Comparison of distance information in [TOAC1 , Glu(OMe)7, 18, 19 ] alamethicin F50/5 from paramagnetic relaxation enhancement measurements with data obtained from an X-ray diffraction-based model

2011 ◽  
Vol 17 (5) ◽  
pp. 377-382 ◽  
Author(s):  
Rani Alphonsa Jose ◽  
Marta De Zotti ◽  
Cristina Peggion ◽  
Fernando Formaggio ◽  
Claudio Toniolo ◽  
...  
Keyword(s):  
Paramagnetic Relaxation ◽  
Paramagnetic Relaxation Enhancement ◽  
X Ray Diffraction ◽  
Distance Information ◽  
X Ray

scholarly journals Tuning the 1H NMR Paramagnetic Relaxation Enhancement and Local Order of [Aliquat]+-Based Systems Mixed with DMSO

2021 ◽  
Vol 22 (2) ◽  
pp. 706
Author(s):  
Rui Cordeiro ◽  
Maria J. Beira ◽  
Carlos Cruz ◽  
João L. Figueirinhas ◽  
Marta C. Corvo ◽  
...  
Keyword(s):  
1H Nmr ◽  
Molecular Level ◽  
Outer Sphere ◽  
Paramagnetic Relaxation ◽  
Paramagnetic Relaxation Enhancement ◽  
Local Order ◽  
Large Set ◽  
X Ray ◽  
Nmr Relaxometry ◽  
Ionic Systems

Understanding the behavior of a chemical compound at a molecular level is fundamental, not only to explain its macroscopic properties, but also to enable the control and optimization of these properties. The present work aims to characterize a set of systems based on the ionic liquids [Aliquat][Cl] and [Aliquat][FeCl4] and on mixtures of these with different concentrations of DMSO by means of 1H NMR relaxometry, diffusometry and X-ray diffractometry. Without DMSO, the compounds reveal locally ordered domains, which are large enough to induce order fluctuation as a significant relaxation pathway, and present paramagnetic relaxation enhancement for the [Aliquat][Cl] and [Aliquat][FeCl4] mixture. The addition of DMSO provides a way of tuning both the local order of these systems and the relaxation enhancement produced by the tetrachloroferrate anion. Very small DMSO volume concentrations (at least up to 1%) lead to enhanced paramagnetic relaxation without compromising the locally ordered domains. Larger DMSO concentrations gradually destroy these domains and reduce the effect of paramagnetic relaxation, while solvating the ions present in the mixtures. The paramagnetic relaxation was explained as a correlated combination of inner and outer-sphere mechanisms, in line with the size and structure differences between cation and anion. This study presents a robust method of characterizing paramagnetic ionic systems and obtaining a consistent analysis for a large set of samples having different co-solvent concentrations.

scholarly journals Refining RNA solution structures with the integrative use of label-free paramagnetic relaxation enhancement NMR

2019 ◽  
Vol 5 (5-6) ◽  
pp. 244-253
Author(s):  
Zhou Gong ◽  
Shuai Yang ◽  
Qing-Fen Yang ◽  
Yue-Ling Zhu ◽  
Jing Jiang ◽  
...  
Keyword(s):  
Rna Structure ◽  
Paramagnetic Relaxation ◽  
Structure Characterization ◽  
Paramagnetic Relaxation Enhancement ◽  
Label Free ◽  
Rna Structures ◽  
Distance Information ◽  
Solution Structures ◽  
Paramagnetic Probe

AbstractNMR structure calculation is inherently integrative, and can incorporate new experimental data as restraints. As RNAs have lower proton densities and are more conformational heterogenous than proteins, the refinement of RNA structures can benefit from additional types of restraints. Paramagnetic relaxation enhancement (PRE) provides distance information between a paramagnetic probe and protein or RNA nuclei. However, covalent conjugation of a paramagnetic probe is difficult for RNAs, thus limiting the use of PRE NMR for RNA structure characterization. Here, we show that the solvent PRE can be accurately measured for RNA labile imino protons, simply with the addition of an inert paramagnetic cosolute. Demonstrated on three RNAs that have increasingly complex topologies, we show that the incorporation of the solvent PRE restraints can significantly improve the precision and accuracy of RNA structures. Importantly, the solvent PRE data can be collected for RNAs without isotope enrichment. Thus, the solvent PRE method can work integratively with other biophysical techniques for better characterization of RNA structures.

scholarly journals NMR Study of Repair Mechanism of DNA Photolyase by FAD-induced Paramagnetic Relaxation Enhancement

2004 ◽  
Vol 279 (50) ◽  
pp. 52574-52579 ◽  
Author(s):  
Takumi Ueda ◽  
Akira Kato ◽  
Yuuta Ogawa ◽  
Takuya Torizawa ◽  
Seiki Kuramitsu ◽  
...  
Keyword(s):  
Thermus Thermophilus ◽  
Paramagnetic Relaxation ◽  
Paramagnetic Relaxation Enhancement ◽  
Pyrimidine Dimer ◽  
Dna Photolyase ◽  
X Ray ◽  
Double Stranded Dna ◽  
Nmr Study ◽  
Tryptophan Residues ◽  
Dna Complex

Cyclobutane pyrimidine dimer (CPD) photolyases, which contain FAD as a cofactor, use light to repair CPDs. We performed structural analyses of the catalytic site of theThermus thermophilusCPD photolyase-DNA complex, using FAD-induced paramagnetic relaxation enhancement (PRE). The distances between the tryptophan residues and the FAD calculated from the PRE agree well with those observed in the x-ray structure (with an error of <3 Å). Subsequently, a single-stranded DNA containing13C-labeled CPD was prepared, and the FAD-induced PRE of the NMR resonances from the CPD lesion in complex with the CPD photolyase was investigated. The distance between the FAD and the CPD calculated from the PRE is 16 ± 3 Å. The FAD-induced PRE was also observed in the CPD photolyase-double-stranded DNA complex. Based on these results, a model of the CPD photolyase-DNA complex was constructed, and the roles of Arg-201, Lys-240, Trp-247, and Trp-353 in the CPD-repair reaction are discussed.

The Use of Advanced Analytical Techniques for Characterization of the Chemical, Physical, and Crystallographic Nature of a Surface

1973 ◽  
Vol 31 ◽  
pp. 132-133 ◽  
Author(s):  
R. E. Herfert
Keyword(s):  
Surface Characterization ◽  
Analytical Techniques ◽  
X Ray Diffraction ◽  
Depth Of Penetration ◽  
X Ray ◽  
The Past ◽  
Transmission Electron ◽  
Scanning Electron

Studies of the nature of a surface, either metallic or nonmetallic, in the past, have been limited to the instrumentation available for these measurements. In the past, optical microscopy, replica transmission electron microscopy, electron or X-ray diffraction and optical or X-ray spectroscopy have provided the means of surface characterization. Actually, some of these techniques are not purely surface; the depth of penetration may be a few thousands of an inch. Within the last five years, instrumentation has been made available which now makes it practical for use to study the outer few 100A of layers and characterize it completely from a chemical, physical, and crystallographic standpoint. The scanning electron microscope (SEM) provides a means of viewing the surface of a material in situ to magnifications as high as 250,000X.

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.

Electron Microscopy of Human Gallstones

1971 ◽  
Vol 29 ◽  
pp. 296-297
Author(s):  
C. Wolpers ◽  
R. Blaschke
Keyword(s):  
Electron Microscopy ◽  
Room Temperature ◽  
Bile Pigment ◽  
X Ray Diffraction ◽  
Triclinic Crystal System ◽  
X Ray ◽  
Follow Up Study ◽  
Infra Red ◽  
Main Components

Scanning microscopy was used to study the surface of human gallstones and the surface of fractures. The specimens were obtained by operation, washed with water, dried at room temperature and shadowcasted with carbon and aluminum. Most of the specimens belong to patients from a series of X-ray follow-up study, examined during the last twenty years. So it was possible to evaluate approximately the age of these gallstones and to get information on the intensity of growing and solving.Cholesterol, a group of bile pigment substances and different salts of calcium, are the main components of human gallstones. By X-ray diffraction technique, infra-red spectroscopy and by chemical analysis it was demonstrated that all three components can be found in any gallstone. In the presence of water cholesterol crystallizes in pane-like plates of the triclinic crystal system.

High Resolution Replication of Organoclay Surfaces

1982 ◽  
Vol 40 ◽  
pp. 576-577
Author(s):  
W. W. Barker ◽  
W. E. Rigsby ◽  
V. J. Hurst ◽  
W. J. Humphreys
Keyword(s):  
Clay Mineral ◽  
Organic Molecule ◽  
Organic Molecules ◽  
X Ray Diffraction ◽  
Xrd Pattern ◽  
X Ray ◽  
Naturally Occurring ◽  
Silicate Layers ◽  
Mineral Identification

Experimental clay mineral-organic molecule complexes long have been known and some of them have been extensively studied by X-ray diffraction methods. The organic molecules are adsorbed onto the surfaces of the clay minerals, or intercalated between the silicate layers. Natural organo-clays also are widely recognized but generally have not been well characterized. Widely used techniques for clay mineral identification involve treatment of the sample with H2 O2 or other oxidant to destroy any associated organics. This generally simplifies and intensifies the XRD pattern of the clay residue, but helps little with the characterization of the original organoclay. Adequate techniques for the direct observation of synthetic and naturally occurring organoclays are yet to be developed.

Electron Microscopy of Shock Loaded Polycrystalline Beryllium

1974 ◽  
Vol 32 ◽  
pp. 506-507 ◽  
Author(s):  
J. M. Galbraith ◽  
L. E. Murr ◽  
A. L. Stevens
Keyword(s):  
Electron Microscopy ◽  
Wave Propagation ◽  
Structural Change ◽  
Single Crystal ◽  
Diffraction Pattern ◽  
Shock Loading ◽  
Slip Systems ◽  
Compression Tests ◽  
X Ray Diffraction ◽  
X Ray

Uniaxial compression tests and hydrostatic tests at pressures up to 27 kbars have been performed to determine operating slip systems in single crystal and polycrystal1ine beryllium. A recent study has been made of wave propagation in single crystal beryllium by shock loading to selectively activate various slip systems, and this has been followed by a study of wave propagation and spallation in textured, polycrystal1ine beryllium. An alteration in the X-ray diffraction pattern has been noted after shock loading, but this alteration has not yet been correlated with any structural change occurring during shock loading of polycrystal1ine beryllium.This study is being conducted in an effort to characterize the effects of shock loading on textured, polycrystal1ine beryllium. Samples were fabricated from a billet of Kawecki-Berylco hot pressed HP-10 beryllium.

Chemical modification of the bacterial wall to determine sites of metal deposition

1978 ◽  
Vol 36 (2) ◽  
pp. 350-351
Author(s):  
T. J. Beveridge
Keyword(s):  
Electron Scattering ◽  
Metal Salt ◽  
Metal Deposition ◽  
Suitable Model ◽  
X Ray Diffraction ◽  
Subtilis Cell ◽  
Thin Sections ◽  
X Ray ◽  
Section Data ◽  
Metal Impregnation

The Bacillus subtilis cell wall provides a protective sacculus about the vital constituents of the bacterium and consists of a collection of anionic hetero- and homopolymers which are mainly polysaccharidic. We recently demonstrated that unfixed walls were able to trap and retain substantial amounts of metal when suspended in aqueous metal salt solutions. These walls were briefly mixed with low concentration metal solutions (5mM for 10 min at 22°C), were well washed with deionized distilled water, and the quantity of metal uptake (atomic absorption and X-ray fluorescence), the type of staining response (electron scattering profile of thin-sections), and the crystallinity of the deposition product (X-ray diffraction of embedded specimens) determined.Since most biological material possesses little electron scattering ability electron microscopists have been forced to depend on heavy metal impregnation of the specimen before obtaining thin-section data. Our experience with these walls suggested that they may provide a suitable model system with which to study the sites of reaction for this metal deposition.

Polygonal profiles of ferritin molecules

1983 ◽  
Vol 41 ◽  
pp. 600-601
Author(s):  
William H. Massover
Keyword(s):  
Axial Ratio ◽  
X Ray Diffraction ◽  
Rhombic Dodecahedron ◽  
Apparent Contradiction ◽  
Iron Storage ◽  
X Ray ◽  
Hexagonal Shape ◽  
Axes Of Symmetry ◽  
Apparent Conflict ◽  
Iron Storage Protein

The molecular structure of the iron-storage protein, ferritin, is becoming known in ever finer detail. The 24 apoferritin subunits (MW ca. 20,000) have a 2:1 axial ratio and are polymerized with 4:3:2 symmetry to form an outer shell surrounding a variable amount of microcrystalline iron, Recent x-ray diffraction results indicate that the projected outline of the native molecule has a quasi-hexagonal shape when viewed down the 3-fold axes of symmetry, and a quasi-square shape when looking down the 4-fold axes. To date, no electron microscope study has reported observing anything other than circular profiles, which would indicate that ferritin is strictly spherical. The apparent conflict between the "hollow sphere" of electron microscopy (E.M.) and the "truncated rhombic dodecahedron" of x-ray diffraction could reflect the poorer effective resolution of E.M. coming from radiation damage, staining, drying, etc. The present study investigates the detailed shape of individual ferritin molecules in order to search for the predicted aspherical profiles and to interpret the nature of this apparent contradiction.

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