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Article ; Online: Special issue for Klaus Gawrisch.

Zimmerberg, Joshua / Soubias, Olivier / Pastor, Richard W

2023 Volume 122, Issue 6, Page(s) E1–E8

Language	English
Publishing date	2023-03-15
Publishing country	United States
Document type	Editorial
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2023.02.022
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Article ; Online: Designing antimalarials that break into cells to lock down parasites.

Glushakova, Svetlana / Zimmerberg, Joshua

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 26

MeSH term(s)	Animals ; Antimalarials/pharmacology ; Cell Membrane/drug effects ; Cells/parasitology ; Drug Design ; Erythrocytes/drug effects ; Erythrocytes/parasitology ; Humans ; Parasites/drug effects ; Parasites/growth & development ; Plasmodium falciparum/drug effects
Chemical Substances	Antimalarials
Language	English
Publishing date	2021-06-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2108103118
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Article: Defining the EM-signature of successful cell-transfection.

Pemberton, Joshua G / Tenkova, Tatyana / Felgner, Philip / Zimmerberg, Josh / Balla, Tamas / Heuser, John

bioRxiv : the preprint server for biology

2024

Abstract: In this report, we describe the architecture of Lipofectamine 2000 and 3000 transfection- reagents, as they appear inside of transfected cells, using classical transmission electron microscopy (EM). We also demonstrate that they provoke consistent ... ...

Abstract	In this report, we describe the architecture of Lipofectamine 2000 and 3000 transfection- reagents, as they appear inside of transfected cells, using classical transmission electron microscopy (EM). We also demonstrate that they provoke consistent structural changes after they have entered cells, changes that not only provide new insights into the mechanism of action of these particular transfection-reagents, but also provide a convenient and robust method for identifying by EM which cells in any culture have been successfully transfected. This also provides clues to the mechanism(s) of their toxic effects, when they are applied in excess. We demonstrate that after being bulk-endocytosed by cells, the cationic spheroids of Lipofectamine remain intact throughout the entire time of culturing, but escape from their endosomes and penetrate directly into the cytoplasm of the cell. In so doing, they provoke a stereotypical recruitment and rearrangement of endoplasmic reticulum (ER), and they ultimately end up escaping into the cytoplasm and forming unique 'inclusion-bodies.' Once free in the cytoplasm, they also invariably develop dense and uniform coatings of cytoplasmic ribosomes on their surfaces, and finally, they become surrounded by 'annulate' lamellae' of the ER. In the end, these annulate-lamellar enclosures become the ultrastructural 'signatures' of these inclusion-bodies, and serve to positively and definitively identify all cells that have been effectively transfected. Importantly, these new EM-observations define several new and unique properties of these classical Lipofectamines, and allow them to be discriminated from other lipoidal or particulate transfection-reagents, which we find do not physically break out of endosomes or end up in inclusion bodies, and in fact, provoke absolutely none of these 'signature' cytoplasmic reactions.
Language	English
Publishing date	2024-03-07
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.07.583927
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Article ; Online: Initiation and evolution of pores formed by influenza fusion peptides probed by lysolipid inclusion.

Rice, Amy / Zimmerberg, Joshua / Pastor, Richard W

Biophysical journal

2022 Volume 122, Issue 6, Page(s) 1018–1032

Abstract: The fusion peptide (FP) domain is necessary for the fusogenic activity of spike proteins in a variety of enveloped viruses, allowing the virus to infect the host cell, and is the only part of the protein that interacts directly with the target membrane ... ...

Abstract	The fusion peptide (FP) domain is necessary for the fusogenic activity of spike proteins in a variety of enveloped viruses, allowing the virus to infect the host cell, and is the only part of the protein that interacts directly with the target membrane lipid tails during fusion. There are consistent findings of poration by this domain in experimental model membrane systems, and, in certain conditions, the isolated FPs can generate pores. Here, we use molecular dynamics simulations to investigate the specifics of how these FP-induced pores form in membranes with different compositions of lysolipid and POPC. The simulations show that pores form spontaneously at high lysolipid concentrations via hybrid intermediates, where FP aggregates in the cis leaflet tilt to form a funnel-like structure that spans the leaflet and locally reduces the hydrophobic thickness that must be traversed by water to form a pore. By restraining a single FP within an FP aggregate to this tilted conformation, pores can be formed in lower-lysolipid-content membranes, including pure POPC, on the 100-ns timescale, much more rapidly than in unbiased simulations in bilayers with the same composition. The pore formation pathway is similar to the spontaneous formation in high lysolipid concentrations. Depending on the membrane composition, the pores can be metastable (as seen in POPC) or lead to membrane rupture.
MeSH term(s)	Humans ; Lipid Bilayers/chemistry ; Influenza, Human/metabolism ; Peptides/chemistry ; Cell Membrane/metabolism ; Membrane Lipids/metabolism ; Membrane Fusion
Chemical Substances	Lipid Bilayers ; Peptides ; Membrane Lipids
Language	English
Publishing date	2022-12-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2022.12.029
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Article ; Online: Relative quantification of progressive changes in healthy and dysferlin-deficient mouse skeletal muscle proteomes.

Golding, Adriana E / Li, Wenping / Blank, Paul S / Cologna, Stephanie M / Zimmerberg, Joshua

Muscle & nerve

2023 Volume 68, Issue 5, Page(s) 805–816

Abstract: Introduction/aims: Individuals with dysferlinopathies, a group of genetic muscle diseases, experience delay in the onset of muscle weakness. The cause of this delay and subsequent muscle wasting are unknown, and there are currently no clinical ... ...

Abstract	Introduction/aims: Individuals with dysferlinopathies, a group of genetic muscle diseases, experience delay in the onset of muscle weakness. The cause of this delay and subsequent muscle wasting are unknown, and there are currently no clinical interventions to limit or prevent muscle weakness. To better understand molecular drivers of dysferlinopathies, age-dependent changes in the proteomic profile of skeletal muscle (SM) in wild-type (WT) and dysferlin-deficient mice were identified. Methods: Quadriceps were isolated from 6-, 18-, 42-, and 77-wk-old C57BL/6 (WT, Dysf Results: Over 3200 proteins were identified between 6-, 18-, 42-, and 77-wk-old mice. In total, 46 proteins varied in aging WT SM (p < .01), while 365 varied in dysferlin-deficient SM. However, 569 proteins varied between aged-matched WT and dysferlin-deficient SM. Proteins with significant variation in expression across all comparisons followed distinct temporal trends. Discussion: Proteins involved in sarcolemma repair and regeneration underwent significant changes in SM over the lifespan of WT mice, while those associated with immune infiltration and inflammation were overly represented over the lifespan of dysferlin-deficient mice. The proteins identified herein are likely to contribute to our overall understanding of SM aging and dysferlinopathy disease progression.
Language	English
Publishing date	2023-09-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	438353-9
ISSN	1097-4598 ; 0148-639X
ISSN (online)	1097-4598
ISSN	0148-639X
DOI	10.1002/mus.27975
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Article ; Online: Hardly Vacuous: The Parasitophorous Vacuolar Membrane of Malaria Parasites.

Goldberg, Daniel E / Zimmerberg, Joshua

Trends in parasitology

2019 Volume 36, Issue 2, Page(s) 138–146

Abstract: When a malaria parasite invades a host erythrocyte it pushes itself in and invaginates a portion of the host membrane, thereby sealing itself inside and establishing itself in the resulting vacuole. The parasitophorous vacuolar membrane (PVM) that ... ...

Abstract	When a malaria parasite invades a host erythrocyte it pushes itself in and invaginates a portion of the host membrane, thereby sealing itself inside and establishing itself in the resulting vacuole. The parasitophorous vacuolar membrane (PVM) that surrounds the parasite is modified by the parasite, using its secretory organelles. To survive within this enveloping membrane, the organism must take in nutrients, secrete wastes, export proteins into the host cell, and eventually egress. Here, we review current understanding of the unique solutions Plasmodium has evolved to these challenges and discuss the remaining questions.
MeSH term(s)	Erythrocytes/parasitology ; Host-Parasite Interactions/physiology ; Humans ; Malaria/parasitology ; Plasmodium/physiology ; Vacuoles/parasitology
Language	English
Publishing date	2019-12-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	2036227-4
ISSN	1471-5007 ; 1471-4922
ISSN (online)	1471-5007
ISSN	1471-4922
DOI	10.1016/j.pt.2019.11.006
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Article ; Online: Dynamic Relationship of the SNARE Complex with a Membrane.

Holz, Ronald W / Zimmerberg, Joshua

Biophysical journal

2019 Volume 117, Issue 4, Page(s) 627–630

Abstract: Fusion of secretory granules and synaptic vesicles with the plasma membrane is driven by SNARE protein interactions. Intensive investigations in vitro, which include x-ray crystallography, cryoelectron microscopy, and NMR analyses by numerous groups, ... ...

Abstract	Fusion of secretory granules and synaptic vesicles with the plasma membrane is driven by SNARE protein interactions. Intensive investigations in vitro, which include x-ray crystallography, cryoelectron microscopy, and NMR analyses by numerous groups, have elucidated structures relevant to the function of these proteins. Although function depends on the proteins being membrane bound, for experimental reasons, most of the studies have used cytosolic domains, as exemplified by the groundbreaking studies that elucidated the structure of a tetrapeptide helical bundle formed by interaction of the cytosolic domains of syntaxin1A, SNAP25 (two peptides) and synaptobrevin 2. Because the cytosolic fragments were unfettered by membrane attachments, it is likely that the tetrapeptide helical bundle reflects the lowest energy state, such as that found in the "cis" interactions of the SNARE motifs after fusion when they co-localize in the plasma membrane. Much more difficult to study and still poorly understood are critical "trans" interactions between the synaptic vesicle SNARE protein synaptobrevin 2 and the plasma membrane syntaxin1A/SNAP25 complex that initiate the fusion event. In a series of articles from the laboratory of Lukas Tamm, the spontaneous orientation of the SNARE motif of membrane-bound, full-length syntaxin1A with respect to the membrane hosting syntaxin's transmembrane domain was investigated with nanometer precision under a variety of conditions, including those that model aspects of the "trans" configuration. The studies rely on fluorescence interference-contrast microscopy, a technique that utilizes the pattern of constructive and destructive interference arising from incoming and reflected excitation and emission light at the surface of a silicon chip that has been layered with oxidized silicon of varying depths. This Perspective discusses their findings, including the unexpected influence of the degree of lipid unsaturation on the orientation of the SNARE complex.
MeSH term(s)	Animals ; Humans ; SNARE Proteins/chemistry ; SNARE Proteins/metabolism ; Synaptic Membranes/metabolism ; Synaptic Vesicles/metabolism
Chemical Substances	SNARE Proteins
Language	English
Publishing date	2019-07-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2019.07.010
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Article ; Online: Phosphatidylinositol 4,5-Bisphosphate Mediates the Co-Distribution of Influenza A Hemagglutinin and Matrix Protein M1 at the Plasma Membrane.

Raut, Prakash / Obeng, Bright / Waters, Hang / Zimmerberg, Joshua / Gosse, Julie A / Hess, Samuel T

Viruses

2022 Volume 14, Issue 11

Abstract: The fully assembled influenza A virus (IAV) has on its surface the highest density of a single membrane protein found in nature-the glycoprotein hemagglutinin (HA) that mediates viral binding, entry, and assembly. HA clusters at the plasma membrane of ... ...

Abstract	The fully assembled influenza A virus (IAV) has on its surface the highest density of a single membrane protein found in nature-the glycoprotein hemagglutinin (HA) that mediates viral binding, entry, and assembly. HA clusters at the plasma membrane of infected cells, and the HA density (number of molecules per unit area) of these clusters correlates with the infectivity of the virus. Dense HA clusters are considered to mark the assembly site and ultimately lead to the budding of infectious IAV. The mechanism of spontaneous HA clustering, which occurs with or without other viral components, has not been elucidated. Using super-resolution fluorescence photoactivation localization microscopy (FPALM), we have previously shown that these HA clusters are interdependent on phosphatidylinositol 4,5-biphosphate (PIP2). Here, we show that the IAV matrix protein M1 co-clusters with PIP2, visualized using the pleckstrin homology domain. We find that cetylpyridinium chloride (CPC), which is a positively charged quaternary ammonium compound known for its antibacterial and antiviral properties at millimolar concentrations, disrupts M1 clustering and M1-PIP2 co-clustering at micromolar concentrations well below the critical micelle concentration (CMC). CPC also disrupts the co-clustering of M1 with HA at the plasma membrane, suggesting the role of host cell PIP2 clusters as scaffolds for gathering and concentrating M1 and HA to achieve their unusually high cluster densities in the IAV envelope.
MeSH term(s)	Humans ; Hemagglutinins/metabolism ; Phosphatidylinositols/metabolism ; Influenza, Human/metabolism ; Hemagglutinin Glycoproteins, Influenza Virus/metabolism ; Virus Assembly ; Cell Membrane/metabolism ; Influenza A virus/physiology
Chemical Substances	Hemagglutinins ; Phosphatidylinositols ; Hemagglutinin Glycoproteins, Influenza Virus
Language	English
Publishing date	2022-11-12
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14112509
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Article: Hardly Vacuous: The Parasitophorous Vacuolar Membrane of Malaria Parasites

Goldberg, Daniel E / Zimmerberg, Joshua

Trends in parasitology. 2020 Feb., v. 36, no. 2

2020

Abstract	When a malaria parasite invades a host erythrocyte it pushes itself in and invaginates a portion of the host membrane, thereby sealing itself inside and establishing itself in the resulting vacuole. The parasitophorous vacuolar membrane (PVM) that surrounds the parasite is modified by the parasite, using its secretory organelles. To survive within this enveloping membrane, the organism must take in nutrients, secrete wastes, export proteins into the host cell, and eventually egress. Here, we review current understanding of the unique solutions Plasmodium has evolved to these challenges and discuss the remaining questions.
Keywords	Plasmodium ; erythrocytes ; malaria ; nutrients ; parasites ; proteins ; vacuoles ; wastes
Language	English
Dates of publication	2020-02
Size	p. 138-146.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2036227-4
ISSN	1471-5007 ; 1471-4922
ISSN (online)	1471-5007
ISSN	1471-4922
DOI	10.1016/j.pt.2019.11.006
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Ectodomain Pulling Combines with Fusion Peptide Inserting to Provide Cooperative Fusion for Influenza Virus and HIV.

Akimov, Sergey A / Kondrashov, Oleg V / Zimmerberg, Joshua / Batishchev, Oleg V

International journal of molecular sciences

2020 Volume 21, Issue 15

Abstract: Enveloped viruses include the most dangerous human and animal pathogens, in particular coronavirus, influenza virus, and human immunodeficiency virus (HIV). For these viruses, receptor binding and entry are accomplished by a single viral envelope protein ...

Abstract	Enveloped viruses include the most dangerous human and animal pathogens, in particular coronavirus, influenza virus, and human immunodeficiency virus (HIV). For these viruses, receptor binding and entry are accomplished by a single viral envelope protein (termed the fusion protein), the structural changes of which trigger the remodeling and merger of the viral and target cellular membranes. The number of fusion proteins required for fusion activity is still under debate, and several studies report this value to range from 1 to 9 for type I fusion proteins. Here, we consider the earliest stage of viral fusion based on the continuum theory of membrane elasticity. We demonstrate that membrane deformations induced by the oblique insertion of amphipathic fusion peptides mediate the lateral interaction of these peptides and drive them to form into a symmetric fusion rosette. The pulling force produced by the structural rearrangements of the fusion protein ectodomains gives additional torque, which deforms the membrane and additionally stabilizes the symmetric fusion rosette, thus allowing a reduction in the number of fusion peptides needed for fusion. These findings can resolve the large range of published cooperativity indices for HIV, influenza, and other type I fusion proteins.
MeSH term(s)	Anisotropy ; Cell Membrane/virology ; HIV/physiology ; HIV Infections/virology ; Humans ; Influenza A virus/physiology ; Influenza, Human/virology ; Models, Theoretical ; Peptides/chemistry ; Protein Domains ; Viral Envelope Proteins/chemistry ; Virus Internalization
Chemical Substances	Peptides ; Viral Envelope Proteins
Keywords	covid19
Language	English
Publishing date	2020-07-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21155411
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