scholarly journals Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

2020 ◽  
Author(s):  
Haroldas Bagdonas ◽  
Daniel Ungar ◽  
Jon Agirre
Keyword(s):  
Structural Biology ◽  
Large Scale ◽  
3D Structure ◽  
Structure Validation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Glycosidic Bonds ◽  
Cryo Electron Microscopy ◽  
Structure Solution ◽  
Solution Methods

The heterogeneity, mobility and complexity of glycans in glycoproteins have been, and currently remain, significant challenges in structural biology. Those aspects present unique problems to the two most prolific techniques: X-ray crystallography and cryo-electron microscopy. At the same time, advances in mass spectrometry have made it possible to get deeper insights on precisely the information that is most difficult to recover by structure solution methods: full-length glycan composition, including linkage details for the glycosidic bonds. These developments have given rise to glycomics. Thankfully, several large scale glycomics initiatives have stored results in publicly-available databases, some of which can be accessed through API interfaces. In the present work, we will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve the validation of 3D glycoprotein structures.

scholarly journals Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

2020 ◽  
Vol 16 ◽  
pp. 2523-2533 ◽  
Author(s):  
Haroldas Bagdonas ◽  
Daniel Ungar ◽  
Jon Agirre
Keyword(s):  
Structural Biology ◽  
Large Scale ◽  
3D Structure ◽  
Structure Validation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Glycosidic Bonds ◽  
Cryo Electron Microscopy ◽  
Structure Solution ◽  
Solution Methods

The heterogeneity, mobility and complexity of glycans in glycoproteins have been, and currently remain, significant challenges in structural biology. These aspects present unique problems to the two most prolific techniques: X-ray crystallography and cryo-electron microscopy. At the same time, advances in mass spectrometry have made it possible to get deeper insights on precisely the information that is most difficult to recover by structure solution methods: the full-length glycan composition, including linkage details for the glycosidic bonds. The developments have given rise to glycomics. Thankfully, several large scale glycomics initiatives have stored results in publicly available databases, some of which can be accessed through API interfaces. In the present work, we will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve the validation of 3D glycoprotein structures.

scholarly journals From X-ray crystallography to cryo-electron microscopy: computing infrastructure in structural biology

2018 ◽  
Vol 74 (a1) ◽  
pp. a224-a224
Author(s):  
Jason Key ◽  
Peter A. Meyer ◽  
Carol Herre ◽  
Michael Timony ◽  
Dimitry Filonov ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Structural Biology ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Computing Infrastructure

scholarly journals A basic introduction to single particles cryo-electron microscopy

2021 ◽  
Vol 9 (1) ◽  
pp. 5-20
Author(s):  
Vittoria Raimondi ◽  
◽  
Alessandro Grinzato ◽  
◽  
Keyword(s):  
Electron Microscopy ◽  
Structural Biology ◽  
Protein Complexes ◽  
Computational Power ◽  
Single Particles ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
First Choice ◽  
New Generation

<abstract> <p>In the last years, cryogenic-electron microscopy (cryo-EM) underwent the most impressive improvement compared to other techniques used in structural biology, such as X-ray crystallography and NMR. Electron microscopy was invented nearly one century ago but, up to the beginning of the last decades, the 3D maps produced through this technique were poorly detailed, justifying the term “blobbology” to appeal to cryo-EM. Recently, thanks to a new generation of microscopes and detectors, more efficient algorithms, and easier access to computational power, single particles cryo-EM can routinely produce 3D structures at resolutions comparable to those obtained with X-ray crystallography. However, unlike X-ray crystallography, which needs crystallized proteins, cryo-EM exploits purified samples in solution, allowing the study of proteins and protein complexes that are hard or even impossible to crystallize. For these reasons, single-particle cryo-EM is often the first choice of structural biologists today. Nevertheless, before starting a cryo-EM experiment, many drawbacks and limitations must be considered. Moreover, in practice, the process between the purified sample and the final structure could be trickier than initially expected. Based on these observations, this review aims to offer an overview of the principal technical aspects and setups to be considered while planning and performing a cryo-EM experiment.</p> </abstract>

scholarly journals Introduction to high-resolution cryo-electron microscopy

2016 ◽  
Vol 62 (3) ◽  
pp. 383-394
Author(s):  
Mariusz Czarnocki-Cieciura ◽  
Marcin Nowotny
Keyword(s):  
Electron Microscopy ◽  
Nmr Spectroscopy ◽  
Structural Biology ◽  
Atomic Resolution ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Transmission Electron ◽  
Electron Microscopes

For many years two techniques have dominated structural biology – X-ray crystallography and NMR spectroscopy. Traditional cryo-electron microscopy of biological macromolecules produced macromolecular reconstructions at resolution limited to 6–10 Å. Recent development of transmission electron microscopes, in particular the development of direct electron detectors, and continuous improvements in the available software, have led to the “resolution revolution” in cryo-EM. It is now possible to routinely obtain near-atomic-resolution 3D maps of intact biological macromolecules as small as ~100 kDa. Thus, cryo-EM is now becoming the method of choice for structural analysis of many complex assemblies that are unsuitable for structure determination by other methods.

scholarly journals LA RIVOLUZIONE DELLA CRIO-MICROSCOPIA ELETTRONICA NELLO STUDIO STRUTTURALE DI PROTEINE E ACIDI NUCLEICI

2020 ◽  
Author(s):  
Martino Bolognesi
Keyword(s):  
Electron Microscopy ◽  
Amino Acids ◽  
Structural Biology ◽  
Molecular Structures ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Past ◽  
Cryo Electron Microscopy ◽  
Resolution Level ◽  
Nello Studio

Observing the fine details of molecular structures (e.g. in proteins and in nucleic acids) has been a central part of Structural Biology over the past 50 years. The recent advent of single particle cryo-electron microscopy brought a revolution in this field, that previously relied on X-ray crystallography and nuclear magnetic resonance. It is now possible to explore the structures of large subcellular assemblies, such as the ribosome, resolving details on the scale of amino acids and nucleotides, in favorable cases reaching the 2 Å resolution level.

scholarly journals X-ray crystallography to cryo-electron microscopy: computing infrastructure in structural biology

2018 ◽  
Vol 74 (a2) ◽  
pp. e412-e412
Author(s):  
Jason Key ◽  
Peter Meyer ◽  
Carol Herre ◽  
Michael Timony ◽  
Dimitry Filonov ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Structural Biology ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Computing Infrastructure

scholarly journals Macromolecular X-ray crystallography: soon to be a road less travelled?

2020 ◽  
Vol 76 (5) ◽  
pp. 400-405 ◽  
Author(s):  
John H. Beale
Keyword(s):  
Electron Microscopy ◽  
Life Expectancy ◽  
Protein Data Bank ◽  
Structural Biology ◽  
Data Bank ◽  
New Labour ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy

The number of new X-ray crystallography-based submissions to the Protein Data Bank appears to be at the beginning of a decline, perhaps signalling an end to the era of the dominance of X-ray crystallography within structural biology. This letter, from the viewpoint of a young structural biologist, applies the Copernican method to the life expectancy of crystallography and asks whether the technique is still the mainstay of structural biology. A study of the rate of Protein Data Bank depositions allows a more nuanced analysis of the fortunes of macromolecular X-ray crystallography and shows that cryo-electron microscopy might now be outcompeting crystallography for new labour and talent, perhaps heralding a change in the landscape of the field.

scholarly journals Advances in methods for atomic resolution macromolecular structure determination

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 667
Author(s):  
Michael C. Thompson ◽  
Todd O. Yeates ◽  
Jose A. Rodriguez
Keyword(s):  
Electron Microscopy ◽  
Structural Biology ◽  
Atomic Resolution ◽  
Macromolecular Structure ◽  
New Developments ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Technical Advances ◽  
Dynamical Properties

Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. Here we highlight some of the latest advances and current challenges at the frontiers of atomic resolution methods for elucidating the structures and dynamical properties of macromolecules and their complexes.

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