The three dimensional structure and biological domains of the p53 C-terminus.

It was expected that there are a coil (289 similar to 325) and two a helix (alpha(1)368 similar to 373, alpha(2)381 similar to 388) structures in p53 protein C-terminal region based on its mRNA secondary structure template and Chou-Fasman's protein secondary structure principle of prediction. The result was conformed by the other four methods of protein secondary structure prediction that are based on the multiple sequence alignment (accuracy = 73.20%). Combine with the 31 amino acids crystal structure of the oligomerization, the three dimensional conformation of p53 C-terminal 108 residues was built using the SGI INDIGO(2) computer. This structure further expounds the relationship among those biological function domains of p53 C- terminus at three-dimensional level.

A three-dimensional metal-organic framework based on a triazine derivative: syntheses, structure analysis, and sorption studies

A novel metal-organic framework [Cu-3(m-TATB)(2)Py(CH3OH)(2)] (1) constructed of a triazine-based trigonal-planar ligand, 3,3',3 ''-s-triazine-2,4,6- triyltribenzoate (m-H(3)TATB), has been synthesized and structurally characterized. Compound 1 features three-dimensional (3D) channels and cavities together, and exhibits high carbon dioxide sorption at normal pressure.

Two- and three-dimensional Au nanoparticle/CoTMPyP self-assembled nanotructured materials: Film structure, tunable electrocatalytic activity, and plasmonic properties

Two- and three-dimensional Au nanoparticle/[tetrakis(N-methylpyridyl)porphyrinato]cobalt (CoTMPyP) nanostructured materials were prepared by "bottom-up" self-assembly. The electrocatalytic and plasmonic properties of the Au nanoparticle/CoTMPyP self-assembled nanostructured materials (abbreviated as Au/CoTMPyP SANMs) are tunable by controlled self-assembly of the An nanoparticles and CoTMPyP on indium tin oxide (ITO) electrode. The electrocatalytic activity of the Au/CoTMPyP SANMs can be tuned in two ways. One way is that citrate-stabilized An nanoparticles are positioned first on ITO surface with tunable number density, and then positively charged CoTMPyP ions are planted selectively on these gold sites. The other way is that An nanoparticles and CoTMPyP are deposited by virtue of layer-by-layer assembly, which can also tune the amount of the as-deposited electrocatalysts. FE-SEM studies showed that three-dimensional SANMs grow in the lateral expansion mode, and thermal annealing resulted in both surface diffusion of nanoparticles and atomic rearrangement to generate larger gold nanostructures with predominant (I 11) facets.

Peripheries of molecular projection in three-dimensional space and studies of quantitative structure-activity relationships

A new index, i.e., the periphery representation of the projection of a molecule from 3D space to a 2D plane is described. The results, correlation with toxicity of substituted nitrobenzenes, obtained by using periphery descriptors are much better than that obtained by using the areas (i.e., shadows) of projections of the compounds. Even better results were achieved by using the combination of periphery descriptors and the projections areas as well as the indicated variable K reflecting the action of group NO position on the benzene ring.

Synthesis and structure of a novel open-framework zincophosphate with intersecting three-dimensional helical channels

A new open-framework zincophosphate, Zn-0.5(H2PO4).0.5H(2)O (denoted as FJ-13), possessing intersecting three-dimensional helical channels, has been synthesized under solvothermal conditions.

Applications of the method of three-dimensional projection of a molecule in quantitative structure-activity relationship of phenol derivatives

Five variables for phenol derivatives were calculated by molecular projection in three-dimensional space which were combined with eight quantum-chemical parameters and three Am indices. These variables were selected by using leaps-and-bounds regression analysis. Multiple linear regression analysis and artificial neural networks' were performed, and the results obtained by using. artificial neural networks are superior than that obtained by using multiple linear regression.

Three-dimensional quantitative structure-activity relationship of the opioid antagonist with potent anorectant activity of 3,4-dimethyl-4-(3-hydroxyphenyl) piperidine

A series of 3,4-dimethyl-4-(3-hydroxyphenyl) piperidine opioid antagonists with varying substituents on the nitrogen were evaluated for their effect on food consumption in obese Zucker rats. In developing three-dimensional quantitative structure-activity relationship (3D-QSAR) studies for this series of opioid antagonists, different structure alignments have been tested to predict the anorectant activities. The interaction energies between molecules and the probe atom were then correlated with anorectant activity using partial least squares (PLS) method. The steric and electrostatic features of the 3D-QSAR were presented in the form of standard deviation coefficient contour maps of steric and electrostatic fields. The results showed that 3D-QSAR results are much better than the results obtained by 2D-QSAR.

Preparation, structure, and properties of three-dimensional ordered alpha-Fe2O3 nanoparticulate film

alpha-Fe2O3 nanoparticulate films could be formed on the surface of alpha-Fe2O3 hydrosol after aging of the hydrosol or by compressing of the nanoparticles on the sol surface, in. which a three-dimensional ordered structure was constructed by the Langmuir-Blodgett; technique and colloid chemical methods. The structure of the LB film was characterized by AFM, TEM, XPS, and UV-vis spectra and small-angle X-ray diffraction. Gas-sensing measurement shows that the LB film has good sensitivity to alcohols at room temperature,

Three dimensional solution structure of neurotoxin CM-11 from the Ophiophagus hannah

The Ophiophagus hannah (King Cobra) neurotoxin CM-11 is a small protein with 72 amino acid residues, Based on complete assignments of H-1-NMR resonances and determination of secondary structures of CM-11, 349 distance and 27 dihedral angle constraints including 19 phi's and 8 chi's were collected from NOESY and DQF-COSY , and the chemical stereospecific assignment of beta(1)H was partially achieved, Twelve structures with lower energy was obtained via metric matrix distance geometry and refinement with simulated annealing, These structures have a low RMSD of 0.14 nm for backbone atoms and 0.20 nm for heavy atoms, with no distance constraint violation more than 0.05 nm, and no dihedral angle violation more than 3 degrees.

Studies on three-dimensional quantitative structure-activity relationship of PDE inhibitory activity of imidazopyridines

In recent years there has been a resurgence of interest in inhibitors of cyclic nucleotide phosphodiesterases (PDE) and enzymes responsible for the intracellular hydrolysis of the second messenger cAMP and cGMP. In this study, a series of 2-substituted phenyllimidazo[4,5-b]pyridines have been made to investigate 3D-QSAR of PDE activity using CoMFA. CoMFA resulted in a quantitative description of the major steric and electrostatic field effects, and gave significant new insights to factors governing PDE inhibition activity. The model was used to predict the PDE inhibition activity of imidazopyridines with satisfactory results.

Studies on three-dimensional quantitative structure-activity relationships between the structures of N-nitroso compounds and their carcinogenic activities

Comparative molecular fiels analysis (CoMFA) has been applied to the studies of the correlation of the N-nitroso compounds and their carcinogenic activities, The comparison of CoMFA results with different lattice spacing and different atom probes was investigated, CoMFA resulted in a quantitative description of the major steric and electrostatic field effects and gave significant new insights to factors governing potency.

Evolution of three-dimensional coherent structures in compressible axisymmetric jet

A high order difference scheme is used to simulate the spatially developing compressible axisymmetric jet. The results show that the Kelvin-Helmholtz instability appears first when the jet loses its stability, and then with development of jet the increase in nonlinear effects leads to the secondary instability and the formation of the streamwise vortices. The evolution of the three-dimensional coherent structure is presented. The computed results verify that in axisymmetric jet the secondary instability and formation of the streamwise vortices are the important physical mechanism of enhancing the flow mixing and transition occurring.

Three-dimensional finite element analysis of composites with coated spherical inclusions

A three-dimensional finite element analysis has been used to determine the internal stresses in a three-phase composite. The stresses have been determined for a variety of interphase properties, the thicknesses of the interphase and the volume fractions of particles. Young's modulus has been calculated from a knowledge of these stresses and the applied deformation. The calculations show that stress distributions in the matrix and the mechanical properties are sensitive to the interphase property in the three-phase composites. The interfacial stresses in the three-dimensional analysis are in agreement with results obtained by an axisymmetric analysis. The predicted bulk modulus in three-dimensional analysis agrees well with the theoretical solution obtained by Qui and Weng, but it presents a great divergence from that in axisymmetric analyses. An investigation indicates that this divergence may be caused by the difference in the unit cell structure between two models. A comparison of the numerically predicted bulk and shear modulus for two-phase composites with the theoretical results indicates that the three-dimensional analysis gives quite satisfactory results.

Protein three-dimensional structural databases: Domains, structurally aligned homologues and superfamilies

This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the program DIAL [Sowdhamini & Blundell (1995), Protein Sci. 4, 506-520]. The alignment of proteins in superfamilies has been performed on the basis of the structural features and relationships of individual residues using the program COMPARER [Sali & Blundell (1990), J. Mol. Biol. 212, 403-428]. The alignment databases contain information on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed structures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in the comparison of newly determined protein structures with previously identified protein domains or existing families.