scholarly journals Vibrational spectroscopy and computer modeling of proteins: solving structure of α1-acid glycoprotein

2004 ◽  
Vol 18 (2) ◽  
pp. 323-330 ◽  
Author(s):  
Vladimír Kopecký ◽  
Rüdiger Ettrich ◽  
Kateřina Hofbauerová ◽  
Vladimír Baumruk
Keyword(s):  
Vibrational Spectroscopy ◽  
Preliminary Analysis ◽  
Three Dimensional ◽  
Nmr Analysis ◽  
New Approach ◽  
X Ray ◽  
Acid Glycoprotein ◽  
High Carbohydrate ◽  
Unknown Structure ◽  
Protein Models

This work introduces a new approach connecting vibrational spectroscopy with homology and energetic molecular modeling of proteins. Combination of both methods can compensate their disadvantages and result in realistic three-dimensional protein models. The approach is most powerful for membrane proteins or glycoproteins with high carbohydrate content where X-ray or NMR analysis is not always successful. Nevertheless, it can also serve as a tool of preliminary analysis of any protein with unknown structure. Power of the approach is demonstrated on human α1-acid glycoprotein. Its predicted structure published in [V. Kopecký Jr. et al.,Biochem. Biophys. Res. Commun.300(2003), 41–46] is discussed in detail with respect to the approach and its general employment.

Micro X-ray fluorescence in materials characterization

2004 ◽  
Vol 19 (2) ◽  
pp. 119-126 ◽  
Author(s):  
George J. Havrilla ◽  
Thomasin Miller
Keyword(s):  
Single Point ◽  
Three Dimensional ◽  
Chemical Imaging ◽  
Materials Characterization ◽  
New Approach ◽  
X Ray ◽  
Elemental Imaging ◽  
X Ray Imaging ◽  
Point Analysis ◽  
Comprehensive Characterization

Micro X-ray fluorescence (MXRF) offers the analyst a new approach to materials characterization. The range of applications is expanding rapidly. Single point analysis has been demonstrated for nanoliter volumes with detection limits at the 0.5 ng level. MXRF can be used as an element specific detector for capillary electrophoresis. Elemental imaging applications include analysis of sample corrosion and polymers, use as a combinatorial chemistry screening tool, and integration with molecular spectroscopic imaging methods to provide a more comprehensive characterization. Three-dimensional elemental imaging is a reality with the development of a confocal X-ray fluorescence microscope. Stereoview elemental X-ray imaging can provide unique views of materials that flat two-dimensional images cannot achieve. Spectral imaging offers chemical imaging capability, moving MXRF into a higher level of information content. The future is bright for MXRF as a materials characterization tool.

NMR analysis of a series of 1,2-bis(1-R-5-oxo-2,3-dihydro-1H-pyrrol-4-ylidene)ethanes and X-ray crystal structure analysis of theR= mesityl compound

2014 ◽  
Vol 70 (10) ◽  
pp. 965-970 ◽  
Author(s):  
Qi Liu ◽  
Xiu-Qing Song ◽  
Hong Yan
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Crystal Structure Analysis ◽  
Nmr Analysis ◽  
X Ray ◽  
H Nmr ◽  
Class 1 ◽  
Heterocyclic Group ◽  
C Nmr ◽  
Dyes And Pigments

Four tetramethyl 4,4′-(ethane-1,2-diylidene)bis[1-R-5-oxo-4,5-dihydro-1H-pyrrole-2,3-dicarboxylate] compounds, denoted class (1), are a series of conjugated buta-1,3-dienes substituted with a heterocyclic group. The compounds can be used as dyes and pigments due to their long-range conjugated systems. Four structures were studied using1H NMR,13C NMR and mass spectroscopy,viz.withR= 2,4,6-trimethylphenyl, (1a),R = cyclohexyl, (1b),R=tert-butyl, (1c), andR= isopropyl, (1d). A detailed discussion is presented regarding the characteristics of the three-dimensional structures based on NMR analysis and the X-ray crystal structure of (1a), namely tetramethyl 4,4′-(ethane-1,2-diylidene)bis[5-oxo-1-(2,4,6-trimethylphenyl)-4,5-dihydro-1H-pyrrole-2,3-dicarboxylate], C36H36N2O10. The conjugation plane and stability were also studiedviaquantum chemical calculations.

scholarly journals High-fidelity X-ray micro-tomography reconstruction of siderite-hosted Carboniferous arachnids

2009 ◽  
Vol 5 (6) ◽  
pp. 841-844 ◽  
Author(s):  
Russell Garwood ◽  
Jason A. Dunlop ◽  
Mark D. Sutton
Keyword(s):  
Three Dimensional ◽  
Data Recovery ◽  
High Fidelity ◽  
New Approach ◽  
Computer Reconstruction ◽  
X Ray ◽  
Tomography Reconstruction ◽  
Micro Tomography ◽  
Coal Measures ◽  
Crab Spiders

A new approach to maximize data recovery from siderite-hosted fossils is presented. Late Carboniferous trigonotarbids (Arachnida: Trigonotarbida) from Coseley, UK, were chosen to assess the potential of high-resolution X-ray micro-tomography (XMT). Three-dimensional computer reconstruction visualizes the animals at 20 µm or better resolution, resolving subtle and previously unseen details. Novel data recovered includes (possibly plesiomorphic) retention of endites on leg coxae of Cryptomartus hindi (Anthracomartidae) and highlights further similarities between this family and the Devonian Palaeocharinidae. Also revealed is a flattened body with robust anterior limbs, implying a hunting stance similar to modern crab spiders (Thomisidae). Eophrynus prestvicii (Eophrynidae) had more gracile limbs but a heavily ornamented body, with newly identified upward-pointing marginal spines on the opisthosoma. Its habitus is comparable with certain modern laniatorid harvestmen (Opiliones). These findings demonstrate the potential of XMT to revolutionize the study of siderite-hosted Coal Measures fossils.

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.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

X-ray microtomography

1988 ◽  
Vol 46 ◽  
pp. 998-999
Author(s):  
H.W. Deckman ◽  
B.F. Flannery ◽  
J.H. Dunsmuir ◽  
K.D' Amico
Keyword(s):  
Computed Tomography ◽  
Internal Structure ◽  
Imaging Technique ◽  
Three Dimensional ◽  
Tissue Structure ◽  
Individual Element ◽  
X Ray ◽  
Non Invasive ◽  
Panoramic Imaging ◽  
Three Dimensional Images

We have developed a new X-ray microscope which produces complete three dimensional images of samples. The microscope operates by performing X-ray tomography with unprecedented resolution. Tomography is a non-invasive imaging technique that creates maps of the internal structure of samples from measurement of the attenuation of penetrating radiation. As conventionally practiced in medical Computed Tomography (CT), radiologists produce maps of bone and tissue structure in several planar sections that reveal features with 1mm resolution and 1% contrast. Microtomography extends the capability of CT in several ways. First, the resolution which approaches one micron, is one thousand times higher than that of the medical CT. Second, our approach acquires and analyses the data in a panoramic imaging format that directly produces three-dimensional maps in a series of contiguous stacked planes. Typical maps available today consist of three hundred planar sections each containing 512x512 pixels. Finally, and perhaps of most import scientifically, microtomography using a synchrotron X-ray source, allows us to generate maps of individual element.

Revealing gross three-dimensional structure in the SEM

1987 ◽  
Vol 45 ◽  
pp. 656-657
Author(s):  
Sterling P. Newberry
Keyword(s):  
Freeze Drying ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Small Object ◽  
Final Solution ◽  
Dimensional Representation ◽  
X Ray ◽  
Three Dimensional Representation ◽  
Freeze Dried ◽  
Critical Point Drying

The beautiful three dimensional representation of small object surfaces by the SEM leads one to search for ways to open up the sample and look inside. Could this be the answer to a better microscopy for gross biological 3-D structure? We know from X-Ray microscope images that Freeze Drying and Critical Point Drying give promise of adequately preserving gross structure. Can we slice such preparations open for SEM inspection? In general these preparations crush more readily than they slice. Russell and Dagihlian got around the problem by “deembedding” a section before imaging. This some what defeats the advantages of direct dry preparation, thus we are reluctant to accept it as the final solution to our problem. Alternatively, consider fig 1 wherein a freeze dried onion root has a window cut in its surface by a micromanipulator during observation in the SEM.

X-ray Structure Refinement and Vibrational Spectroscopy of Ca8Gd2 (PO4)6 O2

2013 ◽  
Vol 12 (10) ◽  
pp. 719-726
Author(s):  
R. Ayadi ◽  
Mohamed Boujelbene ◽  
T. Mhiri
Keyword(s):  
Solid State ◽  
General Formula ◽  
Vibrational Spectroscopy ◽  
Powder Diffraction ◽  
Infrared Spectra ◽  
Solid State Reaction ◽  
Structure Refinement ◽  
Unit Cell ◽  
Cell Group ◽  
X Ray

The present paper is interested in the study of compounds from the apatite family with the general formula Ca10 (PO4)6A2. It particularly brings to light the exploitation of the distinctive stereochemistries of two Ca positions in apatite. In fact, Gd-Bearing oxyapatiteCa8 Gd2 (PO4)6O2 has been synthesized by solid state reaction and characterized by X-ray powder diffraction. The site occupancies of substituents is0.3333 in Gd and 0.3333 for Ca in the Ca(1) position and 0. 5 for Gd in the Ca (2) position.  Besides, the observed frequencies in the Raman and infrared spectra were explained and discussed on the basis of unit-cell group analyses.

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