Purine 3′:5′-cyclic nucleotides with the nucleobase in asynorientation: cAMP, cGMP and cIMP

2016 ◽  
Vol 72 (6) ◽  
pp. 465-479 ◽  
Author(s):  
Katarzyna Anna Ślepokura
Keyword(s):  
Cyclic Nucleotides ◽  
Three Dimensional ◽  
Purine Nucleotides ◽  
Conformational Preferences ◽  
Cellular Signal ◽  
Structural Database ◽  
Cyclic Phosphate ◽  
Base Orientation ◽  
Chemical Groups ◽  
Made In

Purine 3′:5′-cyclic nucleotides are very well known for their role as the secondary messengers in hormone action and cellular signal transduction. Nonetheless, their solid-state conformational details still require investigation. Five crystals containing purine 3′:5′-cyclic nucleotides have been obtained and structurally characterized, namely adenosine 3′:5′-cyclic phosphate dihydrate, C10H12N5O6P·2H2O or cAMP·2H2O, (I), adenosine 3′:5′-cyclic phosphate 0.3-hydrate, C10H12N5O6P·0.3H2O or cAMP·0.3H2O, (II), guanosine 3′:5′-cyclic phosphate pentahydrate, C10H12N5O7P·5H2O or cGMP·5H2O, (III), sodium guanosine 3′:5′-cyclic phosphate tetrahydrate, Na+·C10H11N5O7P−·4H2O or Na(cGMP)·4H2O, (IV), and sodium inosine 3′:5′-cyclic phosphate tetrahydrate, Na+·C10H10N4O7P−·4H2O or Na(cIMP)·4H2O, (V). Most of the cyclic nucleotide zwitterions/anions [two from four cAMP present in total in (I) and (II), cGMP in (III), cGMP−in (IV) and cIMP−in (V)] aresynconformers about the N-glycosidic bond, and this nucleobase arrangement is accompanied by Crib—H...Npurhydrogen bonds (rib = ribose and pur = purine). The base orientation is tuned by the ribose pucker. An analysis of data obtained from the Cambridge Structural Database made in the context ofsyn–anticonformational preferences has revealed that among thesynconformers of various purine nucleotides, cyclic nucleotides and dinucleotides predominate significantly. The interactions stabilizing thesynconformation have been indicated. The inter-nucleotide contacts in (I)–(V) have been systematized in terms of the chemical groups involved. All five structures display three-dimensional hydrogen-bonded networks.

scholarly journals 3D IMAGING OF INDIVIDUAL PARTICLES: A REVIEW

2012 ◽  
Vol 31 (2) ◽  
pp. 65 ◽  
Author(s):  
Eric Pirard
Keyword(s):  
Literature Review ◽  
Digital Imaging ◽  
Systems Analysis ◽  
3D Imaging ◽  
Materials Science ◽  
Recent Literature ◽  
Three Dimensional ◽  
Shape Estimation ◽  
Individual Particles ◽  
Made In

In recent years, impressive progress has been made in digital imaging and in particular in three dimensional visualisation and analysis of objects. This paper reviews the most recent literature on three dimensional imaging with a special attention to particulate systems analysis. After an introduction recalling some important concepts in spatial sampling and digital imaging, the paper reviews a series of techniques with a clear distinction between the surfometric and volumetric principles. The literature review is as broad as possible covering materials science as well as biology while keeping an eye on emerging technologies in optics and physics. The paper should be of interest to any scientist trying to picture particles in 3D with the best possible resolution for accurate size and shape estimation. Though techniques are adequate for nanoscopic and microscopic particles, no special size limit has been considered while compiling the review.

Iodo-nitroarenesulfonamides: interplay of hard and soft hydrogen bonds, I...O interactions and aromatic π...π stacking interactions

2001 ◽  
Vol 58 (1) ◽  
pp. 94-108 ◽  
Author(s):  
Craig J. Kelly ◽  
Janet M. S. Skakle ◽  
James L. Wardell ◽  
Solange M. S. V. Wardell ◽  
John N. Low ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Stacking Interactions ◽  
Asymmetric Unit ◽  
Space Group ◽  
Rotation Axes ◽  
Π Stacking ◽  
Structural Database ◽  
A Chain

Molecules of N-(4′-iodophenylsulfonyl)-4-nitroaniline, 4-O2NC6H4NHSO2C6H4I-4′ (1), are linked by three-centre I...O2N interactions into chains and these chains are linked into a three-dimensional framework by C—H...O hydrogen bonds. In the isomeric N-(4′-nitrophenylsulfonyl)-4-iodoaniline, 4-IC6H4NHSO2C6H4NO2-4′ (2), the chains generated by the I...O2N interactions are again linked into a three-dimensional framework by C—H...O hydrogen bonds. Molecules of N,N-bis(3′-nitrophenylsulfonyl)-4-iodoaniline, 4-IC6H4N(SO2C6H4NO2-3′)2 (3), lie across twofold rotation axes in space group C2/c and they are linked into chains by paired I...O=S interactions: these chains are linked into sheets by a C—H...O hydrogen bond, and the sheets are linked into a three-dimensional framework by aromatic π...π stacking interactions. In N-(4′-iodophenylsulfonyl)-3-nitroaniline, 3-O2NC6H4NHSO2C6H4I-4′ (4), there are R^2_2(8) rings formed by hard N—H...O=S hydrogen bonds and R^2_2(24) rings formed by two-centre I...nitro interactions, which together generate a chain of fused rings: the combination of a C—H...O hydrogen bond and aromatic π...π stacking interactions links the chains into sheets. Molecules of N-(4′-iodophenylsulfonyl)-4-methyl-2-nitroaniline, 4-CH3-2-O2NC6H3NHSO2C6H4I-4′ (5), are linked by N—H...O=S and C—H...O(nitro) hydrogen bonds into a chain containing alternating R^2_2(8) and R^2_2(10) rings, but there are no I...O interactions of either type. There are two molecules in the asymmetric unit of N-(4′-iodophenylsulfonyl)-2-nitroaniline, 2-O2NC6H4NHSO2C6H4I-4′ (6), and the combination of an I...O=S interaction and a hard N—H...O(nitro) hydrogen bond links the two types of molecule to form a cyclic, centrosymmetric four-component aggregate. C—H...O hydrogen bonds link these four-molecule aggregates to form a molecular ladder. Comparisons are made with structures retrieved from the Cambridge Structural Database.

Spacer conformation in biologically active molecules

2004 ◽  
Vol 76 (5) ◽  
pp. 959-964 ◽  
Author(s):  
J. Karolak-Wojciechowska ◽  
A. Fruzinski
Keyword(s):  
Statistical Data ◽  
Population Analysis ◽  
Cambridge Structural Database ◽  
Biologically Active ◽  
Aliphatic Chain ◽  
X Ray ◽  
Flexible Spacer ◽  
Conformational Preferences ◽  
Structural Database ◽  
The One

Based on our contemporary studies on the structures of biologically active molecules, we focus our attention on the aliphatic chain and its conformation. That flexible spacer definitely influenced the balanced position of all pharmacophoric points in molecules of biological ligands. The one atomic linker and two or three atomic spacers with one heteroatom X =O, S, CH2, NH have been taken into account. The conformational preferences clearly depend on the heteroatom X. In the discussion, we utilize our own X-ray data, computation chemistry methods, population analysis, and statistical data from the Cambridge Structural Database (CSD).

scholarly journals In-Depth Verification of a Numerical Model for an Axisymmetric RC Dome

Symmetry ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2152
Author(s):  
Przemysław Czumaj ◽  
Sławomir Dudziak ◽  
Zbigniew Kacprzyk
Keyword(s):  
Three Dimensional ◽  
Spatial Models ◽  
Detailed Comparison ◽  
The Finite Element Method ◽  
Robot System ◽  
Engineering Structures ◽  
Computational Analyses ◽  
Computational Systems ◽  
Good Agreement ◽  
Made In

The designers of civil engineering structures often have to face the problem of the reliability of complex computational analyses performed most often with the Finite Element Method (FEM). Any assessment of reliability of such analyses is difficult and can only be approximate. The present paper puts forward a new method of verification and validation of the structural analyses upon an illustrative example of a dome strengthened by circumferential ribs along the upper and lower edges. Four computational systems were used, namely Abaqus, Autodesk Robot, Dlubal RFEM, and FEAS. Different models were also analyzed—two-dimensional (2D) and three-dimensional (3D) ones using continuum, bar, and shell finite elements. The results of the static (with two kinds of load—self-weight and load distributed along the upper ring) and modal analyses are presented. A detailed comparison between the systems’ and models’ predictions was made. In general, the spatial models predicted a less stiff behavior of the analyzed dome than the planar models. The good agreement between different models and systems was obtained for the first natural frequency with axisymmetric eigenmodes (except from the Autodesk Robot system). The presented approach to the verification of complex shell–bar models can be effectively applied by structural designers.

scholarly journals Reconstructing intragranular strain fields in polycrystalline materials from scanning 3DXRD data

2020 ◽  
Vol 53 (2) ◽  
pp. 314-325 ◽  
Author(s):  
N. Axel Henningsson ◽  
Stephen A. Hall ◽  
Jonathan P. Wright ◽  
Johan Hektor
Keyword(s):  
Three Dimensional ◽  
Polycrystalline Materials ◽  
Reconstruction Method ◽  
X Ray Diffraction ◽  
Reconstruction Accuracy ◽  
Strain Fields ◽  
Spatial Properties ◽  
Reconstruction Methods ◽  
Reconstruction Quality ◽  
Made In

Two methods for reconstructing intragranular strain fields are developed for scanning three-dimensional X-ray diffraction (3DXRD). The methods are compared with a third approach where voxels are reconstructed independently of their neighbours [Hayashi, Setoyama & Seno (2017). Mater. Sci. Forum, 905, 157–164]. The 3D strain field of a tin grain, located within a sample of approximately 70 grains, is analysed and compared across reconstruction methods. Implicit assumptions of sub-problem independence, made in the independent voxel reconstruction method, are demonstrated to introduce bias and reduce reconstruction accuracy. It is verified that the two proposed methods remedy these problems by taking the spatial properties of the inverse problem into account. Improvements in reconstruction quality achieved by the two proposed methods are further supported by reconstructions using synthetic diffraction data.

Structural characterization of intrinsically disordered proteins by the combined use of NMR and SAXS

2012 ◽  
Vol 40 (5) ◽  
pp. 955-962 ◽  
Author(s):  
Nathalie Sibille ◽  
Pau Bernadó
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Dynamic Models ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Main Tool ◽  
Structural Features ◽  
Disordered Proteins ◽  
Dimensional Structure ◽  
Intrinsically Disordered ◽  
Conformational Preferences

In recent years, IDPs (intrinsically disordered proteins) have emerged as pivotal actors in biology. Despite IDPs being present in all kingdoms of life, they are more abundant in eukaryotes where they are involved in the vast majority of regulation and signalling processes. The realization that, in some cases, functional states of proteins were partly or fully disordered was in contradiction to the traditional view where a well defined three-dimensional structure was required for activity. Several experimental evidences indicate, however, that structural features in IDPs such as transient secondary-structural elements and overall dimensions are crucial to their function. NMR has been the main tool to study IDP structure by probing conformational preferences at residue level. Additionally, SAXS (small-angle X-ray scattering) has the capacity to report on the three-dimensional space sampled by disordered states and therefore complements the local information provided by NMR. The present review describes how the synergy between NMR and SAXS can be exploited to obtain more detailed structural and dynamic models of IDPs in solution. These combined strategies, embedded into computational approaches, promise the elucidation of the structure–function properties of this important, but elusive, family of biomolecules.

scholarly journals Gravity Measurements on the Athabaska Glacier, Alberta, Canada

1963 ◽  
Vol 4 (35) ◽  
pp. 617-631
Author(s):  
E. R. Kanasewich
Keyword(s):  
Cross Section ◽  
Three Dimensional ◽  
Gravity Anomalies ◽  
Independent Data ◽  
Surface Slope ◽  
Average Shear Stress ◽  
Glacier Valley ◽  
Gravity Measurements ◽  
Average Shear ◽  
Made In

AbstractThe thickness of the Athabaska Glacier has been obtained along eight transverse profiles by an investigation of gravity anomalies. Three-dimensional computations with a low-speed digital computer were made in this study to acquire more precise results than previously obtained. The thickness of the glacier varies front 326 m. on a line below the lower ice fall to 49 m. near the terminus. The accuracy of the results is discussed and compared with independent data from bore holes and a seismic program. The cross-section of the glacier valley was found to approximate a parabola on several lines. From a knowledge of the thickness. shape and surface slope of the glacier, the average shear stress exerted by the bed on the ice was found to be 1.0 bar.

3′:5′-Cyclic nucleotides: two sodium salts of cdTMP

2016 ◽  
Vol 72 (1) ◽  
pp. 35-47 ◽  
Author(s):  
Katarzyna Anna Ślepokura
Keyword(s):  
Hydrogen Bonds ◽  
Self Assembly ◽  
Cyclic Nucleotides ◽  
Cellular Level ◽  
Sodium Salts ◽  
Comprehensive Knowledge ◽  
Cyclic Phosphate ◽  
Nucleobase Orientation ◽  
Direct Inter

3′:5′-Cyclic nucleotides play an outstanding role in signal transduction at the cellular level but, in spite of comprehensive knowledge of the biological role of cyclic nucleotides, their structures are not established fully. Two hydrated sodium salts of thymidine 3′:5′-cyclic phosphate (cdTMP, C10H12N2O7P), namely sodium thymidine 3′:5′-cyclic phosphate heptahydrate, Na+·C10H12N2O7P−·7H2O or Na(cdTMP)·7H2O, (I), and sodium thymidine 3′:5′-cyclic phosphate 3.7-hydrate, Na+·C10H12N2O7P−·3.7H2O or Na(cdTMP)·3.7H2O, (II), have been obtained in crystalline form and structurally characterized, revealing one nucleotide in the asymmetric unit of (I) and eight different nucleotides in (II). All the cyclic nucleotide anions adopt a similar conformation with regard to nucleobase orientation, sugar conformation and 1,3,2-dioxaphosphorinane ring puckering. In (I), no direct inter-nucleotide hydrogen bonds are present, and adjacent nucleotide anions interactviawater-mediated and Na+-mediated contacts. In contrast, in (II), direct thymine–phosphate N—H...O inter-nucleotide hydrogen bonds occur and these are assisted by numerous inter-nucleotide C—H...O contacts, giving rise to the self-assembly of cdTMP−anions into three different ribbons. Two of these three ribbons run in the same direction, while the third is antiparallel.

Pressure-Probe Interference in a Vortex Flow

1978 ◽  
Vol 5 (2) ◽  
pp. 106-110
Author(s):  
O.O. Mojola
Keyword(s):  
Vortex Flow ◽  
Static Pressure ◽  
Vertical Wall ◽  
Three Dimensional ◽  
Flow Region ◽  
Pressure Probe ◽  
Pressure Data ◽  
Pressure Sensing ◽  
Recirculation Flow ◽  
Made In

This paper examines the sensitivity of vortex-flows to disturbances arising from the insertion of conventional pressure-sensing probes into the flows. With a wide variety of pitot-tubes, static-pressure probes, and transverse-cylinder yawmeters, measurements were made in the vortex (recirculation) flow region of a separated, three-dimensional, turbulent boundary layer upstream of a vertical wall. The measurements, which included both local and surface pressure data, have been analysed to reveal how the shape, size, and alignment of probes independently and collectively contribute to the probe interference.

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