scholarly journals CryoEM analysis of small plant biocatalysts at sub-2 Å resolution

2022 ◽  
Vol 78 (1) ◽  
Author(s):  
Nicole Dimos ◽  
Carl P. O. Helmer ◽  
Andrea M. Chánique ◽  
Markus C. Wahl ◽  
Robert Kourist ◽  
...  
Keyword(s):  
Structural Analysis ◽  
High Resolution ◽  
Structural Biology ◽  
Enzyme Catalysis ◽  
Rapid Development ◽  
Small Plant ◽  
Key Technology ◽  
Cryo Electron Microscopy ◽  
Pharmaceutical Industries ◽  
Exquisite Specificity

Enzyme catalysis has emerged as a key technology for developing efficient, sustainable processes in the chemical, biotechnological and pharmaceutical industries. Plants provide large and diverse pools of biosynthetic enzymes that facilitate complex reactions, such as the formation of intricate terpene carbon skeletons, with exquisite specificity. High-resolution structural analysis of these enzymes is crucial in order to understand their mechanisms and modulate their properties by targeted engineering. Although cryo-electron microscopy (cryoEM) has revolutionized structural biology, its applicability to high-resolution structural analysis of comparatively small enzymes has so far been largely unexplored. Here, it is shown that cryoEM can reveal the structures of plant borneol dehydrogenases of ∼120 kDa at or below 2 Å resolution, paving the way for the rapid development of new biocatalysts that can provide access to bioactive terpenes and terpenoids.

scholarly journals Rapid high-resolution structure analysis of small, biotechnologically relevant enzymes by cryo-electron microscopy

2021 ◽  
Author(s):  
Nicole Dimos ◽  
Carl P.O. Helmer ◽  
Andrea M. Chanique ◽  
Markus C. Wahl ◽  
Robert Kourist ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Structural Biology ◽  
Structure Analysis ◽  
Cryo Electron Microscopy ◽  
High Resolution Structure ◽  
Fast Development ◽  
Pharmaceutical Industries ◽  
Exquisite Specificity ◽  
Resolution Structure

Enzyme catalysis has emerged as a key technology for developing efficient, sustainable processes in the chemical, biotechnological and pharmaceutical industries. Plants provide large and diverse pools of biosynthetic enzymes that facilitate complex reactions, such as the formation of intricate terpene carbon skeletons, with exquisite specificity. High-resolution structural analysis of these enzymes is crucial to understand their mechanisms and modulate their properties by targeted engineering. Although cryo-electron microscopy (cryo-EM) has revolutionized structural biology, its applicability to high-resolution structure analysis of comparatively small enzymes is so far largely unexplored. Here, we show that cryo-EM can reveal the structures of ~120 kDa plant borneol dehydrogenases at or below 2 Å resolution, paving the way for the fast development of new biocatalysts that provide access to bioactive terpenes and terpenoids.

scholarly journals Programming new geometry restraints: parallelity of atomic groups

2015 ◽  
Vol 48 (4) ◽  
pp. 1130-1141 ◽  
Author(s):  
Oleg V. Sobolev ◽  
Pavel V. Afonine ◽  
Paul D. Adams ◽  
Alexandre Urzhumtsev
Keyword(s):  
Electron Microscopy ◽  
Experimental Data ◽  
High Resolution ◽  
Structural Biology ◽  
Data Structures ◽  
A Priori ◽  
Low Resolution ◽  
Cryo Electron Microscopy ◽  
Model Geometry ◽  
Associated Data

Improvements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to usea prioriinformation about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they can be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in theComputational Crystallography Toolbox(cctbx) are presented.

Structural analysis of the surface-layer protein of spirillum serpens by high-resolution electron microscopy

1983 ◽  
Vol 41 ◽  
pp. 738-739
Author(s):  
W. H. Wu ◽  
R. M. Glaeser
Keyword(s):  
Electron Microscopy ◽  
Surface Layer ◽  
Structural Analysis ◽  
High Resolution ◽  
Low Dose ◽  
High Resolution Electron Microscopy ◽  
Optical Diffraction ◽  
Surface Layer Protein ◽  
Morphological Unit ◽  
Resolution Electron

Spirillum serpens possesses a surface layer protein which exhibits a regular hexagonal packing of the morphological subunits. A morphological model of the structure of the protein has been proposed at a resolution of about 25 Å, in which the morphological unit might be described as having the appearance of a flared-out, hollow cylinder with six ÅspokesÅ at the flared end. In order to understand the detailed association of the macromolecules, it is necessary to do a high resolution structural analysis. Large, single layered arrays of the surface layer protein have been obtained for this purpose by means of extensive heating in high CaCl2, a procedure derived from that of Buckmire and Murray. Low dose, low temperature electron microscopy has been applied to the large arrays.As a first step, the samples were negatively stained with neutralized phosphotungstic acid, and the specimens were imaged at 40,000 magnification by use of a high resolution cold stage on a JE0L 100B. Low dose images were recorded with exposures of 7-9 electrons/Å2. The micrographs obtained (Fig. 1) were examined by use of optical diffraction (Fig. 2) to tell what areas were especially well ordered.

Computer processing of high-resolution images of periodic specimens

1986 ◽  
Vol 44 ◽  
pp. 2-5
Author(s):  
W. Chiu ◽  
M.F. Schmid ◽  
T.-W. Jeng
Keyword(s):  
High Resolution ◽  
Fourier Transforms ◽  
Complex Structure ◽  
Distribution Functions ◽  
Multiple Image ◽  
Cryo Electron Microscopy ◽  
Structure Factors ◽  
Unit Cells ◽  
High Resolution Images ◽  
Phase Probability Distribution

Cryo-electron microscopy has been developed to the point where one can image thin protein crystals to 3.5 Å resolution. In our study of the crotoxin complex crystal, we can confirm this structural resolution from optical diffractograms of the low dose images. To retrieve high resolution phases from images, we have to include as many unit cells as possible in order to detect the weak signals in the Fourier transforms of the image. Hayward and Stroud proposed to superimpose multiple image areas by combining phase probability distribution functions for each reflection. The reliability of their phase determination was evaluated in terms of a crystallographic “figure of merit”. Grant and co-workers used a different procedure to enhance the signals from multiple image areas by vector summation of the complex structure factors in reciprocal space.

On the devaluation of expert opinion or why do we need a law about the basics of expert activity

2020 ◽  
Vol 22 (3) ◽  
pp. 19-24
Author(s):  
MARAT R. BIKTIMIROV ◽  
◽  
OLGA V. PILIPENKO ◽  
MAXIM S. SAFONOV ◽  
◽  
...  
Keyword(s):  
Project Management ◽  
Structural Analysis ◽  
Expert Opinion ◽  
Knowledge Economy ◽  
Rapid Development ◽  
Digital Technologies ◽  
Accurate Assessment ◽  
Industrial Management ◽  
The Impact ◽  
Creative Construction

Taking practical responsible decisions in the field of social and industrial management in the context of rapid development of digital technologies in the era of the knowledge economy is impossible without reliance on expertise. A kind of organization of activities for the production of ‘predictions’ is required, when not only an accurate assessment of the impact of certain factors and their possible interactions with each other is given, but also as a result of creative construction of scenarios for the development of processes and events, an understanding comes which factors need to be taken into account. At the same time, the expertise constantly faces criticism, calling the conclusions of experts arbitrary, unreliable and subjective. Often, expertise is confused with monitoring, evaluation, diagnosis, inspection or counseling. The authors of the article carried out a structural analysis of the content of the expertise processes in the project management vector in the digitalization era and came to the conclusion that the effectiveness of the expertise is significantly increased in case of clear regulation of this type of activity, providing the necessary status.

Cryo-EM Is a Powerful Tool, But Helical Applications Can Have Pitfalls

Soft Matter ◽  
2021 ◽  
Author(s):  
Edward Egelman ◽  
Fengbin Wang
Keyword(s):  
Electron Microscopy ◽  
Structural Biology ◽  
Macromolecular Complexes ◽  
Atomic Structures ◽  
Cryo Electron Microscopy ◽  
Main Technique

In structural biology, cryo-electron microscopy (cryo-EM) has emerged as the main technique for determining the atomic structures of macromolecular complexes. This has largely been due to the introduction of direct...

Europium-Doped Ceria–Gadolinium Mixed Oxides: PARAFAC Analysis and High-Resolution Emission Spectroscopy under Cryogenic Conditions for Structural Analysis

2020 ◽  
Vol 124 (24) ◽  
pp. 4972-4983
Author(s):  
Sitshengisiwe Chemura ◽  
Toni Haubitz ◽  
Philipp A. Primus ◽  
Martin Underberg ◽  
Tim Hülser ◽  
...  
Keyword(s):  
Structural Analysis ◽  
High Resolution ◽  
Emission Spectroscopy ◽  
Mixed Oxides ◽  
Doped Ceria ◽  
Cryogenic Conditions

X-ray computed microtomography for the structural analysis of jewelry from the Museum “Royal Tombs of Sipán”

2020 ◽  
Vol 35 (S1) ◽  
pp. S38-S42
Author(s):  
Soraia Rodrigues de Azeredo ◽  
Roberto Cesareo ◽  
Angel Guillermo Bustamante Dominguez ◽  
Ricardo Tadeu Lopes
Keyword(s):  
Structural Analysis ◽  
High Resolution ◽  
Copper Alloys ◽  
North Coast ◽  
Flat Panel ◽  
X Ray ◽  
The North ◽  
Gold Silver ◽  
Computed Microtomography ◽  
X Ray Computed

Precious ornaments from the Museum Royal Tombs of Sipán were analyzed by X-ray computed microtomography (microCT). The ornaments analyzed were golden earrings produced by the Moche culture that flourished along the north coast of present-day Peru between approximately 100 and 600 AD. Sipán, also known as Huava Rajada, is a mochica archaeological complex in the north of Peru. In particular, the spectacular jewelry, mainly composed of gold, silver, and copper alloys, gilded copper, and tumbaga, from the Museum “Royal Tombs of Sipán,” in Lambayeque, north of Peru, are some of the most sophisticated metalworking ever produced of pre-Columbian America. A portable microCT system consisting of a high-resolution flat panel detector and a mini X-ray tube were used for the structural analysis of these ornaments. The microCT images show parts of the internal structure, highlighting the manufacturing technique and gold sheets joining techniques of the Moche artisans. Furthermore, the advantage of using the portable microCT system for nondestructive testing is clear when the sample cannot be taken to the laboratory.

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