Protein Structure and Function: Looking through the Network of Side-Chain Interactions

Network theory has become an excellent method of choice through which biological data are smoothly integrated to gain insights into complex biological problems. Understanding protein structure, folding, and function has been an important problem, which is being extensively investigated by the network approach. Since the sequence uniquely determines the structure, this review focuses on the networks of non-covalently connected amino acid side chains in proteins. Questions in structural biology are addressed within the framework of such a formalism. While general applications are mentioned in this review, challenging problems which have demanded the attention of scientific community for a long time, such as allostery and protein folding, are considered in greater detail. Our aim has been to explore these important problems through the eyes of networks. Various methods of constructing protein structure networks (PSN) are consolidated. They include the methods based on geometry, edges weighted by different schemes, and also bipartite network of protein-nucleic acid complexes. A number of network metrics that elegantly capture the general features as well as specific features related to phenomena, such as allostery and protein model validation, are described. Additionally, an integration of network theory with ensembles of equilibrium structures of a single protein or that of a large number of structures from the data bank has been presented to perceive complex phenomena from network perspective. Finally, we discuss briefly the capabilities, limitations, and the scope for further explorations of protein structure networks.

The design of an agent for modelling supply chain network dynamics

A useful insight into managerial decision making can be found from simulation of business systems, but existing work on simulation of supply chain behaviour has largely considered non-competitive chains. Where competitive agents have been examined, they have generally had a simple structure and been used for fundamental examination of stability and equilibria rather than providing practical guidance to managers. In this paper, a new agent for the study of competitive supply chain network dynamics is proposed. The novel features of the agent include the ability to select between competing vendors, distribute orders preferentially among many customers, manage production and inventory, and determine price based on competitive behaviour. The structure of the agent is related to existing business models and sufficient details are provided to allow implementation. The agent is tested to demonstrate that it recreates the main results of the existing modelling and management literature on supply chain dynamics. A brief exploration of competitive dynamics is given to confirm that the proposed agent can respond to competition. The results demonstrate that overall profitability for a supply chain network is maximised when businesses operate collectively. It is possible for an individual business to achieve higher profits by adopting a more competitive stance, but the consequence of this is that the overall profitability of the network is reduced. The agent will be of use for a broad range of studies on the long-run effect of management decisions on their network of suppliers and customers.

Synthesis and potency of long end-associative polymers for mist control

Long linear polymers that are end-functionalized with associative groups were studied as additives to hydrocarbon fluids to mitigate the fire hazard associated with the presence of mist in a crash scenario. These polymers were molecularly designed to overcome both the shear-degradation of long polymer chains in turbulent flows, and the chain collapse induced by the random placement of associative groups along polymer backbones. Architectures of associative groups on the polymer chain ends that were tested included clusters of self-associative carboxyl groups and pairs of hetero-complementary associative units.

Linear polymers with clusters of discrete numbers of carboxyl groups on their chain ends were investigated first: an innovative synthetic strategy was devised to achieve unprecedented backbone lengths and precise control of the number of carboxyl groups on chain ends (N). We found that a very narrow range of N allows the co-existence of sufficient end-association strength and polymer solubility in apolar media. Subsequent steady-flow rheological study on solution behavior of such soluble polymers in apolar media revealed that the end-association of very long chains in apolar media leads to the formation of flower-like micelles interconnected by bridging chains, which trap significant fraction of polymer chains into looped structures with low contribution to mist-control. The efficacy of very long 1,4-polybutadiene chains end-functionalized with clusters of four carboxyl groups as mist-control additives for jet fuel was further tested. In addition to being shear-resistant, the polymer was found capable of providing fire-protection to jet fuel at concentrations as low as 0.3wt%. We also found that this polymer has excellent solubility in jet fuel over a wide range of temperature (-30 to +70°C) and negligible interference with dewatering of jet fuel. It does not cause an adverse increase in viscosity at concentrations where mist-control efficacy exists.

Four pairs of hetero-complementary associative end-groups of varying strengths were subsequently investigated, in the hopes of achieving supramolecular aggregates with both mist-control ability and better utilization of polymer building blocks. Rheological study of solutions of the corresponding complementary associative polymer pairs in apolar media revealed the strength of complementary end-association required to achieve supramolecular aggregates capable of modulating rheological properties of the solution.

Both self-associating and complementary associating polymers have therefore been found to resist shear degradation. The successful strategy of building soluble, end-associative polymers with either self-associative or complementary associative groups will guide the next generation of mist-control technology.

Novel catalysis of TiO2 for the catalytic alcohols synthesis from CO and H2O

Direct synthesis of alcohols from CO and H2O was investigated using TiO2 catalyst. MeOH (about 24 mg g(-1) h(-1)) and EtOH (about 8 mg g(-1) h(-1)) could be produced under the reaction conditions of T= 573 K, P= 0.5 MPa, CO flow rate of 30 ml min(-1) and CO/H2O = 3/2 during the period of 12 to 44 h time-on-stream. Compared with PbO, TiO2 could preserve stable catalytic activity during a long time of reaction. For the same catalyst TiO2, the reaction performance of alkali carbonates increased with their solubility (K2CO3>Na2CO3>Li2CO3). The corresponding catalytic activity was found to increase with the alkalescence of solvent. The formation mechanism of alcohols was proposed as well. (C) 2004 Elsevier B.V. All rights reserved.

Microphase Separation of Mixed Polymer Brushes: Dependence of the Morphology on Grafting Density, Composition, Chain-Length Asymmetry, Solvent Quality, and Selectivity

Microphase separation of binary mixed A/B polymer brushes exposed to different solvents is studied using Single-Chain-in-Mean-Field simulations. Effects of solvent quality and selectivity, grafting density, composition, and chain-length asymmetry are systematically investigated, and diagrams of morphologies in various solvents are constructed as a function of grafting density and composition or chain-length asymmetry. The structure of the microphase segregated morphologies lacks long-range periodic order, and it is analyzed quantitatively Using Minkowski measures.

Synthesis and chain-length dependent properties of monodisperse oligo(9,9-di-n-octylfluorene-2,7-vinylene)s

A series of monodisperse oligo(9,9-di-n-octylfluorene-2,7-vinylene)s (OFVs) with fluorene units up to 11 has been synthesized following a divergent approach. Chain length was found to affect not only photophysical properties but also thermal properties. Absorption and photoluminescence spectra are red-shifted with increasing chain length. The effective conjugated length has been extrapolated to be as long as 19 fluorene vinylene units, indicative of a well-conjugated system. With the number of fluorene units > 5, the oligomers exhibit nematic mesomorphism. Glass transition temperature (T-g) and clearing point temperature (T-c) increase with increasing molecular length and with those of OFV11 up to 71 and 230 degrees C, respectively. The oligomers can form uniform films by solution casting for fabrication of light-emitting diodes. With a device structure of ITO/ PEDOT:PSS/OFV11/Ca/Al, a current efficiency of 0.8 cd.A(-1) at a brightness of 1300 cd.m(-2) along with a maximum brightness of 2690 cd.m(-2) have been realized. This performance is notably superior to that of the corresponding polymer.

Ordering-induced micro-bands in thin films of a main-chain liquid crystalline chloro-poly(aryl ether ketone)

Micro-banded textures developed from thin films of a main-chain thermotropic liquid crystalline chloro-poly(aryl ether ketone) in the melt were investigated using transmission electron microscopy (TEM). selective area electron diffraction, and atomic force microscopy techniques. The micro-banded textures were formed in the copolymer thin films after annealing at temperatures between 320 and 330degreesC, where a highly ordered smectic crystalline phase is formed without mechanical shearing. The micro-banded textures displayed a sinusoidal-like periodicity with a spacing of 150 nm and an amplitude of 2 rim. The long axis of the banded texture was parallel to the b-axis of an orthorhombic unit cell. In the convex regions, the molecular chains exhibited a homeotropic alignment, i.e. the chain direction was parallel to the film normal. In the concave re-ions, the molecular chains possessed a tilted alignment. In addition to the effects of annealing temperatures and times, the thickness of the film played a vital role in the formation of the banded texture. A possible formation mechanism of this banded texture vas also suggested and discussed. It was suggested that the micro-bands were formed during cooling.

Helical single-lamellar crystals thermotropically formed in a synthetic nonracemic chiral main-chain polyester

Phase structures and transformation mechanisms of nonracemic chiral biological and synthetic polymers are fundamentally important topics in understanding their macroscopic responses in different environments. It has been known for many years that helical structures and morphologies can exist in low-ordered chiral liquid crystalline (LC) phases. However, when the chiral liquid crystals form highly ordered smectic liquid crystal phases, the helical morphology is suppressed due to the crystallization process. A double-twisted morphology has been observed in many liquid crystalline biopolymers such as dinoflaggellate chromosomes (in Prorocentrum micans) in an in vivo arrangement. Helical crystals grown from solution have been reported in the case of Bombyx mori silk fibroin crystals having the beta modification. This study describes a synthetic nonracemic chiral main-chain LC polyester that is able to thermotropically form helical single lamellar crystals. Flat single lamellar crystals can also be observed under the same crystallization condition. Moreover, flat and helical lamellae can coexist in one single lamellar crystal, within which one form can smoothly transform to the other. Both of these crystals possess the same structure, although translational symmetry is broken in the helical crystals. The polymer chain folding direction in both flat and helical lamellar crystals is determined to be identical, and it is always along the long axis of the lamellae. This finding provides an opportunity to study the chirality effect on phase structure, morphology, and transformation in condensed states of chiral materials. [S0163-1829(99)01042-5].

NMR investigation of phenolphthalein polyether ether ketone .1. The chain structure and assignments of H-1, C-13 NMR lines of PEK-C

Amorphous samples of polyether ketone with cardo(PEK-C) have been studied in the solution state by C-13, H-1 high-resolution NMR, The H-1 and C-13 1D NMR spectra were assigned using two dimensional chemical shift correlated spectroscopy, 2D homonuclear correlated(COSY) and heteronuclear correlated (HETCOR) spectroscopy present important information. In this work, the structural units of PEK-C was determined by NMR. For some peaks, these assignments are confirmed by two dimensional long-range heteronuclear correlation experiments, A little modification is made on the original C-13 peak assignments for the main chain, The symmetry and the isotacticity of the chain structure for PEK-C are obvious on NMR data.

INVESTIGATION OF ELECTRIC DICHROISM OF CETYLPYRIDINIUM BROMIDE BY SPECTROELECTROCHEMISTRY WITH A LONG OPTICAL-PATH LENGTH THIN-LAYER CELL

In this paper, the electric dichroism of cetylpyridinium bromide (CPB) has been found and studied by spectroelectrochemistry with a long optical path length thin-layer cell (LOPTLC) for the first time. The CPB molecule with a long carbon chain and a polar pyridinium ring is anisotropic in molecular configuration or in polarizability. In the electric field of a thin-layer cell, the CPB molecule reorientates along the direction of the electric field and exhibits electric dichroism, which results in the increase of absorbance of CPB in the UV-vis range. By use of in situ measurement of spectroelectrochemistry, the order parameters of long molecular axis (S = 0.845) and short molecular axis (D = 0.155) and the angle between the long axis direction of the CPB molecule and the direction normal to the electrode surface (theta = 18-degrees 44') have been determined. These data were used to describe the state of arrangement of the molecules in the solution. The reorientation of CPB molecules is the result of the interaction between the anisotropic molecules and electric field. The effects of the concentration of CPB and of the applied electric field on the electric dichroism have been investigated.

MOLECULAR CHAIN STRUCTURE OF DOPED POLYANILINE

The chain structure of polyaniline doped with HCl or CF_3COOH has been investigated by FTIR, solid state ~(13)CNMR, resonance laser Raman and UV-VIS spectroscopies. The results show that during the protonic acid doping, a partial redox reaction takes place between the quinone-diimine and benzene-diamine units and it leads to a long conjugate system with a certain charge distribution.

Improving cold chain technologies through the use of phase change material

Gemstone Team FRESH

Mechanisms of long-term decline in size of lesser sandeels in the North Sea explored using a growth and phenology model

The lesser sandeel Ammodytes marinus is a key species in the North Sea ecosystem, transferring energy from planktonic producers to top predators. Previous studies have shown a long-term decline in the size of 0-group sandeels in the western North Sea, but they were unable to pinpoint the mechanism (later hatching, slower growth or changes in size-dependent mortality) or cause. To investigate the first 2 possibilities we combined 2 independent time series of sandeel size, namely data from chick-feeding Atlantic puffins Fratercula arctica and from the Continuous Plankton Recorder (CPR), in a novel statistical model implemented using Markov Chain Monte Carlo (MCMC). The model estimated annual mean length on 1 July, as well as hatching date and growth rate for sandeels from 1973 to 2006. Mean length-at-date declined by 22% over this period, corresponding to a 60% decrease in energy content, with a sharper decline since 2002. Up to the mid-1990s, the decline was associated with a trend towards later hatching. Subsequently, hatching became earlier again, and the continued trend towards smaller size appears to have been driven by lower growth rates, particularly in the most recent years, although we could not rule out changes in size-dependent mortality. Our findings point to major changes in key aspects of sandeel life history, which we consider are most likely due to direct and indirect temperature-related changes over a range of biotic factors, including the seasonal distribution of copepods and intra- and inter-specific competition with planktivorous fish. The results have implications both for the many predators of sandeels and for age and size of maturation in this aggregation of North Sea sandeels.

Evaluation of the antidiabetic activity of DPP IV resistant N-terminally modified versus mid-chain acylated analogues of glucose-dependent insulinotropic polypeptide

Glucose dependent insulinotropic polypeptide (GIP) is a gastrointestinal hormone with therapeutic potential for type 2 diabetes due to its insulin-releasing and antihyperglycaemic actions. However, development of GIP-based therapies is limited by N-terminal degradation by DPP IV resulting in a very short circulating half-life. Numerous GIP analogues have now been generated exhibiting DPP IV resistance and extended bioactivity profiles. In this study, we report a direct comparison of the long-term antidiabetic actions of three such GIP molecules, N-AcGIP, GIP(LyS(37)PAL) and N-AcGIP(LyS(37)PAL) in obese diabetic (ob/ob) mice. An extended duration of action of each GIP analogue was demonstrated prior to examining the effects of once daily injections (25 nmol kg(-1) body weight) over a 14-day period. Administration of either N-AcGIP, GIP(LyS(37)PAL) or N-AcGIP(LyS37PAL) significantly decreased non-fasting plasma glucose and improved glucose tolerance compared to saline treated controls. All three analogues significantly enhanced glucose and nutrient-induced insulin release, and improved insulin sensitivity. The metabolic and insulin secretory responses to native GIP were also enhanced in 14-day analogue treated mice, revealing no evidence of GIP-receptor desensitization. These effects were accompanied by significantly enhanced pancreatic insulin following N-AcGIP(Lys(37)PAL) and increased islet number and islet size in all three groups. Body weight, food intake and circulating glucagon were unchanged. These data demonstrate the therapeutic potential of once daily injection of enzyme resistant GIP analogues and indicate that N-AcGIP is equally as effective as related palmitate derivatised analogues of GIP. (c) 2006 Elsevier Inc. All rights reserved.

Volumetric properties and enthalpies of solution of alcohols CkH2k+1OH (k = 1, 2, 6) in 1-methyl-3-alkylimidazolium bis(trifluoromethylsulfonyl)imide {[C1CnIm][NTf2] n = 2, 4, 6, 8, 10} ionic liquids

We present a study on the effect of the alkyl chain length of the imidazolium ring in 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquids, [C1CnIm][NTf2] (n = 2 to 10), on the mixing properties of (ionic liquid + alcohol) mixtures (enthalpy and volume). We have measured small excess molar volumes with highly asymmetric curves as a function of mole fraction composition (S-shape) with more negative values in the alcohol-rich regions. The excess molar volumes increase with the increase of the alkyl-chain length of the imidazolium cation of the ionic liquid. The values of the partial molar excess enthalpy and the enthalpy of mixing are positive and, for the case of methanol, do not vary monotonously with the length of the alkyl side-chain of the cation on the ionic liquid – increasing from n = 2 to 6 and then decreasing from n = 8. This non-monotonous variation is explained by a more favourable interaction of methanol with the cation head group of the ionic liquid for alkyl chains longer than eight carbon atoms. It is also observed that the mixing is less favourable for the smaller alcohols, the enthalpy of mixing decreasing to less positive values as the alkyl chain of the alcohol increases. Based on the data from this work and on the knowledge of the vapour pressure of {[C1CnIm][NTf2] + alcohol} binary mixtures at T = 298 K reported in the literature, the excess Gibbs free energy, excess enthalpy and excess entropy could be then calculated and it was observed that these mixtures behave like the ones constituted by a non-associating and a non-polar component, with its solution behaviour being determined by the enthalpy.