Directing peptide conformation with centrally positioned pre-organized dipeptide segments: studies of a 12-residue helix and beta-hairpin

Secondary structure formation in oligopeptides can be induced by short nucleating segments with a high propensity to form hydrogen bonded turn conformations. Type I/III turns facilitate helical folding while type II'/I' turns favour hairpin formation. This principle is experimentally verified by studies of two designed dodecapeptides, Boc-Val-Phe-Leu-Phe-Val-Aib-Aib-Val-Phe-Leu-Phe-Val-OMe 1 and Boc-Val-Phe-Leu-Phe-Val- (D) Pro- (L) Pro-Val-Phe-Leu-Phe-Val-OMe 2. The N- and C-terminal flanking pentapeptide sequences in both cases are identical. Peptide 1 adopts a largely alpha-helical conformation in crystals, with a small 3(10) helical segment at the N-terminus. The overall helical fold is maintained in methanol solution as evidenced by NMR studies. Peptide 2 adopts an antiparallel beta-hairpin conformation stabilized by 6 interstrand hydrogen bonds. Key nuclear Overhauser effects (NOEs) provide evidence for the antiparallel beta-hairpin structure. Aromatic proton chemical shifts provide a clear distinction between the conformation of peptides 1 (helical) and 2 (beta-hairpin). The proximity of facing aromatic residues positioned at non-hydrogen bonding positions in the hairpin results in extensively ring current shifted proton resonances in peptide 2.

Discharge Plasma Combined With Bauxite Residue for Biodiesel Exhaust Cleaning: A Case Study on NOx Removal

Experiments were conducted at laboratory level to treat the oxides of nitrogen (NOx) present in raw and dry biodiesel exhaust utilizing a combination of electric discharge plasma and bauxite residue, i. e., red mud, an industrial waste byproduct from the aluminum industry. In this paper, the adsorption and a possible catalytic property of bauxite residue are discussed. Nonthermal plasma was generated using dielectric barrier discharges initiated by ac/repetitive pulse energization. The effect of corona electrodes on the plasma generation was qualitatively studied through NOx cleaning. The plasma reactor and adsorbent reactors were connected in cascade while treating the exhaust. The diesel generator, running on biodiesel fuel, was electrically loaded to study the effectiveness of the cascade system in cleaning the exhaust. Interestingly, under the laboratory conditions studied, plasma-bauxite residue combination has shown good synergistic properties and enhanced the NOx removal up to about 90%. With proper scaling up, the suggested cascade system may become an economically feasible option to treat the exhaust in larger installations. The results were discussed emphasizing the role of bauxite residue as an adsorbent and as a room temperature catalyst.

Ab Initio MD Simulations of the Bronsted Acidity of Glutathione in Aqueous Solutions: Predicting pK(a) Shifts of the Cysteine Residue

The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pK(a) value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides shift in the dissociation constant values as compared with the isolated accurate estimates of the pK(a) and correctly predicts the cysteine amino acid.

Luffa acutangula agglutinin: Primary structure determination and identification of a tryptophan residue involved in its carbohydrate-binding activity using mass spectrometry

A lectin from phloem exudates of Luffa acutangula (ridge gourd) was purified on chitin affinity chromatography and characterized for its amino acid sequence and to study the role of tryptophan in its activity. The purified lectin was subjected to various proteolytic digestions, and the resulting peptides were analyzed by liquid chromatography coupled electrospray ionization ion trap mass spectrometer. The peptide precursor ions were fragmented by collision-induced dissociation or electron transfer dissociation experiments, and a manual interpretation of MS/MS was performed to deduce amino acid sequence. This gave rise to almost complete sequence coverage of the lectin which showed high-sequence similarity with deduced sequences of phloem lectins present in the database. Chemical modification of lysine, tyrosine, histidine, arginine, aspartic acid, and glutamic acid residues did not inhibit the hemagglutinating activity. However, the modification of tryptophan residues using N-bromosuccinimide showed the loss of hemagglutinating activity. Additionally, the mapping of tryptophan residues was performed to determine the extent and number of residues modified, which revealed that six residues per molecule were oxidized suggesting their accessibility. The retention of the lectin activity was seen when the modifications were performed in the presence of chitooligosaccharides due to protection of a tryptophan residue (W-102) in the protein. These studies taken together have led to the identification of a particular tryptophan residue (W-102) in the activity of the lectin. (c) 2015 IUBMB Life, 67(12):943-953, 2015

Ischaemic concentrations of lactate increase TREK1 channel activity by interacting with a single histidine residue in the carboxy terminal domain

Key points The physiological metabolite, lactate and the two-pore domain leak potassium channel, TREK1 are known neuroprotectants against cerebral ischaemia. However, it is not known whether lactate interacts with TREK1 channel to provide neuroprotection. In this study we show that lactate increases TREK1 channel activity and hyperpolarizes CA1 stratum radiatum astrocytes in hippocampal slices. Lactate increases open probability and decreases longer close time of the human (h)TREK1 channel in a concentration dependent manner. Lactate interacts with histidine 328 (H328) in the carboxy terminal domain of hTREK1 channel to decrease its dwell time in the longer closed state. This interaction was dependent on the charge on H328. Lactate-insensitive mutant H328A hTREK1 showed pH sensitivity similar to wild-type hTREK1, indicating that the effect of lactate on hTREK1 is independent of pH change. AbstractA rise in lactate concentration and the leak potassium channel TREK1 have been independently associated with cerebral ischaemia. Recent literature suggests lactate to be neuroprotective and TREK1 knockout mice show an increased sensitivity to brain and spinal cord ischaemia; however, the connecting link between the two is missing. Therefore we hypothesized that lactate might interact with TREK1 channels. In the present study, we show that lactate at ischaemic concentrations (15-30mm) at pH7.4 increases TREK1 current in CA1 stratum radiatum astrocytes and causes membrane hyperpolarization. We confirm the intracellular action of lactate on TREK1 in hippocampal slices using monocarboxylate transporter blockers and at single channel level in cell-free inside-out membrane patches. The intracellular effect of lactate on TREK1 is specific since other monocarboxylates such as pyruvate and acetate at pH7.4 failed to increase TREK1 current. Deletion and point mutation experiments suggest that lactate decreases the longer close dwell time incrementally with increase in lactate concentration by interacting with the histidine residue at position 328 (H328) in the carboxy terminal domain of the TREK1 channel. The interaction of lactate with H328 is dependent on the charge on the histidine residue since isosteric mutation of H328 to glutamine did not show an increase in TREK1 channel activity with lactate. This is the first demonstration of a direct effect of lactate on ion channel activity. The action of lactate on the TREK1 channel signifies a separate neuroprotective mechanism in ischaemia since it was found to be independent of the effect of acidic pH on channel activity. Key points The physiological metabolite, lactate and the two-pore domain leak potassium channel, TREK1 are known neuroprotectants against cerebral ischaemia. However, it is not known whether lactate interacts with TREK1 channel to provide neuroprotection. In this study we show that lactate increases TREK1 channel activity and hyperpolarizes CA1 stratum radiatum astrocytes in hippocampal slices. Lactate increases open probability and decreases longer close time of the human (h)TREK1 channel in a concentration dependent manner. Lactate interacts with histidine 328 (H328) in the carboxy terminal domain of hTREK1 channel to decrease its dwell time in the longer closed state. This interaction was dependent on the charge on H328. Lactate-insensitive mutant H328A hTREK1 showed pH sensitivity similar to wild-type hTREK1, indicating that the effect of lactate on hTREK1 is independent of pH change.

Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis

Identification of residue-residue contacts from primary sequence can be used to guide protein structure prediction. Using Escherichia coli CcdB as the test case, we describe an experimental method termed saturation-suppressor mutagenesis to acquire residue contact information. In this methodology, for each of five inactive CcdB mutants, exhaustive screens for suppressors were performed. Proximal suppressors were accurately discriminated from distal suppressors based on their phenotypes when present as single mutants. Experimentally identified putative proximal pairs formed spatial constraints to recover >98% of native-like models of CcdB from a decoy dataset. Suppressor methodology was also applied to the integral membrane protein, diacylglycerol kinase A where the structures determined by X-ray crystallography and NMR were significantly different. Suppressor as well as sequence co-variation data clearly point to the Xray structure being the functional one adopted in vivo. The methodology is applicable to any macromolecular system for which a convenient phenotypic assay exists.

Spatial determination of gold catalyst residue used in the production of ZnO nanowires by SIMS depth profiling analysis

In this paper we demonstrate how secondary ion mass spectrometry (SIMS) can be applied to ZnO nanowire structures for gold catalyst residue determination. Gold plays a significant role in determining the structural properties of such nanowires, with the location of the gold after growth being a strong indicator of the growth mechanism. For the material investigated here, we find that the gold remains at the substrate-nanowire interface. This was not anticipated as the usual growth mechanism associated with catalyst growth is of a vapour-liquid-solid (VLS) type. The results presented here favour a vapour-solid (VS) growth mechanism instead. Copyright © 2007 John Wiley & Sons, Ltd.

Application of insecticide in various volumes of waterat stages of Sorghum development for control of fall armyworm (Lepidóptera: Noctuidae)

Una debilidad en las aplicaciones de insecticidas para el control de plagas del sorgo, es el desconocimiento existente acerca del efecto de los volúmenes de agua sobre la efectividad del producto químico aplicado. El objetivo de esta investigación fue determinar el efecto de diferentes volúmenes de agua aplicados en diferentes etapas fonológicas del cultivo sobre la efectividad de clorpirifos sobre el gusano cogollero (Spodoptera frugiperda (J. E. Smith) (lnsecta: Lepidoptera: Noctuidae)) . El ensayo se estableció el 20 de Septiembre de 2001, en terrenos de la es~ación experimental numero 2 del Centro Nacional de Tecnología Agropecuaria y Forestal (CENTA), ubicado en SanAndrés, departamento de la Libertad, El Salvador .. Se efectuaron aplicaciones de chlorpyrifos en dosis de ~ .4 1 ha·, utilizando 285 y ~42 litros de agua, aplicado en dos etapas de crecimiento del cultivo de sorgo (25 y 45 días después de siembra). Los tratamientos incluyeron una aplicación a un determinado volumen y tiempo (25 días después de siembra), y dos a aplicaciones a determinados volúmenes y tiempo, una a los 25 y otra a los 45 días después de siembra. La aplicación de Chlorpyrifos redujo de significativamente la intestación de larvas a las 24 horas después de la primera aplicación, cuando se le compara con el tratamiento control. Sin embargo, no se determinaron diferencias significativas en la eficacia del insecticida, cuando se comparó la infestación de larvas en parcelas tratadas con diferentes cantidades de agua. El volumen mayor de agua pareciera que mejora la distribución del producto qufmico sobre la planta, lo que conduce a una mayor mortalidad de larvas. Una segunda aplicación de insecticida, 20 días después de la primera aplicación, redujo significativamente la infestación de larvas comparada con una sola aplicación. Esta información indica que el incremento en los volúmenes de agua mejora la eficacia del insecticida Chlorpyrifos contra el gusano cogollero en el cultivo de sorgo. Una segunda aplicación del tratamiento insecticida es efectiva contra relnfestaciones de larvas y sugiere que el cogollero que se alimenta de estructuras vegetativas del sorgo, en los ntveles encontrados en este estudio en el Salvador, puede reducir la producción de grano del sorgo.

Frequency of insecticide spray application for control of fall armyworm (Lepidóptera: Noctuidae) on sorghum

Existe desconocimiento del efecto de frecuencias de aplicación de los insecticidas sobre el comportamiento de las poblaciones del gu· sano cogollero ( Spodoptera frugipercta) y la repercusión de estas en los rendimientos del sorgo granifero (Sorghum bicolor l. Moench). El estudio se realizó en la Estación Experimental dos del Centro Nacional de Tecnología Agropecuaria y Forestal (CENTA), ubicado en San Andrés, departamento de La Libertad, El Salvador, durante los meses de septiembre del año 2001 y enero de 2002. El objetivo de la investigación fue determinar el efecto del numero de aplicaciones de clorpirifos sobre las poblaciones de larvas de gusano cogollero en el cultivo del sorgo. Para este ensayo se estableció un diseño de bloques al azar con cinco tratamientos y cuatro repeticiones. Se realizaron aplicaciones de Chlorpyrifos en el cultivo del sorgo, en dosis de 1.4 1 ha·1, en 285 1 de agua durante cuatro fechas (4 estados de desarrollo de la planta), específicamente a los 15, 25, 35 y 45 días después de la siembra. Las parcelas contratamientos recibieron 1 , 2, 3 y 4 aplicaciones de insecticidas y fueron comparadas con una parcela sin aplicación. Cada tratamiento insecticida inicialmente tuvo reducciones significativas en las poblaciones de cogollero, comparados con la parcela sin aplicación. Tratamientos con cada aplicación adicional tuvo reducciones significativas en las poblaciones de larvas vivas, comparados con tratamientos que tuvieron menor numero de aplicaciones. El cogollero, tuvo reinfestaciones, en las parcelas que recibieron ya sea una, dos o tres aplicaciones de insecticidas, durante el periodo de observación después de cada uno de los tres tratamientos. Estos resultados muestran las reinfecciones de las poblaciones de cogollero después de las aplicaciones de insecticidas, y la carencia de efecto residual de los mismos. A pesar de que no se determinaron diferencias significativas en el rendimiento de grano, las diferencias numéricas oscilaron desde 555 a 1 674 kg ha·1 mas allá del rendimiento observado en el tratamiento sin aplicación, lo cual sugiere que el manejo efectivo del daño ocasionado por el cogollero en el cultivo de sorgo, puede resultar en mejora de los rendimientos.

Significant Residue Features Revealed By Eigenvalue Decomposition Analysis Of Blosum Matrices

Here we attempt to characterize protein evolution by residue features which dominate residue substitution in homologous proteins. Evolutionary information contained in residue substitution matrix is abstracted with the method of eigenvalue decomposition. Top eigenvectors in the eigenvalue spectrums are analyzed as function of the level of similarity, i.e. sequence identity (SI) between homologous proteins. It is found that hydrophobicity and volume are two significant residue features conserved in protein evolution. There is a transition point at SI approximate to 45%. Residue hydrophobicity is a feature governing residue substitution as SI >= 45%. Whereas below this SI level, residue volume is a dominant feature. (C) 2007 Elsevier B.V. All rights reserved.

Efficacy and Residue Comparisons between Two Slow-release Formulations of Fluridone

Residue profiles and efficacy of Avast and Sonar, two slow release pellet formulations of fluridone {1-methyl-3-phenyl-5- [3-(trifluoromethyl)phenly]-4(1H)-pyridinone}, were compared in outdoor tanks. Hydrilla (Hydrilla verticillata (L.f.) Royle) and southern naiad (Najas guadalupensis (Sprengel) Magnus) were treated with a split application of 6, 12, 18 and 24 μg/l a.i. fluridone and the concentrations of both formulations compared over a 134-day period. Both pellet formulations exhibited very similar residues over time for each respective treatment, resulted in peak concentrations of fluridone 40 to 50 days after application, and effectively and similarly controlled southern naiad and hydrilla at all rates tested by 92 days after initial application. (PDF contains 3 pages.)

Studies on shark liver oil and its residue

Seasonal variation in oil and moisture contents and vitamin A potency of oil in livers from different species of sharks landed at Veraval coast were studied. Values of moisture, protein, ash and vitamins in defatted liver residue were determined.

Responses of Cyprinus carpio var. communis to Cyhalothrin, a pyrethroid insecticide

Haematological and biochemical profiles in a freshwater teleost, Cyprinus carpio var. communis, exposed to sub-lethal toxicity of the insecticide cyhalothrin were studied. During the treatment, erythrocyte count, haemoglobin content and protein content decreased, whereas leucocyte count and glucose level increased. The data are discussed in relation to the significance of haematological and biochemical changes as non-specific biomarkers against anthropogenic stress.