Tuning the beta-turn segment in designed peptide beta-hairpins: Construction of a stable type I ' beta-turn nucleus and hairpin-helix transition promoting segments

Designed octapeptides Boc-Leu-Val-Val-Aib-(D)Xxx-Leu- Val-Val-OMe ((D)Xxx = (D)Ala, 3a; (D)Val, 3c and (D)Pro, 5a) and Boc-Leu-Phe-Val-Aib-DAla-Leu-Phe-Val-OMe (3b) have been investigated to construct models of a stable type I' beta-turn nucleated hairpin and to generate systems for investigating helix-hairpin conformational transitions. Peptide 5a, which contains a central Aib-(D)Pro segment, is shown to adopt a stable type I' beta-turn nucleated hairpin structure, stabilized by four cross-strand hydrogen bonds. The stability of the structure in diverse solvents is established by the observation of all diagnostic NOEs expected in a beta-hairpin conformation. Replacement of (D)Pro5 by (D)Ala/(D)Val (3a-c) results in sequences that form beta-hairpins in hydrogen bonding solvents like CD3OH and DMSO-d(6). However, in CDCl3 evidence for population of helical conformations is obtained. Peptide 6b (Boc-Leu-Phe-Val-Aib-Aib-Leu-Phe-Val-OMe), which contains a centrally positioned Aib-Aib segment, provides a clear example of a system, which exhibits a helical conformation in CDCl3 and a significant population of both helices and hairpins in CD3OH and DMSO-d(6). The coexistence of multiple conformations is established by the simultaneous observation of diagnostic NOEs. Control over stereochemistry of the central beta-turn permits generation of models for robust beta-hairpins and also for the construction of systems that may be used to probe helix-hairpin conformational transitions. (c) 2006 Wiley Periodicals, Inc.

Synthesis, Structure, Spirocyclization Mechanism, and Glutathione Peroxidase-like Antioxidant Activity of Stable Spirodiazaselenurane and Spirodiazatellurane

The first examples of stable spirodiazaselenurane and spirodiazatellurane were synthesized by oxidative spirocyclization of the corresponding diaryl selenide and telluride and were structurally characterized. X-ray crystal structures of the spirodiazaselenurane and spirodiazatellurane suggest that the structures are distorted trigonal bipyramidal (TBP) with the electronegative nitrogen atoms occupying the apical positions and two carbon atoms and the lone pair of Se/Te occupying the equatorial positions. Interestingly, the spirodiazatellurane underwent spontaneous chiral resolution during crystallization, and the absolute configurations of its enantiomers were confirmed by single-crystal X-ray analyses. A detailed mechanistic study indicates that the cyclization to spirodiazaselenurane and spirodiazatellurane occurs via selenoxide and telluroxide intermediates. The chalcogenoxides cyclize to the corresponding spiro compounds in a stepwise manner via the involvement of hydroxyl chalcogenurane intermediates, and the activation energy for them spirocyclization reaction decreases in the order S > Se > Te. In addition to the synthesis, characterization, and mechanism of cyclization, the glutathione peroxidase (GPx) mimetic activity of the newly synthesized compounds was evaluated. These studies suggest that the tellurium compounds are more effective as GPx mimics than their selenium counterparts due to the fast oxidation of the tellurium center in the presence of peroxide and the involvement of an efficient redox cycle between the telluride and telluroxide intermediate.

Environmental and climatic dependences of stable isotope ratios in tree rings on different temporal scales

This work examines stable isotope ratios of carbon, oxygen and hydrogen in annual growth rings of trees. Isotopic composition in wood cellulose is used as a tool to study past climate. The method benefits from the accurate and precise dating provided by dendrochronology. In this study the origin, nature and the strength of climatic correlations are studied on different temporal scales and at different sites in Finland. The origin of carbon isotopic signal is in photosynthetic fractionation. The basic physical and chemical fractionations involved are reasonably well understood. This was confirmed by measuring instantaneous photosynthetic discrimination on Scots pine (Pinus sylvestris L.). The internal conductance of CO2 was recognized to have a significant impact on the observed fractionation, and further investigations are suggested to quantify its role in controlling the isotopic signal of photosynthates. Isotopic composition of the produced biomass can potentially be affected by variety of external factors that induce physiological changes in trees. Response of carbon isotopic signal in tree ring cellulose to changes in resource availability was assessed in a manipulation experiment. It showed that the signal was relatively stable despite of changes in water and nitrogen availability to the tree. Palaeoclimatic reconstructions are typically based on functions describing empirical relationship between isotopic and climatic parameters. These empirical relationships may change depending on the site conditions, species and timeframe studied. Annual variation in Scots pine tree ring carbon and oxygen isotopic composition was studied in northern and in central eastern Finland and annual variation in tree ring latewood carbon, oxygen and hydrogen isotopic ratio in Oak (Quercus robur L.) was studied in southern Finland. In all of the studied sites at least one of the studied isotope ratios was shown to record climate strongly enough to be used in climatic reconstructions. Using the observed relationships, four-century-long climate reconstructions from living Scots pine were created for northern and central eastern Finland. Also temporal stability of the relationships between three proxy indicators, tree ring growth and carbon and oxygen isotopic composition was studied during the four-hundred-year period. Isotope ratios measured from tree rings in Finland were shown to be sensitive indicators of climate. Increasing understanding of environmental controls and physiological mechanisms affecting tree ring isotopic composition will make possible more accurate interpretation of isotope data. This study also demonstrated that by measuring multiple isotopes and physical proxies from the same tree rings, additional information on tree physiology can be obtained. Thus isotopic ratios measured from tree ring cellulose provide means to improve the reliability of climate reconstructions.

Isolation and characterization of heat-stable allergens from shrimp (Penaeus indicus)

Shrimp are among the more common causes of immediate hypersensitivity reactions to food. To characterize better the allergenic substances within shrimp, extracts from heated shrimp were systematically examined with solid-phase radioimmunoassay and sera from patients clinically sensitive to shrimp. Two heat-stable protein allergens, designated as Sa-I and Sa-II, were identified from boiled shrimp (Penaeus indicus) extracts. Sa-I was isolated by ultrafiltration, Sephadex G-25, and diethylaminoethyl-Sephacel chromatography, whereas Sa-II, the major allergen, was purified by successive chromatography on diethylaminoethyl-Sephacel, Bio-Gel P-200, and Sepharose 4B columns. Sa-I, which was homogeneous by polyacrylamide gel electrophoresis (PAGE), elicited a single band on sodium dodecyl sulfate-PAGE corresponding to a molecular weight of 8.2 kd. Sa-II was also found to be homogeneous by PAGE, crossed immunoelectrophoresis, and immunoblotting. On sodium dodecyl sulfate-PAGE, it elicited a single band with a molecular weight of 34 kd. Sa-II was found to contain 301 amino acid residues and was particularly rich in glutamate/glutamine and aspartate/asparagine. Solid-phase radioimmunoassay-inhibition studies revealed that Sa-I and Sa-II share 54% of the allergenic epitopes, suggesting that Sa-I may be a fragment of Sa-II.SDS-PAGE, Sodium dodecyl sulfate-polyacrylamide gel electrophoresis; MW, Molecular weight; BSA, Bovine serum albumin; DEAE, Diethylaminoethyl; SPRIA, Solid-phase radioimmunoassay; CIE, Crossed immunoelectrophoresis .

Antimicrobial activity of highly stable silver nano particles embedded in agar-agar matrix as a thin film

Highly stable silver nanoparticles (Ag NPs) in agar-agar (Ag/agar) as inorganic-organic hybrid were obtained as free-standing film by in situ reduction of silver nitrate by ethanol. The antimicrobial activity of Ag/agar film on Escherichia coli (E. coil), Staphylococcus aureus (S. aureus), and Candida albicans (C albicans) was evaluated in a nutrient broth and also in saline solution. In particular, films were repeatedly tested for antimicrobial activity after recycling. UV-vis absorption and TEM studies were carried out on films at different stages and morphological studies on microbes were carried out by SEM. Results showed spherical Ag NPs of size 15-25 nm, having sharp surface plasmon resonance (SPR) band. The antimicrobial activity of Ag/agar film was found to be in the order, C. albicans > E. coil > S. aureus, and antimicrobial activity against C. albicans was almost maintained even after the third cycle. Whereas, in case of E. coil and S. aureus there was a sharp decline in antimicrobial activity after the second cycle. Agglomeration of Ag NPs in Ag/agar film on exposure to microbes was observed by TEM studies. Cytotoxic experiments carried out on HeLa cells showed a threshold Ag NPs concentration of 60 mu g/mL, much higher than the minimum inhibition concentration of Ag NPs (25.8 mu g/mL) for E. coli. The mechanical strength of the film determined by nanoindentation technique showed almost retention of the strength even after repeated cycle. (C) 2010 Elsevier Ltd. All rights reserved.

Almost Stable Matchings by Truncating the Gale–Shapley Algorithm

We show that the ratio of matched individuals to blocking pairs grows linearly with the number of propose–accept rounds executed by the Gale–Shapley algorithm for the stable marriage problem. Consequently, the participants can arrive at an almost stable matching even without full information about the problem instance; for each participant, knowing only its local neighbourhood is enough. In distributed-systems parlance, this means that if each person has only a constant number of acceptable partners, an almost stable matching emerges after a constant number of synchronous communication rounds. We apply our results to give a distributed (2 + ε)-approximation algorithm for maximum-weight matching in bicoloured graphs and a centralised randomised constant-time approximation scheme for estimating the size of a stable matching.

Vesicle and Stable Monolayer Formation from Simple ``Click'' Chemistry Adducts in Water

Click chemistry has been successfully extended into the field of molecular design of novel amphiphatic adducts. After their syntheses and characterizations, we have studied their aggregation properties in aqueous medium. Each of these adducts forms stable suspensions in water. These suspensions have been characterized by dynamic light scattering (DLS) studies and transmission electron microscopy (TEM). The presence of inner aqueous compartments in such aggregates has been demonstrated using dye (methylene blue) entrapment studies. These aggregates have been further characterized using X-ray diffraction (XRD), which indicates the existence of bilayer structures in them. Therefore, the resulting aggregates could be described as vesicles. The temperature-induced order-to-disorder transitions of the vesicular aggregates and the accompanying changes in their packing and hydration have been examined using high-sensitivity differential scanning calorimetry, fluorescence anisotropy, and generalized polarization measurements using appropriate membrane-soluble probe, 1,6-diphenylhexatriene, and Paldan, respectively. The findings of these studies are consistent with each other in terms of the apparent phase transition temperatures. Langmuir monolayer studies confirmed that these click adducts also form stable monolayers on buffered aqueous subphase at the air-water interface.

A β,β,β-trialkoxyethyllithium stable towards fragmentation: a carboxyl protected acetic acid dianion equivalent

The novel alkyllithium 1b is not only intriguingly stable towards fragmentation, but also a synthetically useful reagent, complementing current carboxylic ester enolate methodology. Its design is based on interesting mechanistic principles, and harnesses the known stability of the 2,4,10-trioxaadamantane framework.

High level stable expression of rat brain type IIA sodium channel ?-subunit in CHO cells

The neuronal sodium channels are responsible for the rising phase of action potential and are composed of three subunits, of which the alpha-subunit has been shown to be adequate for most of its functional properties. We have stably expressed the rat brain type IIA sodium channel alpha-subunit in CHO cell tine using a CMV promoter-based vector. The expression was confirmed by detecting a 6.5 kb RNA corresponding to sodium channel alpha-subunit using Northern hybridization. The cells stably expressing the alpha-subunit, yield isolated sodium currents of amplitudes greater than 4nA when studied in whole-cell configuration of the patch-clamp technique. The sodium currents are characterized by activation and inactivation properties similar to neuronal sodium channels, and are blocked by the voltage gated sodium channel blocker tetrodotoxin (TTX).

Adaptive optimal tuning of a general class of stable LTI systems with restricted inputs

The problem addressed is one of model reference adaptive control (MRAC) of asymptotically stable plants of unknown order with zeros located anywhere in the s-plane except at the origin. The reference model is also asymptotically stable and lacking zero(s) at s = 0. The control law is to be specified only in terms of the inputs to and outputs of the plant and the reference model. For inputs from a class of functions that approach a non-zero constant, the problem is formulated in an optimal control framework. By successive refinements of the sub-optimal laws proposed here, two schemes are finally design-ed. These schemes are characterized by boundedness, convergence and optimality. Simplicity and total time-domain implementation are the additional striking features. Simulations to demonstrate the efficacy of the control schemes are presented.

Natural Convection Heat Transfer From an Isothermal Vertical Surface to a Stable Thermally Stratified Fluid

Natural convection from an isothermal vertical surface to a thermally stratified fluid is studied numerically. A wide range of stratification levels is considered. It is shown that at high levels of ambient thermal stratification, a portion at the top of the plate absorbs heat, while a horizontal plume forms around a location where the plate temperature equals the ambient temperature. The plume is shown to be inherently unsteady, and its transient nature is investigated in detail. The effect of the temperature defect in striating the plume is discussed. Average Nusselt number data are presented for Pr = 6.0 and 0.7.

Stable carbon isotope ratios in Asian elephant collagen: implications for dietary studies

Stable carbon isotope ratios in bone collagen have been used in a variety of dietary studies in modern and fossil animals, including humans. Inherent in the stable isotope technique is the assumption that the isotopic signature is a reflection of the diet and is persistent in collagen because this is a relatively inert protein. Carbon isotope analyses of bones from a southern Indian population of Asian elephant (Elephas maximus), a long-lived mammal that alternates seasonally between a predominantly C3 (browse) and C4 (grass) plant diet, showed two patterns that have important implications for dietary interpretation based on isotopic studies. Relative to the quantity of the two plant types consumed on average, the ?13C signal in collagen indicated that more carbon was incorporated from C3 plants, possibly due to their higher protein contribution. There was a much greater variance in ?13C values of collagen in sub-adult (range -10.5� to-22.7�, variance=14.51) compared to adult animals (range -16.0� to -20.3�, variance=1.85) pointing to high collagen turnover rates and non-persistent isotopic signatures in younger, growing animals. It thus seems important to correct for any significant relative differences in nutritive value of food types and also consider the age of an animal before drawing definite conclusions about its diet from isotope ratios.

Highly Efficient and Thermally Stable Second-Order Nonlinear Optical Chromophores and Electrooptic Polymers

Organic polymeric electro-optic (E-O) materials have attracted significant attention because of their potential use as fast and efficient components of integrated photonic devices (1,2). However, the practical application of these materials in optical devices is somewhat limited by the stringent material requirements imposed by the device design, fabrication processes and operating environments. Among the various material requirements, the most notable ones are large electro-optic coefficients (r(33)) and high thermal stability (3). The design of poled polymeric materials with high electro-optic activity (r(33)) involves the optimization of the percent incorporation of efficient (large beta mu) second order nonlinear optical (NLO) chromophores into the polymer matrices and the effective creation of poling-induced non-centrosymmetric structures. The factors that affect the material stability are a) the inherent thermal stability of the NLO chromophores, b) the chemical stability of the NLO chromophores during the polymer processing conditions, and c) the long-term dipolar alignment stability at high temperatures. Although considerable progress has been made in achieving these properties (4), organic polymeric materials suitable for practical E-O device applications are yet to be developed. This chapter highlights some of our approaches in the optimization of molecular and material nonlinear optical and thermal properties.