scholarly journals GeRelion: GPU-enhanced parallel implementation of single particle cryo-EM image processing

2016 ◽  
Author(s):  
Huayou Su ◽  
Wen Wen ◽  
Xiaoli Du ◽  
Xicheng Lu ◽  
Maofu Liao ◽  
...  
Keyword(s):  
Image Processing ◽  
Single Particle ◽  
Parallel Implementation ◽  
Data Sets ◽  
Structural Details ◽  
High Resolution Structure ◽  
Molecular Machinery ◽  
Speed Up ◽  
And Function ◽  
Resolution Structure

Single particle cryo-EM emerges as a powerful and versatile method to characterize the structure and function of macromolecules, revealing the structural details of critical molecular machinery inside the cells. RELION is a widely used EM image processing software, and most of the recently published single particle cryo-EM structures were generated by using RELION. Due to the massive computational loads and the growing demands for processing much larger cryo-EM data sets, there is a pressing need to speed up image processing. Here we present GeRelion (https://github.com/gpu-pdl¬nudt/GeRelion), an efficient parallel implementation of RELION on GPU system. In the performance tests using two cryo-EM data sets, GeRelion on 4 or 8 GPU cards outperformed RELION on 256 CPU cores, demonstrating dramatically improved speed and superb scalability. By greatly accelerating single particle cryo-EM structural analysis, GeRelion will facilitate both high resolution structure determination and dissection of mixed conformations of dynamic molecular machines.

The ryanodine receptor provides high throughput Ca2+-release but is precisely regulated by networks of associated proteins: a focus on proteins relevant to phosphorylation

2015 ◽  
Vol 43 (3) ◽  
pp. 426-433 ◽  
Author(s):  
Fiona O'Brien ◽  
Elisa Venturi ◽  
Rebecca Sitsapesan
Keyword(s):  
Spatial Organization ◽  
Ryanodine Receptors ◽  
Integrated System ◽  
Fine Tuning ◽  
Control Mechanisms ◽  
Fk 506 ◽  
High Resolution Structure ◽  
Associated Proteins ◽  
And Function ◽  
Resolution Structure

Once opened, ryanodine receptors (RyR) are efficient pathways for the release of Ca2+ from the endoplasmic/sarcoplasmic reticulum (ER/SR). The precise nature of the Ca2+-release event, however, requires fine-tuning for the specific process and type of cell involved. For example, the spatial organization of RyRs, the luminal [Ca2+] and the influence of soluble regulators that fluctuate under physiological and pathophysiological control mechanisms, all affect the amplitude and duration of RyR Ca2+ fluxes. Various proteins are docked tightly to the huge bulky structure of RyR and there is growing evidence that, together, they provide a sophisticated and integrated system for regulating RyR channel gating. This review focuses on those proteins that are relevant to phosphorylation of RyR channels with particular reference to the cardiac isoform of RyR (RyR2). How phosphorylation of RyR affects channel activity and whether proteins such as the FK-506 binding proteins (FKBP12 and FKBP12.6) are involved, have been highly controversial subjects for more than a decade. But that is expected given the large number of participating proteins, the relevance of phosphorylation in heart failure and inherited arrhythmic diseases, and the frustrations of predicting relationships between structure and function before the advent of a high resolution structure of RyR.

Low-dose high-resolution EM of zeolite materials with slow A scan CCD camera

1992 ◽  
Vol 50 (1) ◽  
pp. 302-303
Author(s):  
M. Pan ◽  
P.A. Crozier
Keyword(s):  
Image Processing ◽  
Electron Beam ◽  
High Resolution ◽  
Low Dose ◽  
Ccd Camera ◽  
Low Noise ◽  
Great Sensitivity ◽  
Recording Device ◽  
High Resolution Structure ◽  
Resolution Structure

Zeolite materials are widely used as an important type of catalyst in oil industry. Their catalytic properties and performance are closely related to their unique structures. Use of high resolution electron microscopy (HREM) to characterize structures of zeolite materials has been limited mainly due to the great sensitivity of the framework structures to electron beam irradiation used in the observation. With the recent development in solid state electronics, a new type of image recording device, known as a charge-coupled-device (CCD), has been made possible. Among many of its superior properties, it has been found that the very low noise level present in a slow scan CCD camera offers the possibility of recording high resolution structure images of zeolite materials with very low electron beam dose. The digital storage of CCD images allows on-line image processing to be performed at the microscope, thus making the recording of low dose electron microscope images more efficient. Image processing was also found to be essential in extracting high resolution structure information contained in the noisy low dose HREM CCD images.

scholarly journals Structure and function of the bacterial protein toxin phenomycin

2019 ◽  
Author(s):  
Bente K. Hansen ◽  
Camilla K. Larsen ◽  
Jacob T. Nielsen ◽  
Esben B. Svenningsen ◽  
Lan B. Van ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Endosomal Escape ◽  
Bacterial Protein ◽  
Direct Inhibition ◽  
Uptake Mechanism ◽  
Protein Toxin ◽  
Limiting Step ◽  
High Resolution Structure ◽  
And Function ◽  
Resolution Structure

SummaryPhenomycin is a bacterial mini-protein of 89 amino acids discovered more than 50 years ago with toxicity in the nanomolar regime towards mammalian cells. The protein inhibits the function of the eukaryotic ribosome in cell free systems and appears to target translation initiation. Several fundamental questions concerning the cellular activity of phenomycin have however remained unanswered. In this paper, we have used morphological profiling to show that direct inhibition of translation underlies the toxicity of phenomycin in cells. We have performed studies of the cellular uptake mechanism of phenomycin, showing that endosomal escape is the toxicity-limiting step, and we have solved a solution phase high-resolution structure of the protein using NMR spectroscopy. Through bioinformatic as well as functional comparisons between phenomycin and two homologs, we have identified a peptide segment, which constitutes one of two loops in the structure, that is critical for the toxicity of phenomycin.

scholarly journals Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin

2021 ◽  
Vol 118 (16) ◽  
pp. e2025658118
Author(s):  
Yanting Tang ◽  
An Mu ◽  
Yuying Zhang ◽  
Shan Zhou ◽  
Weiwei Wang ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Mycobacterium Smegmatis ◽  
Structural Features ◽  
Antituberculosis Drug ◽  
Potential Mechanism ◽  
Cargo Protein ◽  
High Resolution Structure ◽  
Axis Of Symmetry ◽  
And Function ◽  
Resolution Structure

Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact and function. Here, we have isolated a native cargo-packaging encapsulin from Mycobacterium smegmatis and determined its complete high-resolution structure by cryogenic electron microscopy (cryo-EM). This encapsulin comprises an icosahedral shell and a dodecameric DyP cargo. The dodecameric DyP consists of two hexamers with a twofold axis of symmetry and stretches across the interior of the encapsulin. Our results reveal that the encapsulin shell plays a role in stabilizing the dodecameric DyP. Furthermore, we have proposed a potential mechanism for removing the hydrogen peroxide based on the structural features. Our study also suggests that the DyP is the primary cargo protein of mycobacterial encapsulins and is a potential target for antituberculosis drug discovery.

scholarly journals Image processing techniques for high-resolution structure determination from badly ordered 2D crystals

2018 ◽  
Vol 203 (2) ◽  
pp. 120-134 ◽  
Author(s):  
Nikhil Biyani ◽  
Sebastian Scherer ◽  
Ricardo D. Righetto ◽  
Julia Kowal ◽  
Mohamed Chami ◽  
...  
Keyword(s):  
Image Processing ◽  
High Resolution ◽  
Structure Determination ◽  
Image Processing Techniques ◽  
High Resolution Structure ◽  
Processing Techniques ◽  
2D Crystals ◽  
Resolution Structure

scholarly journals MicroED with the Falcon III direct electron detector

IUCrJ ◽  
2019 ◽  
Vol 6 (5) ◽  
pp. 921-926 ◽  
Author(s):  
Johan Hattne ◽  
Michael W. Martynowycz ◽  
Pawel A. Penczek ◽  
Tamir Gonen
Keyword(s):  
High Energy ◽  
Proteinase K ◽  
Data Sets ◽  
Electron Detector ◽  
Density Maps ◽  
Transmission Electron ◽  
High Energy Electrons ◽  
High Resolution Structure ◽  
Resolution Structure ◽  
Nanosized Crystals

Microcrystal electron diffraction (MicroED) combines crystallography and electron cryo-microscopy (cryo-EM) into a method that is applicable to high-resolution structure determination. In MicroED, nanosized crystals, which are often intractable using other techniques, are probed by high-energy electrons in a transmission electron microscope. Diffraction data are recorded by a camera in movie mode: the nanocrystal is continuously rotated in the beam, thus creating a sequence of frames that constitute a movie with respect to the rotation angle. Until now, diffraction-optimized cameras have mostly been used for MicroED. Here, the use of a direct electron detector that was designed for imaging is reported. It is demonstrated that data can be collected more rapidly using the Falcon III for MicroED and with markedly lower exposure than has previously been reported. The Falcon III was operated at 40 frames per second and complete data sets reaching atomic resolution were recorded in minutes. The resulting density maps to 2.1 Å resolution of the serine protease proteinase K showed no visible signs of radiation damage. It is thus demonstrated that dedicated diffraction-optimized detectors are not required for MicroED, as shown by the fact that the very same cameras that are used for imaging applications in electron microscopy, such as single-particle cryo-EM, can also be used effectively for diffraction measurements.

Towards understanding the catalytic core structure of the spliceosome

2005 ◽  
Vol 33 (3) ◽  
pp. 447-449 ◽  
Author(s):  
S.E. Butcher ◽  
D.A. Brow
Keyword(s):  
Structure And Function ◽  
Mrna Splicing ◽  
Catalytic Core ◽  
Coding Regions ◽  
High Resolution Structure ◽  
Associated Proteins ◽  
And Function ◽  
Mrna Precursor ◽  
Precursor Mrna ◽  
Resolution Structure

The spliceosome catalyses the splicing of nuclear pre-mRNA (precursor mRNA) in eukaryotes. Pre-mRNA splicing is essential to remove internal non-coding regions of pre-mRNA (introns) and to join the remaining segments (exons) into mRNA before translation. The spliceosome is a complex assembly of five RNAs (U1, U2, U4, U5 and U6) and many dozens of associated proteins. Although a high-resolution structure of the spliceosome is not yet available, inroads have been made towards understanding its structure and function. There is growing evidence suggesting that U2 and U6 RNAs, of the five, may contribute to the catalysis of pre-mRNA splicing. In this review, recent progress towards understanding the structure and function of U2 and U6 RNAs is summarized.

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