Initial Structure (initial + structure)

Distribution by Scientific Domains

Selected Abstracts

ChemInform Abstract: Initial Structure,Activity Relationship Studies of a Novel Series of Pyrrolo[1,2-a]pyrimid-7-ones as GnRH Receptor Antagonists.

CHEMINFORM, Issue 24 2002
Yun-Fei Zhu
Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source]

Total Synthesis and Initial Structure,Activity Relationships of Longicatenamycin,A

CHEMMEDCHEM, Issue 4 2008
Franz von, Nussbaum Dr.
Abstract Natural products have provided the majority of lead structures for marketed antibacterials. In addition, they are biological guide principles to new therapies. Nevertheless, numerous "old" classes of antibiotics such as the longicatenamycins have never been explored by chemical postevolution. Longicatenamycin,A is the first defined longicatenamycin congener that has been totally synthesized and tested in pure form. This venture required the de,novo syntheses of the non-proteinogenic amino acids (2S,3R)-,-hydroxyglutamic acid (HyGlu), 5-chloro- D -tryptophan (D -ClTrp), and (S)-2-amino-6-methylheptanoic acid (hhLeu). In the key step, the sensitive HyGlu building block was coupled as a pentafluorophenyl active ester to the unprotected H- D -ClTrp-Glu-hhLeu- D -Val- D -(Cbz)Orn-OH fragment. This first total synthesis of longicatenamycin,A provided new congeners of the natural product (deacetyllongicatenamycin, dechlorolongicatenamycin, and longicatenamycin-A-amide). [source]

Elevated CO2 and herbivory influence trait integration in Arabidopsis thaliana

M. Gabriela Bidart-Bouzat
Abstract We lack information on how elevated CO2, and its interaction with other factors like herbivory, affect levels and patterns of trait integration in plants. We experimentally tested the hypothesis that elevated CO2 disrupts and restructures functional associations among plant traits, in the selfing annual, Arabidopsis thaliana. We tested for these effects both in the presence and absence of herbivory by larvae of the diamondback moth, Plutella xylostella. Elevated CO2, both alone and combined with moth herbivory, modified integrated trait responses. In addition, integration under different environments was genotype-specific. These results imply that global changes in CO2 are likely to cause divergent evolutionary outcomes among populations of plants that differ in the initial structure of their quantitative genetic variation. [source]

Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

Masaki Kojima
A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data. [source]

Fractal Dimension of Trabecular Bone Projection Texture Is Related to Three-Dimensional Microarchitecture

L. Pothuaud
Abstract The purpose of this work was to understand how fractal dimension of two-dimensional (2D) trabecular bone projection images could be related to three-dimensional (3D) trabecular bone properties such as porosity or connectivity. Two alteration processes were applied to trabecular bone images obtained by magnetic resonance imaging: a trabeculae dilation process and a trabeculae removal process. The trabeculae dilation process was applied from the 3D skeleton graph to the 3D initial structure with constant connectivity. The trabeculae removal process was applied from the initial structure to an altered structure having 99% of porosity, in which both porosity and connectivity were modified during this second process. Gray-level projection images of each of the altered structures were simply obtained by summation of voxels, and fractal dimension (Df) was calculated. Porosity (,) and connectivity per unit volume (Cv) were calculated from the 3D structure. Significant relationships were found between Df, ,, and Cv. Df values increased when porosity increased (dilation and removal processes) and when connectivity decreased (only removal process). These variations were in accordance with all previous clinical studies, suggesting that fractal evaluation of trabecular bone projection has real meaning in terms of porosity and connectivity of the 3D architecture. Furthermore, there was a statistically significant linear dependence between Df and Cv when , remained constant. Porosity is directly related to bone mineral density and fractal dimension can be easily evaluated in clinical routine. These two parameters could be associated to evaluate the connectivity of the structure. [source]

Identifying native-like protein structures using physics-based potentials

Brian N. Dominy
Abstract As the field of structural genomics matures, new methods will be required that can accurately and rapidly distinguish reliable structure predictions from those that are more dubious. We present a method based on the CHARMM gas phase implicit hydrogen force field in conjunction with a generalized Born implicit solvation term that allows one to make such discrimination. We begin by analyzing pairs of threaded structures from the EMBL database, and find that it is possible to identify the misfolded structures with over 90% accuracy. Further, we find that misfolded states are generally favored by the solvation term due to the mispairing of favorable intramolecular ionic contacts. We also examine 29 sets of 29 misfolded globin sequences from Levitt's "Decoys ,R' Us" database generated using a sequence homology-based method. Again, we find that discrimination is possible with approximately 90% accuracy. Also, even in these less distorted structures, mispairing of ionic contacts results in a more favorable solvation energy for misfolded states. This is also found to be the case for collapsed, partially folded conformations of CspA and protein G taken from folding free energy calculations. We also find that the inclusion of the generalized Born solvation term, in postprocess energy evaluation, improves the correlation between structural similarity and energy in the globin database. This significantly improves the reliability of the hypothesis that more energetically favorable structures are also more similar to the native conformation. Additionally, we examine seven extensive collections of misfolded structures created by Park and Levitt using a four-state reduced model also contained in the "Decoys ,R' Us" database. Results from these large databases confirm those obtained in the EMBL and misfolded globin databases concerning predictive accuracy, the energetic advantage of misfolded proteins regarding the solvation component, and the improved correlation between energy and structural similarity due to implicit solvation. Z-scores computed for these databases are improved by including the generalized Born implicit solvation term, and are found to be comparable to trained and knowledge-based scoring functions. Finally, we briefly explore the dynamic behavior of a misfolded protein relative to properly folded conformations. We demonstrate that the misfolded conformation diverges quickly from its initial structure while the properly folded states remain stable. Proteins in this study are shown to be more stable than their misfolded counterparts and readily identified based on energetic as well as dynamic criteria. In summary, we demonstrate the utility of physics-based force fields in identifying native-like conformations in a variety of preconstructed structural databases. The details of this discrimination are shown to be dependent on the construction of the structural database. 2002 Wiley Periodicals, Inc. J Comput Chem 23: 147,160, 2002 [source]

Wideband printed dipole antenna using a novel PBG structure

H.-W. Yuan
Abstract A wideband printed dipole antenna with an integrated balun feed is given. To further get larger bandwidth capabilities of this antenna, a novel low-cost smaller unit-cell planar photonic bandgap (PBG) structure is etched onto the antenna surface, and a better dipole antenna is fabricated. Through optimizing the sizes of PBG structure, a 56.7% bandwidth is obtained where voltage standing wave ratio (VSWR) is less than 1.5 while a 36% bandwidth is obtained from initial structure. Agreement between calculations and measurements is very good. The result indicates that the novel design may obtain better wideband characteristic. 2009 Wiley Periodicals, Inc. Microwave Opt Technol Lett 51: 1862,1865, 2009; Published online in Wiley InterScience ( DOI 10.1002/mop.24466 [source]

Fault Diagnosis Based on the Fuzzy-Recurrent Neural Network

Zhao Xiang
ABSTRACT A fuzzy-recurrent neural network (FRNN) has been constructed by adding some feedback connections to a feedforward fuzzy neural network (FNN). The FRNN expands the modeling ability of a FNN in order to deal with temporal problems. A basic concept of the FRNN is first to use process or expert knowledge, including appropriate fuzzy logic rules and membership functions, to construct an initial structure and to then use parameter-learning algorithms to fine-tune the membership functions and other parameters. Its recurrent property makes it suitable for dealing with temporal problems, such as on-line fault diagnosis. In addition, it also provides human-understandable meaning to the normal feedforward multilayer neural network, in which the internal units are always opaque to users. In a word, the trained FRNN has good interpreting ability and one-step-ahead predicting ability. To demonstrate the performance of the FRNN in diagnosis, a comparison is made with a conventional feedforward network. The efficiency of the FRNN is verified by the results. [source]

Topography Mediated Patterning of Inorganic Materials by Spray Pyrolysis,

D. Beckel
Microstructured ceramic thin films are produced by spray pyrolysis of metal salt solutions onto micromachined substrates. The ceramic structures built on the substrate result from preferential assembly of particles on the edge of the initially micromachined structures, leading to smaller lateral dimensions (1,2 ,m in width) than the initial structures on the substrate (see figure). The assembly process amplifies the height of the initial structures by a factor of approximately thirty, resulting in features with an aspect ratio of three. [source]

Generation and characterization of low-energy structures in atomic clusters

J. M. C. Marques
Abstract Factors relevant for controlling the structures determined in the local optimization of argon clusters are investigated. In particular, the role of volume and shape for the box where initial structures are generated is assessed. A thorough characterization of the optimization is also presented, based on a nearest-neighbor analysis, in clusters ranging from 30 to 55 atoms. This includes the assessment of the degree of preservation of aspects of the initial randomly generated structure in the final optimized counterpart, and the correlation between optimized energy and the number of nearest neighbors and average departure from the diatomic reference distance. The usefulness of this analysis to explore the energy landscape of atomic clusters is also highlighted. 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source]

Learning from Directed Evolution: Theoretical Investigations into Cooperative Mutations in Lipase Enantioselectivity

CHEMBIOCHEM, Issue 2 2004
Marco Bocola Dr.
Abstract Molecular modeling with classical force-fields has been used to study the reactant complex and the tetrahedral intermediate in lipase-catalyzed ester hydrolysis in 20 enzyme/substrate combinations. The R and S enantiomers of,-methyldecanoic acid ester served as substrates for the wild-type lipase from Pseudomonas aeruginosa and nine selected mutants. After suitable preparation of initial structures from an available wild-type crystal structure, each system was subjected to 1 ns CHARMM force-field molecular dynamics simulations. The resulting geometric and energetic changes allow interpretation of some experimentally observed effects of mutations, particularly with regard to the "hot spots" at residues 155 and 162. The replacement S155F enhances S enantiopreference through a steric relay involving Leu162. The double mutation S53P + L162G improves S enantioselectivity by creating a new binding pocket for the S enantiomer with an additional stabilizing hydrogen bond to His83. The simulations provide insight into remote and cooperative effects of mutations. [source]