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Article ; Online: Morphofunctional changes at the active zone during synaptic vesicle exocytosis.

Radecke, Julika / Seeger, Raphaela / Kádková, Anna / Laugks, Ulrike / Khosrozadeh, Amin / Goldie, Kenneth N / Lučić, Vladan / Sørensen, Jakob B / Zuber, Benoît

EMBO reports

2023 Volume 24, Issue 5, Page(s) e55719

Abstract: Synaptic vesicle (SV) fusion with the plasma membrane (PM) proceeds through intermediate steps that remain poorly resolved. The effect of persistent high or low exocytosis activity on intermediate steps remains unknown. Using spray-mixing plunge-freezing ...

Abstract	Synaptic vesicle (SV) fusion with the plasma membrane (PM) proceeds through intermediate steps that remain poorly resolved. The effect of persistent high or low exocytosis activity on intermediate steps remains unknown. Using spray-mixing plunge-freezing cryo-electron tomography we observe events following synaptic stimulation at nanometer resolution in near-native samples. Our data suggest that during the stage that immediately follows stimulation, termed early fusion, PM and SV membrane curvature changes to establish a point contact. The next stage-late fusion-shows fusion pore opening and SV collapse. During early fusion, proximal tethered SVs form additional tethers with the PM and increase the inter-SV connector number. In the late-fusion stage, PM-proximal SVs lose their interconnections, allowing them to move toward the PM. Two SNAP-25 mutations, one arresting and one disinhibiting spontaneous release, cause connector loss. The disinhibiting mutation causes loss of membrane-proximal multiple-tethered SVs. Overall, tether formation and connector dissolution are triggered by stimulation and respond to spontaneous fusion rate manipulation. These morphological observations likely correspond to SV transition from one functional pool to another.
MeSH term(s)	Synaptic Vesicles/physiology ; Synaptic Transmission/physiology ; Exocytosis/physiology ; Cell Membrane ; Membrane Fusion
Language	English
Publishing date	2023-03-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.202255719
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Article ; Online: Identification of a Dps contamination in Mitomycin-C-induced expression of Colicin Ia.

Pipercevic, Joka / Jakob, Roman P / Righetto, Ricardo D / Goldie, Kenneth N / Stahlberg, Henning / Maier, Timm / Hiller, Sebastian

Biochimica et biophysica acta. Biomembranes

2021 Volume 1863, Issue 7, Page(s) 183607

Abstract: Colicins are bacterial toxins targeting Gram-negative bacteria, including E. coli and related Enterobacteriaceae strains. Some colicins form ion-gated pores in the inner membrane of attacked bacteria that are lethal to their target. Colicin Ia was the ... ...

Abstract	Colicins are bacterial toxins targeting Gram-negative bacteria, including E. coli and related Enterobacteriaceae strains. Some colicins form ion-gated pores in the inner membrane of attacked bacteria that are lethal to their target. Colicin Ia was the first pore-forming E. coli toxin, for which a high-resolution structure of the monomeric full-length protein was determined. It is so far also the only colicin, for which a low-resolution structure of its membrane-inserted pore was reported by negative-stain electron microscopy. Resolving this structure at the atomic level would allow an understanding of the mechanism of toxin pore formation. Here, we report an observation that we made during an attempt to determine the Colicin Ia pore structure at atomic resolution. Colicin Ia was natively expressed by mitomycin-C induction under a native SOS promotor and purified following published protocols. The visual appearance in the electron microscope of negatively stained preparations and the lattice parameters of 2D crystals obtained from the material were highly similar to those reported earlier resulting from the same purification protocol. However, a higher-resolution structural analysis revealed that the protein is Dps (DNA-binding protein from starved cells), a dodecameric E. coli protein. This finding suggests that the previously reported low-resolution structure of a "Colicin Ia oligomeric pore" actually shows Dps.
MeSH term(s)	Colicins/chemistry ; Colicins/genetics ; Colicins/metabolism ; Cryoelectron Microscopy ; Crystallization ; DNA-Binding Proteins/chemistry ; Escherichia coli/metabolism ; Gene Expression/drug effects ; Mitomycin/pharmacology ; Protein Structure, Quaternary ; Recombinant Proteins/biosynthesis ; Recombinant Proteins/isolation & purification
Chemical Substances	Colicins ; DNA-Binding Proteins ; Recombinant Proteins ; Mitomycin (50SG953SK6)
Language	English
Publishing date	2021-03-26
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	60-7
ISSN	1879-2642 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2618 ; 1879-2650 ; 0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
ISSN (online)	1879-2642 ; 1879-2596 ; 1879-260X ; 1872-8006 ; 1879-2618 ; 1879-2650
ISSN	0006-3002 ; 0005-2728 ; 0005-2736 ; 0304-4165 ; 0167-4838 ; 1388-1981 ; 0167-4889 ; 0167-4781 ; 0304-419X ; 1570-9639 ; 0925-4439 ; 1874-9399
DOI	10.1016/j.bbamem.2021.183607
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Article ; Online: Deuterium induces a distinctive

Opitz, Christian / Ahrné, Erik / Goldie, Kenneth N / Schmidt, Alexander / Grzesiek, Stephan

The Journal of biological chemistry

2018 Volume 294, Issue 7, Page(s) 2279–2292

Abstract: Substitution of protium (H) for deuterium (D) strongly affects biological systems. Whereas higher eukaryotes such as plants and mammals hardly survive a deuterium content of >30%, many microorganisms can grow on fully deuterated media, albeit at reduced ... ...

Abstract	Substitution of protium (H) for deuterium (D) strongly affects biological systems. Whereas higher eukaryotes such as plants and mammals hardly survive a deuterium content of >30%, many microorganisms can grow on fully deuterated media, albeit at reduced rates. Very little is known about how the H/D replacement influences life at the systems level. Here, we used MS-based analysis to follow the adaptation of a large part of the
MeSH term(s)	Cell Proliferation/drug effects ; Deuterium/pharmacology ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Proteome/genetics ; Proteome/metabolism
Chemical Substances	Escherichia coli Proteins ; Proteome ; Deuterium (AR09D82C7G)
Language	English
Publishing date	2018-12-13
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA118.006914
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Article ; Online: Cryo-EM reconstruction of Type VI secretion system baseplate and sheath distal end.

Nazarov, Sergey / Schneider, Johannes P / Brackmann, Maximilian / Goldie, Kenneth N / Stahlberg, Henning / Basler, Marek

The EMBO journal

2017 Volume 37, Issue 4

Abstract: The bacterial Type VI secretion system (T6SS) assembles from three major parts: a membrane complex that spans inner and outer membranes, a baseplate, and a sheath-tube polymer. The baseplate assembles around a tip complex with associated effectors and ... ...

Abstract	The bacterial Type VI secretion system (T6SS) assembles from three major parts: a membrane complex that spans inner and outer membranes, a baseplate, and a sheath-tube polymer. The baseplate assembles around a tip complex with associated effectors and connects to the membrane complex by TssK. The baseplate assembly initiates sheath-tube polymerization, which in some organisms requires TssA. Here, we analyzed both ends of isolated non-contractile
MeSH term(s)	Bacterial Proteins/chemistry ; Cryoelectron Microscopy/methods ; Membrane Proteins/chemistry ; Type VI Secretion Systems/ultrastructure ; Vibrio cholerae/cytology ; Vibrio cholerae/metabolism ; Vibrio cholerae/ultrastructure
Chemical Substances	Bacterial Proteins ; Membrane Proteins ; Type VI Secretion Systems
Language	English
Publishing date	2017-12-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.201797103
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Article ; Online: Poly(N-isopropylacrylamide)/poly(dopamine) capsules.

Zhang, Yan / Teo, Boon M / Goldie, Kenneth N / Städler, Brigitte

Langmuir : the ACS journal of surfaces and colloids

2014 Volume 30, Issue 19, Page(s) 5592–5598

Abstract: Polymer capsules are an interesting concept considered in nanobiotechnology. Approaches that facilitate their assembly remain sought after. Poly(dopamine) (PDA) has been considered and successfully applied in this context. We recently demonstrated that ... ...

Abstract	Polymer capsules are an interesting concept considered in nanobiotechnology. Approaches that facilitate their assembly remain sought after. Poly(dopamine) (PDA) has been considered and successfully applied in this context. We recently demonstrated that PDA could be copolymerized with different types of poly(N-isopropylacrylamide) (pNiPAAm) to assemble mixed films on planar substrates. Herein, we transferred this approach onto colloidal substrates and characterized the film thickness depending on the film composition and template particles size. While the membrane of capsules assembled using 5 μm template particles exhibited strong dependency on the film composition, smaller templates led to capsules with similar membrane thickness. We then compared the permeability of different capsules using fluorescently labeled dextran and fluorescein. We found that the permeability of capsules was heavily dependent on the polymer composition and the template particle size. These fundamental findings contribute to the potential of these capsules, assembled in one-step, for biomedical applications.
MeSH term(s)	Acrylic Resins/chemistry ; Capsules/chemistry ; Indoles/chemistry ; Polymers/chemistry
Chemical Substances	Acrylic Resins ; Capsules ; Indoles ; Polymers ; polydopamine ; poly-N-isopropylacrylamide (25189-55-3)
Language	English
Publishing date	2014-05-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2005937-1
ISSN	1520-5827 ; 0743-7463
ISSN (online)	1520-5827
ISSN	0743-7463
DOI	10.1021/la5005227
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Article ; Online: 3D correlative electron microscopy reveals continuity of

Sedzicki, Jaroslaw / Tschon, Therese / Low, Shyan Huey / Willemart, Kevin / Goldie, Kenneth N / Letesson, Jean-Jacques / Stahlberg, Henning / Dehio, Christoph

Journal of cell science

2018 Volume 131, Issue 4

Abstract: Entry of the facultative intracellular ... ...

Abstract	Entry of the facultative intracellular pathogen
MeSH term(s)	Animals ; Brucella abortus/pathogenicity ; Brucella abortus/ultrastructure ; Brucella melitensis/pathogenicity ; Brucella melitensis/ultrastructure ; Cytoplasm/microbiology ; Endoplasmic Reticulum/microbiology ; Endoplasmic Reticulum/ultrastructure ; HeLa Cells ; Host-Pathogen Interactions/genetics ; Humans ; Mice ; Microscopy, Electron, Scanning ; Trophoblasts/microbiology ; Trophoblasts/ultrastructure ; Type IV Secretion Systems/ultrastructure ; Vacuoles/microbiology ; Vacuoles/ultrastructure
Chemical Substances	Type IV Secretion Systems
Language	English
Publishing date	2018-02-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.210799
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Article ; Online: Miniaturizing EM Sample Preparation: Opportunities, Challenges, and "Visual Proteomics".

Arnold, Stefan A / Müller, Shirley A / Schmidli, Claudio / Syntychaki, Anastasia / Rima, Luca / Chami, Mohamed / Stahlberg, Henning / Goldie, Kenneth N / Braun, Thomas

Proteomics

2018 Volume 18, Issue 5-6, Page(s) e1700176

Abstract: This review compares and discusses conventional versus miniaturized specimen preparation methods for transmission electron microscopy (TEM). The progress brought by direct electron detector cameras, software developments and automation have transformed ... ...

Abstract	This review compares and discusses conventional versus miniaturized specimen preparation methods for transmission electron microscopy (TEM). The progress brought by direct electron detector cameras, software developments and automation have transformed transmission cryo-electron microscopy (cryo-EM) and made it an invaluable high-resolution structural analysis tool. In contrast, EM specimen preparation has seen very little progress in the last decades and is now one of the main bottlenecks in cryo-EM. Here, we discuss the challenges faced by specimen preparation for single particle EM, highlight current developments, and show the opportunities resulting from the advanced miniaturized and microfluidic sample grid preparation methods described, such as visual proteomics and time-resolved cryo-EM studies.
MeSH term(s)	Cryoelectron Microscopy/methods ; Humans ; Imaging, Three-Dimensional/methods ; Microfluidics/methods ; Microscopy, Electron, Transmission/methods ; Proteins/ultrastructure ; Proteomics/methods ; Specimen Handling
Chemical Substances	Proteins
Language	English
Publishing date	2018-02-14
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.201700176
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Article: Miniaturized sample preparation for transmission electron microscopy

Schmidli, Claudio / Rima, Luca / Arnold, Stefan A / Stohler, Thomas / Syntychaki, Anastasia / Bieri, Andrej / Albiez, Stefan / Goldie, Kenneth N / Chami, Mohamed / Stahlberg, Henning / Braun, Thomas

Journal of visualized experiments. 2018 July 27, , no. 137

2018

Abstract: Due to recent technological progress, cryo-electron microscopy (cryo-EM) is rapidly becoming a standard method for the structural analysis of protein complexes to atomic resolution. However, protein isolation techniques and sample preparation methods for ...

Abstract	Due to recent technological progress, cryo-electron microscopy (cryo-EM) is rapidly becoming a standard method for the structural analysis of protein complexes to atomic resolution. However, protein isolation techniques and sample preparation methods for EM remain a bottleneck. A relatively small number (100,000 to a few million) of individual protein particles need to be imaged for the high-resolution analysis of proteins by the single particle EM approach, making miniaturized sample handling techniques and microfluidic principles feasible. A miniaturized, paper-blotting-free EM grid preparation method for sample pre-conditioning, EM grid priming and post processing that only consumes nanoliter-volumes of sample is presented. The method uses a dispensing system with sub-nanoliter precision to control liquid uptake and EM grid priming, a platform to control the grid temperature thereby determining the relative humidity above the EM grid, and a pick-and-plunge-mechanism for sample vitrification. For cryo-EM, an EM grid is placed on the temperature-controlled stage and the sample is aspirated into a capillary. The capillary tip is positioned in proximity to the grid surface, the grid is loaded with the sample and excess is re-aspirated into the microcapillary. Subsequently, the sample film is stabilized and slightly thinned by controlled water evaporation regulated by the offset of the platform temperature relative to the dew-point. At a given point the pick-and-plunge mechanism is triggered, rapidly transferring the primed EM grid into liquid ethane for sample vitrification. Alternatively, sample-conditioning methods are available to prepare nanoliter-sized sample volumes for negative stain (NS) EM. The methodologies greatly reduce sample consumption and avoid approaches potentially harmful to proteins, such as the filter paper blotting used in conventional methods. Furthermore, the minuscule amount of sample required allows novel experimental strategies, such as fast sample conditioning, combination with single-cell lysis for "visual proteomics," or "lossless" total sample preparation for quantitative analysis of complex samples.
Keywords	cryo-electron microscopy ; ethane ; evaporation ; isolation techniques ; liquids ; proteins ; proteomics ; quantitative analysis ; relative humidity ; temperature ; transmission electron microscopy ; vitrification
Language	English
Dates of publication	2018-0727
Size	p. e57310.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/57310
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Transmission electron microscopy of amyloid fibrils.

Gras, Sally L / Waddington, Lynne J / Goldie, Kenneth N

Methods in molecular biology (Clifton, N.J.)

2011 Volume 752, Page(s) 197–214

Abstract: Transmission Electron Microscopy of negatively stained and cryo-prepared specimens allows amyloid fibrils to be visualised at high resolution in a dried or a hydrated state, and is an essential method for characterising the morphology of fibrils and pre- ... ...

Abstract	Transmission Electron Microscopy of negatively stained and cryo-prepared specimens allows amyloid fibrils to be visualised at high resolution in a dried or a hydrated state, and is an essential method for characterising the morphology of fibrils and pre-fibrillar species. We outline the key steps involved in the preparation and observation of samples using negative staining and cryo-electron preservation. We also discuss methods to measure fibril characteristics, such as fibril width, from electron micrographs.
MeSH term(s)	Amyloid/chemistry ; Artifacts ; Cryopreservation ; Image Processing, Computer-Assisted ; Microscopy, Electron, Transmission/instrumentation ; Microscopy, Electron, Transmission/methods ; Protein Multimerization ; Protein Structure, Secondary
Chemical Substances	Amyloid
Language	English
Publishing date	2011
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-60327-223-0_13
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Article: Poly(N-isopropylacrylamide)/Poly(dopamine) Capsules

Zhang, Yan / Goldie Kenneth N / StaÌdler Brigitte / Teo Boon M

Langmuir. 2014 May 20, v. 30, no. 19

2014

Abstract	Polymer capsules are an interesting concept considered in nanobiotechnology. Approaches that facilitate their assembly remain sought after. Poly(dopamine) (PDA) has been considered and successfully applied in this context. We recently demonstrated that PDA could be copolymerized with different types of poly(N-isopropylacrylamide) (pNiPAAm) to assemble mixed films on planar substrates. Herein, we transferred this approach onto colloidal substrates and characterized the film thickness depending on the film composition and template particles size. While the membrane of capsules assembled using 5 Î¼m template particles exhibited strong dependency on the film composition, smaller templates led to capsules with similar membrane thickness. We then compared the permeability of different capsules using fluorescently labeled dextran and fluorescein. We found that the permeability of capsules was heavily dependent on the polymer composition and the template particle size. These fundamental findings contribute to the potential of these capsules, assembled in one-step, for biomedical applications.
Keywords	dextran ; dopamine ; fluorescein ; particle size ; permeability ; polymers
Language	English
Dates of publication	2014-0520
Size	p. 5592-5598.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2005937-1
ISSN	1520-5827 ; 0743-7463
ISSN (online)	1520-5827
ISSN	0743-7463
DOI	10.1021%2Fla5005227
Database	NAL-Catalogue (AGRICOLA)

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