scholarly journals Dynamic oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis

2019 ◽  
Author(s):  
Mariusz Madej ◽  
Joshua B. R. White ◽  
Zuzanna Nowakowska ◽  
Shaun Rawson ◽  
Carsten Scavenius ◽  
...  
Keyword(s):  
Porphyromonas Gingivalis ◽  
Direct Evidence ◽  
Inflammatory Diseases ◽  
Extracellular Proteins ◽  
Substrate Selectivity ◽  
Binding Studies ◽  
Uptake Mechanism ◽  
X Ray ◽  
Cryo Electron Microscopy ◽  
Binding Surface

AbstractPorphyromonas gingivalis, an asaccharolytic Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases, such as rheumatoid arthritis, cardiovascular disease and Alzheimer’s disease. P. gingivalis utilizes protease-generated peptides derived from extracellular proteins for growth, but how those peptides enter the cell is not clear. Here we identify RagAB as the outer membrane importer for peptides. X-ray crystal structures show that the transporter forms a dimeric RagA2B2 complex with the RagB substrate binding surface-anchored lipoprotein forming a closed lid on the TonB-dependent transporter RagA. Cryo-electron microscopy structures reveal the opening of the RagB lid and thus provide direct evidence for a “pedal bin” nutrient uptake mechanism. Together with mutagenesis, peptide binding studies and RagAB peptidomics, our work identifies RagAB as a dynamic OM oligopeptide acquisition machine with considerable substrate selectivity that is essential for the efficient utilisation of proteinaceous nutrients by P. gingivalis.

Evidence for ordered Fe3Ni

1987 ◽  
Vol 45 ◽  
pp. 216-217
Author(s):  
K.B. Reuter ◽  
D.B. Williams ◽  
J.I. Goldstein
Keyword(s):  
Experimental Data ◽  
Martensitic Transformation ◽  
Electron Diffraction ◽  
Room Temperature ◽  
Direct Evidence ◽  
Transformation Product ◽  
Iron Meteorites ◽  
X Ray ◽  
Ni Content ◽  
Temperature Transformation

In the Fe-Ni system, although ordered FeNi and ordered Ni3Fe are experimentally well established, direct evidence for ordered Fe3Ni is unconvincing. Little experimental data for Fe3Ni exists because diffusion is sluggish at temperatures below 400°C and because alloys containing less than 29 wt% Ni undergo a martensitic transformation at room temperature. Fe-Ni phases in iron meteorites were examined in this study because iron meteorites have cooled at slow rates of about 10°C/106 years, allowing phase transformations below 400°C to occur. One low temperature transformation product, called clear taenite 2 (CT2), was of particular interest because it contains less than 30 wtZ Ni and is not martensitic. Because CT2 is only a few microns in size, the structure and Ni content were determined through electron diffraction and x-ray microanalysis. A Philips EM400T operated at 120 kV, equipped with a Tracor Northern 2000 multichannel analyzer, was used.

Electron holography of interfaces in electroceramics

1993 ◽  
Vol 51 ◽  
pp. 1088-1089
Author(s):  
Vinayak P. Dravid ◽  
V. Ravikumar ◽  
Richard Plass
Keyword(s):  
Space Charge ◽  
Direct Evidence ◽  
Materials Science ◽  
Theoretical Work ◽  
Electron Holography ◽  
Resolution Limit ◽  
Interference Phenomenon ◽  
X Ray ◽  
Electron Sources ◽  
Science Community

With the advent of coherent electron sources with cold field emission guns (cFEGs), it has become possible to utilize the coherent interference phenomenon and perform “practical” electron holography. Historically, holography was envisioned to extent the resolution limit by compensating coherent aberrations. Indeed such work has been done with reasonable success in a few laboratories around the world. However, it is the ability of electron holography to map electrical and magnetic fields which has caught considerable attention of materials science community.There has been considerable theoretical work on formation of space charge on surfaces and internal interfaces. In particular, formation and nature of space charge have important implications for the performance of numerous electroceramics which derive their useful properties from electrically active grain boundaries. Bonnell and coworkers, in their elegant STM experiments provided the direct evidence for GB space charge and its sign, while Chiang et al. used the indirect but powerful technique of x-ray microchemical profiling across GBs to infer the nature of space charge.

Extracellular Proteins as Enterobacterial Thermometers

2003 ◽  
Vol 86 (1-2) ◽  
pp. 139-156 ◽  
Author(s):  
Robin J. Rowbury
Keyword(s):  
Thermal Stress ◽  
Heat Shock ◽  
Stress Responses ◽  
Direct Evidence ◽  
Experimental Studies ◽  
Extracellular Proteins ◽  
Temperature Changes ◽  
Induction Components ◽  
Cellular Components ◽  
Thermal Stimuli

Biological thermometers are cellular components or structures which sense increasing temperatures, interaction of the thermometer and the thermal stress bringing about the switching-on of inducible responses, with gradually enhanced levels of response induction following gradually increasing temperatures. In enterobacteria, for studies of such thermometers, generally induction of heat shock protein (HSP) synthesis has been examined, with experimental studies aiming to establish (often indirectly) how the temperature changes which initiate HSP synthesis are sensed; numerous other processes and responses show graded induction as temperature is increased, and how the temperature changes which induce these are sensed is also of interest. Several classes of intracellular component and structure have been proposed as enterobacterial thermometers, with the ribosome and the DnaK chaperone being the most favoured, although for many of the proposed intracellular thermometers, most of the evidence for their functioning in this way is indirect. In contrast to the above, the studies reviewed here firmly establish that for four distinct stress responses, which are switched-on gradually as temperature increases, temperature changes are sensed by extracellular components (extracellular sensing components, ESCs) i.e. there is firm and direct evidence for the occurrence of extracellular thermometers. All four thermometers described here are proteins, which appear to be distinct and different from each other, and on sensing thermal stress are activated by it to four distinct extracellular induction components (EICs), which interact with receptors on the surface of organisms to induce the appropriate responses. It is predicted that many other temperature-induced processes, including the synthesis of HSPs, will be switched-on following the activation of similar extracellular thermometers by thermal stimuli.

scholarly journals High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Koji Kato ◽  
Naoyuki Miyazaki ◽  
Tasuku Hamaguchi ◽  
Yoshiki Nakajima ◽  
Fusamichi Akita ◽  
...  
Keyword(s):  
Photosystem Ii ◽  
Physiological State ◽  
High Dose ◽  
Final State ◽  
X Ray ◽  
Redox States ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Redox Active ◽  
Beam Damage

AbstractPhotosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.

Developing structure-based models to predict substrate specificity of D-group (Type II) molybdenum enzymes: application to a molybdo-enzyme of unknown function from Archaeoglobus fulgidus

2006 ◽  
Vol 34 (1) ◽  
pp. 118-121 ◽  
Author(s):  
E.J. Dridge ◽  
D.J. Richardson ◽  
R.J. Lewis ◽  
C.S. Butler
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Archaeoglobus Fulgidus ◽  
Substrate Selectivity ◽  
Type Ii ◽  
Amino Acid Residues ◽  
Sequence Alignments ◽  
X Ray ◽  
Group Type

The AF0174–AF0176 gene cluster in Archaeoglobus fulgidus encodes a putative oxyanion reductase of the D-type (Type II) family of molybdo-enzymes. Sequence analysis reveals that the catalytic subunit AF0176 shares low identity (31–32%) and similarity (41–42%) to both NarG and SerA, the catalytic components of the respiratory nitrate and selenate reductases respectively. Consequently, predicting the oxyanion substrate selectivity of AF0176 has proved difficult based solely on sequence alignments. In the present study, we have modelled both AF0176 and SerA on the recently determined X-ray structure of the NAR (nitrate reductase) from Escherichia coli and have identified a number of key amino acid residues, conserved in all known NAR sequences, including AF0176, that we speculate may enhance selectivity towards trigonal planar (NO3−) rather than tetrahedral (SeO42− and ClO4−) substrates.

scholarly journals Expressed in the Yeast Saccharomyces cerevisiae, Human ERK5 Is a Client of the Hsp90 Chaperone That Complements Loss of the Slt2p (Mpk1p) Cell Integrity Stress-Activated Protein Kinase

2006 ◽  
Vol 5 (11) ◽  
pp. 1914-1924 ◽  
Author(s):  
Andrew W. Truman ◽  
Stefan H. Millson ◽  
James M. Nuttall ◽  
Victoria King ◽  
Mehdi Mollapour ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Map Kinase ◽  
Protein Kinases ◽  
Strong Association ◽  
Active Form ◽  
Cell Integrity ◽  
Binding Studies ◽  
Hsp90 Inhibition ◽  
Binding Surface ◽  
Hsp90 Chaperone

ABSTRACT ERK5 is a mitogen-activated protein (MAP) kinase regulated in human cells by diverse mitogens and stresses but also suspected of mediating the effects of a number of oncogenes. Its expression in the slt2Δ Saccharomyces cerevisiae mutant rescued several of the phenotypes caused by the lack of Slt2p (Mpk1p) cell integrity MAP kinase. ERK5 is able to provide this cell integrity MAP kinase function in yeast, as it is activated by the cell integrity signaling cascade that normally activates Slt2p and, in its active form, able to stimulate at least one key Slt2p target (Rlm1p, the major transcriptional regulator of cell wall genes). In vitro ERK5 kinase activity was abolished by Hsp90 inhibition. ERK5 activity in vivo was also lost in a strain that expresses a mutant Hsp90 chaperone. Therefore, human ERK5 expressed in yeast is an Hsp90 client, despite the widely held belief that the protein kinases of the MAP kinase class are non-Hsp90-dependent activities. Two-hybrid and protein binding studies revealed that strong association of Hsp90 with ERK5 requires the dual phosphorylation of the TEY motif in the MAP kinase activation loop. These phosphorylations, at positions adjacent to the Hsp90-binding surface recently identified for a number of protein kinases, may cause a localized rearrangement of this MAP kinase region that leads to creation of the Hsp90-binding surface. Complementation of the slt2Δ yeast defect by ERK5 expression establishes a new tool with which to screen for novel agonists and antagonists of ERK5 signaling as well as for isolating mutant forms of ERK5.

scholarly journals Radio Supernovae as Direct Evidence of Stellar Evolution in Real Time

1998 ◽  
Vol 11 (1) ◽  
pp. 367-367
Author(s):  
S.D. Van Dyk ◽  
M.J. Montes ◽  
K.W. Weiler ◽  
R.A. Sramek ◽  
N. Panagia
Keyword(s):  
Mass Loss ◽  
Stellar Evolution ◽  
Loss Rate ◽  
Direct Evidence ◽  
Mass Loss Rate ◽  
X Ray ◽  
Stringent Constraint ◽  
Clear Change ◽  
Late Stages ◽  
Circumstellar Environment

The radio emission from supernovae provides a direct probe of a supernova’s circumstellar environment, which presumably was established by mass-loss episodes in the late stages of the progenitor’s presupernova evolution. The observed synchrotron emission is generated by the SN shock interacting with the relatively high-density circumstellar medium which has been fully ionized and heated by the initial UV/X-ray flash. The study of radio supernovae therefore provides many clues to and constraints on stellar evolution. We will present the recent results on several cases, including SN 1980K, whose recent abrupt decline provides us with a stringent constraint on the progenitor’s initial mass; SN 1993J, for which the profile of the wind matter supports the picture of the progenitor’s evolution in an interacting binary system; and SN 1979C, where a clear change in presupernova mass-loss rate occurred about 104 years before explosion. Other examples, such as SNe 19941 and 1996cb, will also be discussed.

Examining the structure of the mature amyloid fibril

2002 ◽  
Vol 30 (4) ◽  
pp. 521-525 ◽  
Author(s):  
O. S. Makin ◽  
L. C. Serpell
Keyword(s):  
Self Assembly ◽  
Rational Design ◽  
Amyloid Fibrils ◽  
Structural Information ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Fibre Diffraction ◽  
Complementary Techniques ◽  
Mature Fibril

The pathogenesis of the group of diseases known collectively as the amyloidoses is characterized by the deposition of insoluble amyloid fibrils. These are straight, unbranching structures about 70–120 å (1 å = 0.1 nm) in diameter and of indeterminate length formed by the self-assembly of a diverse group of normally soluble proteins. Knowledge of the structure of these fibrils is necessary for the understanding of their abnormal assembly and deposition, possibly leading to the rational design of therapeutic agents for their prevention or disaggregation. Structural elucidation is impeded by fibril insolubility and inability to crystallize, thus preventing the use of X-ray crystallography and solution NMR. CD, Fourier-transform infrared spectroscopy and light scattering have been used in the study of the mechanism of fibril formation. This review concentrates on the structural information about the final, mature fibril and in particular the complementary techniques of cryo-electron microscopy, solid-state NMR and X-ray fibre diffraction.

Green rust as a precursor for magnetite: an in situ synchrotron based study

2008 ◽  
Vol 72 (1) ◽  
pp. 201-204 ◽  
Author(s):  
A. Sumoondur ◽  
S. Shaw ◽  
I. Ahmed ◽  
L. G. Benning
Keyword(s):  
Direct Evidence ◽  
Green Rust ◽  
Stable Phase ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
Subsequent Transformation ◽  
Rapid Formation ◽  
Reaction Proceeds

AbstractIn this study, direct evidence for the formation of magnetite via a green rust intermediate is reported. The Fe(II) induced transformation of ferrihydrite, was quantified in situ and under O2-free conditions using synchrotron-based time-resolved energy dispersive X-ray diffraction. At pH 9 and Fe(II)/Fe(III) ratios of 0.5 and 1, rapid growth (6 min) of sulphate green rust and its subsequent transformation to magnetite was observed. Electron microscopy confirmed these results, showing the initial rapid formation of hexagonal sulphate green rust particles, followed by the corrosion of the green rust as magnetite growth occurred, indicating that the reaction proceeds via a dissolution-reprecipitation mechanism. At pH 7 and Fe(II)/Fe(III) ratio of 0.5, sulphate green rust was the stable phase, with no transformation to magnetite.

scholarly journals Cloning, expression, purification, crystallization and preliminary X-ray diffraction of a lysine-specific permease fromPseudomonas aeruginosa

2014 ◽  
Vol 70 (10) ◽  
pp. 1362-1367 ◽  
Author(s):  
Emmanuel Nji ◽  
Dianfan Li ◽  
Declan A. Doyle ◽  
Martin Caffrey
Keyword(s):  
Metal Ion ◽  
Cell Volume Regulation ◽  
Ion Concentration ◽  
Size Exclusion ◽  
Substrate Selectivity ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Exclusion Chromatography

The prokaryotic lysine-specific permease (LysP) belongs to the amino acid–polyamine–organocation (APC) transporter superfamily. In the cell, members of this family are responsible for the uptake and recycling of nutrients, for the maintenance of a constant internal ion concentration and for cell volume regulation. The detailed mechanism of substrate selectivity and transport of L-lysine by LysP is not understood. A high-resolution crystal structure would enormously facilitate such an understanding. To this end, LysP fromPseudomonas aeruginosawas recombinantly expressed inEscherichia coliand purified to near homogeneity by immobilized metal ion-affinity chromatography (IMAC) and size-exclusion chromatography (SEC). Hexagonal- and rod-shaped crystals were obtained in the presence of L-lysine and the L-lysine analogue L-4-thialysine by vapour diffusion and diffracted to 7.5 Å resolution. The diffraction data were indexed in space groupP21, with unit-cell parametersa= 169.53,b= 169.53,c= 290.13 Å, γ = 120°.

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