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 Electron crystallography: imaging and single-crystal diffraction from powders

2007 ◽  
Vol 64 (1) ◽  
pp. 149-160 ◽  
Author(s):  
Xiaodong Zou ◽  
Sven Hovmöller
Keyword(s):  
Three Dimensional ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Crystallographic Structure ◽  
X Ray Diffraction ◽  
Electron Crystallography ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction ◽  
Recent Developments

The study of crystals at atomic level by electrons – electron crystallography – is an important complement to X-ray crystallography. There are two main advantages of structure determinations by electron crystallography compared to X-ray diffraction: (i) crystals millions of times smaller than those needed for X-ray diffraction can be studied and (ii) the phases of the crystallographic structure factors, which are lost in X-ray diffraction, are present in transmission-electron-microscopy (TEM) images. In this paper, some recent developments of electron crystallography and its applications, mainly on inorganic crystals, are shown. Crystal structures can be solved to atomic resolution in two dimensions as well as in three dimensions from both TEM images and electron diffraction. Different techniques developed for electron crystallography, including three-dimensional reconstruction, the electron precession technique and ultrafast electron crystallography, are reviewed. Examples of electron-crystallography applications are given. There is in principle no limitation to the complexity of the structures that can be solved by electron crystallography.

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 4-(4-Chlorophenyl)-4,5-dihydro-1H-1,2,4-triazole-5-thione

Molbank ◽  
10.3390/m1047 ◽  
2019 ◽  
Vol 2019 (1) ◽  
pp. M1047 ◽  
Author(s):  
Chien Yeo ◽  
Ainnul Azizan ◽  
Edward Tiekink
Keyword(s):  
Hydrogen Bonds ◽  
Structure Determination ◽  
Title Compound ◽  
Uv Spectroscopy ◽  
Three Dimensional ◽  
Membered Ring ◽  
X Ray ◽  
X Ray Crystallography ◽  
Orthogonal Relationship ◽  
Ir And Uv Spectroscopy

The title compound, 4-(4-chlorophenyl)-4,5-dihydro-1H-1,2,4-triazole-5-thione (1), was synthesized by a hetero-cyclization reaction of 4-chlorophenyl isothiocyanate and formic hydrazide. Compound 1 was characterized by a single-crystal X-ray structure determination as well as 1H and 13C{1H} NMR, IR, and UV spectroscopy, and microelemental analysis. X-ray crystallography on 1 confirms the molecule exists as the thione tautomer and shows the five-membered ring to be planar and to form a dihedral angle of 82.70(5)° with the appended chlorophenyl ring, indicating an almost orthogonal relationship. In the molecular packing, supramolecular dimers are formed via thioamide-N–H⋯S(thione) hydrogen bonds and these are connected by C=S⋯π(triazolyl) and C-Cl⋯π(triazolyl) interactions, leading to a three-dimensional architecture.

scholarly journals PROBABILISTIC ENSEMBLES FOR IMPROVED INFERENCE IN PROTEIN-STRUCTURE DETERMINATION

2012 ◽  
Vol 10 (01) ◽  
pp. 1240009 ◽  
Author(s):  
AMEET SONI ◽  
JUDE SHAVLIK
Keyword(s):  
Protein Structure ◽  
Structure Determination ◽  
Protein Structures ◽  
Three Dimensional ◽  
Protein Structure Determination ◽  
Complex Problem ◽  
Approximate Inference ◽  
X Ray ◽  
X Ray Crystallography ◽  
Inference Methods

Protein X-ray crystallography — the most popular method for determining protein structures — remains a laborious process requiring a great deal of manual crystallographer effort to interpret low-quality protein images. Automating this process is critical in creating a high-throughput protein-structure determination pipeline. Previously, our group developed ACMI, a probabilistic framework for producing protein-structure models from electron-density maps produced via X-ray crystallography. ACMI uses a Markov Random Field to model the three-dimensional (3D) location of each non-hydrogen atom in a protein. Calculating the best structure in this model is intractable, so ACMI uses approximate inference methods to estimate the optimal structure. While previous results have shown ACMI to be the state-of-the-art method on this task, its approximate inference algorithm remains computationally expensive and susceptible to errors. In this work, we develop Probabilistic Ensembles in ACMI (PEA), a framework for leveraging multiple, independent runs of approximate inference to produce estimates of protein structures. Our results show statistically significant improvements in the accuracy of inference resulting in more complete and accurate protein structures. In addition, PEA provides a general framework for advanced approximate inference methods in complex problem domains.

scholarly journals A suite of software for processing MicroED data of extremely small protein crystals

2014 ◽  
Vol 47 (3) ◽  
pp. 1140-1145 ◽  
Author(s):  
Matthew G. Iadanza ◽  
Tamir Gonen
Keyword(s):  
Structure Determination ◽  
Ad Hoc ◽  
Source Code ◽  
Three Dimensional ◽  
Molecular Replacement ◽  
X Ray ◽  
X Ray Crystallography ◽  
Software Packages ◽  
Transmission Electron ◽  
Standard Software

Electron diffraction of extremely small three-dimensional crystals (MicroED) allows for structure determination from crystals orders of magnitude smaller than those used for X-ray crystallography. MicroED patterns, which are collected in a transmission electron microscope, were initially not amenable to indexing and intensity extraction by standard software, which necessitated the development of a suite of programs for data processing. The MicroED suite was developed to accomplish the tasks of unit-cell determination, indexing, background subtraction, intensity measurement and merging, resulting in data that can be carried forward to molecular replacement and structure determination. Thisad hocsolution has been modified for more general use to provide a means for processing MicroED data until the technique can be fully implemented into existing crystallographic software packages. The suite is written in Python and the source code is available under a GNU General Public License.

scholarly journals Covering complete proteomes with X-ray structures: a current snapshot

2014 ◽  
Vol 70 (11) ◽  
pp. 2781-2793 ◽  
Author(s):  
Marcin J. Mizianty ◽  
Xiao Fan ◽  
Jing Yan ◽  
Eric Chalmers ◽  
Christopher Woloschuk ◽  
...  
Keyword(s):  
Homology Modeling ◽  
Structure Determination ◽  
Large Scale ◽  
Structural Model ◽  
Target Selection ◽  
Three Dimensional ◽  
X Ray ◽  
X Ray Crystallography ◽  
Knowledge Based ◽  
Wide Range

Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.

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.

Beyond X-rays: an overview of emerging structural biology methods

2021 ◽  
Author(s):  
Jason E. Schaffer ◽  
Vandna Kukshal ◽  
Justin J. Miller ◽  
Vivian Kitainda ◽  
Joseph M. Jez
Keyword(s):  
Structure Determination ◽  
De Novo ◽  
Three Dimensional ◽  
Atomic Scale ◽  
X Rays ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography ◽  
New Methods ◽  
Main Technique

Structural biologists rely on X-ray crystallography as the main technique for determining the three-dimensional structures of macromolecules; however, in recent years, new methods that go beyond X-ray-based technologies are broadening the selection of tools to understand molecular structure and function. Simultaneously, national facilities are developing programming tools and maintaining personnel to aid novice structural biologists in de novo structure determination. The combination of X-ray free electron lasers (XFELs) and serial femtosecond crystallography (SFX) now enable time-resolved structure determination that allows for capture of dynamic processes, such as reaction mechanism and conformational flexibility. XFEL and SFX, along with microcrystal electron diffraction (MicroED), help side-step the need for large crystals for structural studies. Moreover, advances in cryogenic electron microscopy (cryo-EM) as a tool for structure determination is revolutionizing how difficult to crystallize macromolecules and/or complexes can be visualized at the atomic scale. This review aims to provide a broad overview of these new methods and to guide readers to more in-depth literature of these methods.

scholarly journals Improving diffraction resolution using a new dehydration method

2016 ◽  
Vol 72 (2) ◽  
pp. 152-159 ◽  
Author(s):  
Qingqiu Huang ◽  
Doletha M. E. Szebenyi
Keyword(s):  
Escherichia Coli ◽  
Structure Determination ◽  
Three Dimensional ◽  
Archaeoglobus Fulgidus ◽  
Dimensional Structure ◽  
High Quality ◽  
X Ray ◽  
Three Dimensional Structure ◽  
X Ray Crystallography ◽  
Dry Out

The production of high-quality crystals is one of the major obstacles in determining the three-dimensional structure of macromolecules by X-ray crystallography. It is fairly common that a visually well formed crystal diffracts poorly to a resolution that is too low to be suitable for structure determination. Dehydration has proven to be an effective post-crystallization treatment for improving crystal diffraction quality. Several dehydration methods have been developed, but no single one of them is suitable for all crystals. Here, a new convenient and effective dehydration method is reported that makes use of a dehydrating solution that will not dry out in air for several hours. Using this dehydration method, the resolution ofArchaeoglobus fulgidusCas5a crystals has been increased from 3.2 to 1.95 Å and the resolution ofEscherichia coliLptA crystals has been increased from <5 to 3.4 Å.

Dihydrofolate Reductase Inhibition. A Study in the Use of X-ray Crystallography, Molecular Graphics, and Quantitative Structure-Activity Relations in Drug Design

1982 ◽  
Vol 16 (5) ◽  
pp. 391-396 ◽  
Author(s):  
Corwin Hansch
Keyword(s):  
Cell Culture ◽  
Dihydrofolate Reductase ◽  
Three Dimensional ◽  
Bovine Liver ◽  
Quantitative Structure ◽  
Molecular Graphics ◽  
X Ray ◽  
X Ray Crystallography ◽  
Structure Activity ◽  
Hydrophobic Barrier

Substituent constants and regression analyses are used to formulate quantitative structure-activity relationships (QSAR) for the inhibition by 4,6-diamino-1,2-dihydro-2,2-dimethyl-1-(3-X-phenyl)- s-triazines of purified dihydrofolate reductase (DHFR) from L. casei cells, bovine liver, and murine leukemia cells (L5178Y). The QSAR for the activity of the triazines on purified DHFR is compared with the QSAR for their action on L. casei cell culture and murine L5178Y cell culture. The QSAR for action on purified DHFR is similar to that on wild type cells; however, the QSAR for these cells differs remarkably from QSAR for both types of cells that are resistant to methotrexate (MTX). The conclusion from these analyses is that cells resistant to MTX protect themselves from this highly hydrophilic drug by developing a hydrophobic barrier. Our understanding of DHFR interaction with drugs is rapidly increasing via QSAR, and X-ray crystallography, combined with the new molecular graphics of Langridge's group, promises to expedite the process. The value of three-dimensional color graphics is discussed, with the aid of color stereo views of L. casei and E. coli DHFR.

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