Complexes of the arginine-rich histone tetramer (H3)2(H4)2with negatively supercoiled DNA: electron microscopy and chemical cross-linking

ATP synthase, also called F(1)F(o)-ATPase, catalyzes the synthesis of ATP during oxidative phosphorylation. The enzyme is reversible and is able to use ATP to drive a proton gradient for transport purposes. Our work has focused on the enzyme from Escherichia coli (ECF(1)F(o)). We have used a combination of methods to study this enzyme, including electron microscopy and chemical cross-linking. The utility of these two approaches in particular, and the important insights they give into the structure and mechanism of the ATP synthase, are reviewed.

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Ultrafast microwave energy fixation for electron microscopy.

Journal of Histochemistry & Cytochemistry ◽

10.1177/34.3.3950387 ◽

1986 ◽

Vol 34 (3) ◽

pp. 381-387 ◽

Cited By ~ 45

Author(s):

G R Login ◽

W B Stavinoha ◽

A M Dvorak

Keyword(s):

Electron Microscopy ◽

Vesicular Transport ◽

Microwave Energy ◽

Cross Linking ◽

Fixation Methods ◽

Temperature Range ◽

Fixation Temperature ◽

Potential Applications ◽

Chemical Cross Linking ◽

Control Samples

We demonstrate that microwave (MW) energy can be used in conjunction with chemical cross-linking agents to fix tissue blocks rapidly for electron microscopy in as brief a time as 26 msec. The optimal ultrafast MW fixation methodology involved immersing tissue blocks up to 2 mm3 in dilute aldehyde fixative and immediately irradiating the specimens in a 7.3 kW MW oven for 26-90 msec, reaching a fixation temperature range of 32-42 degrees C. Ultrastructural preservation of samples irradiated by MW energy was comparable to that of the control samples immersed in aldehyde fixative for 2 hr at 25 degrees C. Potential applications for this new fixation technology include investigation of rapid intracellular processes (e.g., vesicular transport) and preservation of proteins that are difficult to demonstrate with routine fixation methods (e.g., antigens and enzymes).

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Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1811874115 ◽

2018 ◽

Vol 115 (42) ◽

pp. E9792-E9801 ◽

Cited By ~ 59

Author(s):

Saikat Chowdhury ◽

Chinatsu Otomo ◽

Alexander Leitner ◽

Kazuto Ohashi ◽

Ruedi Aebersold ◽

...

Keyword(s):

Electron Microscopy ◽

Mass Spectrometry ◽

Endoplasmic Reticulum ◽

Lipid Membranes ◽

De Novo ◽

Cross Linking ◽

Double Membrane ◽

Membrane Compartments ◽

Biochemical Analyses ◽

Chemical Cross Linking

Autophagy is an enigmatic cellular process in which double-membrane compartments, called “autophagosomes, form de novo adjacent to the endoplasmic reticulum (ER) and package cytoplasmic contents for delivery to lysosomes. Expansion of the precursor membrane phagophore requires autophagy-related 2 (ATG2), which localizes to the PI3P-enriched ER–phagophore junction. We combined single-particle electron microscopy, chemical cross-linking coupled with mass spectrometry, and biochemical analyses to characterize human ATG2A in complex with the PI3P effector WIPI4. ATG2A is a rod-shaped protein that can bridge neighboring vesicles through interactions at each of its tips. WIPI4 binds to one of the tips, enabling the ATG2A-WIPI4 complex to tether a PI3P-containing vesicle to another PI3P-free vesicle. These data suggest that the ATG2A-WIPI4 complex mediates ER–phagophore association and/or tethers vesicles to the ER–phagophore junction, establishing the required organization for phagophore expansion via the transfer of lipid membranes from the ER and/or the vesicles to the phagophore.

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Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2AWIPI4 complex

10.1101/180315 ◽

2017 ◽

Cited By ~ 1

Author(s):

Saikat Chowdhury ◽

Chinatsu Otomo ◽

Alexander Leitner ◽

Kazuto Ohashi ◽

Ruedi Aebersold ◽

...

Keyword(s):

Electron Microscopy ◽

Mass Spectrometry ◽

Endoplasmic Reticulum ◽

Lipid Membranes ◽

De Novo ◽

Cross Linking ◽

Double Membrane ◽

Membrane Compartments ◽

Biochemical Analyses ◽

Chemical Cross Linking

AbstractAutophagy is an enigmatic cellular process in which double-membrane compartments, called autophagosomes, form de novo adjacent to the endoplasmic reticulum (ER) and package cytoplasmic contents for delivery to lysosomes. Expansion of the precursor membrane phagophore requires autophagy-related 2 (ATG2), which localizes to the phosphatidylinositol-3-phosphate (PI3P)-enriched ER-phagophore junction. We combined single-particle electron microscopy, chemical cross-linking coupled with mass spectrometry, and biochemical analyses to characterize human ATG2A in complex with the PI3P effector WIPI4. ATG2A is a rod-shaped protein that can bridge neighboring vesicles through interactions at each of its tips. WIPI4 binds to one of the tips, enabling the ATG2A-WIPI4 complex to tether a PI3P-containing vesicle to another PI3P-free vesicle. These data suggest that the ATG2A-WIPI4 complex mediates ER-phagophore association and/or tethers vesicles to the ER-phagophore junction, establishing the required organization for phagophore expansion via the transfer of lipid membranes from the ER and/or the vesicles to the phagophore.

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Embedding Procedure for Water Swollen Samples

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010006951x ◽

1970 ◽

Vol 28 ◽

pp. 504-505

Author(s):

Ann M. Thomas ◽

Virginia Shemeley

Keyword(s):

Electron Microscopy ◽

Transmission Electron Microscopy ◽

Ion Exchange ◽

Structural Changes ◽

Cross Linking ◽

Ion Exchange Resins ◽

Transmission Electron ◽

First Pass ◽

Exchange Resins

Those samples which swell rapidly when exposed to water are, at best, difficult to section for transmission electron microscopy. Some materials literally burst out of the embedding block with the first pass by the knife, and even the most rapid cutting cycle produces sections of limited value. Many ion exchange resins swell in water; some undergo irreversible structural changes when dried. We developed our embedding procedure to handle this type of sample, but it should be applicable to many materials that present similar sectioning difficulties.The purpose of our embedding procedure is to build up a cross-linking network throughout the sample, while it is in a water swollen state. Our procedure was suggested to us by the work of Rosenberg, where he mentioned the formation of a tridimensional structure by the polymerization of the GMA biproduct, triglycol dimethacrylate.

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The Current Situation in Chemical Stabilization of Biological Materials

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100093912 ◽

1972 ◽

Vol 30 ◽

pp. 132-133

Author(s):

John H. Luft

Keyword(s):

Electron Microscopy ◽

Electron Microscope ◽

Osmium Tetroxide ◽

Molecular Level ◽

Cross Linking ◽

Chemical Stabilization ◽

Specimen Preparation ◽

Sufficient Condition ◽

Radio Telescopes

With information processing devices such as radio telescopes, microscopes or hi-fi systems, the quality of the output often is limited by distortion or noise introduced at the input stage of the device. This analogy can be extended usefully to specimen preparation for the electron microscope; fixation, which initiates the processing sequence, is the single most important step and, unfortunately, is the least well understood. Although there is an abundance of fixation mixtures recommended in the light microscopy literature, osmium tetroxide and glutaraldehyde are favored for electron microscopy. These fixatives react vigorously with proteins at the molecular level. There is clear evidence for the cross-linking of proteins both by osmium tetroxide and glutaraldehyde and cross-linking may be a necessary if not sufficient condition to define fixatives as a class.

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CRYO-Electron Microscopy of the Acto-Myosin-ATP Complex

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100179993 ◽

1990 ◽

Vol 48 (1) ◽

pp. 248-249

Author(s):

John Trinickt ◽

Howard White

Keyword(s):

Electron Microscopy ◽

Atp Hydrolysis ◽

Myosin Head ◽

Bound State ◽

Cross Linking ◽

Weakly Bound ◽

Cryo Electron Microscopy ◽

Myosin Subfragment 1 ◽

Attached State ◽

High Fraction

The primary force of muscle contraction is thought to involve a change in the myosin head whilst attached to actin, the energy coming from ATP hydrolysis. This change in attached state could either be a conformational change in the head or an alteration in the binding angle made with actin. A considerable amount is known about one bound state, the so-called strongly attached state, which occurs in the presence of ADP or in the absence of nucleotide. In this state, which probably corresponds to the last attached state of the force-producing cycle, the angle between the long axis myosin head and the actin filament is roughly 45°. Details of other attached states before and during power production have been difficult to obtain because, even at very high protein concentration, the complex is almost completely dissociated by ATP. Electron micrographs of the complex in the presence of ATP have therefore been obtained only after chemically cross-linking myosin subfragment-1 (S1) to actin filaments to prevent dissociation. But it is unclear then whether the variability in attachment angle observed is due merely to the cross-link acting as a hinge.We have recently found low ionic-strength conditions under which, without resorting to cross-linking, a high fraction of S1 is bound to actin during steady state ATP hydrolysis. The structure of this complex is being studied by cryo-electron microscopy of hydrated specimens. Most advantages of frozen specimens over ambient temperature methods such as negative staining have already been documented. These include improved preservation and fixation rates and the ability to observe protein directly rather than a surrounding stain envelope. In the present experiments, hydrated specimens have the additional benefit that it is feasible to use protein concentrations roughly two orders of magnitude higher than in conventional specimens, thereby reducing dissociation of weakly bound complexes.

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