scholarly journals High-resolution cryo-EM structure of photosystem II: Effects of electron beam damage

2020 ◽  
Author(s):  
Koji Kato ◽  
Naoyuki Miyazaki ◽  
Tasuku Hamaguchi ◽  
Yoshiki Nakajima ◽  
Fusamichi Akita ◽  
...  
Keyword(s):  
Electron Beam ◽  
Photosystem Ii ◽  
Physiological State ◽  
State Transitions ◽  
High Dose ◽  
Final State ◽  
Electron Dose ◽  
X Ray Crystallography ◽  
Redox Active ◽  
Beam Damage

AbstractPhotosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state, and its final state structure has not been solved because of the low efficiencies of the S-state transitions in the crystals. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, which was reduced by reducing the electron dose. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.

scholarly journals High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Koji Kato ◽  
Naoyuki Miyazaki ◽  
Tasuku Hamaguchi ◽  
Yoshiki Nakajima ◽  
Fusamichi Akita ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
Physiological State ◽  
High Dose ◽  
Final State ◽  
X Ray ◽  
Redox States ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Redox Active ◽  
Beam Damage

AbstractPhotosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.

Electron Beam Damage in High-Temperature Polymers

1985 ◽  
Vol 43 ◽  
pp. 84-85
Author(s):  
Satish Kumar ◽  
Stephen J. Krause ◽  
W. W. Adams
Keyword(s):  
Electron Microscopy ◽  
Electron Beam ◽  
Initial Period ◽  
Damage Mechanism ◽  
Diffraction Intensity ◽  
Electron Dose ◽  
Microscopy Imaging ◽  
Optimum Parameters ◽  
Electron Energy Loss ◽  
Beam Damage

Electron microscopy studies of polymers are limited due to beam damage. Two concerns are (i) the damage mechanism in a particular material, and (ii) the maximum dose for a material before damage effects are observed. To understand these aspects of beam damage of polymers several systematic studies have been under taken. From the knowledge of the dose required for damage to the polymer crystals, optimum parameters for electron microscopy imaging can be determined.Electron beam damage can be quantified by changes in (i) mass, (ii) diffraction contrast, (iii) diffraction intensity, and (iv) electron energy loss spectrum (EELS) intensity. Dose required to damage a material depends on which of the above criteria is applied. Therefore to compare the beam damage results for different polymers it is necessary to use the same criteria. We have studied beam damage by measuring the loss of diffraction intensity. Diffraction intensity decreases exponentially with increasing electron dose, after a short initial period. The intensity, I(D), of a particular reflection at a dose, D, can be given by the following equation.

scholarly journals Using Your Beam Efficiently: Reducing Electron Dose in the STEM via Flyback Compensation

2022 ◽  
pp. 1-9
Author(s):  
Tiarnan Mullarkey ◽  
Jonathan J. P. Peters ◽  
Clive Downing ◽  
Lewys Jones
Keyword(s):  
Electron Beam ◽  
Strain Measurement ◽  
Scanning Transmission Electron Microscope ◽  
Absolute Minimum ◽  
Electron Dose ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Dose Efficiency ◽  
Specialized Hardware ◽  
Beam Damage

In the scanning transmission electron microscope, fast-scanning and frame-averaging are two widely used approaches for reducing electron-beam damage and increasing image signal noise ratio which require no additional specialized hardware. Unfortunately, for scans with short pixel dwell-times (less than 5 μs), line flyback time represents an increasingly wasteful overhead. Although beam exposure during flyback causes damage while yielding no useful information, scan coil hysteresis means that eliminating it entirely leads to unacceptably distorted images. In this work, we reduce this flyback to an absolute minimum by calibrating and correcting for this hysteresis in postprocessing. Substantial improvements in dose efficiency can be realized (up to 20%), while crystallographic and spatial fidelity is maintained for displacement/strain measurement.

Photosystem II: the engine of life

2003 ◽  
Vol 36 (1) ◽  
pp. 71-89 ◽  
Author(s):  
James Barber
Keyword(s):  
High Resolution ◽  
Photosystem Ii ◽  
Water Oxidation ◽  
Structural Models ◽  
Reaction Centre ◽  
Ps Ii ◽  
X Ray ◽  
X Ray Crystallography ◽  
Redox Active ◽  
Resolution Electron

1. Introduction 712. Electron transfer in PS II 723. (Mn)4cluster and mechanism of water oxidation 734. Organization and structure of the protein subunits 755. Organization of chlorophylls and redox active cofactors 816. Implications arising from the structural models 827. Perspectives 848. Acknowledgements 869. Addendum 8610. References 87Photosystem II (PS II) is a multisubunit membrane protein complex, which uses light energy to oxidize water and reduce plastoquinone. High-resolution electron cryomicroscopy and X-ray crystallography are revealing the structure of this important molecular machine. Both approaches have contributed to our understanding of the organization of the transmembrane helices of higher plant and cyanobacterial PS II and both indicate that PS II normally functions as a dimer. However the high-resolution electron density maps derived from X-ray crystallography currently at 3·7/3·8 Å, have allowed assignments to be made to the redox active cofactors involved in the light-driven water–plastoquinone oxidoreductase activity and to the chlorophyll molecules that absorb and transfer energy to the reaction centre. In particular the X-ray work has identified density that can accommodate the four manganese atoms which catalyse the water-oxidation process. The Mn cluster is located at the lumenal surface of the D1 protein and approximately 7 Å from the redox active tyrosine residue (YZ) which acts an electron/proton transfer link to the primary oxidant P680.+. The lower resolution electron microscopy studies, however, are providing structural models of larger PS II supercomplexes that are ideal frameworks in which to incorporate the X-ray derived structures.

Temperature Dependence of the Critical Electron Dose for Fatty Acid Monolayers

1982 ◽  
Vol 40 ◽  
pp. 78-79
Author(s):  
Kenneth H. Downing ◽  
Robert M. Glaeser
Keyword(s):  
Electron Beam ◽  
Fatty Acid ◽  
Inelastic Scattering ◽  
Temperature Dependence ◽  
Structural Damage ◽  
Direct Result ◽  
Second Step ◽  
Strong Temperature Dependence ◽  
Electron Dose ◽  
Covalent Bonds

The structural damage of molecules irradiated by electrons is generally considered to occur in two steps. The direct result of inelastic scattering events is the disruption of covalent bonds. Following changes in bond structure, movement of the constituent atoms produces permanent distortions of the molecules. Since at least the second step should show a strong temperature dependence, it was to be expected that cooling a specimen should extend its lifetime in the electron beam. This result has been found in a large number of experiments, but the degree to which cooling the specimen enhances its resistance to radiation damage has been found to vary widely with specimen types.

Lithography below 100 nm

1983 ◽  
Vol 41 ◽  
pp. 96-99
Author(s):  
L. D. Jackel
Keyword(s):  
Spatial Distribution ◽  
Electron Beam ◽  
Electron Scattering ◽  
Electron Beam Lithography ◽  
Substrate Material ◽  
Local Electron ◽  
Electron Dose ◽  
Positive Resist ◽  
Exposure Process

Most production electron beam lithography systems can pattern minimum features a few tenths of a micron across. Linewidth in these systems is usually limited by the quality of the exposing beam and by electron scattering in the resist and substrate. By using a smaller spot along with exposure techniques that minimize scattering and its effects, laboratory e-beam lithography systems can now make features hundredths of a micron wide on standard substrate material. This talk will outline sane of these high- resolution e-beam lithography techniques.We first consider parameters of the exposure process that limit resolution in organic resists. For concreteness suppose that we have a “positive” resist in which exposing electrons break bonds in the resist molecules thus increasing the exposed resist's solubility in a developer. Ihe attainable resolution is obviously limited by the overall width of the exposing beam, but the spatial distribution of the beam intensity, the beam “profile” , also contributes to the resolution. Depending on the local electron dose, more or less resist bonds are broken resulting in slower or faster dissolution in the developer.

Electron Beam Damage of Biomolecules Assessed by Energy Loss Spectroscopy

1978 ◽  
Vol 36 (3) ◽  
pp. 61-69
Author(s):  
M. Isaacson ◽  
M.L. Collins ◽  
M. Listvan
Keyword(s):  
Electron Microscopy ◽  
Radiation Damage ◽  
Structural Integrity ◽  
Analytical Electron Microscopy ◽  
High Dose ◽  
Dose Rates ◽  
Special Cases ◽  
Analytical Electron ◽  
Atom Migration ◽  
Beam Damage

Over the past five years it has become evident that radiation damage provides the fundamental limit to the study of blomolecular structure by electron microscopy. In some special cases structural determinations at very low doses can be achieved through superposition techniques to study periodic (Unwin & Henderson, 1975) and nonperiodic (Saxton & Frank, 1977) specimens. In addition, protection methods such as glucose embedding (Unwin & Henderson, 1975) and maintenance of specimen hydration at low temperatures (Taylor & Glaeser, 1976) have also shown promise. Despite these successes, the basic nature of radiation damage in the electron microscope is far from clear. In general we cannot predict exactly how different structures will behave during electron Irradiation at high dose rates. Moreover, with the rapid rise of analytical electron microscopy over the last few years, nvicroscopists are becoming concerned with questions of compositional as well as structural integrity. It is important to measure changes in elemental composition arising from atom migration in or loss from the specimen as a result of electron bombardment.

Electron-diffraction studies in synthetic polymer materials

1983 ◽  
Vol 41 ◽  
pp. 362-365
Author(s):  
D.T. Grubb
Keyword(s):  
Electron Diffraction ◽  
Synthetic Polymer ◽  
Polymer Materials ◽  
Crystallographic Structure ◽  
High Dose ◽  
Electron Dose ◽  
Dose Rates ◽  
First Case ◽  
Diffraction Patterns ◽  
The Many

Diffraction studies in polymeric and other beam sensitive materials may bring to mind the many experiments where diffracted intensity has been used as a measure of the electron dose required to destroy fine structure in the TEM. But this paper is concerned with a range of cases where the diffraction pattern itself contains the important information.In the first case, electron diffraction from paraffins, degraded polyethylene and polyethylene single crystals, all the samples are highly ordered, and their crystallographic structure is well known. The diffraction patterns fade on irradiation and may also change considerably in a-spacing, increasing the unit cell volume on irradiation. The effect is large and continuous far C94H190 paraffin and for PE, while for shorter chains to C 28H58 the change is less, levelling off at high dose, Fig.l. It is also found that the change in a-spacing increases at higher dose rates and at higher irradiation temperatures.

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