Image Processing and Lattice Determination for Three-Dimensional Nanocrystals

2011 ◽  
Vol 17 (6) ◽  
pp. 879-885 ◽  
Author(s):  
Linhua Jiang ◽  
Dilyana Georgieva ◽  
Igor Nederlof ◽  
Zunfeng Liu ◽  
Jan Pieter Abrahams
Keyword(s):  
Molecular Structure ◽  
Three Dimensional ◽  
X Ray ◽  
X Ray Crystallography ◽  
Hard Materials ◽  
Cryo Electron Microscopy ◽  
Diffraction Patterns ◽  
Radiation Hard ◽  
Orientation Parameters

AbstractThree-dimensional nanocrystals can be studied by electron diffraction using transmission cryo-electron microscopy. For molecular structure determination of proteins, such nanosized crystalline samples are out of reach for traditional single-crystal X-ray crystallography. For the study of materials that are not sensitive to the electron beam, software has been developed for determining the crystal lattice and orientation parameters. These methods require radiation-hard materials that survive careful orienting of the crystals and measuring diffraction of one and the same crystal from different, but known directions. However, as such methods can only deal with well-oriented crystalline samples, a problem exists for three-dimensional (3D) crystals of proteins and other radiation sensitive materials that do not survive careful rotational alignment in the electron microscope. Here, we discuss our newly released software AMP that can deal with nonoriented diffraction patterns, and we discuss the progress of our new preprocessing program that uses autocorrelation patterns of diffraction images for lattice determination and indexing of 3D nanocrystals.

Using cryo-electron microscopy maps for X-ray structure determination of homologues

2020 ◽  
Vol 76 (1) ◽  
pp. 63-72
Author(s):  
Lingxiao Zeng ◽  
Wei Ding ◽  
Quan Hao
Keyword(s):  
Electron Microscopy ◽  
Hybrid Method ◽  
Model Building ◽  
Test Cases ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sequence Identity ◽  
Whole Process ◽  
Cryo Electron Microscopy

The combination of cryo-electron microscopy (cryo-EM) and X-ray crystallography reflects an important trend in structural biology. In a previously published study, a hybrid method for the determination of X-ray structures using initial phases provided by the corresponding parts of cryo-EM maps was presented. However, if the target structure of X-ray crystallography is not identical but homologous to the corresponding molecular model of the cryo-EM map, then the decrease in the accuracy of the starting phases makes the whole process more difficult. Here, a modified hybrid method is presented to handle such cases. The whole process includes three steps: cryo-EM map replacement, phase extension by NCS averaging and dual-space iterative model building. When the resolution gap between the cryo-EM and X-ray crystallographic data is large and the sequence identity is low, an intermediate stage of model building is necessary. Six test cases have been studied with sequence identity between the corresponding molecules in the cryo-EM and X-ray structures ranging from 34 to 52% and with sequence similarity ranging from 86 to 91%. This hybrid method consistently produced models with reasonable R work and R free values which agree well with the previously determined X-ray structures for all test cases, thus indicating the general applicability of the method for X-ray structure determination of homologues using cryo-EM maps as a starting point.

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

scholarly journals Structure of catalase determined by MicroED

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Brent L Nannenga ◽  
Dan Shi ◽  
Johan Hattne ◽  
Francis E Reyes ◽  
Tamir Gonen
Keyword(s):  
Structure Determination ◽  
Three Dimensional ◽  
Bovine Liver ◽  
Electron Crystallography ◽  
X Ray ◽  
X Ray Crystallography ◽  
Continuous Rotation ◽  
Bovine Liver Catalase ◽  
Diffraction Patterns ◽  
Atomic Analysis

MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (<xref ref-type="bibr" rid="bib26">Shi et al., 2013</xref>). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination.

scholarly journals X-ray data processing

2017 ◽  
Vol 37 (5) ◽  
Author(s):  
Harold R. Powell
Keyword(s):  
Molecular Structure ◽  
Data Processing ◽  
Structure Determination ◽  
X Ray ◽  
X Ray Crystallography ◽  
Common Scale ◽  
Diffraction Patterns

The method of molecular structure determination by X-ray crystallography is a little over a century old. The history is described briefly, along with developments in X-ray sources and detectors. The fundamental processes involved in measuring diffraction patterns on area detectors, i.e. autoindexing, refining crystal and detector parameters, integrating the reflections themselves and putting the resultant measurements on to a common scale are discussed, with particular reference to the most commonly used software in the field.

scholarly journals History of protein crystallography in China

2007 ◽  
Vol 362 (1482) ◽  
pp. 1035-1042 ◽  
Author(s):  
Zihe Rao
Keyword(s):  
Protein Crystallography ◽  
Three Dimensional ◽  
Porcine Insulin ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Subsequent Determination ◽  
History Of

China has a strong background in X-ray crystallography dating back to the 1920s. Protein crystallography research in China was first developed following the successful synthesis of insulin in China in 1966. The subsequent determination of the three-dimensional structure of porcine insulin made China one of the few countries which could determine macromolecular structures by X-ray diffraction methods in the late 1960s and early 1970s. After a slow period during the 1970s and 1980s, protein crystallography in China has reached a new climax with a number of outstanding accomplishments. Here, I review the history and progress of protein crystallography in China and detail some of the recent research highlights, including the crystal structures of two membrane proteins as well as the structural genomics initiative in China.

Bacteriophage PRD1 Capsid Structure: Iterative Combination of Threedimensional Electron Microscopy and X-Ray Crystallography

2000 ◽  
Vol 6 (S2) ◽  
pp. 284-285
Author(s):  
Carmen San Martin ◽  
Roger M. Burnett ◽  
Felix de Haas ◽  
Ralph Heinkel ◽  
Twan Rutten ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Three Dimensional ◽  
Cyclic Process ◽  
Particle Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Bacteriophage Prd1 ◽  
Cryo Electron Microscopy ◽  
Moderate Resolution ◽  
Protein Rich

PRD1 is a ds-DNA bacteriophage from the Tectiviridae family with an unusual structural feature: the viral genome is enclosed by a protein-rich membrane, which is in turn enclosed by an external icosahedral protein shell (capsid). Three-dimensional reconstructions from cryo-electron microscopy (cryo-EM) images have revealed the structure of the PRD1 capsid at moderate resolution (28 Å), while X-ray crystallographic studies have recently provided a high resolution (1.85 Å) picture of the major coat protein, P3. We have now combined these results from different imaging methods to obtain a more detailed understanding of the virion organization. The combination has been made in a cyclic process: a preliminary fitting of the atomic structure of P3 to each one of its independent positions in the cryo-EM maps of the capsids provided initial models that could be used to improve the reconstructions; the refined maps then served as a base frame for an optimized fit. This process allows us to study the viral particle structure at “quasi-atomic” resolution.

Microtubules, sickle cell hemoglobin fibers, and various crystal structures

1983 ◽  
Vol 41 ◽  
pp. 422-425
Author(s):  
Stuart J. Edelstein ◽  
Richard H. Crepeau ◽  
Christopher W. Akey ◽  
Thomas A. Ceska
Keyword(s):  
Molecular Structure ◽  
Electron Microscopy ◽  
Cytochrome Oxidase ◽  
Sickle Cell ◽  
Three Dimensional ◽  
Beef Heart ◽  
Structural Studies ◽  
Image Reconstruction Techniques ◽  
X Ray ◽  
X Ray Crystallography

Structural studies involving electron microscopy and image reconstruction techniques are now approaching levels of resolution that had previously been the domain of x-ray crystallography. Studies on purple membrane are a prime example. Although few other systems have reached comparable levels of resolution, progress is being made on several fronts. Citing work from this laboratory, I will illustrate three ways we are using electron microscopy to approach the border with x-ray crystallography, in studies on: three-dimensional crystals (cytochrome oxidase from P. aeruginosa, catalase, and beef heart F1-ATPase); arrays of proteins which do not form three-dimensional crystals (tubulin sheets and microtubules); and the supra-molecular structure of a protein of known atomic structure (sickle cell hemoglobin).A. Electron microscopy as an adjunct to X-ray crystallography for threedimensional crystalsOur applications in this area have primarily consisted of embedding and sectioning techniques with crystals that are too small or otherwise unsuitable for x-ray crystallography, such as occur for cytochrome oxidase from P. aeruginosa or beef heart F1-ATPase.

Membrane protein crystallography in the era of modern structural biology

2020 ◽  
Vol 48 (6) ◽  
pp. 2505-2524
Author(s):  
Tristan O. C. Kwan ◽  
Danny Axford ◽  
Isabel Moraes
Keyword(s):  
Structural Biology ◽  
Molecular Level ◽  
Protein Structures ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cellular Processes ◽  
Biochemical Level

The aim of structural biology has been always the study of biological macromolecules structures and their mechanistic behaviour at molecular level. To achieve its goal, multiple biophysical methods and approaches have become part of the structural biology toolbox. Considered as one of the pillars of structural biology, X-ray crystallography has been the most successful method for solving three-dimensional protein structures at atomic level to date. It is however limited by the success in obtaining well-ordered protein crystals that diffract at high resolution. This is especially true for challenging targets such as membrane proteins (MPs). Understanding structure-function relationships of MPs at the biochemical level is vital for medicine and drug discovery as they play critical roles in many cellular processes. Though difficult, structure determination of MPs by X-ray crystallography has significantly improved in the last two decades, mainly due to many relevant technological and methodological developments. Today, numerous MP crystal structures have been solved, revealing many of their mechanisms of action. Yet the field of structural biology has also been through significant technological breakthroughs in recent years, particularly in the fields of single particle electron microscopy (cryo-EM) and X-ray free electron lasers (XFELs). Here we summarise the most important advancements in the field of MP crystallography and the significance of these developments in the present era of modern structural biology.

Quantitative nanotomography of amorphous and polycrystalline samples using coherent X-ray diffraction

2019 ◽  
Vol 52 (3) ◽  
pp. 571-578 ◽  
Author(s):  
Y. Chushkin ◽  
F. Zontone ◽  
O. Cherkas ◽  
A. Gibaud
Keyword(s):  
Mass Density ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Coherent Diffraction Imaging ◽  
Diffraction Imaging ◽  
Diffraction Patterns ◽  
Better Than

This article presents a combined approach where quantitative forward-scattering coherent diffraction imaging (CDI) is supported by crystal diffraction using 8.1 keV synchrotron X-ray radiation. The method allows the determination of the morphology, mass density and crystallinity of an isolated microscopic specimen. This approach is tested on three homogeneous samples made of different materials with different degrees of crystallinity. The mass density and morphology are revealed using three-dimensional coherent diffraction imaging with a resolution better than 36 nm. The crystallinity is extracted from the diffraction profiles measured simultaneously with coherent diffraction patterns. The presented approach extends CDI to structural characterization of samples when crystallinity aspects are of interest.

scholarly journals John Thomas Finch. 28 February 1930—5 December 2017

2018 ◽  
Vol 66 ◽  
pp. 183-199
Author(s):  
R. A. Crowther ◽  
K. C. Holmes
Keyword(s):  
Molecular Structure ◽  
Electron Microscopy ◽  
Electron Microscope ◽  
Three Dimensional ◽  
Important Place ◽  
Diverse Range ◽  
X Ray ◽  
X Ray Crystallography ◽  
Embedded Particles ◽  
Team Player

John Finch was a gifted experimentalist who used X-ray crystallography and electron microscopy to elucidate the structures of important biological assemblies, particularly viruses and chromatin. When he started research in the 1950s, little was known about the structure of viruses, and the methods for investigating them were fairly limited. His early work on crystals of viruses was important in establishing their symmetry, and later with the electron microscope he mapped out the molecular structure of many virus coats. His observations on negatively stained preparations demonstrated that images of particles prepared in this way represented projections of fully stained embedded particles, not merely one-sided footprints. This was very relevant to the development of methods for making three-dimensional maps of specimens from electron micrographs. Later, besides further studies of viruses, he worked on many other systems, including chromatin, nucleosomes and tRNA. John was very much a team player and held an important place as the key experimentalist in many influential collaborations, investigating a diverse range of biological specimens.

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