottlenecks which have hindered the implementation of advanced sensing technologies in pandemic diseases. We also describe in brief COVID-19 by comparing it with other pandemic strains such as that of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) for the identification of features that enable biosensing. Moreover, we discuss visualization and characterization tools that can potentially be used not only for sensing applications but also to assist in speeding up the drug discovery and vaccine development process. Furthermore, we discuss the emerging monitoring mechanism, namely wastewater-based epidemiology, for early warning of the outbreak, focusing on sensors for rapid and on-site analysis of SARS-CoV2 in sewage. To conclude, we provide holistic insights into challenges associated with the quick translation of sensing technologies, policies, ethical issues, technology adoption, and an overall outlook of the role of the sensing technologies in pandemics.
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Affiliation(s)
- Nikhil Bhalla
- Nanotechnology
and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37
0QB Jordanstown, Northern Ireland, United Kingdom
- Healthcare
Technology Hub, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern
Ireland, United Kingdom
| | - Yuwei Pan
- Cranfield
Water Science Institute, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Zhugen Yang
- Cranfield
Water Science Institute, Cranfield University, Cranfield, Bedfordshire MK43 0AL, United Kingdom
| | - Amir Farokh Payam
- Nanotechnology
and Integrated Bioengineering Centre (NIBEC), School of Engineering, Ulster University, Shore Road, BT37
0QB Jordanstown, Northern Ireland, United Kingdom
- Healthcare
Technology Hub, Ulster University, Shore Road, BT37 0QB Jordanstown, Northern
Ireland, United Kingdom
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20
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Akimov SA, Molotkovsky RJ, Kuzmin PI, Galimzyanov TR, Batishchev OV. Continuum Models of Membrane Fusion: Evolution of the Theory. Int J Mol Sci 2020; 21:E3875. [PMID: 32485905 PMCID: PMC7312925 DOI: 10.3390/ijms21113875] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/24/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
Starting from fertilization, through tissue growth, hormone secretion, synaptic transmission, and sometimes morbid events of carcinogenesis and viral infections, membrane fusion regulates the whole life of high organisms. Despite that, a lot of fusion processes still lack well-established models and even a list of main actors. A merger of membranes requires their topological rearrangements controlled by elastic properties of a lipid bilayer. That is why continuum models based on theories of membrane elasticity are actively applied for the construction of physical models of membrane fusion. Started from the view on the membrane as a structureless film with postulated geometry of fusion intermediates, they developed along with experimental and computational techniques to a powerful tool for prediction of the whole process with molecular accuracy. In the present review, focusing on fusion processes occurring in eukaryotic cells, we scrutinize the history of these models, their evolution and complication, as well as open questions and remaining theoretical problems. We show that modern approaches in this field allow continuum models of membrane fusion to stand shoulder to shoulder with molecular dynamics simulations, and provide the deepest understanding of this process in multiple biological systems.
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Affiliation(s)
- Sergey A. Akimov
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia; (R.J.M.); (P.I.K.); (T.R.G.); (O.V.B.)
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21
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Watanabe H, Yoshida C, Ooishi A, Nakai Y, Ueda M, Isobe Y, Honda S. Histidine-Mediated Intramolecular Electrostatic Repulsion for Controlling pH-Dependent Protein-Protein Interaction. ACS Chem Biol 2019; 14:2729-2736. [PMID: 31596562 DOI: 10.1021/acschembio.9b00652] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein-protein interactions that can be controlled by environmental triggers have immense potential in various biological and industrial applications. In the current study, we aimed to engineer a pH-dependent protein-protein interaction that employs intramolecular electrostatic repulsion through a structure-guided histidine substitution approach. We implemented this strategy on Streptococcal protein G, an affinity ligand for immunoglobulin G, and showed that even a single point mutation effectively improved the pH sensitivity of the binding interactions without adversely affecting its structural stability or its innate binding function. Depending on the pH of the environment, the protein-protein interaction was disrupted by the electrostatic repulsion between the substituted histidine and its neighboring positively charged residues. Structurally, the substituted histidine residue was located adjacent to a lysine residue that could form hydrogen bonds with immunoglobulin G. Thermodynamically, the introduced electrostatic repulsion was reflected in the significant loss of the exothermic heat of the binding under acidic conditions, whereas accompanying enthalpy-entropy compensation partly suppressed the improvement of the pH sensitivity. Thus, the engineered pH-sensitive protein G could enable antibody purification under mildly acidic conditions. This intramolecular design can be combined with conventional protein-protein interface design. Moreover, the method proposed here provides us with additional design criteria for optimization of pH-dependent molecular interactions.
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Affiliation(s)
- Hideki Watanabe
- The National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba 305-8566, Japan
| | - Chuya Yoshida
- The National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba 305-8566, Japan
| | - Ayako Ooishi
- The National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba 305-8566, Japan
| | - Yasuto Nakai
- Daicel Corporation, Innovation Park, 1239, Shinzaike, Aboshi, Himeji, Hyogo 671-1283, Japan
| | - Momoko Ueda
- Daicel Corporation, Innovation Park, 1239, Shinzaike, Aboshi, Himeji, Hyogo 671-1283, Japan
| | - Yutaka Isobe
- Daicel Corporation, Innovation Park, 1239, Shinzaike, Aboshi, Himeji, Hyogo 671-1283, Japan
| | - Shinya Honda
- The National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba 305-8566, Japan
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22
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Liu N, Girvin ME, Brenowitz M, Lai JR. Conformational and lipid bilayer-perturbing properties of Marburg virus GP2 segments containing the fusion loop and membrane-proximal external region/transmembrane domain. Heliyon 2019; 5:e03018. [PMID: 31890962 PMCID: PMC6926192 DOI: 10.1016/j.heliyon.2019.e03018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 11/04/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
Fusion of host and viral membranes is a crucial step during infection by enveloped viruses. In the structurally-defined "class I″ viral glycoproteins, the formation of a highly stable α-helical bundle by the ectodomain of the fusion subunit (e.g., GP2 for Marburg virus, MARV) is postulated to provide the energetic driving force to overcome barriers associated with membrane fusion. Upon cell binding, the fusion subunit is proposed to form an extended intermediate that bridges both the viral and host membranes, and collapse of this extended intermediate brings the two membranes into proximity. While there is much high-resolution structural data available for prefusion and post-fusion structures of viral glycoproteins, little information is available about intermediate conformations especially in the context of the fusion loop/peptide (FL or FP) and membrane-proximal external region (MPER)/transmembrane (TM) segments. We present structural and functional studies on segments of MARV GP2 that encompass the FL and MPER/TM in detergent micelles and lipid bicelles. A protein that contains most elements of GP2 ("MGP2-full") is α-helical in membrane-mimicking environments and has pH-dependent membrane lytic activity. MGP2-full is monomeric under such conditions, contrasting with the trimeric species that has been described previously for MARV GP2 ectodomain in aqueous buffer. Variants of MARV GP2 containing the N- and C-terminal halves ("MGP2-FNL" and "MGP2-CMT", respectively) have similar properties. This work provides novel insight into conformational and membrane-perturbing properties of the MARV fusion subunit and how they may relate to viral membrane fusion.
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Affiliation(s)
- Nina Liu
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Mark E Girvin
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.,Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jonathan R Lai
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
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23
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Antanasijevic A, Durst MA, Lavie A, Caffrey M. Identification of a pH sensor in Influenza hemagglutinin using X-ray crystallography. J Struct Biol 2019; 209:107412. [PMID: 31689502 PMCID: PMC7111647 DOI: 10.1016/j.jsb.2019.107412] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 11/15/2022]
Abstract
X-ray crystallography identifies a conserved histidine, HA1-H38, that changes side chain conformation at low pH. We attribute the observed conformational change to cation-cation repulsion between protonated HA1-H18 and HA1-H38. We suggest that the HA1-H18 and HA1-H38 pair plays a role in the pathway toward the postfusion conformation of HA.
Hemagglutnin (HA) mediates entry of influenza virus through a series of conformational changes triggered by the low pH of the endosome. The residue or combination of residues acting as pH sensors has not yet been fully elucidated. In this work, we assay pH effects on the structure of H5 HA by soaking HA crystallized at pH 6.5 in a series of buffers with lower pH, mimicking the conditions of the endosome. We find that HA1-H38, which is conserved in Group 1 HA, undergoes a striking change in side chain conformation, which we attribute to its protonation and cation-cation repulsion with conserved HA1-H18. This work suggests that x-ray crystallography can be applied for studying small-scale pH-induced conformational changes providing valuable information on the location of pH sensors in HA. Importantly, the observed change in HA1-H38 conformation is further evidence that the pH-induced conformational changes of HA are the result of a series of protonation events to conserved and non-conserved pH sensors.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, 60607 Chicago, USA
| | - Matthew A Durst
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, 60607 Chicago, USA
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, 60607 Chicago, USA.
| | - Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Ave, 60607 Chicago, USA.
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24
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Leidreiter F, Roderer D, Meusch D, Gatsogiannis C, Benz R, Raunser S. Common architecture of Tc toxins from human and insect pathogenic bacteria. SCIENCE ADVANCES 2019; 5:eaax6497. [PMID: 31663026 PMCID: PMC6795518 DOI: 10.1126/sciadv.aax6497] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution structures of TcAs from different bacteria suggest a considerable difference in their architecture and possibly in their mechanism of action. Here, we present high-resolution structures of five TcAs from insect and human pathogens, which show a similar overall composition and domain organization. Essential structural features, including a trefoil protein knot, are present in all TcAs, suggesting a common mechanism of action. All TcAs form functional pores and can be combined with TcB-TcC subunits from other species to form active chimeric holotoxins. We identified a conserved ionic pair that stabilizes the shell, likely operating as a strong latch that only springs open after destabilization of other regions. Our results provide new insights into the architecture and mechanism of the Tc toxin family.
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Affiliation(s)
- F. Leidreiter
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - D. Roderer
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - D. Meusch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - C. Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - R. Benz
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campusring 1, 28759 Bremen, Germany
| | - S. Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
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25
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Li Y, Wu X, Zhu Q, Chen Z, Lu Y, Qi J, Wu W. Improving the hypoglycemic effect of insulin via the nasal administration of deep eutectic solvents. Int J Pharm 2019; 569:118584. [PMID: 31376466 DOI: 10.1016/j.ijpharm.2019.118584] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/30/2019] [Accepted: 07/30/2019] [Indexed: 02/06/2023]
Abstract
This study aimed to develop biocompatible deep eutectic solvents (DESs) as carriers for improving the nasal delivery of insulin. The DES was prepared from malic acid and choline chloride broadly used in foods, drugs, or cosmetics as biocompatible additives. The DES of choline chloride and malic acid (CM-DES) demonstrated lower melting point (-59.1 °C) and higher viscosity (120,000 cP) compared with hydrogels based on sodium carboxyl methyl cellulose (CMC-Na). The conformational structure of insulin does not change in CM-DES as characterized by circular dichroism. The in vitro results showed that CM-DES dissociated gradually but did not disintegrate immediately upon contact with water. CM-DES was able to improve the hypoglycemic effect of insulin significantly at different doses compared with hydrogels or solutions of insulin, which could be ascribed to facilitated penetration of insulin across the nasal epithelia by CM-DES. The hypoglycemic effect of CM-DES loading insulin at a dose of 25 IU/kg was similar to that of subcutaneous insulin at 1 IU/kg. In addition, no evident toxicity to nasal epithelia was observed after nasal administration to rats for seven consecutive days. In conclusion, CM-DES showed promising potential in enhancing the hypoglycemic effect of insulin via the nasal route.
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Affiliation(s)
- Yang Li
- Key Laboratory of Smart Drug Delivery of MOE, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Xiying Wu
- Shanghai Dermatology Hospital, Shanghai 200443, PR China
| | - Quangang Zhu
- Shanghai Dermatology Hospital, Shanghai 200443, PR China
| | - Zhongjian Chen
- Shanghai Dermatology Hospital, Shanghai 200443, PR China
| | - Yi Lu
- Key Laboratory of Smart Drug Delivery of MOE, School of Pharmacy, Fudan University, Shanghai 201203, PR China; Shanghai Dermatology Hospital, Shanghai 200443, PR China
| | - Jianping Qi
- Shanghai Dermatology Hospital, Shanghai 200443, PR China; Key Laboratory of Smart Drug Delivery of MOE, School of Pharmacy, Fudan University, Shanghai 201203, PR China.
| | - Wei Wu
- Key Laboratory of Smart Drug Delivery of MOE, School of Pharmacy, Fudan University, Shanghai 201203, PR China; Shanghai Dermatology Hospital, Shanghai 200443, PR China
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26
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Chang HW, Yang CH, Luo YC, Su BG, Cheng HY, Tung SY, Carillo KJD, Liao YT, Tzou DLM, Wang HC, Chang W. Vaccinia viral A26 protein is a fusion suppressor of mature virus and triggers membrane fusion through conformational change at low pH. PLoS Pathog 2019; 15:e1007826. [PMID: 31220181 PMCID: PMC6605681 DOI: 10.1371/journal.ppat.1007826] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/02/2019] [Accepted: 05/07/2019] [Indexed: 11/24/2022] Open
Abstract
Vaccinia mature virus requires A26 envelope protein to mediate acid-dependent endocytosis into HeLa cells in which we hypothesized that A26 protein functions as an acid-sensitive membrane fusion suppressor. Here, we provide evidence showing that N-terminal domain (aa1-75) of A26 protein is an acid-sensitive region that regulates membrane fusion. Crystal structure of A26 protein revealed that His48 and His53 are in close contact with Lys47, Arg57, His314 and Arg312, suggesting that at low pH these His-cation pairs could initiate conformational changes through protonation of His48 and His53 and subsequent electrostatic repulsion. All the A26 mutant mature viruses that interrupted His-cation pair interactions of His48 and His 53 indeed have lost virion infectivity. Isolation of revertant viruses revealed that second site mutations caused frame shifts and premature termination of A26 protein such that reverent viruses regained cell entry through plasma membrane fusion. Together, we conclude that viral A26 protein functions as an acid-sensitive fusion suppressor during vaccinia mature virus endocytosis. Vaccinia virus is a complex large DNA virus with a large number of viral membrane proteins to facilitate cell entry. Although it is well established that vaccinia mature virus uses endocytosis to enter cells, it remains unclear how it triggers membrane fusion in the acidic environment of endosomes. Recently, we hypothesized that A26 protein in vaccinia mature virus functions as an acid-sensitive membrane fusion suppressor, which suggests a novel viral regulation not present in other enveloped viruses. We postulated that conformational changes of A26 protein at low pH result in de-repression of viral fusion complex activity to trigger viral and endosomal membrane fusion. Here, we provide structural, biochemical and biological evidence demonstrating that vaccinia A26 protein does indeed function as an acid-sensitive fusion suppressor protein to regulate vaccinia mature virus membrane fusion during endocytosis. Our data reveal an important and unique “checkpoint” for vaccinia mature virus endocytosis that has not been described for other viruses. Furthermore, by isolating adaptive vaccinia mutants that escaped endocytic blockage, we discovered that mutations within the A26L gene serve as an effective strategy for switching the viral infection route from endocytosis to plasma membrane fusion, expanding viral host range.
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Affiliation(s)
- Hung-Wei Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Cheng-Han Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chun Luo
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Bo-Gang Su
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Huei-Yin Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Yun Tung
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Kathleen Joyce D. Carillo
- Sustainable Chemical Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, Taiwan
| | - Yi-Ting Liao
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan
| | - Der-Lii M. Tzou
- Sustainable Chemical Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Department of Applied Chemistry, National Chia-Yi University, Chia-Yi, Taiwan
| | - Hao-Ching Wang
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taiwan
- * E-mail: (HCW); (WC)
| | - Wen Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- * E-mail: (HCW); (WC)
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27
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Unraveling the differential structural stability and dynamics features of T7 endolysin partially folded conformations. Biochim Biophys Acta Gen Subj 2018; 1862:924-935. [DOI: 10.1016/j.bbagen.2018.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 01/03/2018] [Accepted: 01/08/2018] [Indexed: 01/21/2023]
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28
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Zhou HX, Pang X. Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation. Chem Rev 2018; 118:1691-1741. [PMID: 29319301 DOI: 10.1021/acs.chemrev.7b00305] [Citation(s) in RCA: 490] [Impact Index Per Article: 81.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago , Chicago, Illinois 60607, United States.,Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
| | - Xiaodong Pang
- Department of Physics and Institute of Molecular Biophysics, Florida State University , Tallahassee, Florida 32306, United States
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29
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Lošdorfer Božič A, Podgornik R. pH Dependence of Charge Multipole Moments in Proteins. Biophys J 2017; 113:1454-1465. [PMID: 28978439 DOI: 10.1016/j.bpj.2017.08.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 11/26/2022] Open
Abstract
Electrostatic interactions play a fundamental role in the structure and function of proteins. Due to ionizable amino acid residues present on the solvent-exposed surfaces of proteins, the protein charge is not constant but varies with the changes in the environment-most notably, the pH of the surrounding solution. We study the effects of pH on the charge of four globular proteins by expanding their surface charge distributions in terms of multipoles. The detailed representation of the charges on the proteins is in this way replaced by the magnitudes and orientations of the multipole moments of varying order. Focusing on the three lowest-order multipoles-the total charge, dipole, and quadrupole moment-we show that the value of pH influences not only their magnitudes, but more notably and importantly also the spatial orientation of their principal axes. Our findings imply important consequences for the study of protein-protein interactions and the assembly of both proteinaceous shells and patchy colloids with dissociable charge groups.
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Affiliation(s)
| | - Rudolf Podgornik
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia
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30
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Battles MB, Más V, Olmedillas E, Cano O, Vázquez M, Rodríguez L, Melero JA, McLellan JS. Structure and immunogenicity of pre-fusion-stabilized human metapneumovirus F glycoprotein. Nat Commun 2017; 8:1528. [PMID: 29142300 PMCID: PMC5688127 DOI: 10.1038/s41467-017-01708-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/06/2017] [Indexed: 01/10/2023] Open
Abstract
Human metapneumovirus (hMPV) is a frequent cause of bronchiolitis in young children. Its F glycoprotein mediates virus-cell membrane fusion and is the primary target of neutralizing antibodies. The inability to produce recombinant hMPV F glycoprotein in the metastable pre-fusion conformation has hindered structural and immunological studies. Here, we engineer a pre-fusion-stabilized hMPV F ectodomain and determine its crystal structure to 2.6 Å resolution. This structure reveals molecular determinants of strain-dependent acid-induced fusion, as well as insights into refolding from pre- to post-fusion conformations. A dense glycan shield at the apex of pre-fusion hMPV F suggests that antibodies against this site may not be elicited by host immune responses, which is confirmed by depletion studies of human immunoglobulins and by mouse immunizations. This is a major difference with pre-fusion F from human respiratory syncytial virus (hRSV), and collectively our results should facilitate development of effective hMPV vaccine candidates.
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Affiliation(s)
- Michael B Battles
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Vicente Más
- Unidad de Biología Viral, Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - Eduardo Olmedillas
- Unidad de Biología Viral, Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - Olga Cano
- Unidad de Biología Viral, Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - Mónica Vázquez
- Unidad de Biología Viral, Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220, Madrid, Spain
| | - Laura Rodríguez
- Unidad de Biología Viral, Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220, Madrid, Spain.,University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - José A Melero
- Unidad de Biología Viral, Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28220, Madrid, Spain.
| | - Jason S McLellan
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
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31
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Roedig P, Ginn HM, Pakendorf T, Sutton G, Harlos K, Walter TS, Meyer J, Fischer P, Duman R, Vartiainen I, Reime B, Warmer M, Brewster AS, Young ID, Michels-Clark T, Sauter NK, Kotecha A, Kelly J, Rowlands DJ, Sikorsky M, Nelson S, Damiani DS, Alonso-Mori R, Ren J, Fry EE, David C, Stuart DI, Wagner A, Meents A. High-speed fixed-target serial virus crystallography. Nat Methods 2017; 14:805-810. [PMID: 28628129 PMCID: PMC5588887 DOI: 10.1038/nmeth.4335] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/15/2017] [Indexed: 12/19/2022]
Abstract
We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.
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Affiliation(s)
- Philip Roedig
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Helen M. Ginn
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Tim Pakendorf
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Geoff Sutton
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Karl Harlos
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Thomas S. Walter
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jan Meyer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Pontus Fischer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Ramona Duman
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Ismo Vartiainen
- Institute of Photonics, University of Eastern Finland, Joensuu, Finland
| | - Bernd Reime
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Martin Warmer
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Iris D. Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - James Kelly
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- The Pirbright Institute, Pirbright, United Kingdom
| | - David J. Rowlands
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Marcin Sikorsky
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Silke Nelson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Daniel S. Damiani
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jingshan Ren
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elizabeth E. Fry
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - David I. Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Armin Wagner
- Diamond Light Source Limited, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Alke Meents
- Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
- Center for Free Electron Laser Science (CFEL), Hamburg, Germany
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32
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Di Lella S, Herrmann A, Mair CM. Modulation of the pH Stability of Influenza Virus Hemagglutinin: A Host Cell Adaptation Strategy. Biophys J 2017; 110:2293-2301. [PMID: 27276248 DOI: 10.1016/j.bpj.2016.04.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 03/15/2016] [Accepted: 04/25/2016] [Indexed: 12/31/2022] Open
Abstract
Proteins undergo dynamic structural changes to function within the range of physical and chemical conditions of their microenvironments. Changes in these environments affect their activity unless the respective mutations preserve their proper function. Here, we examine the influenza A virus spike protein hemagglutinin (HA), which undergoes a dynamic conformational change that is essential to the viral life cycle and is dependent on endosomal pH. Since the cells of different potential hosts exhibit different levels of pH, the virus can only cross species barriers if HA undergoes mutations that still permit the structural change to occur. This key event occurs after influenza A enters the host cell via the endocytic route, during its intracellular transport inside endosomes. The acidic pH inside these vesicles triggers a major structural transition of HA that induces fusion of the viral envelope and the endosomal membrane, and permits the release of the viral genome. HA experiences specific mutations that alter its pH stability and allow the conformational changes required for fusion in different hosts, despite the differences in the degree of acidification of their endosomes. Experimental and theoretical studies over the past few years have provided detailed insights into the structural aspects of the mutational changes that alter its susceptibility to different pH thresholds. We will illustrate how such mutations modify the protein's structure and consequently its pH stability. These changes make HA an excellent model of the way subtle structural modifications affect a protein's stability and enable it to function in diverse environments.
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Affiliation(s)
- Santiago Di Lella
- Institute of Biology, Humboldt Universität zu Berlin, Berlin, Germany; Departamento de Química Biológica e IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Andreas Herrmann
- Institute of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Caroline M Mair
- Institute of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
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33
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Structure of the infectious salmon anemia virus receptor complex illustrates a unique binding strategy for attachment. Proc Natl Acad Sci U S A 2017; 114:E2929-E2936. [PMID: 28320973 DOI: 10.1073/pnas.1617993114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Orthomyxoviruses are an important family of RNA viruses, which include the various influenza viruses. Despite global efforts to eradicate orthomyxoviral pathogens, these infections remain pervasive. One such orthomyxovirus, infectious salmon anemia virus (ISAV), spreads easily throughout farmed and wild salmonids, constituting a significant economic burden. ISAV entry requires the interplay of the virion-attached hemagglutinin-esterase and fusion glycoproteins. Preventing infections will rely on improved understanding of ISAV entry. Here, we present the crystal structures of ISAV hemagglutinin-esterase unbound and complexed with receptor. Several distinctive features observed in ISAV HE are not seen in any other viral glycoprotein. The structures reveal a unique mode of receptor binding that is dependent on the oligomeric assembly of hemagglutinin-esterase. Importantly, ISAV hemagglutinin-esterase receptor engagement does not initiate conformational rearrangements, suggesting a distinct viral entry mechanism. This work improves our understanding of ISAV pathogenesis and expands our knowledge on the overall diversity of viral glycoprotein-mediated entry mechanisms. Finally, it provides an atomic-resolution model of the primary neutralizing antigen critical for vaccine development.
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34
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Knowledge-based entropies improve the identification of native protein structures. Proc Natl Acad Sci U S A 2017; 114:2928-2933. [PMID: 28265078 DOI: 10.1073/pnas.1613331114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Evaluating protein structures requires reliable free energies with good estimates of both potential energies and entropies. Although there are many demonstrated successes from using knowledge-based potential energies, computing entropies of proteins has lagged far behind. Here we take an entirely different approach and evaluate knowledge-based conformational entropies of proteins based on the observed frequencies of contact changes between amino acids in a set of 167 diverse proteins, each of which has two alternative structures. The results show that charged and polar interactions break more often than hydrophobic pairs. This pattern correlates strongly with the average solvent exposure of amino acids in globular proteins, as well as with polarity indices and the sizes of the amino acids. Knowledge-based entropies are derived by using the inverse Boltzmann relationship, in a manner analogous to the way that knowledge-based potentials have been extracted. Including these new knowledge-based entropies almost doubles the performance of knowledge-based potentials in selecting the native protein structures from decoy sets. Beyond the overall energy-entropy compensation, a similar compensation is seen for individual pairs of interacting amino acids. The entropies in this report have immediate applications for 3D structure prediction, protein model assessment, and protein engineering and design.
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35
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Davey RA, Shtanko O, Anantpadma M, Sakurai Y, Chandran K, Maury W. Mechanisms of Filovirus Entry. Curr Top Microbiol Immunol 2017; 411:323-352. [PMID: 28601947 DOI: 10.1007/82_2017_14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Filovirus entry into cells is complex, perhaps as complex as any viral entry mechanism identified to date. However, over the past 10 years, the important events required for filoviruses to enter into the endosomal compartment and fuse with vesicular membranes have been elucidated (Fig. 1). Here, we highlight the important steps that are required for productive entry of filoviruses into mammalian cells.
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Affiliation(s)
- R A Davey
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - O Shtanko
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - M Anantpadma
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Y Sakurai
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - K Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - W Maury
- Department of Microbiology, The University of Iowa, Iowa City, IA, USA.
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36
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Hanč P, Schulz O, Fischbach H, Martin SR, Kjær S, Reis e Sousa C. A pH- and ionic strength-dependent conformational change in the neck region regulates DNGR-1 function in dendritic cells. EMBO J 2016; 35:2484-2497. [PMID: 27753620 PMCID: PMC5109244 DOI: 10.15252/embj.201694695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 08/18/2016] [Accepted: 09/15/2016] [Indexed: 12/30/2022] Open
Abstract
DNGR-1 is receptor expressed by certain dendritic cell (DC) subsets and by DC precursors in mouse. It possesses a C-type lectin-like domain (CTLD) followed by a poorly characterized neck region coupled to a transmembrane region and short intracellular tail. The CTLD of DNGR-1 binds F-actin exposed by dead cell corpses and causes the receptor to signal and potentiate cross-presentation of dead cell-associated antigens by DCs. Here, we describe a conformational change that occurs in the neck region of DNGR-1 in a pH- and ionic strength-dependent manner and that controls cross-presentation of dead cell-associated antigens. We identify residues in the neck region that, when mutated, lock DNGR-1 in one of the two conformational states to potentiate cross-presentation. In contrast, we show that chimeric proteins in which the neck region of DNGR-1 is replaced by that of unrelated C-type lectin receptors fail to promote cross-presentation. Our results suggest that the neck region of DNGR-1 is an integral receptor component that senses receptor progression through the endocytic pathway and has evolved to maximize extraction of antigens from cell corpses, coupling DNGR-1 function to its cellular localization.
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Affiliation(s)
- Pavel Hanč
- Immunobiology Laboratory, The Francis Crick Institute, London, UK
| | - Oliver Schulz
- Immunobiology Laboratory, The Francis Crick Institute, London, UK
| | - Hanna Fischbach
- Immunobiology Laboratory, The Francis Crick Institute, London, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Svend Kjær
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
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37
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Mutational analysis of hepatitis B virus pre-S1 (9-24) fusogenic peptide. Biochem Biophys Res Commun 2016; 474:406-412. [PMID: 27120459 DOI: 10.1016/j.bbrc.2016.04.125] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 04/23/2016] [Indexed: 12/31/2022]
Abstract
A hollow nanoparticle known as a bio-nanocapsule (BNC) consisting of hepatitis B virus (HBV) envelope L protein and liposome (LP) can encapsulate drugs and genes and thereby deliver them in vitro and in vivo to human hepatic tissues, specifically by utilizing the HBV-derived infection machinery. Recently, we identified a low pH-dependent fusogenic domain at the N-terminal part of the pre-S1 region of the HBV L protein (amino acid residues 9 to 24; NPLGFFPDHQLDPAFG), which shows membrane destabilizing activity (i.e., membrane fusion, membrane disruption, and payload release) upon interaction with target LPs. In this study, instead of BNC and HBV, we generated LPs displaying a mutated form of the pre-S1 (9-24) peptide, and performed a membrane disruption assay using target LPs containing pyranine (fluorophore) and p-xylene-bis (N-pyridinium bromide) (DPX) as a quencher. The membrane disruption activity was found to correlate with the hydrophobicity of the whole structure, while the peptide retained a random-coil structure even under low pH condition. One large hydrophobic cluster (I) and one small hydrophobic cluster (II) residing in the peptide would be connected by the protonation of residues D16 and D20, and thereby exhibit strong membrane disruption activity in a low pH-dependent manner. Furthermore, the introduction of a positively charged residue enhanced the activity significantly, suggesting that a sole positively charged residue (H17) may be important for the interaction with target LPs by electrostatic interaction. Collectively, these results suggest that the pre-S1 (9-24) peptide may be involved in the endosomal escape of the BNC's payloads, as well as in the HBV uncoating process.
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38
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Lee J, Gregory SM, Nelson EA, White JM, Tamm LK. The Roles of Histidines and Charged Residues as Potential Triggers of a Conformational Change in the Fusion Loop of Ebola Virus Glycoprotein. PLoS One 2016; 11:e0152527. [PMID: 27023721 PMCID: PMC4811418 DOI: 10.1371/journal.pone.0152527] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/15/2016] [Indexed: 11/23/2022] Open
Abstract
Ebola virus (EBOV) enters cells from late endosomes/lysosomes under mildly acidic conditions. Entry by fusion with the endosomal membrane requires the fusion loop (FL, residues 507–560) of the EBOV surface glycoprotein to undergo a pH-dependent conformational change. To find the pH trigger for this reaction we mutated multiple conserved histidines and charged and uncharged hydrophilic residues in the FL and measured their activity by liposome fusion and cell entry of virus-like particles. The FL location in the membrane was assessed by NMR using soluble and lipid-bound paramagnetic relaxation agents. While we could not identify a single residue to be alone responsible for pH triggering, we propose that a distributed pH effect over multiple residues induces the conformational change that enhances membrane insertion and triggers the fusion activity of the EBOV FL.
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Affiliation(s)
- Jinwoo Lee
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia 22908, United States of America.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States of America
| | - Sonia M Gregory
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia 22908, United States of America.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States of America
| | - Elizabeth A Nelson
- Department Cell Biology, University of Virginia, Charlottesville, Virginia 22908, United States of America
| | - Judith M White
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia 22908, United States of America.,Department Cell Biology, University of Virginia, Charlottesville, Virginia 22908, United States of America
| | - Lukas K Tamm
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia 22908, United States of America.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States of America
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39
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Valéry C, Deville-Foillard S, Lefebvre C, Taberner N, Legrand P, Meneau F, Meriadec C, Delvaux C, Bizien T, Kasotakis E, Lopez-Iglesias C, Gall A, Bressanelli S, Le Du MH, Paternostre M, Artzner F. Atomic view of the histidine environment stabilizing higher-pH conformations of pH-dependent proteins. Nat Commun 2015; 6:7771. [PMID: 26190377 PMCID: PMC4518280 DOI: 10.1038/ncomms8771] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 06/09/2015] [Indexed: 11/17/2022] Open
Abstract
External stimuli are powerful tools that naturally control protein assemblies and functions. For example, during viral entry and exit changes in pH are known to trigger large protein conformational changes. However, the molecular features stabilizing the higher pH structures remain unclear. Here we elucidate the conformational change of a self-assembling peptide that forms either small or large nanotubes dependent on the pH. The sub-angstrom high-pH peptide structure reveals a globular conformation stabilized through a strong histidine-serine H-bond and a tight histidine-aromatic packing. Lowering the pH induces histidine protonation, disrupts these interactions and triggers a large change to an extended β-sheet-based conformation. Re-visiting available structures of proteins with pH-dependent conformations reveals both histidine-containing aromatic pockets and histidine-serine proximity as key motifs in higher pH structures. The mechanism discovered in this study may thus be generally used by pH-dependent proteins and opens new prospects in the field of nanomaterials. In biological systems, large pH-induced conformational changes can be observed in certain proteins, a phenomenon poorly understood at the molecular level. Here the authors describe a peptide with the ability to self-organize into either small or large nanotubes in a pH-dependent manner and detail the mechanism driving the transition.
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Affiliation(s)
- Céline Valéry
- 1] Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, 8140 Christchurch, New zealand [2] Ipsen, 5 Avenue du Canada, 91940 Les Ulis, France
| | - Stéphanie Deville-Foillard
- 1] Ipsen, 5 Avenue du Canada, 91940 Les Ulis, France [2] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [3] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Christelle Lefebvre
- CNRS, UMR 6251, Institut de Physique de Rennes, 263 av. Général Leclerc, Université Rennes I, 35042 Rennes Cedex, France
| | | | | | | | - Cristelle Meriadec
- CNRS, UMR 6251, Institut de Physique de Rennes, 263 av. Général Leclerc, Université Rennes I, 35042 Rennes Cedex, France
| | - Camille Delvaux
- 1] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [2] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Thomas Bizien
- CNRS, UMR 6251, Institut de Physique de Rennes, 263 av. Général Leclerc, Université Rennes I, 35042 Rennes Cedex, France
| | - Emmanouil Kasotakis
- 1] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [2] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Carmen Lopez-Iglesias
- Cryo-Electron Microscopy Unit. Scientific and Tecnological Centers of the University of Barcelona, E-08028 Barcelona, Spain
| | - Andrew Gall
- 1] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [2] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Stéphane Bressanelli
- 1] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [2] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Marie-Hélène Le Du
- 1] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [2] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Maïté Paternostre
- 1] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [2] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Franck Artzner
- CNRS, UMR 6251, Institut de Physique de Rennes, 263 av. Général Leclerc, Université Rennes I, 35042 Rennes Cedex, France
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40
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Lawrence RM, Conrad CE, Zatsepin NA, Grant TD, Liu H, James D, Nelson G, Subramanian G, Aquila A, Hunter MS, Liang M, Boutet S, Coe J, Spence JCH, Weierstall U, Liu W, Fromme P, Cherezov V, Hogue BG. Serial femtosecond X-ray diffraction of enveloped virus microcrystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041720. [PMID: 26798819 PMCID: PMC4711640 DOI: 10.1063/1.4929410] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 08/12/2015] [Indexed: 05/22/2023]
Abstract
Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has produced high-resolution, room temperature, time-resolved protein structures. We report preliminary SFX of Sindbis virus, an enveloped icosahedral RNA virus with ∼700 Å diameter. Microcrystals delivered in viscous agarose medium diffracted to ∼40 Å resolution. Small-angle diffuse X-ray scattering overlaid Bragg peaks and analysis suggests this results from molecular transforms of individual particles. Viral proteins undergo structural changes during entry and infection, which could, in principle, be studied with SFX. This is an important step toward determining room temperature structures from virus microcrystals that may enable time-resolved studies of enveloped viruses.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, California 94025, USA
| | | | | | | | | | | | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California , Los Angeles, California 90089, USA
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41
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Cook JD, Soto-Montoya H, Korpela MK, Lee JE. Electrostatic Architecture of the Infectious Salmon Anemia Virus (ISAV) Core Fusion Protein Illustrates a Carboxyl-Carboxylate pH Sensor. J Biol Chem 2015; 290:18495-504. [PMID: 26082488 DOI: 10.1074/jbc.m115.644781] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Indexed: 11/06/2022] Open
Abstract
Segment 5, ORF 1 of the infectious salmon anemia virus (ISAV) genome, encodes for the ISAV F protein, which is responsible for viral-host endosomal membrane fusion during a productive ISAV infection. The entry machinery of ISAV is composed of a complex of the ISAV F and ISAV hemagglutinin esterase (HE) proteins in an unknown stoichiometry prior to receptor engagement by ISAV HE. Following binding of the receptor to ISAV HE, dissociation of the ISAV F protein from HE, and subsequent endocytosis, the ISAV F protein resolves into a fusion-competent oligomeric state. Here, we present a 2.1 Å crystal structure of the fusion core of the ISAV F protein determined at low pH. This structure has allowed us to unambiguously demonstrate that the ISAV entry machinery exhibits typical class I viral fusion protein architecture. Furthermore, we have determined stabilizing factors that accommodate the pH-dependent mode of ISAV transmission, and our structure has allowed the identification of a central coil that is conserved across numerous and varied post-fusion viral glycoprotein structures. We then discuss a mechanistic model of ISAV fusion that parallels the paramyxoviral class I fusion strategy wherein attachment and fusion are relegated to separate proteins in a similar fashion to ISAV fusion.
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Affiliation(s)
- Jonathan D Cook
- From the Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hazel Soto-Montoya
- From the Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Markus K Korpela
- From the Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jeffrey E Lee
- From the Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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42
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Malashkevich VN, Higgins CD, Almo SC, Lai JR. A switch from parallel to antiparallel strand orientation in a coiled-coil X-ray structure via two core hydrophobic mutations. Biopolymers 2015; 104:178-85. [PMID: 25753192 PMCID: PMC4768791 DOI: 10.1002/bip.22631] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/23/2015] [Indexed: 01/20/2023]
Abstract
The coiled-coil is one of the most ubiquitous and well studied protein structural motifs. Significant effort has been devoted to dissecting subtle variations of the typical heptad repeat sequence pattern that can designate larger topological features such as relative α-helical orientation and oligomer size. Here we report the X-ray structure of a model coiled-coil peptide, HA2-Del-L2seM, which forms an unanticipated core antiparallel dimer with potential sites for discrete higher-order multimerization (trimer or tetramer). In the X-ray structure, a third, partially-ordered α-helix is weakly associated with the antiparallel dimer and analytical ultracentrifugation experiments indicate the peptide forms a well-defined tetramer in solution. The HA2-Del-L2seM sequence is closely related to a parent model peptide, HA2-Del, which we previously reported adopts a parallel trimer; HA2-Del-L2seM differs by only hydrophobic leucine to selenomethione mutations and thus this subtle difference is sufficient to switch both relative α-helical topology and number of α-helices participating in the coiled-coil. Comparison of the X-ray structures of HA2-Del-L2seM (reported here) with the HA2-Del parent (reported previously) reveals novel interactions involving the selenomethionine residues that promote antiparallel coiled-coil configuration and preclude parallel trimer formation. These novel atomic insights are instructive for understanding subtle features that can affect coiled-coil topology and provide additional information for design of antiparallel coiled-coils.
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Affiliation(s)
| | | | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Jonathan R. Lai
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
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43
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Ost KS, O’Meara TR, Huda N, Esher SK, Alspaugh JA. The Cryptococcus neoformans alkaline response pathway: identification of a novel rim pathway activator. PLoS Genet 2015; 11:e1005159. [PMID: 25859664 PMCID: PMC4393102 DOI: 10.1371/journal.pgen.1005159] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 03/19/2015] [Indexed: 12/28/2022] Open
Abstract
The Rim101/PacC transcription factor acts in a fungal-specific signaling pathway responsible for sensing extracellular pH signals. First characterized in ascomycete fungi such as Aspergillus nidulans and Saccharomyces cerevisiae, the Rim/Pal pathway maintains conserved features among very distantly related fungi, where it coordinates cellular adaptation to alkaline pH signals and micronutrient deprivation. However, it also directs species-specific functions in fungal pathogens such as Cryptococcus neoformans, where it controls surface capsule expression. Moreover, disruption of the Rim pathway central transcription factor, Rim101, results in a strain that causes a hyper-inflammatory response in animal infection models. Using targeted gene deletions, we demonstrate that several genes encoding components of the classical Rim/Pal pathway are present in the C. neoformans genome. Many of these genes are in fact required for Rim101 activation, including members of the ESCRT complex (Vps23 and Snf7), ESCRT-interacting proteins (Rim20 and Rim23), and the predicted Rim13 protease. We demonstrate that in neutral/alkaline pH, Rim23 is recruited to punctate regions on the plasma membrane. This change in Rim23 localization requires upstream ESCRT complex components but does not require other Rim101 proteolysis components, such as Rim20 or Rim13. Using a forward genetics screen, we identified the RRA1 gene encoding a novel membrane protein that is also required for Rim101 protein activation and, like the ESCRT complex, is functionally upstream of Rim23-membrane localization. Homologs of RRA1 are present in other Cryptococcus species as well as other basidiomycetes, but closely related genes are not present in ascomycetes. These findings suggest that major branches of the fungal Kingdom developed different mechanisms to sense and respond to very elemental extracellular signals such as changing pH levels.
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Affiliation(s)
- Kyla S. Ost
- Departments of Medicine/ Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Teresa R. O’Meara
- Departments of Medicine/ Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Naureen Huda
- Departments of Medicine/ Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Shannon K. Esher
- Departments of Medicine/ Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - J. Andrew Alspaugh
- Departments of Medicine/ Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail:
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44
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Shi J, Zhang H, Gong R, Xiao G. Characterization of the fusion core in zebrafish endogenous retroviral envelope protein. Biochem Biophys Res Commun 2015; 460:633-8. [PMID: 25804638 PMCID: PMC7092836 DOI: 10.1016/j.bbrc.2015.03.081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 03/14/2015] [Indexed: 10/26/2022]
Abstract
Zebrafish endogenous retrovirus (ZFERV) is the unique endogenous retrovirus in zebrafish, as yet, containing intact open reading frames of its envelope protein gene in zebrafish genome. Similarly, several envelope proteins of endogenous retroviruses in human and other mammalian animal genomes (such as syncytin-1 and 2 in human, syncytin-A and B in mouse) were identified and shown to be functional in induction of cell-cell fusion involved in placental development. ZFERV envelope protein (Env) gene appears to be also functional in vivo because it is expressible. After sequence alignment, we found ZFERV Env shares similar structural profiles with syncytin and other type I viral envelopes, especially in the regions of N- and C-terminal heptad repeats (NHR and CHR) which were crucial for membrane fusion. We expressed the regions of N + C protein in the ZFERV Env (residues 459-567, including predicted NHR and CHR) to characterize the fusion core structure. We found N + C protein could form a stable coiled-coil trimer that consists of three helical NHR regions forming a central trimeric core, and three helical CHR regions packing into the grooves on the surface of the central core. The structural characterization of the fusion core revealed the possible mechanism of fusion mediated by ZFERV Env. These results gave comprehensive explanation of how the ancient virus infects the zebrafish and integrates into the genome million years ago, and showed a rational clue for discovery of physiological significance (e.g., medicate cell-cell fusion).
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Affiliation(s)
- Jian Shi
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Huaidong Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Rui Gong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China.
| | - Gengfu Xiao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China.
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Abstract
![]()
The
Ebolaviruses are members of the family Filoviridae (“filoviruses”) and cause severe hemhorragic fever
with human case fatality rates as high as 90%. Infection requires
attachment of the viral particle to cells and triggering of membrane
fusion between the host and viral membranes, a process that occurs
in the host endosome and is facilitated by the envelope glycoprotein
(GP). One potential strategy for therapeutic intervention is the development
of agents (antibodies, peptides, and small molecules) that can interfere
with viral entry aspects such as attachment, uptake, priming, or membrane
fusion. This paper highlights recent developments in the discovery
and evaluation of therapeutic entry inhibitors and identifies opportunities
moving forward.
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Affiliation(s)
- Elisabeth K. Nyakatura
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Julia C. Frei
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
| | - Jonathan R. Lai
- Department
of Biochemistry, Albert Einstein College of Medicine, 1300 Morris
Park Avenue, Bronx, New York 10461, United States
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46
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Higgins CD, Malashkevich VN, Almo SC, Lai JR. Influence of a heptad repeat stutter on the pH-dependent conformational behavior of the central coiled-coil from influenza hemagglutinin HA2. Proteins 2014; 82:2220-8. [PMID: 24753307 DOI: 10.1002/prot.24585] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/07/2014] [Accepted: 04/14/2014] [Indexed: 11/05/2022]
Abstract
The coiled-coil is one of the most common protein structural motifs. Amino acid sequences of regions that participate in coiled-coils contain a heptad repeat in which every third then forth residue is occupied by a hydrophobic residue. Here we examine the consequences of a "stutter," a deviation of the idealized heptad repeat that is found in the central coiled-coil of influenza hemagluttinin HA2. Characterization of a peptide containing the native stutter-containing HA2 sequence, as well as several variants in which the stutter was engineered out to restore an idealized heptad repeat pattern, revealed that the stutter is important for allowing coiled-coil formation in the WT HA2 at both neutral and low pH (7.1 and 4.5). By contrast, all variants that contained idealized heptad repeats exhibited marked pH-dependent coiled-coil formation with structures forming much more stably at low pH. A crystal structure of one variant containing an idealized heptad repeat, and comparison to the WT HA2 structure, suggest that the stutter distorts the optimal interhelical core packing arrangement, resulting in unwinding of the coiled-coil superhelix. Interactions between acidic side chains, in particular E69 and E74 (present in all peptides studied), are suggested to play a role in mediating these pH-dependent conformational effects. This conclusion is partially supported by studies on HA2 variant peptides in which these positions were altered to aspartic acid. These results provide new insight into the structural role of the heptad repeat stutter in HA2.
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Affiliation(s)
- Chelsea D Higgins
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NewYork, 10461
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47
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Structural characterization of the glycoprotein GP2 core domain from the CAS virus, a novel arenavirus-like species. J Mol Biol 2013; 426:1452-68. [PMID: 24333483 PMCID: PMC3951589 DOI: 10.1016/j.jmb.2013.12.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/02/2013] [Accepted: 12/04/2013] [Indexed: 11/21/2022]
Abstract
Fusion of the viral and host cell membranes is a necessary first step for infection by enveloped viruses and is mediated by the envelope glycoprotein. The transmembrane subunits from the structurally defined “class I” glycoproteins adopt an α-helical “trimer-of-hairpins” conformation during the fusion pathway. Here, we present our studies on the envelope glycoprotein transmembrane subunit, GP2, of the CAS virus (CASV). CASV was recently identified from annulated tree boas (Corallus annulatus) with inclusion body disease and is implicated in the disease etiology. We have generated and characterized two protein constructs consisting of the predicted CASV GP2 core domain. The crystal structure of the CASV GP2 post-fusion conformation indicates a trimeric α-helical bundle that is highly similar to those of Ebola virus and Marburg virus GP2 despite CASV genome homology to arenaviruses. Denaturation studies demonstrate that the stability of CASV GP2 is pH dependent with higher stability at lower pH; we propose that this behavior is due to a network of interactions among acidic residues that would destabilize the α-helical bundle under conditions where the side chains are deprotonated. The pH-dependent stability of the post-fusion structure has been observed in Ebola virus and Marburg virus GP2, as well as other viruses that enter via the endosome. Infection experiments with CASV and the related Golden Gate virus support a mechanism of entry that requires endosomal acidification. Our results suggest that, despite being primarily arenavirus like, the transmembrane subunit of CASV is extremely similar to the filoviruses. CASV is a novel arenavirus with a filovirus-like glycoprotein. Arenaviruses and filoviruses are significant human pathogens. The stability of the CASV GP2 post-fusion structure is dependent on pH. CASV infection requires endosomal acidification. The structure and function of CASV GP2 is similar to filovirus GP2.
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