1
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Park S, Rice A, Im W, Pastor RW. Spontaneous curvature generation by peptides in asymmetric bilayers. J Comput Chem 2024; 45:512-522. [PMID: 37991280 PMCID: PMC10922693 DOI: 10.1002/jcc.27261] [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: 07/11/2023] [Revised: 09/30/2023] [Accepted: 11/05/2023] [Indexed: 11/23/2023]
Abstract
Peptides and proteins play crucial roles in membrane remodeling by inducing spontaneous curvature. However, extracting spontaneous curvatures from simulations of asymmetric bilayers is challenging because differential stress (i.e., the difference of the leaflet surface tensions) arising from leaflet area strains can vary substantially among initial conditions. This study investigates peptide-induced spontaneous curvatureδc 0 p in asymmetric bilayers consisting of a single lipid type and a peptide confined to one leaflet;δc 0 p is calculated from the Helfrich equation using the first moment of the lateral pressure tensor and an alternative expression using the differential stress. It is shown that differential stress introduced during initial system generation is effectively relaxed by equilibrating using P21 periodic boundary conditions, which allows lipids to switch leaflets across cell boundaries and equalize their chemical potentials across leaflets. This procedure leads to robust estimates ofδc 0 p for the systems simulated, and is recommended when equality of chemical potentials between the leaflets is a primary consideration.
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Affiliation(s)
- Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Amy Rice
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Richard W. Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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2
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Carter T, Iqbal M. The Influenza A Virus Replication Cycle: A Comprehensive Review. Viruses 2024; 16:316. [PMID: 38400091 PMCID: PMC10892522 DOI: 10.3390/v16020316] [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: 01/18/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Influenza A virus (IAV) is the primary causative agent of influenza, colloquially called the flu. Each year, it infects up to a billion people, resulting in hundreds of thousands of human deaths, and causes devastating avian outbreaks with worldwide losses worth billions of dollars. Always present is the possibility that a highly pathogenic novel subtype capable of direct human-to-human transmission will spill over into humans, causing a pandemic as devastating if not more so than the 1918 influenza pandemic. While antiviral drugs for influenza do exist, they target very few aspects of IAV replication and risk becoming obsolete due to antiviral resistance. Antivirals targeting other areas of IAV replication are needed to overcome this resistance and combat the yearly epidemics, which exact a serious toll worldwide. This review aims to summarise the key steps in the IAV replication cycle, along with highlighting areas of research that need more focus.
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Affiliation(s)
- Toby Carter
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK;
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3
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Michalski M, Setny P. Molecular Mechanisms behind Conformational Transitions of the Influenza Virus Hemagglutinin Membrane Anchor. J Phys Chem B 2023; 127:9450-9460. [PMID: 37877534 PMCID: PMC10641832 DOI: 10.1021/acs.jpcb.3c05257] [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: 08/03/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]
Abstract
Membrane fusion is a fundamental process that is exploited by enveloped viruses to enter host cells. In the case of the influenza virus, fusion is facilitated by the trimeric viral hemagglutinin protein (HA). So far, major focus has been put on its N-terminal fusion peptides, which are directly responsible for fusion initiation. A growing body of evidence points also to a significant functional role of the HA C-terminal domain, which however remains incompletely understood. Our computational study aimed to elucidate the structural and functional interdependencies within the HA C-terminal region encompassing the transmembrane domain (TMD) and the cytoplasmic tail (CT). In particular, we were interested in the conformational shift of the TMD in response to varying cholesterol concentration in the viral membrane and in its modulation by the presence of CT. Using free-energy calculations based on atomistic molecular dynamics simulations, we characterized transitions between straight and tilted metastable TMD configurations under varying conditions. We found that the presence of CT is essential for achieving a stable, highly tilted TMD configuration. As we demonstrate, such a configuration of HA membrane anchor likely supports the tilting motion of its ectodomain, which needs to be executed during membrane fusion. This finding highlights the functional role of, so far, the relatively overlooked CT region.
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Affiliation(s)
- Michal Michalski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Piotr Setny
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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4
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Azimi FC, Dean TT, Minari K, Basso LGM, Vance TDR, Serrão VHB. A Frame-by-Frame Glance at Membrane Fusion Mechanisms: From Viral Infections to Fertilization. Biomolecules 2023; 13:1130. [PMID: 37509166 PMCID: PMC10377500 DOI: 10.3390/biom13071130] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Viral entry and fertilization are distinct biological processes that share a common mechanism: membrane fusion. In viral entry, enveloped viruses attach to the host cell membrane, triggering a series of conformational changes in the viral fusion proteins. This results in the exposure of a hydrophobic fusion peptide, which inserts into the host membrane and brings the viral and host membranes into close proximity. Subsequent structural rearrangements in opposing membranes lead to their fusion. Similarly, membrane fusion occurs when gametes merge during the fertilization process, though the exact mechanism remains unclear. Structural biology has played a pivotal role in elucidating the molecular mechanisms underlying membrane fusion. High-resolution structures of the viral and fertilization fusion-related proteins have provided valuable insights into the conformational changes that occur during this process. Understanding these mechanisms at a molecular level is essential for the development of antiviral therapeutics and tools to influence fertility. In this review, we will highlight the biological importance of membrane fusion and how protein structures have helped visualize both common elements and subtle divergences in the mechanisms behind fusion; in addition, we will examine the new tools that recent advances in structural biology provide researchers interested in a frame-by-frame understanding of membrane fusion.
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Affiliation(s)
- Farshad C Azimi
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Trevor T Dean
- Pharmaceutical Sciences, University of Illinois Chicago, Chicago, IL 60612, USA
| | - Karine Minari
- Biomolecular Cryo-Electron Microscopy Facility, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Luis G M Basso
- Laboratório de Ciências Físicas, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro 28013-602, Brazil
| | - Tyler D R Vance
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vitor Hugo B Serrão
- Biomolecular Cryo-Electron Microscopy Facility, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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5
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Shi W, Cai Y, Zhu H, Peng H, Voyer J, Rits-Volloch S, Cao H, Mayer ML, Song K, Xu C, Lu J, Zhang J, Chen B. Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane. Nature 2023; 619:403-409. [PMID: 37285872 DOI: 10.1038/s41586-023-06273-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The entry of SARS-CoV-2 into host cells depends on the refolding of the virus-encoded spike protein from a prefusion conformation, which is metastable after cleavage, to a lower-energy stable postfusion conformation1,2. This transition overcomes kinetic barriers for fusion of viral and target cell membranes3,4. Here we report a cryogenic electron microscopy (cryo-EM) structure of the intact postfusion spike in a lipid bilayer that represents the single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membrane-interacting segments, including the fusion peptide and transmembrane anchor. The internal fusion peptide forms a hairpin-like wedge that spans almost the entire lipid bilayer and the transmembrane segment wraps around the fusion peptide at the last stage of membrane fusion. These results advance our understanding of the spike protein in a membrane environment and may guide development of intervention strategies.
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Affiliation(s)
- Wei Shi
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yongfei Cai
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- CSL Seqirus, Waltham, MA, USA
| | - Haisun Zhu
- Institute for Protein Innovation, Harvard Institutes of Medicine, Boston, MA, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Jewel Voyer
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | | | - Hong Cao
- Codex BioSolutions, Rockville, MD, USA
| | - Megan L Mayer
- The Harvard Cryo-EM Center for Structural Biology, Boston, MA, USA
| | - Kangkang Song
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Cryo-EM Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chen Xu
- Department of Biochemistry & Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Cryo-EM Core Facility, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jianming Lu
- Codex BioSolutions, Rockville, MD, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA
| | - Jun Zhang
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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6
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Michalski M, Setny P. Two modes of fusogenic action for influenza virus fusion peptide. PLoS Comput Biol 2023; 19:e1011174. [PMID: 37235589 DOI: 10.1371/journal.pcbi.1011174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
The entry of influenza virus into the host cell requires fusion of its lipid envelope with the host membrane. It is catalysed by viral hemagglutinin protein, whose fragments called fusion peptides become inserted into the target bilayer and initiate its merging with the viral membrane. Isolated fusion peptides are already capable of inducing lipid mixing between liposomes. Years of studies indicate that upon membrane binding they form bend helical structure whose degree of opening fluctuates between tightly closed hairpin and an extended boomerang. The actual way in which they initiate fusion remains elusive. In this work we employ atomistic simulations of wild type and fusion inactive W14A mutant of influenza fusion peptides confined between two closely apposed lipid bilayers. We characterise peptide induced membrane perturbation and determine the potential of mean force for the formation of the first fusion intermediate, an interbilayer lipid bridge called stalk. Our results demonstrate two routes through which the peptides can lower free energy barrier towards fusion. The first one assumes peptides capability to adopt transmembrane configuration which subsequently promotes the creation of a stalk-hole complex. The second involves surface bound peptide configuration and proceeds owing to its ability to stabilise stalk by fitting into the region of extreme negative membrane curvature resulting from its formation. In both cases, the active peptide conformation corresponds to tight helical hairpin, whereas extended boomerang geometry appears to be unable to provide favourable thermodynamic effect. The latter observation offers plausible explanation for long known inactivity of boomerang-stabilising W14A mutation.
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Affiliation(s)
- Michal Michalski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Piotr Setny
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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7
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Zhang Y, Ghosh U, Xie L, Holmes D, Severin KG, Weliky DP. Lipid acyl chain protrusion induced by the influenza virus hemagglutinin fusion peptide detected by NMR paramagnetic relaxation enhancement. Biophys Chem 2023; 299:107028. [PMID: 37247572 DOI: 10.1016/j.bpc.2023.107028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/29/2023] [Accepted: 04/29/2023] [Indexed: 05/31/2023]
Abstract
The glycoprotein spikes of membrane-enveloped viruses include a subunit that catalyzes fusion (joining) of the viral and target cell membranes. For influenza virus, this is subunit 2 of hemagglutinin which has a ∼ 20-residue N-terminal fusion peptide (Fp) region that binds target membrane. An outstanding question is whether there are associated membrane changes important for fusion. Several computational studies have found increased "protrusion" of lipid acyl chains near Fp, i.e. one or more chain carbons are closer to the aqueous region than the headgroup phosphorus. Protrusion may accelerate initial joining of outer leaflets of the two membranes into a stalk intermediate. In this study, higher protrusion probability in membrane with vs. without Fp is convincingly detected by larger Mn2+-associated increases in chain 13C NMR transverse relaxation rates (Γ2's). Data analysis provides a ratio Γ2,neighbor/Γ2,distant for lipids neighboring vs. more distant from the Fp. The calculated ratio depends on the number of Fp-neighboring lipids and the experimentally-derived range of 4 to 24 matches the range of increased protrusion probabilities from different simulations. For samples either with or without Fp, the Γ2 values are well-fitted by an exponential decay as the 13C site moves closer to the chain terminus. The decays correlate with free-energy of protrusion proportional to the number of protruded -CH2 groups, with free energy per -CH2 of ∼0.25 kBT. The NMR data support one major fusion role of the Fp to be much greater protrusion of lipid chains, with highest protrusion probability for chain regions closest to the headgroups.
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Affiliation(s)
- Yijin Zhang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Ujjayini Ghosh
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Li Xie
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Daniel Holmes
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Kathryn G Severin
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - David P Weliky
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.
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8
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Jiang L, Chen H, Li C. Advances in deciphering the interactions between viral proteins of influenza A virus and host cellular proteins. CELL INSIGHT 2023; 2:100079. [PMID: 37193064 PMCID: PMC10134199 DOI: 10.1016/j.cellin.2023.100079] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/28/2023] [Accepted: 01/28/2023] [Indexed: 05/18/2023]
Abstract
Influenza A virus (IAV) poses a severe threat to the health of animals and humans. The genome of IAV consists of eight single-stranded negative-sense RNA segments, encoding ten essential proteins as well as certain accessory proteins. In the process of virus replication, amino acid substitutions continuously accumulate, and genetic reassortment between virus strains readily occurs. Due to this high genetic variability, new viruses that threaten animal and human health can emerge at any time. Therefore, the study on IAV has always been a focus of veterinary medicine and public health. The replication, pathogenesis, and transmission of IAV involve intricate interplay between the virus and host. On one hand, the entire replication cycle of IAV relies on numerous proviral host proteins that effectively allow the virus to adapt to its host and support its replication. On the other hand, some host proteins play restricting roles at different stages of the viral replication cycle. The mechanisms of interaction between viral proteins and host cellular proteins are currently receiving particular interest in IAV research. In this review, we briefly summarize the current advances in our understanding of the mechanisms by which host proteins affect virus replication, pathogenesis, or transmission by interacting with viral proteins. Such information about the interplay between IAV and host proteins could provide insights into how IAV causes disease and spreads, and might help support the development of antiviral drugs or therapeutic approaches.
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Affiliation(s)
- Li Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chengjun Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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9
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Rice A, Zimmerberg J, Pastor RW. Initiation and evolution of pores formed by influenza fusion peptides probed by lysolipid inclusion. Biophys J 2023; 122:1018-1032. [PMID: 36575795 PMCID: PMC10111278 DOI: 10.1016/j.bpj.2022.12.029] [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: 10/18/2022] [Revised: 12/09/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
The fusion peptide (FP) domain is necessary for the fusogenic activity of spike proteins in a variety of enveloped viruses, allowing the virus to infect the host cell, and is the only part of the protein that interacts directly with the target membrane lipid tails during fusion. There are consistent findings of poration by this domain in experimental model membrane systems, and, in certain conditions, the isolated FPs can generate pores. Here, we use molecular dynamics simulations to investigate the specifics of how these FP-induced pores form in membranes with different compositions of lysolipid and POPC. The simulations show that pores form spontaneously at high lysolipid concentrations via hybrid intermediates, where FP aggregates in the cis leaflet tilt to form a funnel-like structure that spans the leaflet and locally reduces the hydrophobic thickness that must be traversed by water to form a pore. By restraining a single FP within an FP aggregate to this tilted conformation, pores can be formed in lower-lysolipid-content membranes, including pure POPC, on the 100-ns timescale, much more rapidly than in unbiased simulations in bilayers with the same composition. The pore formation pathway is similar to the spontaneous formation in high lysolipid concentrations. Depending on the membrane composition, the pores can be metastable (as seen in POPC) or lead to membrane rupture.
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Affiliation(s)
- Amy Rice
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Joshua Zimmerberg
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland.
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10
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Rokonujjaman M, Sahyouni A, Wolfe R, Jia L, Ghosh U, Weliky DP. A large HIV gp41 construct with trimer-of-hairpins structure exhibits V2E mutation-dominant attenuation of vesicle fusion and helicity very similar to V2E attenuation of HIV fusion and infection and supports: (1) hairpin stabilization of membrane apposition with larger distance for V2E; and (2) V2E dominance by an antiparallel β sheet with interleaved fusion peptide strands from two gp41 trimers. Biophys Chem 2023; 293:106933. [PMID: 36508984 PMCID: PMC9879285 DOI: 10.1016/j.bpc.2022.106933] [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: 09/29/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022]
Abstract
There is complete attenuation of fusion and infection mediated by HIV gp160 with gp41 subunit with V2E mutation, and also V2E dominance with WT/V2E mixtures. V2E is at the N-terminus of the ∼25-residue fusion peptide (Fp) which likely binds the target membrane. In this study, large V2E attenuation and dominance were observed for vesicle fusion induced by FP_HM, a large gp41 ectodomain construct with Fp followed by hyperthermostable hairpin with N- and C-helices, and membrane-proximal external region (Mper). FP_HM is a trimer-of-hairpins, the final gp41 structure during fusion. Vesicle fusion and helicity were measured for FP_HM using trimers with different fractions (f's) of WT and V2E proteins. Reductions in FP_HM fusion and helicity vs. fV2E were quantitatively-similar to those for gp160-mediated fusion and infection. Global fitting of all V2E data supports 6 WT gp41 (2 trimers) required for fusion. These data are understood by a model in which the ∼25 kcal/mol free energy for initial membrane apposition is compensated by the thermostable hairpin between the Fp in target membrane and Mper/transmembrane domain in virus membrane. The data support a structural model for V2E dominance with a membrane-bound Fp with antiparallel β sheet and interleaved strands from the two trimers. Relative to fV2E = 0, a longer Fp sheet is stabilized with small fV2E because of salt-bridge and/or hydrogen bonds between E2 on one strand and C-terminal Fp residues on adjacent strands, like R22. A longer Fp sheet results in shorter N- and C-helices, and larger separation during membrane apposition which hinders fusion.
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Affiliation(s)
- Md Rokonujjaman
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Abdulrazak Sahyouni
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Robert Wolfe
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Lihui Jia
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Ujjayini Ghosh
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - David P Weliky
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.
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11
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Shi W, Cai Y, Zhu H, Peng H, Voyer J, Rits-Volloch S, Cao H, Mayer ML, Song K, Xu C, Lu J, Zhang J, Chen B. Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.12.05.519151. [PMID: 36523411 PMCID: PMC9753783 DOI: 10.1101/2022.12.05.519151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into host cells depends on refolding of the virus-encoded spike protein from a prefusion conformation, metastable after cleavage, to a lower energy, stable postfusion conformation. This transition overcomes kinetic barriers for fusion of viral and target cell membranes. We report here a cryo-EM structure of the intact postfusion spike in a lipid bilayer that represents single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membraneinteracting segments, including the fusion peptide and transmembrane anchor. The internal fusion peptide forms a hairpin-like wedge that spans almost the entire lipid bilayer and the transmembrane segment wraps around the fusion peptide at the last stage of membrane fusion. These results advance our understanding of the spike protein in a membrane environment and may guide development of intervention strategies.
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12
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Rice A, Haldar S, Wang E, Blank PS, Akimov SA, Galimzyanov TR, Pastor RW, Zimmerberg J. Planar aggregation of the influenza viral fusion peptide alters membrane structure and hydration, promoting poration. Nat Commun 2022; 13:7336. [PMID: 36470871 PMCID: PMC9722698 DOI: 10.1038/s41467-022-34576-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/28/2022] [Indexed: 12/07/2022] Open
Abstract
To infect, enveloped viruses employ spike protein, spearheaded by its amphipathic fusion peptide (FP), that upon activation extends out from the viral surface to embed into the target cellular membrane. Here we report that synthesized influenza virus FPs are membrane active, generating pores in giant unilamellar vesicles (GUV), and thus potentially explain both influenza virus' hemolytic activity and the liposome poration seen in cryo-electron tomography. Experimentally, FPs are heterogeneously distributed on the GUV at the time of poration. Consistent with this heterogeneous distribution, molecular dynamics (MD) simulations of asymmetric bilayers with different numbers of FPs in one leaflet show FP aggregation. At the center of FP aggregates, a profound change in the membrane structure results in thinning, higher water permeability, and curvature. Ultimately, a hybrid bilayer nanodomain forms with one lipidic leaflet and one peptidic leaflet. Membrane elastic theory predicts a reduced barrier to water pore formation when even a dimer of FPs thins the membrane as above, and the FPs of that dimer tilt, to continue the leaflet bending initiated by the hydrophobic mismatch between the FP dimer and the surrounding lipid.
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Affiliation(s)
- Amy Rice
- grid.94365.3d0000 0001 2297 5165Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Sourav Haldar
- grid.94365.3d0000 0001 2297 5165Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA ,grid.418363.b0000 0004 0506 6543Present Address: Division of Virus Research and Therapeutics, CSIR-Central Drug Research Institute, Lucknow, UP India
| | - Eric Wang
- grid.94365.3d0000 0001 2297 5165Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA ,grid.94365.3d0000 0001 2297 5165Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Paul S. Blank
- grid.94365.3d0000 0001 2297 5165Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Sergey A. Akimov
- grid.4886.20000 0001 2192 9124A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia
| | - Timur R. Galimzyanov
- grid.4886.20000 0001 2192 9124A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russia ,grid.35043.310000 0001 0010 3972National University of Science and Technology “MISiS”, 4 Leninskiy Prospect, Moscow, Russia
| | - Richard W. Pastor
- grid.94365.3d0000 0001 2297 5165Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Joshua Zimmerberg
- grid.94365.3d0000 0001 2297 5165Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
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13
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Surmeier G, Dogan-Surmeier S, Paulus M, Albers C, Latarius J, Sternemann C, Schneider E, Tolan M, Nase J. The interaction of viral fusion peptides with lipid membranes. Biophys J 2022; 121:3811-3825. [PMID: 36110043 PMCID: PMC9674987 DOI: 10.1016/j.bpj.2022.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/13/2022] [Accepted: 09/12/2022] [Indexed: 11/02/2022] Open
Abstract
In this paper, we studied fusogenic peptides of class I-III fusion proteins, which are relevant to membrane fusion for certain enveloped viruses, in contact with model lipid membranes. We resolved the vertical structure and examined the adsorption or penetration behavior of the fusogenic peptides at phospholipid Langmuir monolayers with different initial surface pressures with x-ray reflectometry. We show that the fusion loops of tick-borne encephalitis virus (TBEV) glycoprotein E and vesicular stomatitis virus (VSV) G-protein are not able to insert deeply into model lipid membranes, as they adsorbed mainly underneath the headgroups with only limited penetration depths into the lipid films. In contrast, we observed that the hemagglutinin 2 fusion peptide (HA2-FP) and the VSV-transmembrane domain (VSV-TMD) can penetrate deeply into the membranes. However, in the case of VSV-TMD, the penetration was suppressed already at low surface pressures, whereas HA2-FP was able to insert even into highly compressed films. Membrane fusion is accompanied by drastic changes of the membrane curvature. To investigate how the peptides affect the curvature of model lipid membranes, we examined the effect of the fusogenic peptides on the equilibration of cubic monoolein structures after a phase transition from a lamellar state induced by an abrupt hydrostatic pressure reduction. We monitored this process in presence and absence of the peptides with small-angle x-ray scattering and found that HA2-FP and VSV-TMD drastically accelerate the equilibration, while the fusion loops of TBEV and VSV stabilize the swollen state of the lipid structures. In this work, we show that the class I fusion peptide of HA2 penetrates deeply into the hydrophobic region of membranes and is able to promote and accelerate the formation of negative curvature. In contrast, we found that the class II and III fusion loops of TBEV and VSV tend to counteract negative membrane curvature.
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Affiliation(s)
- Göran Surmeier
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund, Germany
| | | | - Michael Paulus
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund, Germany
| | - Christian Albers
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund, Germany
| | - Jan Latarius
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund, Germany
| | | | - Eric Schneider
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund, Germany
| | - Metin Tolan
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund, Germany
| | - Julia Nase
- Fakultät Physik/DELTA, Technische Universität Dortmund, Dortmund, Germany
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14
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Reversible structural changes in the influenza hemagglutinin precursor at membrane fusion pH. Proc Natl Acad Sci U S A 2022; 119:e2208011119. [PMID: 35939703 PMCID: PMC9388137 DOI: 10.1073/pnas.2208011119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Hemagglutinin (HA) is the receptor binding and membrane fusion glycoprotein of influenza virus. Like other virus fusion glycoproteins such as those of HIV and Ebola, HA is synthesized as a precursor (HA0) that requires cleavage for fusion activity and, for influenza, exposure to low pH. Studies by X-ray and cryogenic electron microscopy (cryo-EM) have characterized conformational changes in HA that occur at membrane fusion pH. Here, using cryo-EM, we report that there are extensive changes to the structure of HA0 at low pH but that, unlike the changes in HA, the changes are reversible on return to neutral pH. The low-pH structure of HA0 is considered an indicator of potential intermediates in the conformational changes in HA at fusion pH. The subunits of the influenza hemagglutinin (HA) trimer are synthesized as single-chain precursors (HA0s) that are proteolytically cleaved into the disulfide-linked polypeptides HA1 and HA2. Cleavage is required for activation of membrane fusion at low pH, which occurs at the beginning of infection following transfer of cell-surface–bound viruses into endosomes. Activation results in extensive changes in the conformation of cleaved HA. To establish the overall contribution of cleavage to the mechanism of HA-mediated membrane fusion, we used cryogenic electron microscopy (cryo-EM) to directly image HA0 at neutral and low pH. We found extensive pH-induced structural changes, some of which were similar to those described for intermediates in the refolding of cleaved HA at low pH. They involve a partial extension of the long central coiled coil formed by melting of the preexisting secondary structure, threading it between the membrane-distal domains, and subsequent refolding as extended helices. The fusion peptide, covalently linked at its N terminus, adopts an amphipathic helical conformation over part of its length and is repositioned and packed against a complementary surface groove of conserved residues. Furthermore, and in contrast to cleaved HA, the changes in HA0 structure at low pH are reversible on reincubation at neutral pH. We discuss the implications of covalently restricted HA0 refolding for the cleaved HA conformational changes that mediate membrane fusion and for the action of antiviral drug candidates and cross-reactive anti-HA antibodies that can block influenza infectivity.
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15
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Michalski M, Setny P. Membrane-Bound Configuration and Lipid Perturbing Effects of Hemagglutinin Subunit 2 N-Terminus Investigated by Computer Simulations. Front Mol Biosci 2022; 9:826366. [PMID: 35155580 PMCID: PMC8830744 DOI: 10.3389/fmolb.2022.826366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/04/2022] [Indexed: 01/08/2023] Open
Abstract
Hemagglutinin (HA) mediated fusion of influenza virus envelope with host lipid membrane is a critical step warrantying virus entry to the cell. Despite tremendous advances in structural biology methods, the knowledge concerning the details of HA2 subunit insertion into the target membrane and its subsequent bilayer perturbing effect is still rather limited. Herein, based on a set of molecular dynamics simulations, we investigate the structure and interaction with lipid membrane of the N-terminal HA2 region comprising a trimer of fusion peptides (HAfps) tethered by flexible linkers to a fragment of coiled-coil stem structure. We find that, prior to insertion into the membrane, HAfps within the trimers do not sample space individually but rather associate into a compact hydrophobic aggregate. Once within the membrane, they fold into tight helical hairpins, which remain at the lipid-water interface. However, they can also assume stable, membrane-spanning configurations of significantly increased membrane-perturbing potential. In this latter case, HAfps trimers centre around the well-hydrated transmembrane channel-forming distinct, symmetric assemblies, whose wedge-like shape may play a role in promoting membrane curvature. We also demonstrate that, following HAfps insertion, the coiled-coil stem spontaneously tilts to almost membrane-parallel orientation, reflecting experimentally observed configuration adopted in the course of membrane fusion by complete HA2 units at the rim of membrane contact zones.
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16
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Chiliveri SC, Robertson AJ, Shen Y, Torchia DA, Bax A. Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems. Chem Rev 2021; 122:9307-9330. [PMID: 34766756 DOI: 10.1021/acs.chemrev.1c00730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The measurement and application of residual dipolar couplings (RDCs) in solution NMR studies of biological macromolecules has become well established over the past quarter of a century. Numerous methods for generating the requisite anisotropic orientational molecular distribution have been demonstrated, each with its specific strengths and weaknesses. In parallel, an enormous number of pulse schemes have been introduced to measure the many different types of RDCs, ranging from the most widely measured backbone amide 15N-1H RDCs, to 1H-1H RDCs and couplings between low-γ nuclei. Applications of RDCs range from structure validation and refinement to the determination of relative domain orientations, the measurement of backbone and domain motions, and de novo structure determination. Nevertheless, it appears that the power of the RDC methodology remains underutilized. This review aims to highlight the practical aspects of sample preparation and RDC measurement while describing some of the most straightforward applications that take advantage of the exceptionally precise information contained in such data. Some emphasis will be placed on more recent developments that enable the accurate measurement of RDCs in larger systems, which is key to the ongoing shift in focus of biological NMR spectroscopy from structure determination toward gaining improved understanding of how molecular flexibility drives protein function.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Angus J Robertson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dennis A Torchia
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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17
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Basso LGM, Zeraik AE, Felizatti AP, Costa-Filho AJ. Membranotropic and biological activities of the membrane fusion peptides from SARS-CoV spike glycoprotein: The importance of the complete internal fusion peptide domain. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183697. [PMID: 34274319 PMCID: PMC8280623 DOI: 10.1016/j.bbamem.2021.183697] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/05/2021] [Accepted: 07/10/2021] [Indexed: 11/28/2022]
Abstract
Fusion peptides (FP) are prominent hydrophobic segments of viral fusion proteins that play critical roles in viral entry. FPs interact with and insert into the host lipid membranes, triggering conformational changes in the viral protein that leads to the viral-cell fusion. Multiple membrane-active domains from the severe acute respiratory syndrome (SARS) coronavirus (CoV) spike protein have been reported to act as the functional fusion peptide such as the peptide sequence located between the S1/S2 and S2' cleavage sites (FP1), the S2'-adjacent fusion peptide domain (FP2), and the internal FP sequence (cIFP). Using a combined biophysical approach, we demonstrated that the α-helical coiled-coil-forming internal cIFP displayed the highest membrane fusion and permeabilizing activities along with membrane ordering effect in phosphatidylcholine (PC)/phosphatidylglycerol (PG) unilamellar vesicles compared to the other two N-proximal fusion peptide counterparts. While the FP1 sequence displayed intermediate membranotropic activities, the well-conserved FP2 peptide was substantially less effective in promoting fusion, leakage, and membrane ordering in PC/PG model membranes. Furthermore, Ca2+ did not enhance the FP2-induced lipid mixing activity in PC/phosphatidylserine/cholesterol lipid membranes, despite its strong erythrocyte membrane perturbation. Nonetheless, we found that the three putative SARS-CoV membrane-active fusion peptide sequences here studied altered the physical properties of model and erythrocyte membranes to different extents. The importance of the distinct membranotropic and biological activities of all SARS-CoV fusion peptide domains and the pronounced effect of the internal fusion peptide sequence to the whole spike-mediated membrane fusion process are discussed.
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Affiliation(s)
- Luis Guilherme Mansor Basso
- Laboratório de Ciências Físicas, Centro de Ciência e Tecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, RJ, Brazil; Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, 14040-901 Ribeirão Preto, SP, Brazil.
| | - Ana Eliza Zeraik
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Avenida Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, RJ, Brazil; Grupo de Biofísica e Biologia Estrutural "Sérgio Mascarenhas", Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Centro, São Carlos, SP, Brazil
| | - Ana Paula Felizatti
- Laboratório de Produtos Naturais, Departamento de Química, Centro de Ciências Exatas e de Tecnologia, Universidade Federal de São Carlos, Rod. Washington Luiz, Km 235, Monjolinho, 13565905, São Carlos, SP, Brazil; Grupo de Biofísica e Biologia Estrutural "Sérgio Mascarenhas", Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense, 400, Centro, São Carlos, SP, Brazil
| | - Antonio José Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes, 3900, 14040-901 Ribeirão Preto, SP, Brazil.
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18
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Lousa D, Soares CM. Molecular mechanisms of the influenza fusion peptide: insights from experimental and simulation studies. FEBS Open Bio 2021; 11:3253-3261. [PMID: 34710289 PMCID: PMC8634857 DOI: 10.1002/2211-5463.13323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/11/2021] [Accepted: 10/27/2021] [Indexed: 12/29/2022] Open
Abstract
A key step in infections by enveloped viruses, such as influenza, is the fusion between the viral envelope and the host cell membrane, which allows the virus to insert its genetic material into the host cell and replicate. The influenza virus fusion process is promoted by hemagglutinin (HA), a glycoprotein that contains three identical monomers composed of two polypeptide chains (HA1 and HA2). Early studies on this protein revealed that HA-mediated fusion involves the insertion of the HA2 N-terminal segment into the host membrane and that this segment, known as the fusion peptide, is a key player in the fusion process. This mini-review highlights the main findings that have been obtained by experimental and computational studies on the HA fusion peptide, which give us a glimpse of its mode of action.
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Affiliation(s)
- Diana Lousa
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Cláudio M Soares
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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19
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Gamblin SJ, Vachieri SG, Xiong X, Zhang J, Martin SR, Skehel JJ. Hemagglutinin Structure and Activities. Cold Spring Harb Perspect Med 2021; 11:a038638. [PMID: 32513673 PMCID: PMC8485738 DOI: 10.1101/cshperspect.a038638] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hemagglutinins (HAs) are the receptor-binding and membrane fusion glycoproteins of influenza viruses. They recognize sialic acid-containing, cell-surface glycoconjugates as receptors but have limited affinity for them, and, as a consequence, virus attachment to cells requires their interaction with several virus HAs. Receptor-bound virus is transferred into endosomes where membrane fusion by HAs is activated at pH between 5 and 6.5, depending on the strain of virus. Fusion activity requires extensive rearrangements in HA conformation that include extrusion of a buried "fusion peptide" to connect with the endosomal membrane, form a bridge to the virus membrane, and eventually bring both membranes close together. In this review, we give an overview of the structures of the 16 genetically and antigenically distinct subtypes of influenza A HA in relation to these two functions in virus replication and in relation to recognition of HA by antibodies that neutralize infection.
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Affiliation(s)
- Steven J Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Sébastien G Vachieri
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Xiaoli Xiong
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Jie Zhang
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Stephen R Martin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - John J Skehel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
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20
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Ghosh U, Weliky DP. Rapid 2H NMR Transverse Relaxation of Perdeuterated Lipid Acyl Chains of Membrane with Bound Viral Fusion Peptide Supports Large-Amplitude Motions of These Chains That Can Catalyze Membrane Fusion. Biochemistry 2021; 60:2637-2651. [PMID: 34436856 DOI: 10.1021/acs.biochem.1c00316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An early step in cellular infection by a membrane-enveloped virus like HIV or influenza is joining (fusion) of the viral and cell membranes. Fusion is catalyzed by a viral protein that typically includes an apolar "fusion peptide" (fp) segment that binds the target membrane prior to fusion. In this study, the effects of nonhomologous HIV and influenza fp's on lipid acyl chain motion are probed with 2H NMR transverse relaxation rates (R2's) of a perdeuterated DMPC membrane. Measurements were made between 35 and 0 °C, which brackets the membrane liquid-crystalline-to-gel phase transitions. Samples were made with either HIV "GPfp" at pH 7 or influenza "HAfp" at pH 5 or 7. GPfp induces vesicle fusion at pH 7, and HAfp induces more fusion at pH 5 vs 7. GPfp bound to DMPC adopts an intermolecular antiparallel β sheet structure, whereas HAfp is a monomer helical hairpin. The R2's of the no peptide and HAfp, pH 7, samples increase gradually as temperature is lowered. The R2's of GPfp and HAfp, pH 5, samples have very different temperature dependence, with a ∼10× increase in R2CD2 when temperature is reduced from 25 to 20 °C and smaller but still substantial R2's at 10 and 0 °C. The large R2's with GPfp and HAfp, pH 5, are consistent with large-amplitude motions of lipid acyl chains that can aid fusion catalysis by increasing the population of chains near the aqueous phase, which is the chain location for transition states between membrane fusion intermediates.
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Affiliation(s)
- Ujjayini Ghosh
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - David P Weliky
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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21
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Koppisetti RK, Fulcher YG, Van Doren SR. Fusion Peptide of SARS-CoV-2 Spike Rearranges into a Wedge Inserted in Bilayered Micelles. J Am Chem Soc 2021; 143:13205-13211. [PMID: 34375093 PMCID: PMC8370118 DOI: 10.1021/jacs.1c05435] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Indexed: 11/28/2022]
Abstract
The receptor binding and proteolysis of Spike of SARS-CoV-2 release its S2 subunit to rearrange and catalyze viral-cell fusion. This deploys the fusion peptide for insertion into the cell membranes targeted. We show that this fusion peptide transforms from intrinsic disorder in solution into a wedge-shaped structure inserted in bilayered micelles, according to chemical shifts, 15N NMR relaxation, and NOEs. The globular fold of three helices contrasts the open, extended forms of this region observed in the electron density of compact prefusion states. In the hydrophobic, narrow end of the wedge, helices 1 and 2 contact the fatty acyl chains of phospholipids, according to NOEs and proximity to a nitroxide spin label deep in the membrane mimic. The polar end of the wedge may engage and displace lipid head groups and bind Ca2+ ions for membrane fusion. Polar helix 3 protrudes from the bilayer where it might be accessible to antibodies.
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Affiliation(s)
| | - Yan G. Fulcher
- Dept. of Biochemistry, University of Missouri, Columbia, MO 65211 USA
| | - Steven R. Van Doren
- Dept. of Biochemistry, University of Missouri, Columbia, MO 65211 USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211 USA
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22
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Moreira P, Sequeira AM, Pereira S, Rodrigues R, Rocha M, Lousa D. ViralFP: A Web Application of Viral Fusion Proteins. FRONTIERS IN MEDICAL TECHNOLOGY 2021; 3:722392. [PMID: 35047951 PMCID: PMC8757699 DOI: 10.3389/fmedt.2021.722392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/19/2021] [Indexed: 12/03/2022] Open
Abstract
Viral fusion proteins are attached to the membrane of enveloped viruses (a group that includes Coronaviruses, Dengue, HIV and Influenza) and catalyze fusion between the viral and host membranes, enabling the virus to insert its genetic material into the host cell. Given the importance of these biomolecules, this work presents a centralized database containing the most relevant information on viral fusion proteins, available through a free-to-use web server accessible through the URL https://viralfp.bio.di.uminho.pt/. This web application contains several bioinformatic tools, such as Clustal sequence alignment and Weblogo, including as well a machine learning-based tool capable of predicting the location of fusion peptides (the component of fusion proteins that inserts into the host's cell membrane) within the fusion protein sequence. Given the crucial role of these proteins in viral infection, their importance as natural targets of our immune system and their potential as therapeutic targets, this web application aims to foster our ability to fight pathogenic viruses.
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Affiliation(s)
- Pedro Moreira
- Centro de Engenharia Biológica, Escola de Engenharia da Universidade do Minho, Braga, Portugal
| | - Ana Marta Sequeira
- Centro de Engenharia Biológica, Escola de Engenharia da Universidade do Minho, Braga, Portugal
| | - Sara Pereira
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Rúben Rodrigues
- Centro de Engenharia Biológica, Escola de Engenharia da Universidade do Minho, Braga, Portugal
| | - Miguel Rocha
- Centro de Engenharia Biológica, Escola de Engenharia da Universidade do Minho, Braga, Portugal
| | - Diana Lousa
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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23
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Transient Excursions to Membrane Core as Determinants of Influenza Virus Fusion Peptide Activity. Int J Mol Sci 2021; 22:ijms22105301. [PMID: 34069905 PMCID: PMC8157580 DOI: 10.3390/ijms22105301] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/06/2021] [Accepted: 05/13/2021] [Indexed: 12/19/2022] Open
Abstract
Fusion of viral and host cell membranes is a critical step in the life cycle of enveloped viruses. In the case of influenza virus, it is mediated by subunit 2 of hemagglutinin (HA) glycoprotein whose N-terminal fragments insert into the target membrane and initiate lipid exchange. These isolated fragments, known as fusion peptides (HAfp), already possess own fusogenic activity towards liposomes. Although they have long been studied with the hope to uncover the details of HA-mediated fusion, their actual mechanism of action remains elusive. Here, we use extensive molecular dynamics simulations combined with experimental studies of three HAfp variants to fully characterize their free energy landscape and interaction with lipid bilayer. In addition to customary assumed peptides localization at lipid-water interface, we characterize membrane-spanning configurations, which turn out to be metastable for active HAfps and unstable for the fusion inactive W14A mutant. We show that, while the degree of membrane perturbation by surface peptide configurations is relatively low and does not show any mutation-related differences, the effect of deeply inserted configurations is significant and correlates with insertion depth of the N-terminal amino group which is the highest for the wild type HAfp. Finally, we demonstrate the feasibility of spontaneous peptide transition to intramembrane location and the critical role of strictly conserved tryptofan residue 14 in this process.
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24
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The role of fusion peptides in depth-dependent membrane organization and dynamics in promoting membrane fusion. Chem Phys Lipids 2020; 234:105025. [PMID: 33301753 DOI: 10.1016/j.chemphyslip.2020.105025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 11/24/2022]
Abstract
Membrane fusion is an important event in the life of eukaryotes; occurs in several processes such as endocytosis, exocytosis, cellular trafficking, compartmentalization, import of nutrients and export of waste, vesiculation, inter cellular communication, and fertilization. The enveloped viruses as well utilize fusion between the viral envelope and host cell membrane for infection. The stretch of 20-25 amino acids located at the N-terminus of the fusion protein, known as fusion peptide, plays a decisive role in the fusion process. The stalk model of membrane fusion postulated a common route of bilayer transformation for stalk, transmembrane contact, and pore formation; and fusion peptide is believed to facilitate bilayer transformation to promote membrane fusion. The peptide-induced change in depth-dependent organization and dynamics could provide important information in understanding the role of fusion peptide in membrane fusion. In this review, we have discussed about three depth-dependent properties of the membrane such as rigidity, polarity and heterogeneity, and the impact of fusion peptide on these three membrane properties.
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25
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Lousa D, Pinto ART, Campos SRR, Baptista AM, Veiga AS, Castanho MARB, Soares CM. Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment. Sci Rep 2020; 10:20082. [PMID: 33208852 PMCID: PMC7674464 DOI: 10.1038/s41598-020-77040-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 11/02/2020] [Indexed: 12/27/2022] Open
Abstract
The influenza virus fusion process, whereby the virus fuses its envelope with the host endosome membrane to release the genetic material, takes place in the acidic late endosome environment. Acidification triggers a large conformational change in the fusion protein, hemagglutinin (HA), which enables the insertion of the N-terminal region of the HA2 subunit, known as the fusion peptide, into the membrane of the host endosome. However, the mechanism by which pH modulates the molecular properties of the fusion peptide remains unclear. To answer this question, we performed the first constant-pH molecular dynamics simulations of the influenza fusion peptide in a membrane, extending for 40 µs of aggregated time. The simulations were combined with spectroscopic data, which showed that the peptide is twofold more active in promoting lipid mixing of model membranes at pH 5 than at pH 7.4. The realistic treatment of protonation introduced by the constant-pH molecular dynamics simulations revealed that low pH stabilizes a vertical membrane-spanning conformation and leads to more frequent contacts between the fusion peptide and the lipid headgroups, which may explain the increase in activity. The study also revealed that the N-terminal region is determinant for the peptide’s effect on the membrane.
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Affiliation(s)
- Diana Lousa
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
| | - Antónia R T Pinto
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Sara R R Campos
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - António M Baptista
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Ana S Veiga
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Miguel A R B Castanho
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Cláudio M Soares
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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26
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Mechanistic insights of host cell fusion of SARS-CoV-1 and SARS-CoV-2 from atomic resolution structure and membrane dynamics. Biophys Chem 2020; 265:106438. [PMID: 32721790 PMCID: PMC7375304 DOI: 10.1016/j.bpc.2020.106438] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 01/04/2023]
Abstract
The emerging and re-emerging viral diseases are continuous threats to the wellbeing of human life. Previous outbreaks of Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS had evidenced potential threats of coronaviruses in human health. The recent pandemic due to SARS-CoV-2 is overwhelming and has been going beyond control. Vaccines and antiviral drugs are ungently required to mitigate the pandemic. Therefore, it is important to comprehend the mechanistic details of viral infection process. The fusion between host cell and virus being the first step of infection, understanding the fusion mechanism could provide crucial information to intervene the infection process. Interestingly, all enveloped viruses contain fusion protein on their envelope that acts as fusion machine. For coronaviruses, the spike or S glycoprotein mediates successful infection through receptor binding and cell fusion. The cell fusion process requires merging of virus and host cell membranes, and that is essentially performed by the S2 domain of the S glycoprotein. In this review, we have discussed cell fusion mechanism of SARS-CoV-1 from available atomic resolution structures and membrane binding of fusion peptides. We have further discussed about the cell fusion of SARS-CoV-2 in the context of present pandemic situation.
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27
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Akimov SA, Kondrashov OV, Zimmerberg J, Batishchev OV. Ectodomain Pulling Combines with Fusion Peptide Inserting to Provide Cooperative Fusion for Influenza Virus and HIV. Int J Mol Sci 2020; 21:ijms21155411. [PMID: 32751407 PMCID: PMC7432320 DOI: 10.3390/ijms21155411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 12/18/2022] Open
Abstract
Enveloped viruses include the most dangerous human and animal pathogens, in particular coronavirus, influenza virus, and human immunodeficiency virus (HIV). For these viruses, receptor binding and entry are accomplished by a single viral envelope protein (termed the fusion protein), the structural changes of which trigger the remodeling and merger of the viral and target cellular membranes. The number of fusion proteins required for fusion activity is still under debate, and several studies report this value to range from 1 to 9 for type I fusion proteins. Here, we consider the earliest stage of viral fusion based on the continuum theory of membrane elasticity. We demonstrate that membrane deformations induced by the oblique insertion of amphipathic fusion peptides mediate the lateral interaction of these peptides and drive them to form into a symmetric fusion rosette. The pulling force produced by the structural rearrangements of the fusion protein ectodomains gives additional torque, which deforms the membrane and additionally stabilizes the symmetric fusion rosette, thus allowing a reduction in the number of fusion peptides needed for fusion. These findings can resolve the large range of published cooperativity indices for HIV, influenza, and other type I fusion proteins.
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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; (O.V.K.); (O.V.B.)
- Correspondence: ; Tel.: +7-495-955-4776
| | - Oleg V. Kondrashov
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia; (O.V.K.); (O.V.B.)
| | - Joshua Zimmerberg
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Oleg V. Batishchev
- Laboratory of Bioelectrochemistry, A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/4 Leninskiy Prospekt, 119071 Moscow, Russia; (O.V.K.); (O.V.B.)
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28
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Ghosh U, Weliky DP. 2H nuclear magnetic resonance spectroscopy supports larger amplitude fast motion and interference with lipid chain ordering for membrane that contains β sheet human immunodeficiency virus gp41 fusion peptide or helical hairpin influenza virus hemagglutinin fusion peptide at fusogenic pH. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183404. [PMID: 32585207 DOI: 10.1016/j.bbamem.2020.183404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/27/2020] [Accepted: 06/19/2020] [Indexed: 01/02/2023]
Abstract
Enveloped viruses are surrounded by a membrane which is obtained from an infected host cell during budding. Infection of a new cell requires joining (fusion) of the virus and cell membranes. This process is mediated by a monotopic viral fusion protein with a large ectodomain outside the virus. The ectodomains of class I enveloped viruses have a N-terminal "fusion peptide" (fp) domain that is critical for fusion and binds to the cell membrane. In this study, 2H NMR spectra are analyzed for deuterated membrane with fp from either HIV gp41 (GP) or influenza hemagglutinin (HA) fusion proteins. In addition, the HAfp samples are studied at more fusogenic pH 5 and less fusogenic pH 7. GPfp adopts intermolecular antiparallel β sheet structure whereas HAfp is a monomeric helical hairpin. The data are obtained for a set of temperatures between 35 and 0 °C using DMPC-d54 lipid with perdeuterated acyl chains. The DMPC has liquid-crystalline (Lα) phase with disordered chains at higher temperature and rippled gel (Pβ') or gel phase (Lβ') with ordered chains at lower temperature. At given temperature T, the no peptide and HAfp, pH 7 samples exhibit similar spectral lineshapes. Spectral broadening with reduced temperature correlates with the transition from Lα to Pβ' and then Lβ' phases. At given T, the lineshapes are narrower for HAfp, pH 5 vs. no peptide and HAfp, pH 7 samples, and even narrower for the GPfp sample. These data support larger-amplitude fast (>105 Hz) lipid acyl chain motion for samples with fusogenic peptides, and peptide interference with chain ordering. The NMR data of the present paper correlate with insertion of these peptides into the hydrocarbon core of the membrane and support a significant fusion contribution from the resultant lipid acyl chain disorder, perhaps because of reduced barriers between the different membrane topologies in the fusion pathway. Membrane insertion and lipid perturbation appear common to both β sheet and helical hairpin peptides.
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Affiliation(s)
- Ujjayini Ghosh
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - David P Weliky
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.
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29
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Benhaim MA, Lee KK. New Biophysical Approaches Reveal the Dynamics and Mechanics of Type I Viral Fusion Machinery and Their Interplay with Membranes. Viruses 2020; 12:E413. [PMID: 32276357 PMCID: PMC7232462 DOI: 10.3390/v12040413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/04/2020] [Accepted: 04/04/2020] [Indexed: 12/27/2022] Open
Abstract
Protein-mediated membrane fusion is a highly regulated biological process essential for cellular and organismal functions and infection by enveloped viruses. During viral entry the membrane fusion reaction is catalyzed by specialized protein machinery on the viral surface. These viral fusion proteins undergo a series of dramatic structural changes during membrane fusion where they engage, remodel, and ultimately fuse with the host membrane. The structural and dynamic nature of these conformational changes and their impact on the membranes have long-eluded characterization. Recent advances in structural and biophysical methodologies have enabled researchers to directly observe viral fusion proteins as they carry out their functions during membrane fusion. Here we review the structure and function of type I viral fusion proteins and mechanisms of protein-mediated membrane fusion. We highlight how recent technological advances and new biophysical approaches are providing unprecedented new insight into the membrane fusion reaction.
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Affiliation(s)
- Mark A. Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, USA;
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195-7610, USA;
- Biological Physics Structure and Design Program, University of Washington, Seattle, WA 98195-7610, USA
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30
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Influenza hemagglutinin drives viral entry via two sequential intramembrane mechanisms. Proc Natl Acad Sci U S A 2020; 117:7200-7207. [PMID: 32188780 DOI: 10.1073/pnas.1914188117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Enveloped viruses enter cells via a process of membrane fusion between the viral envelope and a cellular membrane. For influenza virus, mutational data have shown that the membrane-inserted portions of the hemagglutinin protein play a critical role in achieving fusion. In contrast to the relatively well-understood ectodomain, a predictive mechanistic understanding of the intramembrane mechanisms by which influenza hemagglutinin drives fusion has been elusive. We used molecular dynamics simulations of fusion between a full-length hemagglutinin proteoliposome and a lipid bilayer to analyze these mechanisms. In our simulations, hemagglutinin first acts within the membrane to increase lipid tail protrusion and promote stalk formation and then acts to engage the distal leaflets of each membrane and promote stalk widening, curvature, and eventual fusion. These two sequential mechanisms, one occurring before stalk formation and one after, are consistent with our experimental measurements of single-virus fusion kinetics to liposomes of different sizes. The resulting model also helps explain and integrate previous mutational and biophysical data, particularly the mutational sensitivity of the fusion peptide N terminus and the length sensitivity of the transmembrane domain. We hypothesize that entry by other enveloped viruses may also use sequential processes of acyl tail exposure, followed by membrane curvature and distal leaflet engagement.
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31
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Beckett D, El-Baba TJ, Gilbert K, Clemmer DE, Raghavachari K. Untangling Hydrogen Bond Networks with Ion Mobility Spectrometry and Quantum Chemical Calculations: A Case Study on H +XPGG. J Phys Chem B 2019; 123:5730-5741. [PMID: 31241336 DOI: 10.1021/acs.jpcb.9b03803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ion mobility spectrometry-mass spectrometry and quantum chemical calculations are used to determine the structures and stabilities of singly protonated XaaProGlyGly peptides: H+DPGG, H+NPGG, H+EPGG, and H+QPGG. The IMS distributions are similar, suggesting the peptides adopt closely related structures in the gas phase. Quantum chemical calculations show that all conformers seen in the experimental spectrum correspond to the cis configuration about the Xaa-Pro peptide bond, significantly different from the behavior seen previously for H+GPGG. Density functional theory and quantum theory of atoms in molecules (QTAIM) investigations uncover a silent drama as a minor conformer not observed in the H+DPGG spectrum becomes the preferred conformer in H+QPGG, with both conformers being coincident in collision cross section. Investigation of the highly coupled hydrogen bond network, replete with CH···O interactions and bifurcated hydrogen bonds, reveals the cause of this effect as well as the absence of trans conformers from the spectra. A series of generalized observations are provided to aid in enzyme and ligand design using these coupled hydrogen bond motifs.
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Affiliation(s)
- Daniel Beckett
- Department of Chemistry , Indiana University , Bloomington Indiana 47401 , United States
| | - Tarick J El-Baba
- Department of Chemistry , Indiana University , Bloomington Indiana 47401 , United States
| | - Kevin Gilbert
- Department of Chemistry , Indiana University , Bloomington Indiana 47401 , United States
| | - David E Clemmer
- Department of Chemistry , Indiana University , Bloomington Indiana 47401 , United States
| | - Krishnan Raghavachari
- Department of Chemistry , Indiana University , Bloomington Indiana 47401 , United States
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32
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Algayer B, O'Brien A, Momose A, Murphy DJ, Procopio W, Tellers DM, Tucker TJ. Novel pH Selective, Highly Lytic Peptides Based on a Chimeric Influenza Hemagglutinin Peptide/Cell Penetrating Peptide Motif. Molecules 2019; 24:E2079. [PMID: 31159194 PMCID: PMC6600388 DOI: 10.3390/molecules24112079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 11/17/2022] Open
Abstract
Delivery of macromolecular cargos such as siRNA to the cytosol after endocytosis remains a critical challenge. Numerous approaches including viruses, lipid nanoparticles, polymeric constructs, and various peptide-based approaches have yet to yield a general solution to this delivery issue. In this manuscript, we describe our efforts to design novel endosomolytic peptides that could be used to facilitate the release of cargos from a late endosomal compartment. These amphiphilic peptides, based on a chimeric influenza hemagglutinin peptide/cell-penetrating peptide (CPP) template, utilize a pH-triggering mechanism in which the peptides are protonated after acidification of the endosome, and thereby adopt an alpha-helical conformation. The helical forms of the peptides are lytically active, while the non-protonated forms are much less or non-lytically active at physiological pH. Starting from an initial lead peptide (INF7-Tat), we systematically modified the sequence of the chimeric peptides to obtain peptides with greatly enhanced lytic activity that maintain good pH selectivity in a red blood cell hemolysis assay.
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Affiliation(s)
- Bethany Algayer
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
| | - Ann O'Brien
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
| | - Aaron Momose
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
| | - Dennis J Murphy
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
| | - William Procopio
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
| | - David M Tellers
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
| | - Thomas J Tucker
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
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33
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Ranaweera A, Ratnayake PU, Ekanayaka EAP, Declercq R, Weliky DP. Hydrogen-Deuterium Exchange Supports Independent Membrane-Interfacial Fusion Peptide and Transmembrane Domains in Subunit 2 of Influenza Virus Hemagglutinin Protein, a Structured and Aqueous-Protected Connection between the Fusion Peptide and Soluble Ectodomain, and the Importance of Membrane Apposition by the Trimer-of-Hairpins Structure. Biochemistry 2019; 58:2432-2446. [PMID: 31008587 DOI: 10.1021/acs.biochem.8b01272] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influenza virus hemagglutinin (HA) protein has HA1 and HA2 subunits, which form an initial complex. HA1's bind host cell sialic acids, which triggers endocytosis, HA1/HA2 separation, and HA2-mediated fusion between virus and endosome membranes. We report hydrogen-deuterium exchange mass spectrometry (HDX-MS) on the HA2 subunit without HA1. HA2 contains the fusion peptide (FP), soluble ectodomain (SE), transmembrane domain (TM), and endodomain. FP is a monomer by itself, while SE is a trimer of hairpins that includes an interior bundle of residue 38-105 helices, turns, and residue 154-178 strands packed antiparallel to the bundle. FP and TM extend from the same side of the SE hairpin, and fusion models often depict a FP/TM complex with membrane traversal of both domains that is important for membrane pore expansion. The HDX-MS data of this study do not support this complex and instead support independent FP and TM with respective membrane-interfacial and traversal locations. The data also show a low level of aqueous exposure of the 22-38 segment, consistent with retention of the 23-35 antiparallel β sheet observed in the initial HA1/HA2 complex. We propose the β sheet as a semirigid connector between FP and SE that enables close membrane apposition prior to fusion. The I173E mutant exhibits greater exchange for residues 22-69 and 150-191, consistent with dissociation of SE C-terminal strands from interior N-helices. Similar trends are observed for the G1E mutant as well as less exchange for G1E FP. Fusion is highly impaired with either mutant, which correlates with reduced membrane apposition and, for G1E, FP binding to SE rather than the target membrane.
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Affiliation(s)
- Ahinsa Ranaweera
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Punsisi U Ratnayake
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - E A Prabodha Ekanayaka
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Robin Declercq
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - David P Weliky
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
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34
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Liao SY, Lee M, Hong M. Interplay between membrane curvature and protein conformational equilibrium investigated by solid-state NMR. J Struct Biol 2019; 206:20-28. [PMID: 29501472 PMCID: PMC6119545 DOI: 10.1016/j.jsb.2018.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/19/2018] [Accepted: 02/26/2018] [Indexed: 11/28/2022]
Abstract
Many membrane proteins sense and induce membrane curvature for function, but structural information about how proteins modulate their structures to cause membrane curvature is sparse. We review our recent solid-state NMR studies of two virus membrane proteins whose conformational equilibrium is tightly coupled to membrane curvature. The influenza M2 proton channel has a drug-binding site in the transmembrane (TM) pore. Previous chemical shift data indicated that this pore-binding site is lost in an M2 construct that contains the TM domain and a curvature-inducing amphipathic helix. We have now obtained chemical shift perturbation, protein-drug proximity, and drug orientation data that indicate that the pore-binding site is restored when the full cytoplasmic domain is present. This finding indicates that the curvature-inducing amphipathic helix distorts the TM structure to interfere with drug binding, while the cytoplasmic tail attenuates this effect. In the second example, we review our studies of a parainfluenza virus fusion protein that merges the cell membrane and the virus envelope during virus entry. Chemical shifts of two hydrophobic domains of the protein indicate that both domains have membrane-dependent backbone conformations, with the β-strand structure dominating in negative-curvature phosphatidylethanolamine (PE) membranes. 31P NMR spectra and 1H-31P correlation spectra indicate that the β-strand-rich conformation induces saddle-splay curvature to PE membranes and dehydrates them, thus stabilizing the hemifusion state. These results highlight the indispensable role of solid-state NMR to simultaneously determine membrane protein structures and characterize the membrane curvature in which these protein structures exist.
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Affiliation(s)
- Shu Y Liao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Myungwoon Lee
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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35
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DeLisle CF, Mendis HB, Lorieau JL. Super resolution NOESY spectra of proteins. JOURNAL OF BIOMOLECULAR NMR 2019; 73:105-116. [PMID: 31041648 DOI: 10.1007/s10858-019-00231-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
Spectral resolution remains one of the most significant limitations in the NMR study of biomolecules. We present the srNOESY (super resolution nuclear overhauser effect spectroscopy) experiment, which enhances the resolution of NOESY cross-peaks at the expense of the diagonal peak line-width. We studied two proteins, ubiquitin and the influenza hemagglutinin fusion peptide in bicelles, and we achieved average resolution enhancements of 21-47% and individual peak enhancements as large as ca. 450%. New peaks were observed over the conventional NOESY experiment in both proteins as a result of these improvements, and the final structures generated from the calculated restraints matched published models. We discuss the impact of the experimental parameters, spin diffusion and the information content of the srNOESY lineshape.
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Affiliation(s)
- Charles F DeLisle
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL, 60607, USA
| | - H Bhagya Mendis
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL, 60607, USA
| | - Justin L Lorieau
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL, 60607, USA.
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36
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Lee MW, Lee EY, Ferguson AL, Wong GCL. Machine learning antimicrobial peptide sequences: Some surprising variations on the theme of amphiphilic assembly. Curr Opin Colloid Interface Sci 2018; 38:204-213. [PMID: 31093008 DOI: 10.1016/j.cocis.2018.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Antimicrobial peptides (AMPs) collectively constitute a key component of the host innate immune system. They span a diverse space of sequences and can be α-helical, β-sheet, or unfolded in structure. Despite a wealth of knowledge about them from decades of experiments, it remains difficult to articulate general principles governing such peptides. How are they different from other molecules that are also cationic and amphiphilic? What other functions, in immunity and otherwise, are enabled by these simple sequences? In this short review, we present some recent work that engages these questions using methods not usually applied to AMP studies, such as machine learning. We find that not only do AMP-like sequences confer membrane remodeling activity to an unexpectedly broad range of protein classes, their cationic and amphiphilic signature also allows them to act as meta-antigens and self-assemble with immune ligands into nanocrystalline complexes for multivalent presentation to Toll-like receptors.
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Affiliation(s)
- Michelle W Lee
- Department of Bioengineering, Department of Chemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States
| | - Ernest Y Lee
- Department of Bioengineering, Department of Chemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States
| | - Andrew L Ferguson
- Institute for Molecular Engineering, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, United States
| | - Gerard C L Wong
- Department of Bioengineering, Department of Chemistry, California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States
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37
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Baquero E, Fedry J, Legrand P, Krey T, Rey FA. Species-Specific Functional Regions of the Green Alga Gamete Fusion Protein HAP2 Revealed by Structural Studies. Structure 2018; 27:113-124.e4. [PMID: 30416037 PMCID: PMC6327110 DOI: 10.1016/j.str.2018.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/28/2018] [Accepted: 09/28/2018] [Indexed: 12/25/2022]
Abstract
The cellular fusion protein HAP2, which is structurally homologous to viral class II fusion proteins, drives gamete fusion across several eukaryotic kingdoms. Gamete fusion is a highly controlled process in eukaryotes, and is allowed only between same species gametes. In spite of a conserved architecture, HAP2 displays several species-specific functional regions that were not resolved in the available X-ray structure of the green alga Chlamydomonas reinhardtii HAP2 ectodomain. Here we present an X-ray structure resolving these regions, showing a target membrane interaction surface made by three amphipathic helices in a horseshoe-shaped arrangement. HAP2 from green algae also features additional species-specific motifs inserted in regions that in viral class II proteins are critical for the fusogenic conformational change. Such insertions include a cystine ladder-like module evocative of EGF-like motifs responsible for extracellular protein-protein interactions in animals, and a mucin-like region. These features suggest potential HAP2 interaction sites involved in gamete fusion control. Unprecedented organization of amphipathic α helices in the algal HAP2 fusion loops An inserted EGF-like motif suggests a potential algal-specific fusion control site An adjacent mucin-like region potentially modulates algal-specific interactions Inter-chain stem/domain II interactions stabilize the post-fusion hairpin conformation
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Affiliation(s)
- Eduard Baquero
- Institut Pasteur, Unité de Virologie Structurale, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France; CNRS UMR 3569, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Juliette Fedry
- Institut Pasteur, Unité de Virologie Structurale, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France; CNRS UMR 3569, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Pierre Legrand
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192 Gif-sur-Yvette, France
| | - Thomas Krey
- Institut Pasteur, Unité de Virologie Structurale, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France; CNRS UMR 3569, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Felix A Rey
- Institut Pasteur, Unité de Virologie Structurale, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France; CNRS UMR 3569, 25-28 Rue du Docteur Roux, 75724 Paris Cedex 15, France.
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38
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Ranaweera A, Ratnayake PU, Weliky DP. The Stabilities of the Soluble Ectodomain and Fusion Peptide Hairpins of the Influenza Virus Hemagglutinin Subunit II Protein Are Positively Correlated with Membrane Fusion. Biochemistry 2018; 57:5480-5493. [PMID: 30141905 DOI: 10.1021/acs.biochem.8b00764] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cellular entry of influenza virus is mediated by the viral protein hemagglutinin (HA), which forms an initial complex of three HA1 and three HA2 subunits. Each HA2 includes a fusion peptide (FP), a soluble ectodomain (SE), and a transmembrane domain. HA1 binds to cellular sialic acids, followed by virus endocytosis, pH reduction, dissociation of HA1, and structural rearrangement of HA2 into a final trimer-of-SE hairpins. A decrease in pH also triggers HA2-mediated virus/endosome membrane fusion. SE hairpins have an interior parallel helical bundle and C-terminal strands in the grooves of the exterior of the bundle. FPs are separate helical hairpins. This study compares wild-type HA2 (WT-HA2) with G1E(FP) and I173E(SE strand) mutants. WT-HA2 induces vesicle fusion at pH 5.0, whereas the extent of fusion is greatly reduced for both mutants. Circular dichroism for HA2 and FHA2≡FP+SE constructs shows dramatic losses of stability for the mutants, including a Tm reduced by 40 °C for I173E-FHA2. This is evidence of destabilization of SE hairpins via dissociation of strands from the helical bundle, which is also supported by larger monomer fractions for mutant versus WT proteins. The G1E mutant may have disrupted FP hairpins, with consequent non-native FP binding to dissociated SE strands. It is commonly proposed that free energy released by the HA2 structural rearrangement catalyzes HA-mediated fusion. This study supports an alternate mechanistic model in which fusion is preceded by FP insertion in the target membrane and formation of the final SE hairpin. Less fusion by the mutants is due to the loss of hairpin stability and consequent reduced level of membrane apposition of the virus and target membranes.
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Affiliation(s)
- Ahinsa Ranaweera
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Punsisi U Ratnayake
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - David P Weliky
- Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
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39
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Ye H. Molecular design of antimicrobial peptides based on hemagglutinin fusion domain to combat antibiotic resistance in bacterial infection. J Pept Sci 2018. [PMID: 29542264 DOI: 10.1002/psc.3068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Antimicrobial peptides are derived from the viral fusion domain of influenza virus hemagglutinin based on rational analysis of the intermolecular interaction between peptides and bacterial outer membrane. It is revealed that the isolated viral fusion domain is a negatively charged peptide HAfp1-23 that cannot effectively interact with the anionic membrane. Conversion of the native HAfp1-23 to a positively charged peptide HAfp1-23 _KK by E11K/D19K mutation can promote the peptide-membrane interaction substantially; this confers to the peptide a moderate antibacterial potency against antibiotic-resistant bacterial strains. Cyclization of the linear peptide HAfp1-23 _KK results in a cyclic peptide cHAfp1-23 _KK, which can largely minimize entropy penalty upon the peptide-membrane binding by pre-stabilizing peptide hairpin configuration in solvent, where the linear peptide would incur in a considerable conformational change/folding from intrinsic disorder (in water) to the structured hairpin conformation (in lipid). As might be expected, the cyclization considerably improves peptide antibacterial activity with minimum inhibitory concentration of 67 and 34 μg/mL against multidrug-resistant Pseudomonas aeruginosa and methicillin-resistant Staphylococcus aureus, respectively.
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Affiliation(s)
- Hui Ye
- Center of infectious Diseases, West China Hospital, Sichuan University, Chengdu, 610041, China
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40
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Fedry J, Forcina J, Legrand P, Péhau-Arnaudet G, Haouz A, Johnson M, Rey FA, Krey T. Evolutionary diversification of the HAP2 membrane insertion motifs to drive gamete fusion across eukaryotes. PLoS Biol 2018; 16:e2006357. [PMID: 30102690 PMCID: PMC6089408 DOI: 10.1371/journal.pbio.2006357] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 07/09/2018] [Indexed: 12/20/2022] Open
Abstract
HAPLESS2 (HAP2) is a broadly conserved, gamete-expressed transmembrane protein that was shown recently to be structurally homologous to viral class II fusion proteins, which initiate fusion with host cells via insertion of fusion loops into the host membrane. However, the functional conformation of the HAP2 fusion loops has remained unknown, as the reported X-ray structure of Chlamydomonas reinhardtii HAP2 lacked this critical region. Here, we report a structure-guided alignment that reveals diversification of the proposed HAP2 fusion loops. Representative crystal structures show that in flowering plants, HAP2 has a single prominent fusion loop projecting an amphipathic helix at its apex, while in trypanosomes, three small nonpolar loops of HAP2 are poised to interact with the target membrane. A detailed structure-function analysis of the Arabidopsis HAP2 amphipathic fusion helix defines key residues that are essential for membrane insertion and for gamete fusion. Our study suggests that HAP2 may have evolved multiple modes of membrane insertion to accommodate the diversity of membrane environments it has encountered during eukaryotic evolution. The fusion of gamete plasma membranes is the fundamental cellular event that brings two parental cells together to form a new individual, yet we know surprisingly little about this process at the molecular level. HAPLESS 2 (HAP2) is a conserved sperm plasma membrane protein that is essential for gamete fusion in a diverse array of eukaryotes. It was recently shown to share a common ancestor with viral proteins that drive fusion of the viral envelope with host membranes, but its mechanism of action remained elusive, since the reported structure did not resolve the proposed membrane interaction surface. Here, we report two new HAP2 structures revealing that HAP2 has evolved diverse membrane interaction surfaces. In the flowering plants, HAP2 uses an amphipathic helix that presents nonpolar residues to the target membrane; in trypanosomes, the membrane interaction surface comprises three shallow nonpolar loops.
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Affiliation(s)
- Juliette Fedry
- Unité de Virologie Structurale, Institut Pasteur, Paris, France
- CNRS UMR 3569, Paris, France
- Universite Paris Descartes Sorbonne Paris Cité, Institut Pasteur, Paris, France
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Jennifer Forcina
- Brown University, Department of Molecular Biology, Cell Biology, and Biochemistry, Providence, Rhode Island, United States of America
| | - Pierre Legrand
- Synchrotron SOLEIL, L'Orme des Merisiers, Gif-sur-Yvette, France
| | | | - Ahmed Haouz
- Protéopôle, CNRS UMR 3528, Institut Pasteur, Paris, France
| | - Mark Johnson
- Brown University, Department of Molecular Biology, Cell Biology, and Biochemistry, Providence, Rhode Island, United States of America
- * E-mail: (MJ); (FAR); (TK)
| | - Felix A. Rey
- Unité de Virologie Structurale, Institut Pasteur, Paris, France
- CNRS UMR 3569, Paris, France
- * E-mail: (MJ); (FAR); (TK)
| | - Thomas Krey
- Unité de Virologie Structurale, Institut Pasteur, Paris, France
- CNRS UMR 3569, Paris, France
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Hannover, Germany
- * E-mail: (MJ); (FAR); (TK)
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41
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Shi H, Clay MC, Rangadurai A, Sathyamoorthy B, Case DA, Al-Hashimi HM. Atomic structures of excited state A-T Hoogsteen base pairs in duplex DNA by combining NMR relaxation dispersion, mutagenesis, and chemical shift calculations. JOURNAL OF BIOMOLECULAR NMR 2018; 70:229-244. [PMID: 29675775 PMCID: PMC6048961 DOI: 10.1007/s10858-018-0177-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/29/2018] [Indexed: 05/20/2023]
Abstract
NMR relaxation dispersion studies indicate that in canonical duplex DNA, Watson-Crick base pairs (bps) exist in dynamic equilibrium with short-lived low abundance excited state Hoogsteen bps. N1-methylated adenine (m1A) and guanine (m1G) are naturally occurring forms of damage that stabilize Hoogsteen bps in duplex DNA. NMR dynamic ensembles of DNA duplexes with m1A-T Hoogsteen bps reveal significant changes in sugar pucker and backbone angles in and around the Hoogsteen bp, as well as kinking of the duplex towards the major groove. Whether these structural changes also occur upon forming excited state Hoogsteen bps in unmodified duplexes remains to be established because prior relaxation dispersion probes provided limited information regarding the sugar-backbone conformation. Here, we demonstrate measurements of C3' and C4' spin relaxation in the rotating frame (R1ρ) in uniformly 13C/15N labeled DNA as sensitive probes of the sugar-backbone conformation in DNA excited states. The chemical shifts, combined with structure-based predictions using an automated fragmentation quantum mechanics/molecular mechanics method, show that the dynamic ensemble of DNA duplexes containing m1A-T Hoogsteen bps accurately model the excited state Hoogsteen conformation in two different sequence contexts. Formation of excited state A-T Hoogsteen bps is accompanied by changes in sugar-backbone conformation that allow the flipped syn adenine to form hydrogen-bonds with its partner thymine and this in turn results in overall kinking of the DNA toward the major groove. Results support the assignment of Hoogsteen bps as the excited state observed in canonical duplex DNA, provide an atomic view of DNA dynamics linked to formation of Hoogsteen bps, and lay the groundwork for a potentially general strategy for solving structures of nucleic acid excited states.
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Affiliation(s)
- Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Mary C. Clay
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Bharathwaj Sathyamoorthy
- Department of Chemistry, Duke University, Durham, NC 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - David A. Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
- To whom correspondence should be addressed. Telephone: (919) 660-1113, or
| | - Hashim M. Al-Hashimi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- To whom correspondence should be addressed. Telephone: (919) 660-1113, or
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42
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Guardado-Calvo P, Atkovska K, Jeffers SA, Grau N, Backovic M, Pérez-Vargas J, de Boer SM, Tortorici MA, Pehau-Arnaudet G, Lepault J, England P, Rottier PJ, Bosch BJ, Hub JS, Rey FA. A glycerophospholipid-specific pocket in the RVFV class II fusion protein drives target membrane insertion. Science 2018; 358:663-667. [PMID: 29097548 DOI: 10.1126/science.aal2712] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 07/20/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022]
Abstract
The Rift Valley fever virus (RVFV) is transmitted by infected mosquitoes, causing severe disease in humans and livestock across Africa. We determined the x-ray structure of the RVFV class II fusion protein Gc in its postfusion form and in complex with a glycerophospholipid (GPL) bound in a conserved cavity next to the fusion loop. Site-directed mutagenesis and molecular dynamics simulations further revealed a built-in motif allowing en bloc insertion of the fusion loop into membranes, making few nonpolar side-chain interactions with the aliphatic moiety and multiple polar interactions with lipid head groups upon membrane restructuring. The GPL head-group recognition pocket is conserved in the fusion proteins of other arthropod-borne viruses, such as Zika and chikungunya viruses, which have recently caused major epidemics worldwide.
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Affiliation(s)
- P Guardado-Calvo
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France. .,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - K Atkovska
- Institute for Microbiology and Genetics, University of Goettingen, Justus-von-Liebig weg 11, 37077 Göttingen, Germany
| | - S A Jeffers
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France.,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - N Grau
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France.,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - M Backovic
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France.,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - J Pérez-Vargas
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France.,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - S M de Boer
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - M A Tortorici
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France.,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
| | - G Pehau-Arnaudet
- UMR 3528, CNRS, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France
| | - J Lepault
- Institut de Biologie Intégrative de la Cellule, CNRS (UMR 9198), Gif-sur-Yvette, France
| | - P England
- UMR 3528, CNRS, Institut Pasteur, 25-28 rue du Docteur Roux, 75015 Paris, France.,Proteopole, Plateforme de Biophysique des Macromolécules et de leurs Interactions (PFBMI), Institut Pasteur, 25-28 rue du Dr Roux, F-75724 Paris Cedex 15, France
| | - P J Rottier
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - B J Bosch
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - J S Hub
- Institute for Microbiology and Genetics, University of Goettingen, Justus-von-Liebig weg 11, 37077 Göttingen, Germany.
| | - F A Rey
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale, 75724 Paris Cedex 15, France. .,UMR 3569 Virologie, CNRS-Institut Pasteur, 25-28 Rue du Docteur Roux, 75015 Paris, France
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43
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Domański J, Sansom MSP, Stansfeld PJ, Best RB. Balancing Force Field Protein-Lipid Interactions To Capture Transmembrane Helix-Helix Association. J Chem Theory Comput 2018; 14:1706-1715. [PMID: 29424543 PMCID: PMC5852462 DOI: 10.1021/acs.jctc.7b00983] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Indexed: 01/21/2023]
Abstract
Atomistic simulations have recently been shown to be sufficiently accurate to reversibly fold globular proteins and have provided insights into folding mechanisms. Gaining similar understanding from simulations of membrane protein folding and association would be of great medical interest. All-atom simulations of the folding and assembly of transmembrane protein domains are much more challenging, not least due to very slow diffusion within the lipid bilayer membrane. Here, we focus on a simple and well-characterized prototype of membrane protein folding and assembly, namely the dimerization of glycophorin A, a homodimer of single transmembrane helices. We have determined the free energy landscape for association of the dimer using the CHARMM36 force field. We find that the native structure is a metastable state, but not stable as expected from experimental estimates of the dissociation constant and numerous experimental structures obtained under a variety of conditions. We explore two straightforward approaches to address this problem and demonstrate that they result in stable dimers with dissociation constants consistent with experimental data.
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Affiliation(s)
- Jan Domański
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
| | - Mark S. P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Phillip J. Stansfeld
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Robert B. Best
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
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44
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Boonstra S, Blijleven JS, Roos WH, Onck PR, van der Giessen E, van Oijen AM. Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective. Annu Rev Biophys 2018; 47:153-173. [PMID: 29494252 DOI: 10.1146/annurev-biophys-070317-033018] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Influenza hemagglutinin (HA) is a viral membrane protein responsible for the initial steps of the entry of influenza virus into the host cell. It mediates binding of the virus particle to the host-cell membrane and catalyzes fusion of the viral membrane with that of the host. HA is therefore a major target in the development of antiviral strategies. The fusion of two membranes involves high activation barriers and proceeds through several intermediate states. Here, we provide a biophysical description of the membrane fusion process, relating its kinetic and thermodynamic properties to the large conformational changes taking place in HA and placing these in the context of multiple HA proteins working together to mediate fusion. Furthermore, we highlight the role of novel single-particle experiments and computational approaches in understanding the fusion process and their complementarity with other biophysical approaches.
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Affiliation(s)
- Sander Boonstra
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Jelle S Blijleven
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Wouter H Roos
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Erik van der Giessen
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Antoine M van Oijen
- School of Chemistry; Faculty of Science, Medicine and Health; University of Wollongong, Wollongong, New South Wales 2522, Australia;
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45
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Worch R, Dudek A, Krupa J, Szymaniec A, Setny P. Charged N-terminus of Influenza Fusion Peptide Facilitates Membrane Fusion. Int J Mol Sci 2018; 19:E578. [PMID: 29443945 PMCID: PMC5855800 DOI: 10.3390/ijms19020578] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/29/2018] [Accepted: 02/06/2018] [Indexed: 11/16/2022] Open
Abstract
Cleavage of hemagglutinin precursor (HA0) by cellular proteases results in the formation of two subunits, HA1 and HA2. The N-terminal fragment of HA2, named a fusion peptide (HAfp), possess a charged, amine N-terminus. It has been shown that the N-terminus of HAfp stabilizes the structure of a helical hairpin observed for a 23-amino acid long peptide (HAfp1-23), whose larger activity than HAfp1-20 has been demonstrated recently. In this paper, we analyze the effect of N-terminal charge on peptide-mediated fusion efficiency and conformation changes at the membrane interface by comparison with the corresponding N-acetylated peptides of 20- and 23-amino acid lengths. We found that higher fusogenic activities of peptides with unmodified amino termini correlates with their ability to form helical hairpin structures oriented perpendicularly to the membrane plane. Molecular dynamics simulations showed that acetylated peptides adopt open and surface-bound conformation more often, which induced less disorder of the phospholipid chains, as compared to species with unmodified amino termini.
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Affiliation(s)
- Remigiusz Worch
- Institute of Physics, Polish Academy of Sciences, Lotników 32/46 Avenue, 02-668 Warsaw, Poland.
| | - Anita Dudek
- Centre of New Technologies, University of Warsaw, Banacha 2C Street, 02-097 Warsaw, Poland.
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Joanna Krupa
- Institute of Physics, Polish Academy of Sciences, Lotników 32/46 Avenue, 02-668 Warsaw, Poland.
| | - Anna Szymaniec
- Institute of Physics, Polish Academy of Sciences, Lotników 32/46 Avenue, 02-668 Warsaw, Poland.
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | - Piotr Setny
- Centre of New Technologies, University of Warsaw, Banacha 2C Street, 02-097 Warsaw, Poland.
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46
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Conformation and Trimer Association of the Transmembrane Domain of the Parainfluenza Virus Fusion Protein in Lipid Bilayers from Solid-State NMR: Insights into the Sequence Determinants of Trimer Structure and Fusion Activity. J Mol Biol 2018; 430:695-709. [PMID: 29330069 DOI: 10.1016/j.jmb.2018.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 12/30/2017] [Accepted: 01/02/2018] [Indexed: 01/23/2023]
Abstract
Enveloped viruses enter cells by using their fusion proteins to merge the virus lipid envelope and the cell membrane. While crystal structures of the water-soluble ectodomains of many viral fusion proteins have been determined, the structure and assembly of the C-terminal transmembrane domain (TMD) remains poorly understood. Here we use solid-state NMR to determine the backbone conformation and oligomeric structure of the TMD of the parainfluenza virus 5 fusion protein. 13C chemical shifts indicate that the central leucine-rich segment of the TMD is α-helical in POPC/cholesterol membranes and POPE membranes, while the Ile- and Val-rich termini shift to the β-strand conformation in the POPE membrane. Importantly, lipid mixing assays indicate that the TMD is more fusogenic in the POPE membrane than in the POPC/cholesterol membrane, indicating that the β-strand conformation is important for fusion by inducing membrane curvature. Incorporation of para-fluorinated Phe at three positions of the α-helical core allowed us to measure interhelical distances using 19F spin diffusion NMR. The data indicate that, at peptide:lipid molar ratios of ~1:15, the TMD forms a trimeric helical bundle with inter-helical distances of 8.2-8.4Å for L493F and L504F and 10.5Å for L500F. These data provide high-resolution evidence of trimer formation of a viral fusion protein TMD in phospholipid bilayers, and indicate that the parainfluenza virus 5 fusion protein TMD harbors two functions: the central α-helical core is the trimerization unit of the protein, while the two termini are responsible for inducing membrane curvature by transitioning to a β-sheet conformation.
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47
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Campos SK. Subcellular Trafficking of the Papillomavirus Genome during Initial Infection: The Remarkable Abilities of Minor Capsid Protein L2. Viruses 2017; 9:v9120370. [PMID: 29207511 PMCID: PMC5744145 DOI: 10.3390/v9120370] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/01/2017] [Accepted: 12/02/2017] [Indexed: 12/24/2022] Open
Abstract
Since 2012, our understanding of human papillomavirus (HPV) subcellular trafficking has undergone a drastic paradigm shift. Work from multiple laboratories has revealed that HPV has evolved a unique means to deliver its viral genome (vDNA) to the cell nucleus, relying on myriad host cell proteins and processes. The major breakthrough finding from these recent endeavors has been the realization of L2-dependent utilization of cellular sorting factors for the retrograde transport of vDNA away from degradative endo/lysosomal compartments to the Golgi, prior to mitosis-dependent nuclear accumulation of L2/vDNA. An overview of current models of HPV entry, subcellular trafficking, and the role of L2 during initial infection is provided below, highlighting unresolved questions and gaps in knowledge.
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Affiliation(s)
- Samuel K Campos
- The Department of Immunobiology, The University of Arizona, Tucson, AZ 85721-0240, USA.
- The Department of Molecular & Cellular Biology, The University of Arizona, Tucson, AZ 85721-0240, USA.
- The Cancer Biology Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ 85721-0240, USA.
- The BIO5 Institute, Tucson, AZ 85721-0240, USA.
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48
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Switching between Successful and Dead-End Intermediates in Membrane Fusion. Int J Mol Sci 2017; 18:ijms18122598. [PMID: 29207481 PMCID: PMC5751201 DOI: 10.3390/ijms18122598] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/21/2017] [Accepted: 12/01/2017] [Indexed: 11/16/2022] Open
Abstract
Fusion of cellular membranes during normal biological processes, including proliferation, or synaptic transmission, is mediated and controlled by sophisticated protein machinery ensuring the preservation of the vital barrier function of the membrane throughout the process. Fusion of virus particles with host cell membranes is more sparingly arranged and often mediated by a single fusion protein, and the virus can afford to be less discriminative towards the possible different outcomes of fusion attempts. Formation of leaky intermediates was recently observed in some fusion processes, and an alternative trajectory of the process involving formation of π-shaped structures was suggested. In this study, we apply the methods of elasticity theory and Lagrangian formalism augmented by phenomenological and molecular geometry constraints and boundary conditions to investigate the traits of this trajectory and the drivers behind the choice of one of the possible scenarios depending on the properties of the system. The alternative pathway proved to be a dead end, and, depending on the parameters of the participating membranes and fusion proteins, the system can either reversibly enter the corresponding “leaky” configuration or be trapped in it. A parametric study in the biologically relevant range of variables emphasized the fusion protein properties crucial for the choice of the fusion scenario.
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49
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Lai AL, Millet JK, Daniel S, Freed JH, Whittaker GR. The SARS-CoV Fusion Peptide Forms an Extended Bipartite Fusion Platform that Perturbs Membrane Order in a Calcium-Dependent Manner. J Mol Biol 2017; 429:3875-3892. [PMID: 29056462 PMCID: PMC5705393 DOI: 10.1016/j.jmb.2017.10.017] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/02/2017] [Accepted: 10/12/2017] [Indexed: 01/12/2023]
Abstract
Coronaviruses (CoVs) are a major infectious disease threat and include the pathogenic human pathogens of zoonotic origin: severe acute respiratory syndrome CoV (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV). Entry of CoVs into host cells is mediated by the viral spike (S) protein, which is structurally categorized as a class I viral fusion protein, within the same group as influenza virus and HIV. However, S proteins have two distinct cleavage sites that can be activated by a much wider range of proteases. The exact location of the CoV fusion peptide (FP) has been disputed. However, most evidence suggests that the domain immediately downstream of the S2' cleavage site is the FP (amino acids 798-818 SFIEDLLFNKVTLADAGFMKQY for SARS-CoV, FP1). In our previous electron spin resonance spectroscopic studies, the membrane-ordering effect of influenza virus, HIV, and Dengue virus FPs has been consistently observed. In this study, we used this effect as a criterion to identify and characterize the bona fide SARS-CoV FP. Our results indicate that both FP1 and the region immediately downstream (amino acids 816-835 KQYGECLGDINARDLICAQKF, FP2) induce significant membrane ordering. Furthermore, their effects are calcium dependent, which is consistent with in vivo data showing that calcium is required for SARS-CoV S-mediated fusion. Isothermal titration calorimetry showed a direct interaction between calcium cations and both FPs. This Ca2+-dependency membrane ordering was not observed with influenza FP, indicating that the CoV FP exhibits a mechanistically different behavior. Membrane-ordering effects are greater and penetrate deeper into membranes when FP1 and FP2 act in a concerted manner, suggesting that they form an extended fusion "platform."
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Affiliation(s)
- Alex L Lai
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States
| | - Jean K Millet
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, United States
| | - Susan Daniel
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, United States
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, United States.
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50
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Mahajan M, Chatterjee D, Bhuvaneswari K, Pillay S, Bhattacharjya S. NMR structure and localization of a large fragment of the SARS-CoV fusion protein: Implications in viral cell fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:407-415. [PMID: 28988778 PMCID: PMC7094225 DOI: 10.1016/j.bbamem.2017.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 09/16/2017] [Accepted: 10/03/2017] [Indexed: 01/20/2023]
Abstract
The lethal Coronaviruses (CoVs), Severe Acute Respiratory Syndrome-associated Coronavirus (SARS-CoV) and most recently Middle East Respiratory Syndrome Coronavirus, (MERS-CoV) are serious human health hazard. A successful viral infection requires fusion between virus and host cells carried out by the surface spike glycoprotein or S protein of CoV. Current models propose that the S2 subunit of S protein assembled into a hexameric helical bundle exposing hydrophobic fusogenic peptides or fusion peptides (FPs) for membrane insertion. The N-terminus of S2 subunit of SARS-CoV reported to be active in cell fusion whereby FPs have been identified. Atomic-resolution structure of FPs derived either in model membranes or in membrane mimic environment would glean insights toward viral cell fusion mechanism. Here, we have solved 3D structure, dynamics and micelle localization of a 64-residue long fusion peptide or LFP in DPC detergent micelles by NMR methods. Micelle bound structure of LFP is elucidated by the presence of discretely folded helical and intervening loops. The C-terminus region, residues F42-Y62, displays a long hydrophobic helix, whereas the N-terminus is defined by a short amphipathic helix, residues R4-Q12. The intervening residues of LFP assume stretches of loops and helical turns. The N-terminal helix is sustained by close aromatic and aliphatic sidechain packing interactions at the non-polar face. 15N{1H}NOE studies indicated dynamical motion, at ps-ns timescale, of the helices of LFP in DPC micelles. PRE NMR showed that insertion of several regions of LFP into DPC micelle core. Together, the current study provides insights toward fusion mechanism of SARS-CoV.
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Affiliation(s)
- Mukesh Mahajan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Deepak Chatterjee
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Kannaian Bhuvaneswari
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Shubhadra Pillay
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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