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Article ; Online: CryoEM Structures of Dynamin Proteins Involved in Membrane Fission and Fusion.

Nyenhuis, Sarah B / Jimah, John R / Kundu, Nidhi / Harrison, Jonathan T / Canagarajah, Bertram / Hinshaw, Jenny E

Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada

2023 Volume 29, Issue 29 Suppl 1, Page(s) 911

Language	English
Publishing date	2023-08-08
Publishing country	England
Document type	Journal Article
ZDB-ID	1385710-1
ISSN	1435-8115 ; 1431-9276
ISSN (online)	1435-8115
ISSN	1431-9276
DOI	10.1093/micmic/ozad067.451
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Structural Insights into the Mechanism of Dynamin Superfamily Proteins.

Jimah, John R / Hinshaw, Jenny E

Trends in cell biology

2018 Volume 29, Issue 3, Page(s) 257–273

Abstract: Dynamin superfamily proteins (DSPs) mediate membrane fission and fusion necessary for endocytosis, organelle biogenesis and maintenance, as well as for bacterial cytokinesis. They also function in the innate immune response to pathogens and in organizing ...

Abstract	Dynamin superfamily proteins (DSPs) mediate membrane fission and fusion necessary for endocytosis, organelle biogenesis and maintenance, as well as for bacterial cytokinesis. They also function in the innate immune response to pathogens and in organizing the cytoskeleton. In this review, we summarize the current understanding of the molecular mechanism of DSPs, with emphasis on the structural basis of function. Studies from the past decade on the structure and mechanism of DSPs enable comparative analysis of shared mechanisms and unique features of this protein family.
MeSH term(s)	Animals ; Dynamins/chemistry ; Dynamins/classification ; Dynamins/metabolism ; Humans ; Protein Conformation
Chemical Substances	Dynamins (EC 3.6.5.5)
Language	English
Publishing date	2018-12-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	30122-x
ISSN	1879-3088 ; 0962-8924
ISSN (online)	1879-3088
ISSN	0962-8924
DOI	10.1016/j.tcb.2018.11.003
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Article ; Online: Synthesis and Effect of Conformationally Locked Carbocyclic Guanine Nucleotides on Dynamin.

Toti, Kiran S / Jimah, John R / Salmaso, Veronica / Hinshaw, Jenny E / Jacobson, Kenneth A

Biomolecules

2022 Volume 12, Issue 4

Abstract: Guanine nucleotides can flip between a North and South conformation in the ribose moiety. To test the enzymatic activity of GTPases bound to nucleotides in the two conformations, we generated methanocarba guanine nucleotides in the North or South ... ...

Abstract	Guanine nucleotides can flip between a North and South conformation in the ribose moiety. To test the enzymatic activity of GTPases bound to nucleotides in the two conformations, we generated methanocarba guanine nucleotides in the North or South envelope conformations, i.e., (N)-GTP and (S)-GTP, respectively. With dynamin as a model system, we examined the effects of (N)-GTP and (S)-GTP on dynamin-mediated membrane constriction, an activity essential for endocytosis. Dynamin membrane constriction and fission activity are dependent on GTP binding and hydrolysis, but the effect of the conformational state of the GTP nucleotide on dynamin activity is not known. After reconstituting dynamin-mediated lipid tubulation and membrane constriction in vitro, we observed via cryo-electron microscopy (cryo-EM) that (N)-GTP, but not (S)-GTP, enables the constriction of dynamin-decorated lipid tubules. These findings suggest that the activity of dynamin is dependent on the conformational state of the GTP nucleotide. However, a survey of nucleotide ribose conformations associated with dynamin structures in nature shows almost exclusively the (S)-conformation. The explanation for this mismatch of (N) vs. (S) required for GTP analogues in a dynamin-mediated process will be addressed in future studies.
MeSH term(s)	Cryoelectron Microscopy ; Dynamins/metabolism ; Guanine Nucleotides ; Guanosine Triphosphate/chemistry ; Lipids ; Ribose
Chemical Substances	Guanine Nucleotides ; Lipids ; Ribose (681HV46001) ; Guanosine Triphosphate (86-01-1) ; Dynamins (EC 3.6.5.5)
Language	English
Publishing date	2022-04-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom12040584
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Article ; Online: Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission.

Jimah, John R / Kundu, Nidhi / Stanton, Abigail E / Sochacki, Kem A / Canagarajah, Bertram / Chan, Lieza / Strub, Marie-Paule / Wang, Huaibin / Taraska, Justin W / Hinshaw, Jenny E

Developmental cell

2024

Abstract: Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the plasma membrane. Although atomic models of the dynamin helical ... ...

Abstract	Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the plasma membrane. Although atomic models of the dynamin helical polymer bound to guanosine triphosphate (GTP) analogs define earlier stages of membrane constriction, there are no atomic models of the assembled state post-GTP hydrolysis. Here, we used cryo-EM methods to determine atomic structures of the dynamin helical polymer assembled on lipid tubules, akin to necks of budding endocytic vesicles, in a guanosine diphosphate (GDP)-bound, super-constricted state. In this state, dynamin is assembled as a 2-start helix with an inner lumen of 3.4 nm, primed for spontaneous fission. Additionally, by cryo-electron tomography, we trapped dynamin helical assemblies within HeLa cells using the GTPase-defective dynamin K44A mutant and observed diverse dynamin helices, demonstrating that dynamin can accommodate a range of assembled complexes in cells that likely precede membrane fission.
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2024.04.008
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Article ; Online: Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding.

Doyle, Matthew Thomas / Jimah, John R / Dowdy, Tyrone / Ohlemacher, Shannon I / Larion, Mioara / Hinshaw, Jenny E / Bernstein, Harris D

Cell

2022 Volume 185, Issue 7, Page(s) 1143–1156.e13

Abstract: Transmembrane β barrel proteins are folded into the outer membrane (OM) of Gram-negative bacteria by the β barrel assembly machinery (BAM) via a poorly understood process that occurs without known external energy sources. Here, we used single-particle ... ...

Abstract	Transmembrane β barrel proteins are folded into the outer membrane (OM) of Gram-negative bacteria by the β barrel assembly machinery (BAM) via a poorly understood process that occurs without known external energy sources. Here, we used single-particle cryo-EM to visualize the folding dynamics of a model β barrel protein (EspP) by BAM. We found that BAM binds the highly conserved "β signal" motif of EspP to correctly orient β strands in the OM during folding. We also found that the folding of EspP proceeds via "hybrid-barrel" intermediates in which membrane integrated β sheets are attached to the essential BAM subunit, BamA. The structures show an unprecedented deflection of the membrane surrounding the EspP intermediates and suggest that β sheets progressively fold toward BamA to form a β barrel. Along with in vivo experiments that tracked β barrel folding while the OM tension was modified, our results support a model in which BAM harnesses OM elasticity to accelerate β barrel folding.
MeSH term(s)	Bacterial Outer Membrane Proteins/metabolism ; Bacterial Outer Membrane Proteins/ultrastructure ; Cryoelectron Microscopy ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Protein Folding
Chemical Substances	Bacterial Outer Membrane Proteins ; BamA protein, E coli ; Escherichia coli Proteins
Language	English
Publishing date	2022-03-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2022.02.016
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Article ; Online: Implications of conformational flexibility, lipid binding, and regulatory domains in cell-traversal protein CelTOS for apicomplexan migration.

Kumar, Hirdesh / Jimah, John R / Misal, Santosh A / Salinas, Nichole D / Fried, Michal / Schlesinger, Paul H / Tolia, Niraj H

The Journal of biological chemistry

2022 Volume 298, Issue 9, Page(s) 102241

Abstract: Malaria and other apicomplexan-caused diseases affect millions of humans, agricultural animals, and pets. Cell traversal is a common feature used by multiple apicomplexan parasites to migrate through host cells and can be exploited to develop ... ...

Abstract	Malaria and other apicomplexan-caused diseases affect millions of humans, agricultural animals, and pets. Cell traversal is a common feature used by multiple apicomplexan parasites to migrate through host cells and can be exploited to develop therapeutics against these deadly parasites. Here, we provide insights into the mechanism of the Cell-traversal protein for ookinetes and sporozoites (CelTOS), a conserved cell-traversal protein in apicomplexan parasites and malaria vaccine candidate. CelTOS has previously been shown to form pores in cell membranes to enable traversal of parasites through cells. We establish roles for the distinct protein regions of Plasmodium vivax CelTOS and examine the mechanism of pore formation. We further demonstrate that CelTOS dimer dissociation is required for pore formation, as disulfide bridging between monomers inhibits pore formation, and this inhibition is rescued by disulfide-bridge reduction. We also show that a helix-destabilizing amino acid, Pro127, allows CelTOS to undergo significant conformational changes to assemble into pores. The flexible C terminus of CelTOS is a negative regulator that limits pore formation. Finally, we highlight that lipid binding is a prerequisite for pore assembly as mutation of a phospholipids-binding site in CelTOS resulted in loss of lipid binding and abrogated pore formation. These findings identify critical regions in CelTOS and will aid in understanding the egress mechanism of malaria and other apicomplexan parasites as well as have implications for studying the function of other essential pore-forming proteins.
MeSH term(s)	Binding Sites ; Disulfides/chemistry ; Humans ; Malaria Vaccines/chemistry ; Malaria Vaccines/genetics ; Malaria Vaccines/immunology ; Malaria, Vivax/prevention & control ; Phospholipids/immunology ; Plasmodium vivax/genetics ; Plasmodium vivax/immunology ; Proline/chemistry ; Proline/genetics ; Protein Conformation, alpha-Helical ; Protein Multimerization ; Protozoan Proteins/chemistry ; Protozoan Proteins/genetics ; Protozoan Proteins/immunology ; Sporozoites/genetics ; Sporozoites/immunology
Chemical Substances	CelTOS protein, Plasmodium vivax ; Disulfides ; Malaria Vaccines ; Phospholipids ; Protozoan Proteins ; Proline (9DLQ4CIU6V)
Language	English
Publishing date	2022-07-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.102241
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Article: Liposome Disruption Assay to Examine Lytic Properties of Biomolecules.

Jimah, John R / Schlesinger, Paul H / Tolia, Niraj H

Bio-protocol

2017 Volume 7, Issue 15

Abstract: Proteins may have three dimensional structural or amino acid features that suggest a role in targeting and disrupting lipids within cell membranes. It is often necessary to experimentally investigate if these proteins and biomolecules are able to disrupt ...

Abstract	Proteins may have three dimensional structural or amino acid features that suggest a role in targeting and disrupting lipids within cell membranes. It is often necessary to experimentally investigate if these proteins and biomolecules are able to disrupt membranes in order to conclusively characterize the function of these biomolecules. Here, we describe an
Language	English
Publishing date	2017-09-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.2433
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Article: Membrane Lipid Screen to Identify Molecular Targets of Biomolecules.

Jimah, John R / Schlesinger, Paul H / Tolia, Niraj H

Bio-protocol

2017 Volume 7, Issue 15

Abstract: ... CelTOS disrupts cell membranes by specifically targeting phosphatidic acid (Jimah ...

Abstract	Proteins that bind to and disrupt cell membranes may target specific phospholipids. Here we describe a protocol to identify the lipid targets of proteins and biomolecules. First, we describe a screen to identify lipids in membranes that are specifically bound by the biomolecule of interest. Second, we describe a method for determining if the presence of these lipids within membranes is necessary for membrane disruption. The methods described here were used to determine that the malaria vaccine candidate CelTOS disrupts cell membranes by specifically targeting phosphatidic acid (Jimah
Language	English
Publishing date	2017-09-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.2427
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Article: Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding

Doyle, Matthew Thomas / Jimah, John R. / Dowdy, Tyrone / Ohlemacher, Shannon I. / Larion, Mioara / Hinshaw, Jenny E. / Bernstein, Harris D.

Cell. 2022 Mar. 31, v. 185, no. 7

2022

Abstract	Transmembrane β barrel proteins are folded into the outer membrane (OM) of Gram-negative bacteria by the β barrel assembly machinery (BAM) via a poorly understood process that occurs without known external energy sources. Here, we used single-particle cryo-EM to visualize the folding dynamics of a model β barrel protein (EspP) by BAM. We found that BAM binds the highly conserved “β signal” motif of EspP to correctly orient β strands in the OM during folding. We also found that the folding of EspP proceeds via “hybrid-barrel” intermediates in which membrane integrated β sheets are attached to the essential BAM subunit, BamA. The structures show an unprecedented deflection of the membrane surrounding the EspP intermediates and suggest that β sheets progressively fold toward BamA to form a β barrel. Along with in vivo experiments that tracked β barrel folding while the OM tension was modified, our results support a model in which BAM harnesses OM elasticity to accelerate β barrel folding.
Keywords	bacterial outer membranes ; energy ; models ; outer membrane proteins
Language	English
Dates of publication	2022-0331
Size	p. 1143-1156.e13.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2022.02.016
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The structure and spontaneous curvature of clathrin lattices at the plasma membrane.

Sochacki, Kem A / Heine, Bridgette L / Haber, Gideon J / Jimah, John R / Prasai, Bijeta / Alfonzo-Méndez, Marco A / Roberts, Aleah D / Somasundaram, Agila / Hinshaw, Jenny E / Taraska, Justin W

Developmental cell

2021 Volume 56, Issue 8, Page(s) 1131–1146.e3

Abstract: Clathrin-mediated endocytosis is the primary pathway for receptor and cargo internalization in eukaryotic cells. It is characterized by a polyhedral clathrin lattice that coats budding membranes. The mechanism and control of lattice assembly, curvature, ... ...

Abstract	Clathrin-mediated endocytosis is the primary pathway for receptor and cargo internalization in eukaryotic cells. It is characterized by a polyhedral clathrin lattice that coats budding membranes. The mechanism and control of lattice assembly, curvature, and vesicle formation at the plasma membrane has been a matter of long-standing debate. Here, we use platinum replica and cryoelectron microscopy and tomography to present a structural framework of the pathway. We determine the shape and size parameters common to clathrin-mediated endocytosis. We show that clathrin sites maintain a constant surface area during curvature across multiple cell lines. Flat clathrin is present in all cells and spontaneously curves into coated pits without additional energy sources or recruited factors. Finally, we attribute curvature generation to loosely connected and pentagon-containing flat lattices that can rapidly curve when a flattening force is released. Together, these data present a universal mechanistic model of clathrin-mediated endocytosis.
MeSH term(s)	Adhesiveness ; Animals ; Cell Line ; Cell Membrane/physiology ; Cell Membrane/ultrastructure ; Cholesterol/metabolism ; Clathrin/metabolism ; Cryoelectron Microscopy ; Humans ; Male ; Mice ; Models, Biological ; Rats
Chemical Substances	Clathrin ; Cholesterol (97C5T2UQ7J)
Language	English
Publishing date	2021-04-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2054967-2
ISSN	1878-1551 ; 1534-5807
ISSN (online)	1878-1551
ISSN	1534-5807
DOI	10.1016/j.devcel.2021.03.017
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