scholarly journals TatA complexes exhibit a marked change in organisation in response to expression of the TatBC complex

2017 ◽  
Vol 474 (9) ◽  
pp. 1495-1508 ◽  
Author(s):  
Sarah M. Smith ◽  
Andrew Yarwood ◽  
Roland A. Fleck ◽  
Colin Robinson ◽  
Corinne J. Smith
Keyword(s):  
Dimensional Space ◽  
Membrane Integrity ◽  
Three Dimensional ◽  
Marked Change ◽  
Integral Membrane Protein ◽  
Immunogold Labelling ◽  
Inner Membrane ◽  
E Coli ◽  
Array Tomography ◽  
Insight Into

The twin-arginine translocation (Tat) system is an integral membrane protein complex that accomplishes the remarkable feat of transporting large, fully folded polypeptides across the inner membrane of bacteria, into the periplasm. In Escherichia coli, Tat comprises three membrane proteins: TatA, TatB and TatC. How these proteins arrange themselves in the inner membrane to permit passage of Tat substrates, whilst maintaining membrane integrity, is still poorly understood. TatA is the most abundant component of this complex and facilitates assembly of the transport mechanism. We have utilised immunogold labelling in combination with array tomography to gain insight into the localisation and distribution of the TatA protein in E. coli cells. We show that TatA exhibits a uniform distribution throughout the inner membrane of E. coli and that altering the expression of TatBC shows a previously uncharacterised distribution of TatA in the inner membrane. Array tomography was used to provide our first insight into this altered distribution of TatA in three-dimensional space, revealing that this protein forms linear clusters in the inner membrane of E. coli upon increased expression of TatBC. This is the first indication that TatA organisation in the inner membrane alters in response to changes in Tat subunit stoichiometry.

scholarly journals TatA complexes exhibit a marked change in organisation in response to expression of the TatBC complex

2016 ◽  
Author(s):  
Sarah M. Smith ◽  
Andrew Yarwood ◽  
Roland A. Fleck ◽  
Colin Robinson ◽  
Corinne J. Smith
Keyword(s):  
Escherichia Coli ◽  
Membrane Integrity ◽  
Marked Change ◽  
Integral Membrane Protein ◽  
Immunogold Labelling ◽  
Inner Membrane ◽  
E Coli ◽  
Array Tomography ◽  
Twin Arginine Translocase ◽  
Insight Into

AbstractThe twin arginine translocation (Tat) system is an integral membrane protein complex that accomplishes the remarkable feat of transporting large, fully-folded polypeptides across the inner membrane of bacteria, into the periplasm. In Escherichia coli Tat is comprised of three membrane proteins: TatA, TatB and TatC. How these proteins arrange themselves in the inner membrane to permit passage of Tat substrates, whilst maintaining membrane integrity, is still poorly understood. TatA is the most abundant component of this complex and facilitates assembly of the transport mechanism. We have utilised immunogold labelling in combination with array tomography to gain insight into the localisation and distribution of the TatA protein in E. coli cells. We show that TatA exhibits a uniform distribution throughout the inner membrane of E. coli and that altering the expression of TatBC shows a previously uncharacterised distribution of TatA in the inner membrane. Array tomography was used to provide our first insight into this altered distribution of TatA in 3D space, revealing that this protein forms linear clusters in the inner membrane of E. coli upon increased expression of TatBC. This is the first indication that TatA organisation in the inner membrane alters in response to changes in Tat subunit stoichiometry.Summary statementThe volumetric electron-microscopy technique, array tomography, revealed a novel distribution of TatA protein (from the twin arginine translocase complex), in Escherichia coli.

scholarly journals An in silico structural insights into Plasmodium LytB protein and its inhibition

2014 ◽  
Vol 70 (a1) ◽  
pp. C1791-C1791
Author(s):  
Rajabrata Bhunya ◽  
Suman Nandy ◽  
Alpana Seal
Keyword(s):  
In Silico ◽  
3D Structure ◽  
Three Dimensional ◽  
Comparative Modeling ◽  
Binding Energies ◽  
E Coli ◽  
Dimethylallyl Diphosphate ◽  
In Silico Study ◽  
Structural Insights ◽  
Insight Into

In most of the pathogenic organisms including Plasmodium falciparum, isoprenoids are synthesized via MEP (MethylErythritol 4-Phosphate) pathway. LytB is the last enzyme of this pathway which catalyzes the conversion of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Since the MEP pathway is not used by humans, it represents an attractive target for the development of new antimalarial compounds or inhibitors. Here a systematic in-silico study has been conducted to get an insight into the structure of Plasmodium lytB as well as its affinities towards different inhibitors. We used comparative modeling technique to predict the three dimensional (3D) structure of Plasmodium LytB taking E. Coli LytB protein (PDB ID: 3KE8) as template and the model was subsequently refined through molecular dynamics (MD) simulation. A large ligand dataset containing diphospate group was subjected for virtual screening against the target using GOLD 5.2 program. Considering the mode of binding and affinities, 17 leads were selected on basis of binding energies in comparison to its substrate HMBPP (Gold.Chemscore.DG: -20.9734 kcal/mol). Among them, 5 were discarded because of their inhibitory activity towards other human enzymes. The rest 12 potential leads carry all the properties of any "drug like" molecule and the knowledge of Plasmodium LytB inhibitory mechanism which can provide valuable support for the antimalarial inhibitor design in future.

scholarly journals Spectro-Temporal Responses of Curved Railway Tracks with Variable Radii of Arc Curves

2019 ◽  
Vol 19 (04) ◽  
pp. 1950044 ◽  
Author(s):  
Sakdirat Kaewunruen ◽  
Chayut Ngamkhanong ◽  
Xin Liu
Keyword(s):  
Mode Coupling ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Dynamic Responses ◽  
Lateral Direction ◽  
Rolling Velocity ◽  
Railway Tracks ◽  
Curved Track ◽  
Lateral Displacements ◽  
Insight Into

On curved railway tracks, wheel/rail interface can usually cause a traveling source of sound and vibration, which constitutes high-pitch or tonal noise pollution causing considerable concern to rail asset owners, commuters and people living or working along the railway corridor. The sound and vibration can be in various forms and spectra. The undesirable tonal sound on curves caused by excessive lateral wheel/rail dynamics in resonance with falling friction states are often called ‘squeal noises’. This paper evaluates the transient effect of curve radii on the possible occurrence of lateral track resonances, which is a principal cause of dynamic wheel/rail mode coupling that could trigger ‘curve squeal’. This study is devoted to systems thinking approach and better insight into dynamic phenomena of railway tracks that could resolve the railway curve noise problems. Curved track models in three-dimensional space have been developed using a finite element package, STRAND7. The dynamic responses of curved track have been simulated by applying a moving train load. The transient loading model of a common wheel/rail slip has been adopted. The simulations of railway tracks with different curve radii have been carried out to develop state-of-the-art understanding of lateral track dynamics, including rail dynamics, cant dynamics and overall track responses. Parametric studies have been conducted to evaluate lateral displacements, velocities and accelerations of rail over sleeper and rail at midspan, both in static and dynamic conditions. The study firstly reveals that the lateral resonance of tangent tracks is relatively rare and the mode coupling behavior is unlikely to occur on moderately curved tracks. The lateral vibration responses have been presented in terms of time histories and spectro-temporal responses (also called “Spectogram”). The dynamic lateral responses of the track are found to be sensitive to the change of curved radii. The resonance peak in the lateral direction is related to the agreement of corresponding natural frequencies of rail and the vibration excitation frequencies under an individual rolling velocity. The outcome of this study establishes new insight into the dominant influences of different track parameters to track lateral dynamic behaviors.

Three-dimensional reconstruction of the 30S ribosomal subunit from randomly oriented particles

1983 ◽  
Vol 41 ◽  
pp. 758-759
Author(s):  
A. Verschoor ◽  
J. Frank ◽  
M. Radermacher ◽  
T. Wagenknecht ◽  
M. Boublik
Keyword(s):  
Correspondence Analysis ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Ribosomal Subunit ◽  
Two Dimensional ◽  
Mapping Algorithm ◽  
E Coli ◽  
Wide Range ◽  
Dimensional Reconstruction ◽  
Significant Factors

The small (30S) subunit of prokaryotic ribosomes can assume any of a wide range of tilt positions on the specimen support. Correspondence analysis should make it possible to order views appearing in the electron micrograph according to the angle of tilt.231 individual windowed images from two micrographs showing negatively stained 30S subunits from E. coli ribosomes were subjected to multireference alignment. Correspondence analysis yielded six morphologically significant factors of variance. The second of these related to variations in stain concentrations, which are irrelevant at the level of gross morphology. The coordinates for each image in five-dimensional space (relating to factors 1,3,4,5, and 6) were subjected to a nonlinear mapping algorithm, which calculated an optimal two-dimensional map.The resulting distribution (Fig 1) consisted of two clusters, one of rightfacing, the other of left-facing views. Subaverages along the outer margin of the cluster on the left showed the particle in a range of typical views.

Ribosome Structural Organization

1974 ◽  
Vol 32 ◽  
pp. 332-333
Author(s):  
James A. Lake
Keyword(s):  
Ribosomal Proteins ◽  
Structural Organization ◽  
Three Dimensional ◽  
Small Subunit ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
Specific Antibodies ◽  
X Ray ◽  
E Coli ◽  
Complete Sequences

The understanding of ribosome structure has advanced considerably in the last several years. Biochemists have characterized the constituent proteins and rRNA's of ribosomes. Complete sequences have been determined for some ribosomal proteins and specific antibodies have been prepared against all E. coli small subunit proteins. In addition, a number of naturally occuring systems of three dimensional ribosome crystals which are suitable for structural studies have been observed in eukaryotes. Although the crystals are, in general, too small for X-ray diffraction, their size is ideal for electron microscopy.

Structure and function of neural networks in the retina

1988 ◽  
Vol 46 ◽  
pp. 26-27
Author(s):  
Peter Sterling
Keyword(s):  
Ganglion Cells ◽  
Three Dimensional ◽  
Structure And Function ◽  
Synaptic Connections ◽  
Visual Axis ◽  
One Dimensional ◽  
Cat Retina ◽  
Ultrathin Sections ◽  
And Function ◽  
Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

Structural Role of rRNAs on the Ribosomal Subunits from E. Coli by Scanning Transmission Electron Microscopy

1981 ◽  
Vol 39 ◽  
pp. 424-425
Author(s):  
M. Boublik ◽  
N. Robakis ◽  
J.S. Wall
Keyword(s):  
Three Dimensional ◽  
Uranyl Acetate ◽  
Dimensional Structure ◽  
Electron Microscopic ◽  
Ribosomal Subunits ◽  
E Coli ◽  
Freeze Dried ◽  
16S Rna ◽  
Scanning Transmission ◽  
And Function

The three-dimensional structure and function of biological supramolecular complexes are, in general, determined and stabilized by conformation and interactions of their macromolecular components. In the case of ribosomes, it has been suggested that one of the functions of ribosomal RNAs is to act as a scaffold maintaining the shape of the ribosomal subunits. In order to investigate this question, we have conducted a comparative TEM and STEM study of the structure of the small 30S subunit of E. coli and its 16S RNA.The conventional electron microscopic imaging of nucleic acids is performed by spreading them in the presence of protein or detergent; the particles are contrasted by electron dense solution (uranyl acetate) or by shadowing with metal (tungsten). By using the STEM on freeze-dried specimens we have avoided the shearing forces of the spreading, and minimized both the collapse of rRNA due to air drying and the loss of resolution due to staining or shadowing. Figure 1, is a conventional (TEM) electron micrograph of 30S E. coli subunits contrasted with uranyl acetate.

Three Dimensional structure and organization of diploid chromosomes by optical section microscopy

1987 ◽  
Vol 45 ◽  
pp. 633-635
Author(s):  
David A. Agard ◽  
Yasushi Hiraoka ◽  
John W. Sedat
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Developmental State ◽  
Mitotic Cell ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Specific Gene ◽  
Three Dimensional Structure ◽  
Complementary Techniques ◽  
Dynamic Structures

In an effort to understand the complex relationship between structure and biological function within the nucleus, we have embarked on a program to examine the three-dimensional structure and organization of Drosophila melanogaster embryonic chromosomes. Our overall goal is to determine how DNA and proteins are organized into complex and highly dynamic structures (chromosomes) and how these chromosomes are arranged in three dimensional space within the cell nucleus. Futher, we hope to be able to correlate structual data with such fundamental biological properties as stage in the mitotic cell cycle, developmental state and transcription at specific gene loci.Towards this end, we have been developing methodologies for the three-dimensional analysis of non-crystalline biological specimens using optical and electron microscopy. We feel that the combination of these two complementary techniques allows an unprecedented look at the structural organization of cellular components ranging in size from 100A to 100 microns.

Visualisation of E. coli ribosomal RNA in situ by electron spectroscopic imaging and image averaging

1992 ◽  
Vol 50 (1) ◽  
pp. 466-467
Author(s):  
Daniel Beniac ◽  
George Harauz
Keyword(s):  
Ribosomal Rna ◽  
Three Dimensional ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
E Coli ◽  
Microscopical Technique ◽  
Quantitative Image ◽  
Dimensional Reconstruction ◽  
Image Averaging ◽  
Protein Components

The structures of E. coli ribosomes have been extensively probed by electron microscopy of negatively stained and frozen hydrated preparations. Coupled with quantitative image analysis and three dimensional reconstruction, such approaches are worthwhile in defining size, shape, and quaternary organisation. The important question of how the nucleic acid and protein components are arranged with respect to each other remains difficult to answer, however. A microscopical technique that has been proposed to answer this query is electron spectroscopic imaging (ESI), in which scattered electrons with energy losses characteristic of inner shell ionisations are used to form specific elemental maps. Here, we report the use of image sorting and averaging techniques to determine the extent to which a phosphorus map of isolated ribosomal subunits can define the ribosomal RNA (rRNA) distribution within them.

Polymorphic phase transition of a membrane protein - analysis of continuous diffuse electron diffraction intensity

1986 ◽  
Vol 44 ◽  
pp. 166-167
Author(s):  
Douglas L. Dorset ◽  
Andrew K. Massalski
Keyword(s):  
Molecular Sieve ◽  
Three Dimensional ◽  
Pore Geometry ◽  
Two Dimensional ◽  
Diffraction Intensity ◽  
Polymorphic Phase Transition ◽  
E Coli ◽  
Crystallographic Study ◽  
Hexagonal Form ◽  
Polymorphic Forms

Matrix porin, the ompF gene product of E. coli, has been the object of a electron crystallographic study of its pore geometry in an attempt to understand its function as a membrane molecular sieve. Three polymorphic forms have been found for two-dimensional crystals reconstituted in phospholipid, two hexagonal forms with different lipid content and an orthorhombic form coexisting with and similar to the hexagonal form found after lipid loss. In projection these have been shown to retain the same three-fold pore triplet geometry and analyses of three-dimensional data reveal that the small hexagonal and orthorhombic polymorphs have similar structure as well as unit cell spacings.

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