Visualizing the Structure of Macromolecules and Cell Structures in the Natural State

1972 ◽  
Vol 30 ◽  
pp. 176-177
Author(s):  
D.F. Parsons
Keyword(s):  
Biochemical Analysis ◽  
Natural State ◽  
Biological Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cell Structures ◽  
Speed Up ◽  
Pyrimidine Bases ◽  
The Individual ◽  
And Function

A main objective of biological electron microscopy is the visualization of the internal structure of macromolecules and such structures as membranes, ribosomes etc. With respect to individual molecules it is hoped to see confirmation of the peptide chain in proteins and the chain of bases in nucleic acids. A more optimistic objective is that the individual amino acids and purine or pyrimidine bases will be recognizable from their shape. If achieved, these objectives should greatly speed up progress in the study of biological structure and function especially for materials where biochemical analysis and sequencing is very time consuming and x-ray crystallography not practical. A major effort to develop the electron microscope to this capability should be amply repaid by the structural advances made.

scholarly journals Structure and function study of the complex that synthesizesS-adenosylmethionine

IUCrJ ◽  
2014 ◽  
Vol 1 (4) ◽  
pp. 240-249 ◽  
Author(s):  
Ben Murray ◽  
Svetlana V. Antonyuk ◽  
Alberto Marina ◽  
Sebastiaan M. Van Liempd ◽  
Shelly C. Lu ◽  
...  
Keyword(s):  
Complex Formation ◽  
Structural Data ◽  
Structure Based Drug Design ◽  
X Ray ◽  
X Ray Crystallography ◽  
Methylation Of Dna ◽  
Functional Complex ◽  
Enzyme Subunits ◽  
The Individual ◽  
And Function

S-Adenosylmethionine (SAMe) is the principal methyl donor of the cell and is synthesizedviaan ATP-driven process by methionine adenosyltransferase (MAT) enzymes. It is tightly linked with cell proliferation in liver and colon cancer. In humans, there are three genes,mat1A, mat2Aandmat2B, which encode MAT enzymes.mat2Aandmat2Btranscribe MATα2 and MATβ enzyme subunits, respectively, with catalytic and regulatory roles. The MATα2β complex is expressed in nearly all tissues and is thought to be essential in providing the necessary SAMe flux for methylation of DNA and various proteins including histones. In human hepatocellular carcinomamat2Aandmat2Bgenes are upregulated, highlighting the importance of the MATα2β complex in liver disease. The individual subunits have been structurally characterized but the nature of the complex has remained elusive despite its existence having been postulated for more than 20 years and the observation that MATβ is often co-localized with MATα2. Though SAMe can be produced by MAT(α2)4alone, this paper shows that theVmaxof the MATα2β complex is three- to fourfold higher depending on the variants of MATβ that participate in complex formation. Using X-ray crystallography and solution X-ray scattering, the first structures are provided of this 258 kDa functional complex both in crystals and solution with an unexpected stoichiometry of 4α2 and 2βV2 subunits. It is demonstrated that the N-terminal regulates the activity of the complex and it is shown that complex formation takes place surprisinglyviathe C-terminal of MATβV2 that buries itself in a tunnel created at the interface of the MAT(α2)2. The structural data suggest a unique mechanism of regulation and provide a gateway for structure-based drug design in anticancer therapies.

scholarly journals General discussion summary

2002 ◽  
Vol 357 (1426) ◽  
pp. 1419-1420 ◽  
Keyword(s):  
Water Splitting ◽  
Molecular Mechanisms ◽  
Structure And Function ◽  
X Ray ◽  
X Ray Crystallography ◽  
And Function ◽  
Splitting Process

This general discussion was chaired by A. W. Rutherford ( Service de Bioénergétique, Saclay, France ) and revolved around two major topics: (i) the implications of X–ray crystallography on the relationships between structure and function; (ii) the molecular mechanisms of the water–splitting process.

scholarly journals Structure and function of cement proteins in human adenovirus

2014 ◽  
Vol 70 (a1) ◽  
pp. C1603-C1603
Author(s):  
Vijay Reddy ◽  
Glen Nemerow
Keyword(s):  
Protein Structures ◽  
Human Adenovirus ◽  
Icosahedral Symmetry ◽  
Virion Assembly ◽  
X Ray ◽  
X Ray Crystallography ◽  
Capsid Shell ◽  
Multiple Copies ◽  
And Function ◽  
Cement Protein

Human adenoviruses (HAdVs) are large (~150nm in diameter, 150MDa) nonenveloped double-stranded DNA (dsDNA) viruses that cause respiratory, ocular, and enteric diseases. The capsid shell of adenovirus (Ad) comprises multiple copies of three major capsid proteins (MCP: hexon, penton base and fiber) and four minor/cement proteins (IIIa, VI, VIII and IX) that are organized with pseudo T=25 icosahedral symmetry. In addition, six other proteins (V, VII, μ, IVa2, terminal protein and protease) are encapsidated along with the 36Kb dsDNA genome inside the capsid. The crystal structures of all three MCPs are known and so is their organization in the capsid from prior X-ray crystallography and cryoEM analyses. However structures and locations of various cement proteins are of considerable debate. We have determined and refined the structure of an entire human adenovirus employing X-ray crystallpgraphic methods at 3.8Å resolution. Adenovirus cement proteins play crucial roles in virion assembly, disassembly, cell entry and infection. Based on the refined crystal structure of adenovirus, we have determined the structure of the cement protein VI, a key membrane-lytic molecule and its associations with proteins V and VIII, which together glue peripentonal hexons beneath vertex region and connect them to rest of the capsid. Following virion maturation, the cleaved N-terminal pro-peptide of VI is observed deep in the peripentonal hexon cavity, detached from the membrane-lytic domain. Furthermore, we have significantly revised the recent cryoEM models for proteins IIIa and IX and both are located on the capsid exterior. Together, the cement proteins exclusively stabilize the hexon shell, thus rendering penton vertices the weakest links of the adenovirus capsid. Adenovirus cement protein structures reveal the molecular basis of the maturation cleavage of VI that is needed for endosome rupture and delivery of the virion into cytoplasm.

scholarly journals Chest X-ray image analysis and classification for COVID-19 pneumonia detection using Deep CNN

2020 ◽  
Author(s):  
Terry Gao ◽  
Grace Wang
Keyword(s):  
Training Dataset ◽  
X Rays ◽  
X Ray ◽  
Speed Up ◽  
Chest X Ray ◽  
Coronavirus Infection ◽  
Deep Cnn ◽  
Detection And Diagnosis ◽  
The Individual ◽  
New Diagnosis

Abstract To speed up the discovery of COVID-19 disease mechanisms, this research developed a new diagnosis platform using a deep convolutional neural network (CNN) that is able to assist radiologists with diagnosis by distinguishing COVID-19 pneumonia from non-COVID-19 pneumonia in patients at Middlemore Hospital based on chest X-ray classification and analysis. Such a tool can save time in interpreting chest X-rays and increase the accuracy and thereby enhance our medical capacity for the detection and diagnosis of COVID-19. The research idea is that a set of X-ray medical lung images (which include normal, infected by bacteria, infected by virus including COVID-19) were used to train a deep CNN that can distinguish between the noise and the useful information and then uses this training to interpret new images by recognizing patterns that indicate certain diseases such as coronavirus infection in the individual images. The supervised learning method is used as the process of learning from the training dataset and can be thought of as a doctor supervising the learning process. It becomes more accurate as the number of analyzed images grows. In this way, it imitates the training for a doctor, but the theory is that since it is capable of learning from a far larger set of images than any human, it can have the potential of being more accurate.

scholarly journals Solving a new R2lox protein structure by microcrystal electron diffraction

2019 ◽  
Vol 5 (8) ◽  
pp. eaax4621 ◽  
Author(s):  
Hongyi Xu ◽  
Hugo Lebrette ◽  
Max T. B. Clabbers ◽  
Jingjing Zhao ◽  
Julia J. Griese ◽  
...  
Keyword(s):  
Protein Structure ◽  
Electron Diffraction ◽  
Model Building ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Potential Map ◽  
Metal Cofactor ◽  
And Function

Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be studied by conventional x-ray crystallography. However, to date, MicroED has only been applied to redetermine protein structures that had already been solved previously by x-ray diffraction. Here, we present the first new protein structure—an R2lox enzyme—solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0-Å resolution was of sufficient quality to allow accurate model building and refinement. The dinuclear metal cofactor could be located in the map and was modeled as a heterodinuclear Mn/Fe center based on previous studies. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function.

Crystal structure of the pseudoenzyme PDX1.2 in complex with its cognate enzyme PDX1.3: a total eclipse

2019 ◽  
Vol 75 (4) ◽  
pp. 400-415 ◽  
Author(s):  
Graham C. Robinson ◽  
Markus Kaufmann ◽  
Céline Roux ◽  
Jacobo Martinez-Font ◽  
Michael Hothorn ◽  
...  
Keyword(s):  
Active Sites ◽  
Protein Complexes ◽  
Structural Similarity ◽  
Cellular Protein ◽  
Vitamin B ◽  
Protein Activity ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Individual ◽  
High Degree

Pseudoenzymes have burst into the limelight recently as they provide another dimension to regulation of cellular protein activity. In the eudicot plant lineage, the pseudoenzyme PDX1.2 and its cognate enzyme PDX1.3 interact to regulate vitamin B6 biosynthesis. This partnership is important for plant fitness during environmental stress, in particular heat stress. PDX1.2 increases the catalytic activity of PDX1.3, with an overall increase in vitamin B6 biosynthesis. However, the mechanism by which this is achieved is not known. In this study, the Arabidopsis thaliana PDX1.2–PDX1.3 complex was crystallized in the absence and presence of ligands, and attempts were made to solve the X-ray structures. Three PDX1.2–PDX1.3 complex structures are presented: the PDX1.2–PDX1.3 complex as isolated, PDX1.2–PDX1.3-intermediate (in the presence of substrates) and a catalytically inactive complex, PDX1.2–PDX1.3-K97A. Data were also collected from a crystal of a selenomethionine-substituted complex, PDX1.2–PDX1.3-SeMet. In all cases the protein complexes assemble as dodecamers, similar to the recently reported individual PDX1.3 homomer. Intriguingly, the crystals of the protein complex are statistically disordered owing to the high degree of structural similarity of the individual PDX1 proteins, such that the resulting configuration is a composite of both proteins. Despite the differential methionine content, selenomethionine substitution of the PDX1.2–PDX1.3 complex did not resolve the problem. Furthermore, a comparison of the catalytically competent complex with a noncatalytic complex did not facilitate the resolution of the individual proteins. Interestingly, another catalytic lysine in PDX1.3 (Lys165) that pivots between the two active sites in PDX1 (P1 and P2), and the corresponding glutamine (Gln169) in PDX1.2, point towards P1, which is distinctive to the initial priming for catalytic action. This state was previously only observed upon trapping PDX1.3 in a catalytically operational state, as Lys165 points towards P2 in the resting state. Overall, the study shows that the integration of PDX1.2 into a heteromeric dodecamer assembly with PDX1.3 does not cause a major structural deviation from the overall architecture of the homomeric complex. Nonetheless, the structure of the PDX1.2–PDX1.3 complex highlights enhanced flexibility in key catalytic regions for the initial steps of vitamin B6 biosynthesis. This report highlights what may be an intrinsic limitation of X-ray crystallography in the structural investigation of pseudoenzymes.

scholarly journals Sir Aaron Klug OM. 11 August 1926—20 November 2018

2020 ◽  
Vol 68 ◽  
pp. 273-296
Author(s):  
R. A. Crowther
Keyword(s):  
Electron Microscopy ◽  
Molecular Biology ◽  
Royal Society ◽  
Zinc Fingers ◽  
Three Dimensional ◽  
Transfer Rna ◽  
Biological Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Atomic Structures

Aaron Klug made outstanding contributions to the development of structural molecular biology. An early interest in viruses, stemming from work with Rosalind Franklin, prompted him to think deeply about extracting the information contained in electron micrographs. As a result, he proposed a method for making three-dimensional maps of biological specimens from the projected images given by micrographs. For this development and its application to complex molecular assemblies, he was awarded the 1982 Nobel Prize in Chemistry. The recent revolution in biological structure determination, whereby atomic structures can now be determined from micrographs of frozen hydrated specimens, derives from this initial breakthrough. With colleagues, Aaron applied X-ray crystallography and electron microscopy to determine the structures and thereby understand the functions of many biological assemblies, including viruses, transfer RNA, chromatin and zinc fingers. He also made important forays into the pathogenesis of Alzheimer's disease and related dementias. Aaron was director of the MRC Laboratory of Molecular Biology in Cambridge from 1986 to 1996 and President of the Royal Society from 1995 to 2000.

scholarly journals Solving the first novel protein structure by 3D micro-crystal electron diffraction

2019 ◽  
Author(s):  
H. Xu ◽  
H. Lebrette ◽  
M.T.B. Clabbers ◽  
J. Zhao ◽  
J.J. Griese ◽  
...  
Keyword(s):  
Protein Structure ◽  
Electron Diffraction ◽  
Model Building ◽  
Protein Structures ◽  
X Ray ◽  
X Ray Crystallography ◽  
Unknown Protein ◽  
Potential Map ◽  
Crystal Electron ◽  
And Function

AbstractMicro-crystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables studying biomolecules from micron-sized 3D crystals that are too small to be studied by conventional X-ray crystallography. However, to the best of our knowledge, MicroED has only been applied to re-determine protein structures that had already been solved previously by X-ray diffraction. Here we present the first unknown protein structure – an R2lox enzyme – solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0 Å resolution was of sufficient quality to allow accurate model building and refinement. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function, opening up new opportunities for structural biologists.

Sign in / Sign up

Export Citation Format

Share Document