1
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Spencer RKW, Smirnova YG, Soleimani A, Müller M. Transient pores in hemifusion diaphragms. Biophys J 2024; 123:2455-2475. [PMID: 38867448 PMCID: PMC11365115 DOI: 10.1016/j.bpj.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/07/2024] [Accepted: 06/07/2024] [Indexed: 06/14/2024] Open
Abstract
Exchange of material across two membranes, as in the case of synaptic neurotransmitter release from a vesicle, involves the formation and poration of a hemifusion diaphragm (HD). The nontrivial geometry of the HD leads to environment-dependent control, regarding the stability and dynamics of the pores required for this kind of exocytosis. This work combines particle simulations, field-based calculations, and phenomenological modeling to explore the factors influencing the stability, dynamics, and possible control mechanisms of pores in HDs. We find that pores preferentially form at the HD rim, and that their stability is sensitive to a number of factors, including the three line tensions, membrane tension, HD size, and the ability of lipids to "flip-flop" across leaflets. Along with a detailed analysis of these factors, we discuss ways that vesicles or cells may use them to open and close pores and thereby quickly and efficiently transport material.
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Affiliation(s)
- Russell K W Spencer
- Institute for Theoretical Physics, Georg-August University, Göttingen, Germany.
| | - Yuliya G Smirnova
- Institute for Theoretical Physics, Georg-August University, Göttingen, Germany; Technische Universität Dortmund, Dortmund, Germany
| | - Alireza Soleimani
- Institute for Theoretical Physics, Georg-August University, Göttingen, Germany
| | - Marcus Müller
- Institute for Theoretical Physics, Georg-August University, Göttingen, Germany.
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2
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Rizo J, Sari L, Jaczynska K, Rosenmund C, Lin MM. Molecular mechanism underlying SNARE-mediated membrane fusion enlightened by all-atom molecular dynamics simulations. Proc Natl Acad Sci U S A 2024; 121:e2321447121. [PMID: 38593076 PMCID: PMC11032479 DOI: 10.1073/pnas.2321447121] [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: 12/05/2023] [Accepted: 03/18/2024] [Indexed: 04/11/2024] Open
Abstract
The SNAP receptor (SNARE) proteins syntaxin-1, SNAP-25, and synaptobrevin mediate neurotransmitter release by forming tight SNARE complexes that fuse synaptic vesicles with the plasma membranes in microseconds. Membrane fusion is generally explained by the action of proteins on macroscopic membrane properties such as curvature, elastic modulus, and tension, and a widespread model envisions that the SNARE motifs, juxtamembrane linkers, and C-terminal transmembrane regions of synaptobrevin and syntaxin-1 form continuous helices that act mechanically as semirigid rods, squeezing the membranes together as they assemble ("zipper") from the N to the C termini. However, the mechanism underlying fast SNARE-induced membrane fusion remains unknown. We have used all-atom molecular dynamics simulations to investigate this mechanism. Our results need to be interpreted with caution because of the limited number and length of the simulations, but they suggest a model of membrane fusion that has a natural physicochemical basis, emphasizes local molecular events over general membrane properties, and explains extensive experimental data. In this model, the central event that initiates fast (microsecond scale) membrane fusion occurs when the SNARE helices zipper into the juxtamembrane linkers which, together with the adjacent transmembrane regions, promote encounters of acyl chains from both bilayers at the polar interface. The resulting hydrophobic nucleus rapidly expands into stalk-like structures that gradually progress to form a fusion pore, aided by the SNARE transmembrane regions and without clearly discernible intermediates. The propensity of polyunsaturated lipids to participate in encounters that initiate fusion suggests that these lipids may be important for the high speed of neurotransmitter release.
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Affiliation(s)
- Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75390
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Levent Sari
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Klaudia Jaczynska
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX75390
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Christian Rosenmund
- Institute of Neurophysiology, Charité—Universitätsmedizin Berlin, Berlin10117, Germany
- NeuroCure Cluster of Excellence, Berlin10117, Germany
| | - Milo M. Lin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX75390
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX75390
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3
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Jahn R, Cafiso DC, Tamm LK. Mechanisms of SNARE proteins in membrane fusion. Nat Rev Mol Cell Biol 2024; 25:101-118. [PMID: 37848589 DOI: 10.1038/s41580-023-00668-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2023] [Indexed: 10/19/2023]
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are a family of small conserved eukaryotic proteins that mediate membrane fusion between organelles and with the plasma membrane. SNAREs are directly or indirectly anchored to membranes. Prior to fusion, complementary SNAREs assemble between membranes with the aid of accessory proteins that provide a scaffold to initiate SNARE zippering, pulling the membranes together and mediating fusion. Recent advances have enabled the construction of detailed models describing bilayer transitions and energy barriers along the fusion pathway and have elucidated the structures of SNAREs complexed in various states with regulatory proteins. In this Review, we discuss how these advances are yielding an increasingly detailed picture of the SNARE-mediated fusion pathway, leading from first contact between the membranes via metastable non-bilayer intermediates towards the opening and expansion of a fusion pore. We describe how SNARE proteins assemble into complexes, how this assembly is regulated by accessory proteins and how SNARE complexes overcome the free energy barriers that prevent spontaneous membrane fusion.
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Affiliation(s)
- Reinhard Jahn
- Laboratory of Neurobiology, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - David C Cafiso
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
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4
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Takito J, Nonaka N. Osteoclasts at Bone Remodeling: Order from Order. Results Probl Cell Differ 2024; 71:227-256. [PMID: 37996681 DOI: 10.1007/978-3-031-37936-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Osteoclasts are multinucleated bone-resorbing cells derived from the monocyte/macrophage lineage. The macrophage colony-stimulating factor/receptor activator of nuclear factor κB ligand (M-CSF/RANKL) signaling network governs the differentiation of precursor cells into fusion-competent mononucleated cells. Repetitive fusion of fusion-competent cells produces multinucleated osteoclasts. Osteoclasts are believed to die via apoptosis after bone resorption. However, recent studies have found that osteoclastogenesis in vivo proceeds by replacing the old nucleus of existing osteoclasts with a single newly differentiated mononucleated cell. Thus, the formation of new osteoclasts is minimal. Furthermore, the sizes of osteoclasts can change via cell fusion and fission in response to external conditions. On the other hand, osteoclastogenesis in vitro involves various levels of heterogeneity, including osteoclast precursors, mode of fusion, and properties of the differentiated osteoclasts. To better understand the origin of these heterogeneities and the plasticity of osteoclasts, we examine several processes of osteoclastogenesis in this review. Candidate mechanisms that create heterogeneity involve asymmetric cell division, osteoclast niche, self-organization, and mode of fusion and fission. Elucidation of the plasticity or fluctuation of the M-CSF/RANKL network should be an important topic for future researches.
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Affiliation(s)
- Jiro Takito
- Department of Oral Anatomy and Developmental Biology, School of Dentistry, Showa University, Tokyo, Japan.
| | - Naoko Nonaka
- Department of Oral Anatomy and Developmental Biology, School of Dentistry, Showa University, Tokyo, Japan
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5
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Tror S, Jeon S, Nguyen HT, Huh E, Shin K. A Self-Regenerating Artificial Cell, that is One Step Closer to Living Cells: Challenges and Perspectives. SMALL METHODS 2023; 7:e2300182. [PMID: 37246263 DOI: 10.1002/smtd.202300182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/29/2023] [Indexed: 05/30/2023]
Abstract
Controllable, self-regenerating artificial cells (SRACs) can be a vital advancement in the field of synthetic biology, which seeks to create living cells by recombining various biological molecules in the lab. This represents, more importantly, the first step on a long journey toward creating reproductive cells from rather fragmentary biochemical mimics. However, it is still a difficult task to replicate the complex processes involved in cell regeneration, such as genetic material replication and cell membrane division, in artificially created spaces. This review highlights recent advances in the field of controllable, SRACs and the strategies to achieve the goal of creating such cells. Self-regenerating cells start by replicating DNA and transferring it to a location where proteins can be synthesized. Functional but essential proteins must be synthesized for sustained energy generation and survival needs and function in the same liposomal space. Finally, self-division and repeated cycling lead to autonomous, self-regenerating cells. The pursuit of controllable, SRACs will enable authors to make bold advances in understanding life at the cellular level, ultimately providing an opportunity to use this knowledge to understand the nature of life.
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Affiliation(s)
- Seangly Tror
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - SeonMin Jeon
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Huong Thanh Nguyen
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Eunjin Huh
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Kwanwoo Shin
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
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6
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Stanton AE, Hughson FM. The machinery of vesicle fusion. Curr Opin Cell Biol 2023; 83:102191. [PMID: 37421936 PMCID: PMC10529041 DOI: 10.1016/j.ceb.2023.102191] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 07/10/2023]
Abstract
The compartmentalization of eukaryotic cells is reliant on the fidelity of vesicle-mediated intracellular transport. Vesicles deliver their cargo via membrane fusion, a process requiring membrane tethers, Sec1/Munc18 (SM) proteins, and SNAREs. These components function in concert to ensure that membrane fusion is efficient and accurate, but the mechanisms underlying their cooperative action are still in many respects mysterious. In this brief review, we highlight recent progress toward a more integrative understanding of the vesicle fusion machinery. We focus particular attention on cryo-electron microscopy structures of intact multisubunit tethers in complex with SNAREs or SM proteins, as well as a structure of an SM protein bound to multiple SNAREs. The insights gained from this work emphasize the advantages of studying the fusion machinery intact and in context.
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Affiliation(s)
- Abigail E Stanton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Frederick M Hughson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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7
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Zheng L, Bandara SR, Tan Z, Leal C. Lipid nanoparticle topology regulates endosomal escape and delivery of RNA to the cytoplasm. Proc Natl Acad Sci U S A 2023; 120:e2301067120. [PMID: 37364130 PMCID: PMC10318962 DOI: 10.1073/pnas.2301067120] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/04/2023] [Indexed: 06/28/2023] Open
Abstract
RNA therapeutics have the potential to resolve a myriad of genetic diseases. Lipid nanoparticles (LNPs) are among the most successful RNA delivery systems. Expanding their use for the treatment of more genetic diseases hinges on our ability to continuously evolve the design of LNPs with high potency, cellular-specific targeting, and low side effects. Overcoming the difficulty of releasing cargo from endocytosed LNPs remains a significant hurdle. Here, we investigate the fundamental properties of nonviral RNA nanoparticles pertaining to the activation of topological transformations of endosomal membranes and RNA translocation into the cytosol. We show that, beyond composition, LNP fusogenicity can be prescribed by designing LNP nanostructures that lower the energetic cost of fusion and fusion-pore formation with a target membrane. The inclusion of structurally active lipids leads to enhanced LNP endosomal fusion, fast evasion of endosomal entrapment, and efficacious RNA delivery. For example, conserving the lipid make-up, RNA-LNPs having cuboplex nanostructures are significantly more efficacious at endosomal escape than traditional lipoplex constructs.
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Affiliation(s)
- Lining Zheng
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Sarith R. Bandara
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Zhengzhong Tan
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Cecilia Leal
- Department of Materials Science and Engineering, University of Illinois Urbana-Champaign, Urbana, IL61801
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8
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Zhang Y, York J, Brindley MA, Nunberg JH, Melikyan GB. Fusogenic structural changes in arenavirus glycoproteins are associated with viroporin activity. PLoS Pathog 2023; 19:e1011217. [PMID: 37494374 PMCID: PMC10406333 DOI: 10.1371/journal.ppat.1011217] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 08/07/2023] [Accepted: 07/04/2023] [Indexed: 07/28/2023] Open
Abstract
Many enveloped viruses enter host cells by fusing with acidic endosomes. The fusion activity of multiple viral envelope glycoproteins does not generally affect viral membrane permeability. However, fusion induced by the Lassa virus (LASV) glycoprotein complex (GPc) is always preceded by an increase in viral membrane permeability and the ensuing acidification of the virion interior. Here, systematic investigation of this LASV fusion phenotype using single pseudovirus tracking in live cells reveals that the change in membrane barrier function is associated with the fusogenic conformational reorganization of GPc. We show that a small-molecule fusion inhibitor or mutations that impair viral fusion by interfering with GPc refolding into the post-fusion structure prevent the increase in membrane permeability. We find that the increase in virion membrane permeability occurs early during endosomal maturation and is facilitated by virus-cell contact. This increase is observed using diverse arenavirus glycoproteins, whether presented on lentivirus-based pseudoviruses or arenavirus-like particles, and in multiple different cell types. Collectively, these results suggest that conformational changes in GPc triggered by low pH and cell factor binding are responsible for virion membrane permeabilization and acidification of the virion core prior to fusion. We propose that this viroporin-like activity may augment viral fusion and/or post-fusion steps of infection, including ribonucleoprotein release into the cytoplasm.
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Affiliation(s)
- You Zhang
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Joanne York
- Montana Biotechnology Center, University of Montana, Missoula, Montana, United States of America
| | - Melinda A. Brindley
- Department of Infectious Diseases, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Jack H. Nunberg
- Montana Biotechnology Center, University of Montana, Missoula, Montana, United States of America
| | - Gregory B. Melikyan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
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9
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Romani A, Sergi D, Zauli E, Voltan R, Lodi G, Vaccarezza M, Caruso L, Previati M, Zauli G. Nutrients, herbal bioactive derivatives and commensal microbiota as tools to lower the risk of SARS-CoV-2 infection. Front Nutr 2023; 10:1152254. [PMID: 37324739 PMCID: PMC10267353 DOI: 10.3389/fnut.2023.1152254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
The SARS-CoV-2 outbreak has infected a vast population across the world, causing more than 664 million cases and 6.7 million deaths by January 2023. Vaccination has been effective in reducing the most critical aftermath of this infection, but some issues are still present regarding re-infection prevention, effectiveness against variants, vaccine hesitancy and worldwide accessibility. Moreover, although several old and new antiviral drugs have been tested, we still lack robust and specific treatment modalities. It appears of utmost importance, facing this continuously growing pandemic, to focus on alternative practices grounded on firm scientific bases. In this article, we aim to outline a rigorous scientific background and propose complementary nutritional tools useful toward containment, and ultimately control, of SARS-CoV-2 infection. In particular, we review the mechanisms of viral entry and discuss the role of polyunsaturated fatty acids derived from α-linolenic acid and other nutrients in preventing the interaction of SARS-CoV-2 with its entry gateways. In a similar way, we analyze in detail the role of herbal-derived pharmacological compounds and specific microbial strains or microbial-derived polypeptides in the prevention of SARS-CoV-2 entry. In addition, we highlight the role of probiotics, nutrients and herbal-derived compounds in stimulating the immunity response.
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Affiliation(s)
- Arianna Romani
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Domenico Sergi
- Department of Translational Medicine and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Enrico Zauli
- Department of Translational Medicine and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Rebecca Voltan
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Giada Lodi
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Mauro Vaccarezza
- Curtin Medical School & Curtin Health Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Perth, WA, Australia
| | - Lorenzo Caruso
- Department of Environmental and Prevention Sciences and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Maurizio Previati
- Department of Translational Medicine and LTTA Centre, University of Ferrara, Ferrara, Italy
| | - Giorgio Zauli
- Research Department, King Khaled Eye Specialistic Hospital, Riyadh, Saudi Arabia
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10
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Osetrina DA, Kusova AM, Bikmullin AG, Klochkova EA, Yulmetov AR, Semenova EA, Mukhametzyanov TA, Usachev KS, Klochkov VV, Blokhin DS. Extent of N-Terminus Folding of Semenogelin 1 Cleavage Product Determines Tendency to Amyloid Formation. Int J Mol Sci 2023; 24:ijms24108949. [PMID: 37240295 DOI: 10.3390/ijms24108949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
It is known that four peptide fragments of predominant protein in human semen Semenogelin 1 (SEM1) (SEM1(86-107), SEM1(68-107), SEM1(49-107) and SEM1(45-107)) are involved in fertilization and amyloid formation processes. In this work, the structure and dynamic behavior of SEM1(45-107) and SEM1(49-107) peptides and their N-domains were described. According to ThT fluorescence spectroscopy data, it was shown that the amyloid formation of SEM1(45-107) starts immediately after purification, which is not observed for SEM1(49-107). Seeing that the peptide amino acid sequence of SEM1(45-107) differs from SEM1(49-107) only by the presence of four additional amino acid residues in the N domain, these domains of both peptides were obtained via solid-phase synthesis and the difference in their dynamics and structure was investigated. SEM1(45-67) and SEM1(49-67) showed no principal difference in dynamic behavior in water solution. Furthermore, we obtained mostly disordered structures of SEM1(45-67) and SEM1(49-67). However, SEM1(45-67) contains a helix (E58-K60) and helix-like (S49-Q51) fragments. These helical fragments may rearrange into β-strands during amyloid formation process. Thus, the difference in full-length peptides' (SEM1(45-107) and SEM1(49-107)) amyloid-forming behavior may be explained by the presence of a structured helix at the SEM1(45-107) N-terminus, which contributes to an increased rate of amyloid formation.
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Affiliation(s)
- Daria A Osetrina
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Aleksandra M Kusova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan 420111, Russia
| | - Aydar G Bikmullin
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
| | - Evelina A Klochkova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
| | - Aydar R Yulmetov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Evgenia A Semenova
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Timur A Mukhametzyanov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Konstantin S Usachev
- Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420021, Russia
- Laboratory for Structural Analysis of Biomacromolecules, Federal Research Center "Kazan Scientific Center of Russian Academy of Sciences", Kazan 420111, Russia
| | - Vladimir V Klochkov
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Dmitriy S Blokhin
- NMR Laboratory, Medical Physics Department, Institute of Physics, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
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11
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Caliari A, Hanczyc MM, Imai M, Xu J, Yomo T. Quantification of Giant Unilamellar Vesicle Fusion Products by High-Throughput Image Analysis. Int J Mol Sci 2023; 24:ijms24098241. [PMID: 37175944 PMCID: PMC10179211 DOI: 10.3390/ijms24098241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Artificial cells are based on dynamic compartmentalized systems. Thus, remodeling of membrane-bound systems, such as giant unilamellar vesicles, is finding applications beyond biological studies, to engineer cell-mimicking structures. Giant unilamellar vesicle fusion is rapidly becoming an essential experimental step as artificial cells gain prominence in synthetic biology. Several techniques have been developed to accomplish this step, with varying efficiency and selectivity. To date, characterization of vesicle fusion has relied on small samples of giant vesicles, examined either manually or by fluorometric assays on suspensions of small and large unilamellar vesicles. Automation of the detection and characterization of fusion products is now necessary for the screening and optimization of these fusion protocols. To this end, we implemented a fusion assay based on fluorophore colocalization on the membranes and in the lumen of vesicles. Fluorescence colocalization was evaluated within single compartments by image segmentation with minimal user input, allowing the application of the technique to high-throughput screenings. After detection, statistical information on vesicle fluorescence and morphological properties can be summarized and visualized, assessing lipid and content transfer for each object by the correlation coefficient of different fluorescence channels. Using this tool, we report and characterize the unexpected fusogenic activity of sodium chloride on phosphatidylcholine giant vesicles. Lipid transfer in most of the vesicles could be detected after 20 h of incubation, while content exchange only occurred with additional stimuli in around 8% of vesicles.
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Affiliation(s)
- Adriano Caliari
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, China
- Laboratory for Artificial Biology, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Polo Scientifico e Tecnologico Fabio Ferrari, Polo B, Via Sommarive 9, 38123 Povo, Italy
| | - Martin M Hanczyc
- Laboratory for Artificial Biology, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Polo Scientifico e Tecnologico Fabio Ferrari, Polo B, Via Sommarive 9, 38123 Povo, Italy
| | - Masayuki Imai
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aramaki, Aoba, Sendai 980-8578, Japan
| | - Jian Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, China
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12
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Milogrodzka I, Nguyen Pham DT, Sama GR, Samadian H, Zhai J, de Campo L, Kirby NM, Scott TF, Banaszak Holl MM, van 't Hag L. Effect of Cholesterol on Biomimetic Membrane Curvature and Coronavirus Fusion Peptide Encapsulation. ACS NANO 2023; 17:8598-8612. [PMID: 37078604 DOI: 10.1021/acsnano.3c01095] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Biomimetic cubic phases can be used for protein encapsulation in a variety of applications such as biosensors and drug delivery. Cubic phases with a high concentration of cholesterol and phospholipids were obtained herein. It is shown that the cubic phase structure can be maintained with a higher concentration of biomimetic membrane additives than has been reported previously. Opposing effects on the curvature of the membrane were observed upon the addition of phospholipids and cholesterol. Furthermore, the coronavirus fusion peptide significantly increased the negative curvature of the biomimetic membrane with cholesterol. We show that the viral fusion peptide can undergo structural changes leading to the formation of hydrophobic α-helices that insert into the lipid bilayer. This is of high importance, as a fusion peptide that induces increased negative curvature as shown by the formation of inverse hexagonal phases allows for greater contact area between two membranes, which is required for viral fusion to occur. The cytotoxicity assay showed that the toxicity toward HeLa cells was dramatically decreased when the cholesterol or peptide level in the nanoparticles increased. This suggests that the addition of cholesterol can improve the biocompatibility of the cubic phase nanoparticles, making them safer for use in biomedical applications. As the results, this work improves the potential for the biomedical end-use applications of the nonlamellar lipid nanoparticles and shows the need of systematic formulation studies due to the complex interplay of all components.
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Affiliation(s)
- Izabela Milogrodzka
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Duy Tue Nguyen Pham
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Gopal R Sama
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Hajar Samadian
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Jiali Zhai
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Liliana de Campo
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Kirrawee, NSW 2234, Australia
| | - Nigel M Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Timothy F Scott
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
- Department of Materials Science and Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Mark M Banaszak Holl
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
- Department of Mechanical and Materials Engineering, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Leonie van 't Hag
- Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
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13
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Cano-Ortiz L, Luedde T, Münk C. HIV-1 restriction by SERINC5. Med Microbiol Immunol 2023; 212:133-140. [PMID: 35333966 PMCID: PMC10085909 DOI: 10.1007/s00430-022-00732-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/08/2022] [Indexed: 11/25/2022]
Abstract
Serine incorporator 5 (SERINC5 or SER5) is a multipass transmembrane protein with ill-defined cellular activities. SER5 was recently described as a human immunodeficiency virus 1 (HIV-1) restriction factor capable of inhibiting HIV-1 that does not express its accessory protein Nef (Δ Nef). SER5 incorporated into the viral membrane impairs the entry of HIV-1 by disrupting the fusion between the viral and the plasma membrane after envelope receptor interaction induced the first steps of the fusion process. The mechanisms of how SER5 prevents membrane fusion are not fully understood and viral envelope proteins were identified that escape the SER5-mediated restriction. Primate lentiviruses, such as HIV-1 and simian immunodeficiency viruses (SIVs), use their accessory protein Nef to downregulate SER5 from the plasma membrane by inducing an endocytic pathway. In addition to being directly antiviral, recent data suggest that SER5 is an important adapter protein in innate signaling pathways leading to the induction of inflammatory cytokines. This review discusses the current knowledge about HIV-1 restriction by SER5.
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Affiliation(s)
- Lucía Cano-Ortiz
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Tom Luedde
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Building 23.12.U1.82, Moorenstr. 5, 40225, Düsseldorf, Germany.
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14
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Joardar A, Chakraborty H. Differential Behavior of Eicosapentaenoic and Docosahexaenoic Acids on the Organization, Dynamics, and Fusion of Homogeneous and Heterogeneous Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4439-4449. [PMID: 36931902 DOI: 10.1021/acs.langmuir.3c00119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Membrane fusion is a common course in innumerable biological processes that helps in the survival of eukaryotes. Enveloped viruses utilize this process to enter the host cells. Generally, the membrane lipid compositions play an important role in membrane fusion by modulating the membrane's physical properties and the behavior of membrane proteins in the cellular milieu. In this work, we have demonstrated the role of polyunsaturated fatty acids (PUFAs), such as eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids, on the organization, dynamics, and fusion of homogeneous and heterogeneous membranes. We have exploited arrays of steady-state and time-resolved fluorescence spectroscopic methods and polyethylene glycol-induced membrane fusion assay to elucidate the behavior of EPA and DHA on dioleoyl phosphatidylcholine (DOPC)/cholesterol (CH) homogeneous and DOPC/sphingomyelin/CH heterogeneous membranes. Our results suggest that EPA and DHA display differential effects on two different membranes. The effects of PUFAs in homogeneous membranes are majorly attributed to their flexible chain dynamics, whereas the ability of PUFA-induced cholesterol transfer from the lo to the ld phase rules their behavior in heterogeneous membranes. Overall, our results provide detailed information on the effect of PUFAs on homogeneous and heterogeneous membranes.
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Affiliation(s)
- Ankita Joardar
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
| | - Hirak Chakraborty
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
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15
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Joardar A, Pandia S, Chakraborty H. Effect of polyunsaturated free fatty acids on the membrane fusion mechanism. SOFT MATTER 2023; 19:733-742. [PMID: 36617878 DOI: 10.1039/d2sm01474b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Membrane fusion is one of the important processes for the survival of eukaryotic cells and the entry of enveloped viruses into the host cells. Lipid composition plays a crucial role by modulating the organization and dynamics of the membrane, as well as the structure and conformation of membrane proteins. The diversity of the lipid acyl chain in its length and degree of unsaturation originates from the variation in free fatty acids (FFAs). We have studied the effect of linoleic (LA) and alpha-linolenic (ALA) acids on the depth-dependent organization, dynamics, and fusion of DOPC/DOPE (70/30 mol%) membranes utilizing steady-state and time-resolved fluorescence spectroscopic methods. Our results suggest that membranes with 5 mol% LA stabilize the stalk-intermediate and promote lipid mixing at the early stage of the process, i.e., the fusion follows the classical stalk model. Conversely, the extents of lipid and content mixing at the stalk intermediate are similar in the presence of 5 mol% of ALA, indicating the fusion mechanism as a nonclassical one like in the DOPC/DOPE (70/30 mol%) membranes. Our results provide an in-depth insight into the effect of the increasing degree of fatty acid tail unsaturation on membrane organization and dynamics and their impact on the membrane fusion mechanism.
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Affiliation(s)
- Ankita Joardar
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India.
| | - Swaratmika Pandia
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India.
| | - Hirak Chakraborty
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India.
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16
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Palfreyman MT, West SE, Jorgensen EM. SNARE Proteins in Synaptic Vesicle Fusion. ADVANCES IN NEUROBIOLOGY 2023; 33:63-118. [PMID: 37615864 DOI: 10.1007/978-3-031-34229-5_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Neurotransmitters are stored in small membrane-bound vesicles at synapses; a subset of synaptic vesicles is docked at release sites. Fusion of docked vesicles with the plasma membrane releases neurotransmitters. Membrane fusion at synapses, as well as all trafficking steps of the secretory pathway, is mediated by SNARE proteins. The SNAREs are the minimal fusion machinery. They zipper from N-termini to membrane-anchored C-termini to form a 4-helix bundle that forces the apposed membranes to fuse. At synapses, the SNAREs comprise a single helix from syntaxin and synaptobrevin; SNAP-25 contributes the other two helices to complete the bundle. Unc13 mediates synaptic vesicle docking and converts syntaxin into the permissive "open" configuration. The SM protein, Unc18, is required to initiate and proofread SNARE assembly. The SNAREs are then held in a half-zippered state by synaptotagmin and complexin. Calcium removes the synaptotagmin and complexin block, and the SNAREs drive vesicle fusion. After fusion, NSF and alpha-SNAP unwind the SNAREs and thereby recharge the system for further rounds of fusion. In this chapter, we will describe the discovery of the SNAREs, their relevant structural features, models for their function, and the central role of Unc18. In addition, we will touch upon the regulation of SNARE complex formation by Unc13, complexin, and synaptotagmin.
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Affiliation(s)
- Mark T Palfreyman
- School of Biological Sciences, and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Sam E West
- School of Biological Sciences, and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Erik M Jorgensen
- School of Biological Sciences, and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA.
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17
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Villamil Giraldo AM, Mannsverk S, Kasson PM. Measuring single-virus fusion kinetics using an assay for nucleic acid exposure. Biophys J 2022; 121:4467-4475. [PMID: 36330566 PMCID: PMC9748363 DOI: 10.1016/j.bpj.2022.11.002] [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: 05/23/2022] [Revised: 09/26/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022] Open
Abstract
The kinetics by which individual enveloped viruses fuse with membranes provide an important window into viral-entry mechanisms. We have developed a real-time assay using fluorescent probes for single-virus genome exposure than can report on stages of viral entry including or subsequent to fusion pore formation and prior to viral genome trafficking. We accomplish this using oxazole yellow nucleic-acid-binding dyes, which can be encapsulated in the lumen of target membranes to permit specific detection of fusion events. Since increased fluorescence of the dye occurs only when it encounters viral genome via a fusion pore and binds, this assay excludes content leakage without fusion. Using this assay, we show that influenza virus fuses with liposomes of different sizes with indistinguishable kinetics by both testing liposomes extruded through pores of different radii and showing that the fusion kinetics of individual liposomes are uncorrelated with the size of the liposome. These results suggest that the starting curvature of such liposomes does not control the rate-limiting steps in influenza entry.
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Affiliation(s)
- Ana M Villamil Giraldo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Steinar Mannsverk
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Peter M Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden; Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia.
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18
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McCann N, Castellino FJ. Cell Entry and Unusual Replication of SARS-CoV-2. Curr Drug Targets 2022; 23:1539-1554. [PMID: 36239725 DOI: 10.2174/1389450124666221014102927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND SARS-CoV-2 is the causative virus for the CoVID-19 pandemic that has frequently mutated to continue to infect and resist available vaccines. Emerging new variants of the virus have complicated notions of immunity conferred by vaccines versus immunity that results from infection. While we continue to progress from epidemic to endemic as a result of this collective immunity, the pandemic remains a morbid and mortal problem. OBJECTIVE The SARS-CoV-2 virus has a very complex manner of replication. The spike protein, one of the four structural proteins of the encapsulated virus, is central to the ability of the virus to penetrate cells to replicate. The objective of this review is to summarize these complex features of viral replication. METHODS A review of the recent literature was performed on the biology of SARS-CoV-2 infection from published work from PubMed and works reported to preprint servers, e.g., bioRxiv and medRxiv. RESULTS AND CONCLUSION The complex molecular and cellular biology involved in SARS-CoV-2 replication and the origination of >30 proteins from a single open reading frame (ORF) have been summarized, as well as the structural biology of spike protein, a critical factor in the cellular entry of the virus, which is a necessary feature for it to replicate and cause disease.
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Affiliation(s)
- Nathan McCann
- Department of Chemistry and Biochemistry and W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46530, USA
| | - Francis J Castellino
- Department of Chemistry and Biochemistry and W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46530, USA
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19
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Molotkovsky RJ, Kuzmin PI. Fusion of Peroxisome and Lipid Droplet Membranes: Expansion of a π-Shaped Structure. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2022. [DOI: 10.1134/s1990747822050105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Kalutsky MA, Galimzyanov TR, Molotkovsky RJ. A Model of Lipid Monolayer-Bilayer Fusion of Lipid Droplets and Peroxisomes. MEMBRANES 2022; 12:membranes12100992. [PMID: 36295751 PMCID: PMC9612070 DOI: 10.3390/membranes12100992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 06/01/2023]
Abstract
Lipid droplets are unique organelles that store neutral lipids encapsulated by the lipid monolayer. In some processes of cellular metabolism, lipid droplets interact with peroxisomes resulting in the fusion of their envelopes and the formation of protrusions of the peroxisome monolayer, called pexopodia. The formation of pexopodia is facilitated by free fatty acids generated during lipolysis within lipid droplets. In this work, we studied the fusion of monolayer and bilayer membranes during the interaction between lipid droplets and peroxisomes. To this end, we built the energy trajectory of this process using the continuum elasticity theory and investigated the molecular details of the fusion structures utilizing molecular dynamics. We divided the fusion process into two stages: formation of a stalk and its consequent expansion into pexopodia. We found that in the considered system, the stalk was energetically more stable and had a lower energy barrier of formation compared to the case of bilayer fusion. The further evolution of the stalk depended on the value of the spontaneous curvature of the membrane in a threshold manner. We attributed the possible expansion of the stalk to the incorporation of free fatty acids into the stalk region. The developed model allowed describing quantitatively the process of monolayer-bilayer fusion.
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Affiliation(s)
- Maksim A. Kalutsky
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy Prospekt, 119071 Moscow, Russia
- Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Timur R. Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy Prospekt, 119071 Moscow, Russia
| | - Rodion J. Molotkovsky
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy Prospekt, 119071 Moscow, Russia
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21
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Di Bartolo AL, Tomes CN, Mayorga LS, Masone D. Enhanced Expansion and Reduced Kiss-and-Run Events in Fusion Pores Steered by Synaptotagmin-1 C2B Domains. J Chem Theory Comput 2022; 18:4544-4554. [PMID: 35759758 DOI: 10.1021/acs.jctc.2c00424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fusion pore controls the release of exocytotic vesicle contents through a precise orchestration of lipids from the fusing membranes and proteins. There is a major lipid reorganization during the different stages in life of the fusion pore (membrane fusion, nucleation, and expansion) that can be scrutinized thermodynamically. In this work, using umbrella sampling simulations we describe the expansion of the fusion pore. We have calculated free energy profiles to drive a nascent, just nucleated, fusion pore to its expanded configuration. We have quantified the effects on the free energy of one and two Synaptotagmin-1 C2B domains in the cytosolic space. We show that C2B domains cumulatively reduce the cost for expansion, favoring the system to evolve toward full fusion. Finally, by conducting thousands of unbiased molecular dynamics simulations, we show that C2B domains significantly decrease the probability of kiss-and-run events.
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Affiliation(s)
- Ary Lautaro Di Bartolo
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Claudia N Tomes
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Luis S Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
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22
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Abstract
Major recent advances and previous data have led to a plausible model of how key proteins mediate neurotransmitter release. In this model, the soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptor (SNARE) proteins syntaxin-1, SNAP-25, and synaptobrevin form tight complexes that bring the membranes together and are crucial for membrane fusion. NSF and SNAPs disassemble SNARE complexes and ensure that fusion occurs through an exquisitely regulated pathway that starts with Munc18-1 bound to a closed conformation of syntaxin-1. Munc18-1 also binds to synaptobrevin, forming a template to assemble the SNARE complex when Munc13-1 opens syntaxin-1 while bridging the vesicle and plasma membranes. Synaptotagmin-1 and complexin bind to partially assembled SNARE complexes, likely stabilizing them and preventing fusion until Ca2+ binding to synaptotagmin-1 causes dissociation from the SNARE complex and induces interactions with phospholipids that help trigger release. Although fundamental questions remain about the mechanism of membrane fusion, these advances provide a framework to investigate the mechanisms underlying presynaptic plasticity.
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Affiliation(s)
- Josep Rizo
- Departments of Biophysics, Biochemistry, and Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA;
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23
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SNARE proteins: zip codes in vesicle targeting? Biochem J 2022; 479:273-288. [PMID: 35119456 PMCID: PMC8883487 DOI: 10.1042/bcj20210719] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/01/2021] [Accepted: 12/22/2021] [Indexed: 12/17/2022]
Abstract
Membrane traffic in eukaryotic cells is mediated by transport vesicles that bud from a precursor compartment and are transported to their destination compartment where they dock and fuse. To reach their intracellular destination, transport vesicles contain targeting signals such as Rab GTPases and polyphosphoinositides that are recognized by tethering factors in the cytoplasm and that connect the vesicles with their respective destination compartment. The final step, membrane fusion, is mediated by SNARE proteins. SNAREs are connected to targeting signals and tethering factors by multiple interactions. However, it is still debated whether SNAREs only function downstream of targeting and tethering or whether they also participate in regulating targeting specificity. Here, we review the evidence and discuss recent data supporting a role of SNARE proteins as targeting signals in vesicle traffic.
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24
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Nikolaus J, Hancock K, Tsemperouli M, Baddeley D, Karatekin E. Optimal Detection of Fusion Pore Dynamics Using Polarized Total Internal Reflection Fluorescence Microscopy. Front Mol Biosci 2021; 8:740408. [PMID: 34859048 PMCID: PMC8631473 DOI: 10.3389/fmolb.2021.740408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/06/2021] [Indexed: 11/13/2022] Open
Abstract
The fusion pore is the initial narrow connection that forms between fusing membranes. During vesicular release of hormones or neurotransmitters, the nanometer-sized fusion pore may open-close repeatedly (flicker) before resealing or dilating irreversibly, leading to kiss-and-run or full-fusion events, respectively. Pore dynamics govern vesicle cargo release and the mode of vesicle recycling, but the mechanisms are poorly understood. This is partly due to a lack of reconstituted assays that combine single-pore sensitivity and high time resolution. Total internal reflection fluorescence (TIRF) microscopy offers unique advantages for characterizing single membrane fusion events, but signals depend on effects that are difficult to disentangle, including the polarization of the excitation electric field, vesicle size, photobleaching, orientation of the excitation dipoles of the fluorophores with respect to the membrane, and the evanescent field depth. Commercial TIRF microscopes do not allow control of excitation polarization, further complicating analysis. To overcome these challenges, we built a polarization-controlled total internal reflection fluorescence (pTIRF) microscope and monitored fusion of proteoliposomes with planar lipid bilayers with single molecule sensitivity and ∼15 ms temporal resolution. Using pTIRF microscopy, we detected docking and fusion of fluorescently labeled small unilamellar vesicles, reconstituted with exocytotic/neuronal v-SNARE proteins (vSUVs), with a supported bilayer containing the cognate t-SNAREs (tSBL). By varying the excitation polarization angle, we were able to identify a dye-dependent optimal polarization at which the fluorescence increase upon fusion was maximal, facilitating event detection and analysis of lipid transfer kinetics. An improved algorithm allowed us to estimate the size of the fusing vSUV and the fusion pore openness (the fraction of time the pore is open) for every event. For most events, lipid transfer was much slower than expected for diffusion through an open pore, suggesting that fusion pore flickering limits lipid release. We find a weak correlation between fusion pore openness and vesicle area. The approach can be used to study mechanisms governing fusion pore dynamics in a wide range of membrane fusion processes.
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Affiliation(s)
- Joerg Nikolaus
- Cellular and Molecular Physiology, Yale University, New Haven, CT, United States
- Nanobiology Institute, Yale University, West Haven, CT, United States
| | - Kasey Hancock
- Cellular and Molecular Physiology, Yale University, New Haven, CT, United States
- Nanobiology Institute, Yale University, West Haven, CT, United States
- Integrated Physical and Engineering Biology Program, Yale University, New Haven, CT, United States
| | - Maria Tsemperouli
- Cellular and Molecular Physiology, Yale University, New Haven, CT, United States
- Nanobiology Institute, Yale University, West Haven, CT, United States
| | - David Baddeley
- Nanobiology Institute, Yale University, West Haven, CT, United States
- Cell Biology, Yale University, New Haven, CT, United States
| | - Erdem Karatekin
- Cellular and Molecular Physiology, Yale University, New Haven, CT, United States
- Nanobiology Institute, Yale University, West Haven, CT, United States
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Saints-Pères Paris Institute for the Neurosciences (SPPIN), Université de Paris, Centre National de la Recherche Scientifique (CNRS), Paris, France
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25
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The late endosome-resident lipid bis(monoacylglycero)phosphate is a cofactor for Lassa virus fusion. PLoS Pathog 2021; 17:e1009488. [PMID: 34492091 PMCID: PMC8448326 DOI: 10.1371/journal.ppat.1009488] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/17/2021] [Accepted: 08/25/2021] [Indexed: 11/20/2022] Open
Abstract
Arenavirus entry into host cells occurs through a low pH-dependent fusion with late endosomes that is mediated by the viral glycoprotein complex (GPC). The mechanisms of GPC-mediated membrane fusion and of virus targeting to late endosomes are not well understood. To gain insights into arenavirus fusion, we examined cell-cell fusion induced by the Old World Lassa virus (LASV) GPC complex. LASV GPC-mediated cell fusion is more efficient and occurs at higher pH with target cells expressing human LAMP1 compared to cells lacking this cognate receptor. However, human LAMP1 is not absolutely required for cell-cell fusion or LASV entry. We found that GPC-induced fusion progresses through the same lipid intermediates as fusion mediated by other viral glycoproteins–a lipid curvature-sensitive intermediate upstream of hemifusion and a hemifusion intermediate downstream of acid-dependent steps that can be arrested in the cold. Importantly, GPC-mediated fusion and LASV pseudovirus entry are specifically augmented by an anionic lipid, bis(monoacylglycero)phosphate (BMP), which is highly enriched in late endosomes. This lipid also specifically promotes cell fusion mediated by Junin virus GPC, an unrelated New World arenavirus. We show that BMP promotes late steps of LASV fusion downstream of hemifusion–the formation and enlargement of fusion pores. The BMP-dependence of post-hemifusion stages of arenavirus fusion suggests that these viruses evolved to use this lipid as a cofactor to selectively fuse with late endosomes. Pathogenic arenaviruses pose a serious health threat. The viral envelope glycoprotein GPC mediates attachment to host cells and drives virus entry via endocytosis and low pH-dependent fusion within late endosomes. Understanding the host factors and processes that are essential for arenavirus fusion may identify novel therapeutic targets. To delineate the mechanism of arenavirus entry, we examined cell-cell fusion induced by the Old World Lassa virus GPC proteins at low pH. Lassa GPC-mediated fusion was augmented by the human LAMP1 receptor and progressed through lipid curvature-sensitive intermediates, such as hemifusion (merger of contacting leaflets of viral and cell membrane without the formation of a fusion pore). We found that most GPC-mediated fusion events were off-path hemifusion structures and that the transition from hemifusion to full fusion and fusion pore enlargement were specifically promoted by an anionic lipid, bis(monoacylglycero)phosphate, which is highly enriched in late endosomes. This lipid also specifically promotes fusion of unrelated New World Junin arenavirus. Our results imply that arenaviruses evolved to use bis(monoacylglycero)phosphate to enter cells from late endosomes.
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26
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Hadpech S, Moonmuang S, Chupradit K, Yasamut U, Tayapiwatana C. Updating on Roles of HIV Intrinsic Factors: A Review of Their Antiviral Mechanisms and Emerging Functions. Intervirology 2021; 65:67-79. [PMID: 34464956 DOI: 10.1159/000519241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 08/24/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Host restriction factors are cellular proteins that inhibit specific steps of the viral life cycle. Since the 1970s, several new factors have been identified, including human immunodeficiency virus-1 (HIV-1) replication restriction. Evidence accumulated in the last decade has substantially broadened our understanding of the molecular mechanisms utilized to abrogate the HIV-1 life cycle. SUMMARY In this review, we focus on the interaction between host restriction factors participating in the early phase of HIV-1 infection, particularly CA-targeting proteins. Host factors involved in the late phase of the replication cycle, such as viral assembly and egress factors, are also described. Additionally, current reports on well-known antiviral intrinsic factors, as well as other viral restriction factors with their emerging roles, are included. CONCLUSION A comprehensive understanding of the interactions between viruses and hosts is expected to provide insight into the design of novel HIV-1 therapeutic interventions.
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Affiliation(s)
- Sudarat Hadpech
- Division of Pharmacology and Biopharmacy, Faculty of Pharmaceutical Sciences, Burapha University, Chon Buri, Thailand
| | - Sutpirat Moonmuang
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Koollawat Chupradit
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Siriraj Center for Regenerative Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Umpa Yasamut
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.,Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
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27
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Sutherland M, Kwon B, Hong M. Interactions of HIV gp41's membrane-proximal external region and transmembrane domain with phospholipid membranes from 31P NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183723. [PMID: 34352242 DOI: 10.1016/j.bbamem.2021.183723] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/22/2021] [Accepted: 07/30/2021] [Indexed: 11/30/2022]
Abstract
HIV-1 entry into cells requires coordinated changes of the conformation and dynamics of both the fusion protein, gp41, and the lipids in the cell membrane and virus envelope. Commonly proposed features of membrane deformation during fusion include high membrane curvature, lipid disorder, and membrane surface dehydration. The virus envelope and target cell membrane contain a diverse set of phospholipids and cholesterol. To dissect how different lipids interact with gp41 to contribute to membrane fusion, here we use 31P solid-state NMR spectroscopy to investigate the curvature, dynamics, and hydration of POPE, POPC and POPS membranes, with and without cholesterol, in the presence of a peptide comprising the membrane proximal external region (MPER) and transmembrane domain (TMD) of gp41. Static 31P NMR spectra indicate that the MPER-TMD induces strong negative Gaussian curvature (NGC) to the POPE membrane but little curvature to POPC and POPC:POPS membranes. The NGC manifests as an isotropic peak in the static NMR spectra, whose intensity increases with the peptide concentration. Cholesterol inhibits the NGC formation and stabilizes the lamellar phase. Relative intensities of magic-angle spinning 31P cross-polarization and direct-polarization spectra indicate that all three phospholipids become more mobile upon peptide binding. Finally, 2D 1H-31P correlation spectra show that the MPER-TMD enhances water 1H polarization transfer to the lipids, indicating that the membrane surfaces become more hydrated. These results suggest that POPE is an essential component of the high-curvature fusion site, and lipid dynamic disorder is a general feature of membrane restructuring during fusion.
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Affiliation(s)
- Madeleine Sutherland
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Byungsu Kwon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
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28
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Wu Z, Dharan N, McDargh ZA, Thiyagarajan S, O'Shaughnessy B, Karatekin E. The neuronal calcium sensor Synaptotagmin-1 and SNARE proteins cooperate to dilate fusion pores. eLife 2021; 10:68215. [PMID: 34190041 PMCID: PMC8294851 DOI: 10.7554/elife.68215] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
All membrane fusion reactions proceed through an initial fusion pore, including calcium-triggered release of neurotransmitters and hormones. Expansion of this small pore to release cargo is energetically costly and regulated by cells, but the mechanisms are poorly understood. Here, we show that the neuronal/exocytic calcium sensor Synaptotagmin-1 (Syt1) promotes expansion of fusion pores induced by SNARE proteins. Pore dilation relied on calcium-induced insertion of the tandem C2 domain hydrophobic loops of Syt1 into the membrane, previously shown to reorient the C2 domain. Mathematical modelling suggests that C2B reorientation rotates a bound SNARE complex so that it exerts force on the membranes in a mechanical lever action that increases the height of the fusion pore, provoking pore dilation to offset the bending energy penalty. We conclude that Syt1 exerts novel non-local calcium-dependent mechanical forces on fusion pores that dilate pores and assist neurotransmitter and hormone release.
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Affiliation(s)
- Zhenyong Wu
- Department of Cellular and Molecular Physiology, Yale University, New Haven, United States.,Nanobiology Institute, Yale University, West Haven, United States
| | - Nadiv Dharan
- Department of Chemical Engineering, Columbia University, New York, United States
| | - Zachary A McDargh
- Department of Chemical Engineering, Columbia University, New York, United States
| | - Sathish Thiyagarajan
- Department of Chemical Engineering, Columbia University, New York, United States
| | - Ben O'Shaughnessy
- Department of Chemical Engineering, Columbia University, New York, United States
| | - Erdem Karatekin
- Department of Cellular and Molecular Physiology, Yale University, New Haven, United States.,Nanobiology Institute, Yale University, West Haven, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States.,Saints-Pères Paris Institute for the Neurosciences (SPPIN), Université de Paris, Centre National de la Recherche Scientifique (CNRS) UMR 8003, Paris, France
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29
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Kruglova N, Siniavin A, Gushchin V, Mazurov D. Different Neutralization Sensitivity of SARS-CoV-2 Cell-to-Cell and Cell-Free Modes of Infection to Convalescent Sera. Viruses 2021; 13:1133. [PMID: 34204732 PMCID: PMC8231521 DOI: 10.3390/v13061133] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has posed a global threat to human lives and economics. One of the best ways to determine protection against the infection is to quantify the neutralizing activity of serum antibodies. Multiple assays have been developed to validate SARS-CoV-2 neutralization; most of them utilized lentiviral or vesicular stomatitis virus-based particles pseudotyped with the spike (S) protein, making them safe and acceptable to work with in many labs. However, these systems are only capable of measuring infection with purified particles. This study has developed a pseudoviral assay with replication-dependent reporter vectors that can accurately quantify the level of infection directly from the virus producing cell to the permissive target cell. Comparative analysis of cell-free and cell-to-cell infection revealed that the neutralizing activity of convalescent sera was more than tenfold lower in cell cocultures than in the cell-free mode of infection. As the pseudoviral system could not properly model the mechanisms of SARS-CoV-2 transmission, similar experiments were performed with replication-competent coronavirus, which detected nearly complete SARS-CoV-2 cell-to-cell infection resistance to neutralization by convalescent sera. These findings suggest that the cell-to-cell mode of SARS-CoV-2 transmission, for which the mechanisms are largely unknown, could be of great importance for treatment and prevention of COVID-19.
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Affiliation(s)
- Natalia Kruglova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, 119334 Moscow, Russia;
| | - Andrei Siniavin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (A.S.); (V.G.)
- Department of Molecular Neuroimmune Signalling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Vladimir Gushchin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia; (A.S.); (V.G.)
| | - Dmitriy Mazurov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, 119334 Moscow, Russia;
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30
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Serrão VHB, Cook JD, Lee JE. Snapshot of an influenza virus glycoprotein fusion intermediate. Cell Rep 2021; 35:109152. [PMID: 34010634 DOI: 10.1016/j.celrep.2021.109152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/31/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022] Open
Abstract
Enveloped virus entry requires the fusion of cellular and viral membranes, a process directed by their viral fusion glycoproteins. Our current knowledge of this process has been shaped by structural studies of the pre- and post-fusion conformations of these viral fusogens. These structural snapshots have revealed the start and end states necessary for fusion, but the dynamics of the intermediate conformations have remained unclear. Using the influenza C virus hemagglutinin-esterase-fusion glycoprotein as a model, we report the structural and biophysical characterization of a trapped intermediate. Crystallographic studies revealed a structural reorganization of the C terminus to create a second chain reversal region, resulting in the N and C termini being positioned in opposing directions. Intrinsic tryptophan fluorescence and bimane-induced quenching measurements suggest intermediate formation is mediated by conserved hydrophobic residues. Our study reveals a late-stage extended intermediate structural event. This work adds to our understanding of virus cell fusion.
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Affiliation(s)
- Vitor Hugo B Serrão
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jonathan D Cook
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada.
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31
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Witt H, Savić F, Verbeek S, Dietz J, Tarantola G, Oelkers M, Geil B, Janshoff A. Membrane fusion studied by colloidal probes. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:223-237. [PMID: 33599795 PMCID: PMC8071799 DOI: 10.1007/s00249-020-01490-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/19/2020] [Indexed: 12/12/2022]
Abstract
Membrane-coated colloidal probes combine the benefits of solid-supported membranes with a more complex three-dimensional geometry. This combination makes them a powerful model system that enables the visualization of dynamic biological processes with high throughput and minimal reliance on fluorescent labels. Here, we want to review recent applications of colloidal probes for the study of membrane fusion. After discussing the advantages and disadvantages of some classical vesicle-based fusion assays, we introduce an assay using optical detection of fusion between membrane-coated glass microspheres in a quasi two-dimensional assembly. Then, we discuss free energy considerations of membrane fusion between supported bilayers, and show how colloidal probes can be combined with atomic force microscopy or optical tweezers to access the fusion process with even greater detail.
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Affiliation(s)
- Hannes Witt
- Institute for Physical Chemistry, University of Göttingen, 37075, Göttingen, Germany
- Physics of Living Systems, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Filip Savić
- Institute for Physical Chemistry, University of Göttingen, 37075, Göttingen, Germany
| | - Sarah Verbeek
- Institute for Physical Chemistry, University of Göttingen, 37075, Göttingen, Germany
| | - Jörn Dietz
- Institute for Physical Chemistry, University of Göttingen, 37075, Göttingen, Germany
| | - Gesa Tarantola
- Institute for Physical Chemistry, University of Göttingen, 37075, Göttingen, Germany
| | - Marieelen Oelkers
- Institute for Physical Chemistry, University of Göttingen, 37075, Göttingen, Germany
| | - Burkhard Geil
- Institute for Physical Chemistry, University of Göttingen, 37075, Göttingen, Germany
| | - Andreas Janshoff
- Institute for Physical Chemistry, University of Göttingen, 37075, Göttingen, Germany.
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32
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Roychoudhury S, Das A, Sengupta P, Dutta S, Roychoudhury S, Choudhury AP, Ahmed ABF, Bhattacharjee S, Slama P. Viral Pandemics of the Last Four Decades: Pathophysiology, Health Impacts and Perspectives. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E9411. [PMID: 33333995 PMCID: PMC7765415 DOI: 10.3390/ijerph17249411] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/08/2023]
Abstract
The twenty-first century has witnessed some of the deadliest viral pandemics with far-reaching consequences. These include the Human Immunodeficiency Virus (HIV) (1981), Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) (2002), Influenza A virus subtype H1N1 (A/H1N1) (2009), Middle East Respiratory Syndrome Coronavirus (MERS-CoV) (2012) and Ebola virus (2013) and the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) (2019-present). Age- and gender-based characterizations suggest that SARS-CoV-2 resembles SARS-CoV and MERS-CoV with regard tohigher fatality rates in males, and in the older population with comorbidities. The invasion-mechanism of SARS-CoV-2 and SARS-CoV, involves binding of its spike protein with angiotensin-converting enzyme 2 (ACE2) receptors; MERS-CoV utilizes dipeptidyl peptidase 4 (DPP4), whereas H1N1 influenza is equipped with hemagglutinin protein. The viral infections-mediated immunomodulation, and progressive inflammatory state may affect the functions of several other organs. Although no effective commercial vaccine is available for any of the viruses, those against SARS-CoV-2 are being developed at an unprecedented speed. Until now, only Pfizer/BioNTech's vaccine has received temporary authorization from the UK Medicines and Healthcare products Regulatory Agency. Given the frequent emergence of viral pandemics in the 21st century, proper understanding of their characteristics and modes of action are essential to address the immediate and long-term health consequences.
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Affiliation(s)
| | - Anandan Das
- Department of Life Science and Bioinformatics, Assam University, Silchar 788011, India;
| | - Pallav Sengupta
- Department of Physiology, Faculty of Medicine and Biomedical Sciences, MAHSA University, SP2, Bandar Saujana Putra, Jenjarom, Selangor 42610, Malaysia;
| | - Sulagna Dutta
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, MAHSA University, SP2, Bandar Saujana Putra, Jenjarom, Selangor 42610, Malaysia;
| | - Shatabhisha Roychoudhury
- Department of Microbiology, R. G. Kar Medical College and Hospital, Kolkata 700004, India;
- Health Centre, Assam University, Silchar 788011, India
| | - Arun Paul Choudhury
- Department of Obstetrics and Gynecology, Silchar Medical College and Hospital, Silchar 788014, India; (A.P.C.); (A.B.F.A.)
| | - A. B. Fuzayel Ahmed
- Department of Obstetrics and Gynecology, Silchar Medical College and Hospital, Silchar 788014, India; (A.P.C.); (A.B.F.A.)
| | | | - Petr Slama
- Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 613 00 Brno, Czech Republic;
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33
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Caparotta M, Tomes CN, Mayorga LS, Masone D. The Synaptotagmin-1 C2B Domain Is a Key Regulator in the Stabilization of the Fusion Pore. J Chem Theory Comput 2020; 16:7840-7851. [DOI: 10.1021/acs.jctc.0c00734] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Marcelo Caparotta
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
| | - Claudia N. Tomes
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
| | - Luis S. Mayorga
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), Mendoza 5500, Argentina
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34
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Ward AE, Kiessling V, Pornillos O, White JM, Ganser-Pornillos BK, Tamm LK. HIV-cell membrane fusion intermediates are restricted by Serincs as revealed by cryo-electron and TIRF microscopy. J Biol Chem 2020; 295:15183-15195. [PMID: 32788212 PMCID: PMC7650252 DOI: 10.1074/jbc.ra120.014466] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/19/2020] [Indexed: 12/13/2022] Open
Abstract
To enter a cell and establish infection, HIV must first fuse its lipid envelope with the host cell plasma membrane. Whereas the process of HIV membrane fusion can be tracked by fluorescence microscopy, the 3D configuration of proteins and lipids at intermediate steps can only be resolved with cryo-electron tomography (cryoET). However, cryoET of whole cells is technically difficult. To overcome this problem, we have adapted giant plasma membrane vesicles (or blebs) from native cell membranes expressing appropriate receptors as targets for fusion with HIV envelope glycoprotein-expressing pseudovirus particles with and without Serinc host restriction factors. The fusion behavior of these particles was probed by TIRF microscopy on bleb-derived supported membranes. Timed snapshots of fusion of the same particles with blebs were examined by cryo-ET. The combination of these methods allowed us to characterize the structures of various intermediates on the fusion pathway and showed that when Serinc3 or Serinc5 (but not Serinc2) were present, later fusion products were more prevalent, suggesting that Serinc3/5 act at multiple steps to prevent progression to full fusion. In addition, the antifungal amphotericin B reversed Serinc restriction, presumably by intercalation into the fusing membranes. Our results provide a highly detailed view of Serinc restriction of HIV-cell membrane fusion and thus extend current structural and functional information on Serinc as a lipid-binding protein.
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Affiliation(s)
- Amanda E Ward
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Volker Kiessling
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Owen Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Judith M White
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Barbie K Ganser-Pornillos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA.
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia, USA; Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.
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35
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Light-induced lipid mixing implies a causal role of lipid splay in membrane fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183438. [PMID: 32781156 DOI: 10.1016/j.bbamem.2020.183438] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 11/23/2022]
Abstract
The fusion of lipid membranes is central to many biological processes and requires substantial structural reorganization of lipids brought about by the action of fusogenic proteins. Previous molecular dynamics simulations have suggested that splayed lipids, whose tails transiently contact the headgroup region of the bilayer, initiate lipid mixing. Here, we explore the lipid splay hypothesis experimentally. We show that the light-induced trans/cis conversion of the azobenzene-based tail of a model lipid molecule enhances the probability by which its own acyl chains, or the acyl chains of the host lipid, transiently contact the lipid headgroup in a liposomal bilayer. At the same time, the trans/cis conversion triggers lipid mixing of sonicated or extruded liposomes, without requiring fusogenic proteins. This establishes a causal relationship between lipid splay and membrane fusion.
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36
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Chen YC, Sood C, Marin M, Aaron J, Gratton E, Salaita K, Melikyan GB. Super-Resolution Fluorescence Imaging Reveals That Serine Incorporator Protein 5 Inhibits Human Immunodeficiency Virus Fusion by Disrupting Envelope Glycoprotein Clusters. ACS NANO 2020; 14:10929-10943. [PMID: 32441921 PMCID: PMC8274448 DOI: 10.1021/acsnano.0c02699] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Serine incorporator protein 5 (SERINC5) is the host antiretroviral factor that reduces HIV-1 infectivity by incorporating into virions and inhibiting the envelope glycoprotein (Env) mediated virus fusion with target cells. We and others have shown that SERINC5 incorporation into virions alters the Env structure and sensitizes the virus to broadly neutralizing antibodies targeting cryptic Env epitopes. We have also found that SERINC5 accelerates the loss of Env function over time compared to control viruses. However, the exact mechanism by which SERINC5 inhibits HIV-1 fusion is not understood. Here, we utilized 2D and 3D super-resolution microscopy to examine the effect of SERINC5 on the distribution of Env glycoproteins on single HIV-1 particles. We find that, in agreement with a previous report, Env glycoproteins form clusters on the surface of mature virions. Importantly, incorporation of SERINC5, but not SERINC2, which lacks antiviral activity, disrupted Env clusters without affecting the overall Env content. We also show that SERINC5 and SERINC2 also form clusters on single virions. Unexpectedly, Env and SERINC molecules exhibited poor codistribution on virions, as evidenced by much greater Env-SERINC pairwise distances compared to Env-Env distances. This observation is inconsistent with the previously reported interaction between Env and SERINC5 and suggests an indirect effect of SERINC5 on Env cluster formation. Collectively, our results reveal a multifaceted mechanism of SERINC5-mediated restriction of HIV-1 fusion that, aside from the effects on individual Env trimers, involves disruption of Env clusters, which likely serve as sites of viral fusion with target cells.
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Affiliation(s)
- Yen-Cheng Chen
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Chetan Sood
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mariana Marin
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jesse Aaron
- Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, CA 92617, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Gregory B. Melikyan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
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37
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SNAREs, tethers and SM proteins: how to overcome the final barriers to membrane fusion? Biochem J 2020; 477:243-258. [PMID: 31951000 DOI: 10.1042/bcj20190050] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/04/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022]
Abstract
Physiological membrane vesicles are built to separate reaction spaces in a stable manner, even when they accidentally collide or are kept in apposition by spatial constraints in the cell. This requires a natural resistance to fusion and mixing of their content, which originates from substantial energetic barriers to membrane fusion [1]. To facilitate intracellular membrane fusion reactions in a controlled manner, proteinaceous fusion machineries have evolved. An important open question is whether protein fusion machineries actively pull the fusion reaction over the present free energy barriers, or whether they rather catalyze fusion by lowering those barriers. At first sight, fusion proteins such as SNARE complexes and viral fusion proteins appear to act as nano-machines, which mechanically transduce force to the membranes and thereby overcome the free energy barriers [2,3]. Whether fusion proteins additionally alter the free energy landscape of the fusion reaction via catalytic roles is less obvious. This is a question that we shall discuss in this review, with particular focus on the influence of the eukaryotic SNARE-dependent fusion machinery on the final step of the reaction, the formation and expansion of the fusion pore.
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38
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López-Murcia FJ, Reim K, Jahn O, Taschenberger H, Brose N. Acute Complexin Knockout Abates Spontaneous and Evoked Transmitter Release. Cell Rep 2020; 26:2521-2530.e5. [PMID: 30840877 DOI: 10.1016/j.celrep.2019.02.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/05/2018] [Accepted: 02/07/2019] [Indexed: 12/21/2022] Open
Abstract
SNARE-mediated synaptic vesicle (SV) fusion is controlled by multiple regulatory proteins that determine neurotransmitter release efficiency. Complexins are essential SNARE regulators whose mode of action is unclear, as available evidence indicates positive SV fusion facilitation and negative "fusion clamp"-like activities, with the latter occurring only in certain contexts. Because these contradictory findings likely originate in part from different experimental perturbation strategies, we attempted to resolve them by examining a conditional complexin-knockout mouse line as the most stringent genetic perturbation model available. We found that acute complexin loss after synaptogenesis in autaptic and mass-cultured hippocampal neurons reduces SV fusion probability and thus abates the rates of spontaneous, synchronous, asynchronous, and delayed transmitter release but does not affect SV priming or cause "unclamping" of spontaneous SV fusion. Thus, complexins act as facilitators of SV fusion but are dispensable for "fusion clamping" in mammalian forebrain neurons.
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Affiliation(s)
- Francisco José López-Murcia
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Kerstin Reim
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Olaf Jahn
- Proteomics Group, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany; DFG-Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain, 37073 Göttingen, Germany
| | - Holger Taschenberger
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany; DFG-Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain, 37073 Göttingen, Germany.
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany; DFG-Research Center for Nanoscale Microscopy and Molecular Physiology of the Brain, 37073 Göttingen, Germany.
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39
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Tang T, Bidon M, Jaimes JA, Whittaker GR, Daniel S. Coronavirus membrane fusion mechanism offers a potential target for antiviral development. Antiviral Res 2020. [PMID: 32272173 DOI: 10.1016/j.antiviral.2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has focused attention on the need to develop effective therapies against the causative agent, SARS-CoV-2, and also against other pathogenic coronaviruses (CoV) that have emerged in the past or might appear in future. Researchers are therefore focusing on steps in the CoV replication cycle that may be vulnerable to inhibition by broad-spectrum or specific antiviral agents. The conserved nature of the fusion domain and mechanism across the CoV family make it a valuable target to elucidate and develop pan-CoV therapeutics. In this article, we review the role of the CoV spike protein in mediating fusion of the viral and host cell membranes, summarizing the results of research on SARS-CoV, MERS-CoV, and recent peer-reviewed studies of SARS-CoV-2, and suggest that the fusion mechanism be investigated as a potential antiviral target. We also provide a supplemental file containing background information on the biology, epidemiology, and clinical features of all human-infecting coronaviruses, along with a phylogenetic tree of these coronaviruses.
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Affiliation(s)
- Tiffany Tang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Miya Bidon
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Javier A Jaimes
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, 14853, USA
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA.
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Tang T, Bidon M, Jaimes JA, Whittaker GR, Daniel S. Coronavirus membrane fusion mechanism offers a potential target for antiviral development. Antiviral Res 2020; 178:104792. [PMID: 32272173 PMCID: PMC7194977 DOI: 10.1016/j.antiviral.2020.104792] [Citation(s) in RCA: 521] [Impact Index Per Article: 130.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/05/2020] [Accepted: 04/05/2020] [Indexed: 12/14/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has focused attention on the need to develop effective therapies against the causative agent, SARS-CoV-2, and also against other pathogenic coronaviruses (CoV) that have emerged in the past or might appear in future. Researchers are therefore focusing on steps in the CoV replication cycle that may be vulnerable to inhibition by broad-spectrum or specific antiviral agents. The conserved nature of the fusion domain and mechanism across the CoV family make it a valuable target to elucidate and develop pan-CoV therapeutics. In this article, we review the role of the CoV spike protein in mediating fusion of the viral and host cell membranes, summarizing the results of research on SARS-CoV, MERS-CoV, and recent peer-reviewed studies of SARS-CoV-2, and suggest that the fusion mechanism be investigated as a potential antiviral target. We also provide a supplemental file containing background information on the biology, epidemiology, and clinical features of all human-infecting coronaviruses, along with a phylogenetic tree of these coronaviruses.
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Affiliation(s)
- Tiffany Tang
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Miya Bidon
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Javier A Jaimes
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, 14853, USA
| | - Gary R Whittaker
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, 14853, USA
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA.
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Bruininks BM, Souza PC, Ingolfsson H, Marrink SJ. A molecular view on the escape of lipoplexed DNA from the endosome. eLife 2020; 9:52012. [PMID: 32297853 PMCID: PMC7170654 DOI: 10.7554/elife.52012] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/24/2020] [Indexed: 12/23/2022] Open
Abstract
The use of non-viral vectors for in vivo gene therapy could drastically increase safety, whilst reducing the cost of preparing the vectors. A promising approach to non-viral vectors makes use of DNA/cationic liposome complexes (lipoplexes) to deliver the genetic material. Here we use coarse-grained molecular dynamics simulations to investigate the molecular mechanism underlying efficient DNA transfer from lipoplexes. Our computational fusion experiments of lipoplexes with endosomal membrane models show two distinct modes of transfection: parallel and perpendicular. In the parallel fusion pathway, DNA aligns with the membrane surface, showing very quick release of genetic material shortly after the initial fusion pore is formed. The perpendicular pathway also leads to transfection, but release is slower. We further show that the composition and size of the lipoplex, as well as the lipid composition of the endosomal membrane, have a significant impact on fusion efficiency in our models.
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Affiliation(s)
- Bart Mh Bruininks
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh, Netherlands
| | - Paulo Ct Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh, Netherlands
| | - Helgi Ingolfsson
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh, Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh, Netherlands
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42
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Neutralization Breadth and Potency of Single-Chain Variable Fragments Derived from Broadly Neutralizing Antibodies Targeting Multiple Epitopes on the HIV-1 Envelope. J Virol 2020; 94:JVI.01533-19. [PMID: 31619559 DOI: 10.1128/jvi.01533-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 10/08/2019] [Indexed: 12/25/2022] Open
Abstract
Passive administration of HIV-directed broadly neutralizing antibodies (bNAbs) can prevent infection in animal models, and human efficacy trials are under way. Single-chain variable fragments (scFv), comprised of only the variable regions of antibody heavy and light chains, are smaller molecules that may offer advantages over full-length IgG. We designed and expressed scFv of HIV bNAbs prioritized for clinical testing that target the V2-apex (CAP256-VRC26.25), V3-glycan supersite (PGT121), CD4 binding site (3BNC117), and MPER (10E8v4). The use of either a 15- or 18-amino-acid glycine-serine linker between the heavy- and light-chain fragments provided adequate levels of scFv expression. When tested against a 45-multisubtype virus panel, all four scFv retained good neutralizing activity, although there was variable loss of function compared to the parental IgG antibodies. For CAP256-VRC26.25, there was a significant 138-fold loss of potency that was in part related to differential interaction with charged amino acids at positions 169 and 170 in the V2 epitope. Potency was reduced for the 3BNC117 (13-fold) and PGT121 (4-fold) scFv among viruses lacking the N276 and N332 glycans, respectively, and in viruses with a longer V1 loop for PGT121. This suggested that scFv interacted with their epitopes in subtly different ways, with variation at key residues affecting scFv neutralization more than the matched IgGs. Remarkably, the scFv of 10E8v4 maintained breadth of 100% with only a minor reduction in potency. Overall, scFv of clinically relevant bNAbs had significant neutralizing activity, indicating that they are suitable for passive immunization to prevent HIV-1 infection.IMPORTANCE Monoclonal antibodies have been isolated against conserved epitopes on the HIV trimer and are being investigated for passive immunization. Some of the challenges associated with full-sized antibody proteins may be overcome by using single-chain variable fragments (scFv). These smaller forms of antibodies can be produced more efficiently, may show fewer off-target effects with increased tissue penetration, and are more adaptable to vectored-mediated expression than IgG. Here, we demonstrate that scFv of four HIV-directed bNAbs (CAP256-VRC26.25, PGT121, 3BNC117, and 10E8v4) had significant neutralizing activity against diverse global strains of HIV. Loss of potency and/or breadth was shown to be due to increased dependence of the scFv on key residues within the epitope. These smaller antibody molecules with functional activity in the therapeutic range may be suitable for further development as passive immunity for HIV prevention.
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Vadakkan KI. From cells to sensations: A window to the physics of mind. Phys Life Rev 2019; 31:44-78. [PMID: 31759872 DOI: 10.1016/j.plrev.2019.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/06/2019] [Accepted: 10/16/2019] [Indexed: 12/14/2022]
Abstract
Principles of methods for studying particles and fields that cannot be sensed by third-person observers by routine methods can be used to understand the physics of first-person properties of mind. Accordingly, whenever a system exhibits disparate features at multiple levels, unique combination of constraints offered by them direct us towards a solution that will be the first principle of that system. Using this method, it was possible to arrive at a third-person observable solution-point of brain-mind interface. Examination of this location identified a set of unique features that can allow an associatively learned (cue) stimulus to spark hallucinations that form units of first-person internal (inner) sensations reminiscent of stimuli from the associatively learned second item in timescales of milliseconds. It allows us to peep into a virtual space of mind where different modifications and integrations of units of internal sensations generate their different net conformations ranging from perception to an inner sense of hidden relationships that form a hypothesis. Since sparking of inner sensations of the late arriving (when far away) or non-arriving (when hidden) features of items started providing survival advantage, the focus of evolution might have been to optimize this property. Hence, the circuity that generates it can be considered as the primary circuitry of the system. The solution provides several testable predictions. By taking readers through the process of deriving the solution and by explaining how it interconnects disparate findings, it is hoped that the factors determining the physics of mind will become evident.
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Affiliation(s)
- Kunjumon I Vadakkan
- Division of Neurology, Department of Medicine, QEII Health Sciences Centre, 1796 Summer Street, Dalhousie University, Halifax, NS, B3H 3A7, Canada.
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Biochemical Analysis of Coronavirus Spike Glycoprotein Conformational Intermediates during Membrane Fusion. J Virol 2019; 93:JVI.00785-19. [PMID: 31315988 PMCID: PMC6744234 DOI: 10.1128/jvi.00785-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/05/2019] [Indexed: 11/20/2022] Open
Abstract
A fusion protein expressed on the surface of enveloped viruses mediates fusion of the viral and cellular membranes to facilitate virus infection. Pre- and postfusion structures of viral fusion proteins have been characterized, but conformational changes between them remain poorly understood. Here, we examined the intermediate conformation of the murine coronavirus fusion protein, called the spike protein, which must be cleaved by a cellular protease following receptor binding. Western blot analysis of protease digestion products revealed that two subunits (67 and 69 kDa) are produced from a single spike protein (180 kDa). These two subunits were considered to be by-products derived from conformational changes and were useful for probing the intermediate conformation of the spike protein. Interaction with a heptad repeat (HR) peptide revealed that these subunits adopt packed and unpacked conformations, respectively, and two-dimensional electrophoresis revealed a trimeric assembly. Based on biochemical observations, we propose an asymmetric trimer model for the intermediate structure of the spike protein. Receptor binding induces the membrane-binding potential of the trimer, in which at least one HR motif forms a packed-hairpin structure, while membrane fusion subunits are covered by the receptor-binding subunit, thereby preventing the spike protein from forming the typical homotrimeric prehairpin structure predicted by the current model of class I viral fusion protein. Subsequent proteolysis induces simultaneous packing of the remaining unpacked HRs upon assembly of three HRs at the central axis to generate a six-helix bundle. Our model proposes a key mechanism for membrane fusion of enveloped viruses.IMPORTANCE Recent studies using single-particle cryo-electron microscopy (cryoEM) revealed the mechanism underlying activation of viral fusion protein at the priming stage. However, characterizing the subsequent triggering stage underpinning transition from pre- to postfusion structures is difficult because single-particle cryoEM excludes unstable structures that appear as heterogeneous shapes. Therefore, population-based biochemical analysis is needed to capture features of unstable proteins. Here, we analyzed protease digestion products of a coronavirus fusion protein during activation; their sizes appear to be affected directly by the conformational state. We propose a model for the viral fusion protein in the intermediate state, which involves a compact structure and conformational changes that overcome steric hindrance within the three fusion protein subunits.
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Abstract
With no limiting membrane surrounding virions, nonenveloped viruses have no need for membrane fusion to gain access to intracellular replication compartments. Consequently, nonenveloped viruses do not encode membrane fusion proteins. The only exception to this dogma is the fusogenic reoviruses that encode fusion-associated small transmembrane (FAST) proteins that induce syncytium formation. FAST proteins are the smallest viral membrane fusion proteins and, unlike their enveloped virus counterparts, are nonstructural proteins that evolved specifically to induce cell-to-cell, not virus-cell, membrane fusion. This distinct evolutionary imperative is reflected in structural and functional features that distinguish this singular family of viral fusogens from all other protein fusogens. These rudimentary fusogens comprise specific combinations of different membrane effector motifs assembled into small, modular membrane fusogens. FAST proteins offer a minimalist model to better understand the ubiquitous process of protein-mediated membrane fusion and to reveal novel mechanisms of nonenveloped virus dissemination that contribute to virulence.
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Affiliation(s)
- Roy Duncan
- Department of Microbiology & Immunology, Department of Biochemistry & Molecular Biology, and Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 4R2;
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46
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Nishida‐Fukuda H. The Exocyst: Dynamic Machine or Static Tethering Complex? Bioessays 2019; 41:e1900056. [DOI: 10.1002/bies.201900056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/14/2019] [Indexed: 01/15/2023]
Affiliation(s)
- Hisayo Nishida‐Fukuda
- Department of Genome Editing, Institute of Biomedical ScienceKansai Medical University2‐5‐1 Shin‐machi, Hirakata Osaka 5731010 Japan
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Firrito C, Bertelli C, Vanzo T, Chande A, Pizzato M. SERINC5 as a New Restriction Factor for Human Immunodeficiency Virus and Murine Leukemia Virus. Annu Rev Virol 2019; 5:323-340. [PMID: 30265629 DOI: 10.1146/annurev-virology-092917-043308] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
SERINC genes encode for homologous multipass transmembrane proteins with unknown cellular function, despite being highly conserved across eukaryotes. Among the five SERINC genes found in humans, SERINC5 was shown to act as a powerful inhibitor of retroviruses. It is efficiently incorporated into virions and blocks the penetration of the viral core into target cells, by impairing the fusion process with a yet unclear mechanism. SERINC5 was also found to promote human immunodeficiency virus 1 (HIV-1) virion neutralization by antibodies, indicating a pleiotropic activity, which remains mostly unexplored. Counteracting factors have emerged independently in at least three retrovirus lineages, underscoring their fundamental importance during retrovirus evolution. Nef and S2 of primate and equine lentiviruses, and glycoGag of gammaretroviruses, act similarly by targeting SERINC5 to endosomes and excluding it from virions. Here, we discuss the features that distinguish SERINC5 from other known restriction factors, delineating a yet unique class of antiviral inhibitors.
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Affiliation(s)
- Claudia Firrito
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy ; , , ,
| | - Cinzia Bertelli
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy ; , , ,
| | - Teresa Vanzo
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy ; , , ,
| | - Ajit Chande
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal 462 066, Madhya Pradesh, India;
| | - Massimo Pizzato
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy ; , , ,
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48
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Nguyen TT, Cramb DT. Elucidation of the mechanism and energy barrier for anesthetic triggered membrane fusion in model membranes. CAN J CHEM 2019. [DOI: 10.1139/cjc-2018-0405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Membrane fusion is vital for cellular function and is generally mediated via fusogenic proteins and peptides. The mechanistic details and subsequently the transition state dynamics of membrane fusion will be dependent on the type of the fusogenic agent. We have previously established the potential of general anesthetics as a new class of fusion triggering agents in model membranes. We employed two-photon excitation fluorescence cross-correlation spectroscopy (TPE-FCCS) to report on vesicle association kinetics and steady-state fluorescence dequenching assays to monitor lipid mixing kinetics. Using halothane to trigger fusion in 110 nm diameter dioleoylphosphatidylcholine (DOPC) liposomes, we found that lipid rearrangement towards the formation of the fusion stalk was rate limiting. The activation barrier for halothane induced membrane fusion in 110 nm vesicles was found to be ∼40 kJ mol−1. We calculated the enthalpy and entropy of the transition state to be ∼40 kJ mol−1and ∼180 J mol−1K−1, respectively. We have found that the addition of halothane effectively lowers the energy barrier for membrane fusion in less curved vesicles largely due to entropic advantages.
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Affiliation(s)
- Trinh T. Nguyen
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - David T. Cramb
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
- Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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49
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Lu T, Guo H. How the Membranes Fuse: From Spontaneous to Induced. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Teng Lu
- Beijing National Laboratory for Molecular SciencesJoint Laboratory of Polymer Sciences and MaterialsState Key Laboratory of Polymer Physics and ChemistryInstitute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
| | - Hongxia Guo
- Beijing National Laboratory for Molecular SciencesJoint Laboratory of Polymer Sciences and MaterialsState Key Laboratory of Polymer Physics and ChemistryInstitute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
- Division of Polymer Science and MaterialsSchool of Chemical SciencesUniversity of Chinese Academy of Sciences Beijing 100049 China
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50
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Zhang Z, Yang Y, Pincet F, Llaguno MC, Lin C. Placing and shaping liposomes with reconfigurable DNA nanocages. Nat Chem 2019. [PMID: 28644472 DOI: 10.1038/nchem.2802] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The diverse structure and regulated deformation of lipid bilayer membranes are among a cell's most fascinating features. Artificial membrane-bound vesicles, known as liposomes, are versatile tools for modelling biological membranes and delivering foreign objects to cells. To fully mimic the complexity of cell membranes and optimize the efficiency of delivery vesicles, controlling liposome shape (both statically and dynamically) is of utmost importance. Here we report the assembly, arrangement and remodelling of liposomes with designer geometry: all of which are exquisitely controlled by a set of modular, reconfigurable DNA nanocages. Tubular and toroid shapes, among others, are transcribed from DNA cages to liposomes with high fidelity, giving rise to membrane curvatures present in cells yet previously difficult to construct in vitro. Moreover, the conformational changes of DNA cages drive membrane fusion and bending with predictable outcomes, opening up opportunities for the systematic study of membrane mechanics.
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Affiliation(s)
- Zhao Zhang
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA.,Nanobiology Institute, Yale University; West Haven, Connecticut 06516, USA
| | - Yang Yang
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA.,Nanobiology Institute, Yale University; West Haven, Connecticut 06516, USA
| | - Frederic Pincet
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA.,Nanobiology Institute, Yale University; West Haven, Connecticut 06516, USA.,Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University, Université Paris Diderot Sorbonne Paris Cité, Sorbonne Universités UPMC Univ Paris 06, CNRS, 24 rue Lhomond, 75005 Paris, France
| | - Marc C Llaguno
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06510, USA.,Nanobiology Institute, Yale University; West Haven, Connecticut 06516, USA
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