Identifying functionally important cis-peptide containing segments in proteins and their utility in molecular function annotation

Cis-peptide embedded segments are rare in proteins but often highlight their important role in molecular function when they do occur. The high evolutionary conservation of these segments illustrates this observation almost universally, although no attempt has been made to systematically use this information for the purpose of function annotation. In the present study, we demonstrate how geometric clustering and level-specific Gene Ontology molecular-function terms (also known as annotations) can be used in a statistically significant manner to identify cis-embedded segments in a protein linked to its molecular function. The present study identifies novel cis-peptide fragments, which are subsequently used for fragment-based function annotation. Annotation recall benchmarks interpreted using the receiver-operator characteristic plot returned an area-under-curve >0.9, corroborating the utility of the annotation method. In addition, we identified cis-peptide fragments occurring in conjunction with functionally important trans-peptide fragments, providing additional insights into molecular function. We further illustrate the applicability of our method in function annotation where homology-based annotation transfer is not possible. The findings of the present study add to the repertoire of function annotation approaches and also facilitate engineering, design and allied studies around the cis-peptide neighborhood of proteins.

Friedel-Crafts Arylation of a-Hydroxy Ketones: Synthesis of 1,2,2,2-Tetraarylethanones

Friedel-Crafts arylation of a-hydroxy ketones such as 2-hydroxy- 1,2,2-triarylethanones has been achieved with a variety of arenes and heteroarenes in the presence of Lewis or Bronsted acids. Both sterically hindered and unhindered 1,2,2,2-tetrarylethanones are formed in good to excellent yields by using a stoichiometric amount of triflic acid. The intermediacy of an a-keto carbenium ion has been proposed.

A cis-Regulatory Mutation in Troponin-I of Drosophila Reveals the Importance of Proper Stoichiometry of Structural Proteins During Muscle Assembly

Rapid and high wing-beat frequencies achieved during insect flight are powered by the indirect flight muscles, the largest group of muscles present in the thorax. Any anomaly during the assembly and/or structural impairment of the indirect flight muscles gives rise to a flightless phenotype. Multiple mutagenesis screens in Drosophila melanogaster for defective flight behavior have led to the isolation and characterization of mutations that have been instrumental in the identification of many proteins and residues that are important for muscle assembly, function, and disease. In this article, we present a molecular-genetic characterization of a flightless mutation, flightless-H (fliH), originally designated as heldup-a (hdp-a). We show that fliH is a cis-regulatory mutation of the wings up A (wupA) gene, which codes for the troponin-I protein, one of the troponin complex proteins, involved in regulation of muscle contraction. The mutation leads to reduced levels of troponin-I transcript and protein. In addition to this, there is also coordinated reduction in transcript and protein levels of other structural protein isoforms that are part of the troponin complex. The altered transcript and protein stoichiometry ultimately culminates in unregulated acto-myosin interactions and a hypercontraction muscle phenotype. Our results shed new insights into the importance of maintaining the stoichiometry of structural proteins during muscle assembly for proper function with implications for the identification of mutations and disease phenotypes in other species, including humans.

An Easy Access to Benzofurans via DBU Induced Condensation Reaction of Active 2-Hydroxy Acetophenones with Phenacyl Chlorides: A Novel Class of Antioxidant Agents

A convenient and efficient one-pot synthesis of benzofurans 3a, 3b, 3c, 3d, 3e, 3f, 3g, 3h, 3i, 3j, 3k, 3l, 3m, 3n, 3o, 3p, 3q, 3r, 3s, 3t has been described from 2-hydroxy acetophenones and phenacyl chlorides in the presence of DBU. The procedure was applicable for a variety of phenacyl chlorides and provides a variety of benzofurans with higher yields. DBU acts as a base and as well as nucleophiles. All the derivatives were subjected to in vitro antioxidant screenings against representative 2,2-diphenyl-1-picryl-hydrazyl and 2,2-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) radicals and results worth for further investigations.

A simple and rapid approach for testing enantiopurity of hydroxy acids and their derivatives using H-1 NMR spectroscopy

A rapid and the simple chiral derivatizing protocol involving the coupling of 2-formylphenylboronic acid and an optically pure 1,1-binaphthalene]-2,2-diamine is introduced for the accurate determination of the enantiopurity of hydroxy acids and their derivatives, possessing one or two optically active centers, using H-1 NMR spectroscopy.

The cis-Diammineplatinum(II) Complex of Curcumin: A Dual Action DNA Crosslinking and Photochemotherapeutic Agent

Pt(cur)(NH3)(2)](NO3) (1), a curcumin-bound cis-diammineplatinum(II) complex, nicknamed Platicur, as a novel photoactivated chemotherapeutic agent releases photoactive curcumin and an active platinum(II) species upon irradiation with visible light. The hydrolytic instability of free curcumin reduces upon binding to platinum(II). Interactions of 1 with 5'-GMP and ct-DNA indicated formation of platinum-bound DNA adducts upon exposure to visible light (lambda = 400-700 nm). It showed apoptotic photocytotoxicity in cancer cells (IC50 approximate to 15 mu M), thus forming (OH)-O-center dot, while remaining passive in the darkness (IC50 > 200 mu M). A comet assay and platinum estimation suggest Pt-DNA crosslink formation. The fluorescence microscopic images showed cytosolic localization of curcumin, thus implying possibility of dual action as a chemo-and phototherapeutic agent.

Synthetic scope and DFT analysis of the chiral binap-gold(I) complex-catalyzed 1,3-dipolar cycloaddition of azlactones with alkenes

he 1,3-dipolar cycloaddition between glycine-derived azlactones with maleimides is efficiently catalyzed by the dimeric chiral complex [(S-a)-Binap.AuTFA](2). The alanine-derived oxazolone only reacts with tert-butyl acrylate giving anomalous regiochemistry, which is explained and supported by Natural Resonance Theory and Nucleus Independent Chemical Shifts calculations. The origin of the high enantiodiscrimination observed with maleimides and tert-butyl acrylate is analyzed using DFT computed at M06/Lanl2dz//ONIOM(b3lyp/Lanl2dz:UFF) level. Several applications of these cycloadducts in the synthesis of new proline derivatives with a 2,5-trans-arrangement and in the preparation of complex fused polycyclic molecules are described.

Modulation of the effectiveness of 17-alpha-hydroxy-20-beta-dihydroprogesterone or of a gonadotrophic extract on the in vitro intrafollicular maturation of oocytes of the rainbow trout Salmo gairdnerii by various non-maturing steroids [Translation from: Compte Rendu Hebdomadaire des Seances de l'Academie des Sciences, Paris, Series D 281, 811-814, 1975]

The effectiveness of 17 α-hydroxy-20 β-dihydroprogesterone (17 α-20 β Pg) or of a trout hypophyseal gonadotrophic extract on the in vitro intrafollicular maturation of trout oocytes can be modulated by steroids which do not have a direct maturing effect; the effectiveness of the gonadotrophic extract is lowered by oestradiol and oestrone and increased by testosterone. As these steroids have no significant effect on maturation induced by 17 α-20 β Pg, the site of their activity is probably in the follicular envelopes. Corticosteroids, and Cortisol and cortisone in particular increase the effectiveness of the gonadotrophic extract, but increase the effectiveness of 17 α-20 β Pg even more strongly, suggesting that this 'progestagen' has a direct effect on oocyte sensitivity.

Photochemical cis-trans isomerization of β-styrylferrocene

The effect of metal atoms on photochemical transformations has been investigated by studies of the cis-trans isomerization of β-styrylferrocene.

The photostationary state lies entirely on the side of the trans isomer in the cases of direct irradiation at 3130 Å or at 3660 Å. The quantum yield at 3130 Å is 0.00650 and does not vary with concentration. In the presence of benzophenon as sensitizer the quantum yield is 0.00540. On the other hand, the quantum yield for direct irradiation at 3660 Å decreases with increasing concentration of cis β- styrylferrocene varying from 0.00365 to 0.00198.

These results lead to the suggestion that the isomerization takes place from a triplet state of β-styrylferrocene which probably has higher energy than the lowest triplet; reaction from the third triplet seems most likely.

Photosensitized CIS-TRANS isomerization of 2,3-diphenylbutene-2 investigation of anomalous sensitizers for substituted Stilbene isometrization

The behavior of the photosensitized cis-trans isomerization of 2,3-diphenylbutene-2 was studied as a function of sensitizer energy by previously established methods. In addition, certain sensitizers for which parameters other than energy transfer are operative in inducting isomerizations, were studied in more detail. Sensitization of various stilbenes and substituted stilbenes by triphenylene is discussed in terms of excited state complex formation with stilbene. Sensitization by quinones, halogen-containing aromatics and 1,2-diketones is discussed in terms of attack by photolytically produced free radicals, either by addition to and elimination from the double bond, or in the cases of 1,2-diphenylpropene and 2,3-diphenylbutene-2, by hydrogen abstraction from one of the methyl groups and reversible abstraction by the allylic radical to produce cis-trans isomerized substrate and the structurally isomerized products, 2,3-diphenylpropene and 2,3-diphenylbutene-1.

反式和顺式-1，2-二氰-（4-乙基苯）乙烯结构的谱学分析

合成了2种新型的可溶性四氮杂卟啉中间体：反式-1，2二氰-（4-乙基苯）乙烯和顺式-1，2-二氰（4-乙基苯）乙烯。通过UV-Vis，FFIR，GC／MS，^1H NMR等方法对这2种化合物的结构进行了表征，给出了它们完整的结构信息。分析比较了顺、反异构体结构上的差异，分析两者的紫外-可见光谱（UV-Vis）、红外光谱（FTIR）和核磁共振光谱（^1H NMR）谱图的差异及其产生原因。

Efficiency improvement of organic light-emitting diodes using 8-hydroxy-quinolinato lithium as an electron injection layer

Organic light-emitting diodes (OLEDs) using tris-(8-hydroxy-quinolinato) aluminum (Alq(3)) as an emitter, 8-hydroxy-quinolinato lithium (Liq) as an electron injection layer, were prepared. Experimental results show that the efficiency of device with Liq is three times higher than that without Liq. The device using Liq as an injection layer is less sensitive in efficiency to the Liq thickness than that using LiF. In addition to the Alq3 based devices, Liq is also very effective as an electron injection layer for 4,4'-bis(2,2-diphenylvinyl)-1,1'-biphenyl based blue OLED and poly (2-methoxy,5-(2-ethyl-hexyloxy)-1,4-phenylenevinylene) based orange polymer OLED. (c) 2004 Elsevier B.V. All rights reserved.

Vanadyl arsenates as catalysts for selective oxidation of organic sulfides and alkenes

artículo científico (postprint)

Dynamics in dye-doped LC systems in presence of trans-cis isomerism

The excitation as well as relaxation dynamics of dye-doped nematic liquid crystal cells has been explored both experimentally and theoretically. Overshoots in the build up of the probe signal diffracted from gratings written onto dye-doped liquid crystal systems have often been observed. The overshoot behaviour makes the accurate measurement of nonlinear optical (NLO) response magnitude difficult and ambiguous. Moreover, it complicates the understanding of the dynamics and the physics of the NLO processes. On the basis of the system with trans-cis isomerisation as a mechanism of the NLO effect the quantitative model has been built to describe the experimental results which we observe. The two unknown material parameters: diffusion coefficient and cis species lifetime are calculated from the relaxation data. A quantitative model of the signal build-up uses these parameters. The calculated dynamic behaviour based on this model correlates very well with the experimental data. The model is used to predict the performance of the system with various dopant diffusion properties.