Ultrasonic Degradation of Poly(acrylic acid)

The ultrasonic degradation of poly(acrylic acid), a water-soluble polymer, was studied in the presence of persulfates at different temperatures in binary solvent Mixtures of methanol and water. The degraded samples were analyzed by gel permeation chromatography for the time evolution of the molecular weight distributions. A continuous distribution kinetics model based on midpoint chain scission was developed, and the degradation rate coefficients were determined. The decline in the rate of degradation of poly(acrylic acid) with increasing temperature and with an increment in the methanol content in the binary solvent mixture of methanol and water was attributed to the increased vapor pressure of the solutions. The experimental data showed an augmentation of the degradation rate of the polymer with increasing oxidizing agent (persulfate) concentrations. Different concentrations of three persulfates-potassium persulfate, ammonium persulfate, and sodium persulfate-were used. It was found that the ratio of the polymer degradation rate coefficient to the dissociation rate constant of the persulfate was constant. This implies that the ultrasonic degradation rate of poly(acrylic acid) can be determined a priori in the presence of any initiator.

Oxidative and photooxidative degradation of poly(acrylic acid)

The oxidative degradation of poly(acrylic acid) (PAA), a water soluble polymer, was studied at various temperatures with different concentrations of persulfates, potassium persulfate (KPS), ammonium persulfate (APS) and sodium persulfate (SPS). The photodegradation of PAA was also examined with APS as oxidizer. The degraded samples were analyzed for the time evolution of molecular weight distribution by gel permeation chromatography. A theoretical model based on the continuous distribution kinetics was developed that accounted for the polymer degradation and the dissociation of persulfate. The rate coefficients for the oxidative and photooxidative degradation of PAA were determined from the parametric fit of the model with experimental data. The rate of degradation increased with increasing amount of persulfate in both oxidative and photooxidative degradation. The rate of degradation also increased with increasing temperature in the case of oxidative degradation.

Role of glutamine synthetase in citric acid fermentation byAspergillus niger

The activity of glutamine synthetase fromAspergillus niger was significantly lowered under conditions of citric acid fermentation. The intracellular pH of the organism as determined by bromophenol blue dye distribution and fluorescein diacetate uptake methods was relatively constant between 6•0–6•5, when the pH of the external medium was varied between 2•3–7•0.Aspergillus niger glutamine synthetase was rapidly inactivated under acidic pH conditions and Mn2+ ions partially protected the enzyme against this inactivation. Mn2+-dependent glutamine synthetase activity was higher at acidic pH (6•0) compared to Mg2+-supported activity. While the concentration of Mg2+ required to optimally activate glutamine synthetase at pH 6•0 was very high (≥ 50 mM), Mn2+ was effective at 4 mM. Higher concentrations of Mn2+ were inhibitory. The inhibition of both Mn2+ and Mg2+-dependent reactions by citrate, 2-oxoglutarate and ATP were probably due to their ability to chelate divalent ions rather than as regulatory molecules. This suggestion was supported by the observation that a metal ion chelator, EDTA also produced similar effects. Of the end-products of the pathway, only histidine, carbamyl phosphate, AMP and ADP inhibitedAspergillus niger glutamine synthetase. The inhibitions were more pronounced when Mn2+ was the metal ion activator and greater inhibition was observed at lower pH values. These results permit us to postulate that glutamine synthesis may be markedly inhibited when the fungus is grown under conditions suitable for citric acid production and this block may result in delinking carbon and nitrogen metabolism leading to acidogenesis.

Conformational analysis of D-pantothenic acid

The conformational analysis of d-pantothenic acid using classical semiempirical methods has been carried out. The pantothenic acid molecule can exist in the neutral form (I) or in the ionised form (II) with a deprotonated negatively charged carboxyl group. The neutral molecule as well as the anion is highly flexible and has an ensemble of several allowed conformations rather than one or two unique conformations. The distribution of allowed conformations indicate that the β-alanine as well as the pantoic acid part of the molecule prefers partially folded conformations. The conformation of the former is greatly affected by the ionisation state of the carboxyl group whereas that of the latter is not. Possibility of intramolecular hydrogen bonding in different allowed conformations has also been explored. A bifurcated hydrogen bond involving a carboxyl (or carboxylate) oxygen atom and a hydroxyl oxygen atom, as acceptors, and the amide nitrogen atom as the donor occurs frequently in both I and II. Amongst the two crystal structures containing pantothenic acid reported so far, the conformation of the molecule in l-lysine d-pantothenate lies in the allowed region and is stabilised by a bifurcated intramolecular hydrogen bond, whereas that in the calcium bromide salt falls in a disallowed region, presumably due to the requirement of tridentate metal coordination.

Identification of alpha- and beta-Hydroxy Acid Containing Cyclodepsipeptides in Natural Peptide Mixtures Using Negative Ion Mass Spectrometry

Natural peptide libraries often contain cyclodepsipeptides containing alpha or beta hydroxy residues. Extracts of fungal hyphae of Isaria yield a microheterogenous cyclodepsipeptide mixture in which two classes of molecules can be identified by mass spectral fragmentation of negative ions. In the case of isaridins, which contain an alpha-hydroxy residue and a beta-amino acid residue, a characteristic product ion corresponding to a neutral loss of 72 Da is obtained. hi addition, neutral loss of water followed by a 72 Da loss is also observed. Two distinct modes of fragmentation rationalize the observed product ion distribution. The neutral loss of 72 Da has also been obtained for a roseotoxin component, which is also an alpha-hydroxy residue containing cyclodepsipeptide. In the case of isariins, which contain a beta-hydroxy acid residue, ring opening and subsequent loss of the terminal residue as an unsaturated ketene fragment, rationalizes the observed product ion formation. Fragmentation of negative ions provide characteristic neutral losses, which are diagnostic of the presence of alpha-hydroxy or beta-hydroxy residues.

Disallowed Ramachandran Conformations of Amino Acid Residues in Protein Structures

An analysis of the nature and distribution of disallowed Ramachandran conformations of amino acid residues observed in high resolution protein crystal structures has been carried out. A data set consisting of 110 high resolution, non-homologous, protein crystal structures from the Brookhaven Protein Data Bank was examined. The data set consisted of a total of 18,708 non-Gly residues, which were characterized on the basis of their backbone dihedral angles (φ, ψ). Residues falling outside the defined “broad allowed limits” on the Ramachandran map were chosen and the reportedB-factor value of the α-carbon atom was used to further select well defined disallowed conformations. The conformations of the selected 66 disallowed residues clustered in distinct regions of the Ramachandran map indicating that specific φ, ψ angle distortions are preferred under compulsions imposed by local constraints. The distribution of various amino acid residues in the disallowed residue data set showed a predominance of small polar/charged residues, with bulky hydrophobic residues being infrequent. As a further check, for all the 66 cases non-hydrogen van der Waals short contacts in the protein structures were evaluated and compared with the ideal “Ala-dipeptide” constructed using disallowed dihedral angle (φ, ψ) values. The analysis reveals that short contacts are eliminated in most cases by local distortions of bond angles. An analysis of the conformation of the identified disallowed residues in related protein structures reveals instances of conservation of unusual stereochemistry.

Mass Spectrometry-Based Systems Approach for Identification of Inhibitors of Plasmodium falciparum Fatty Acid Synthase{triangledown}

The emergence of strains of Plasmodium falciparum resistant to the commonly used antimalarials warrants the development of new antimalarial agents. The discovery of type II fatty acid synthase (FAS) in Plasmodium distinct from the FAS in its human host (type I FAS) opened up new avenues for the development of novel antimalarials. The process of fatty acid synthesis takes place by iterative elongation of butyryl-acyl carrier protein (butyryl-ACP) by two carbon units, with the successive action of four enzymes constituting the elongation module of FAS until the desired acyl length is obtained. The study of the fatty acid synthesis machinery of the parasite inside the red blood cell culture has always been a challenging task. Here, we report the in vitro reconstitution of the elongation module of the FAS of malaria parasite involving all four enzymes, FabB/F (β-ketoacyl-ACP synthase), FabG (β-ketoacyl-ACP reductase), FabZ (β-ketoacyl-ACP dehydratase), and FabI (enoyl-ACP reductase), and its analysis by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS). That this in vitro systems approach completely mimics the in vivo machinery is confirmed by the distribution of acyl products. Using known inhibitors of the enzymes of the elongation module, cerulenin, triclosan, NAS-21/91, and (–)-catechin gallate, we demonstrate that accumulation of intermediates resulting from the inhibition of any of the enzymes can be unambiguously followed by MALDI-TOF MS. Thus, this work not only offers a powerful tool for easier and faster throughput screening of inhibitors but also allows for the study of the biochemical properties of the FAS pathway of the malaria parasite.

Mass Spectrometry-Based Systems Approach for Identification of Inhibitors of Plasmodium falciparum Fatty Acid Synthase{triangledown}

The emergence of strains of Plasmodium falciparum resistant to the commonly used antimalarials warrants the development of new antimalarial agents. The discovery of type II fatty acid synthase (FAS) in Plasmodium distinct from the FAS in its human host (type I FAS) opened up new avenues for the development of novel antimalarials. The process of fatty acid synthesis takes place by iterative elongation of butyryl-acyl carrier protein (butyryl-ACP) by two carbon units, with the successive action of four enzymes constituting the elongation module of FAS until the desired acyl length is obtained. The study of the fatty acid synthesis machinery of the parasite inside the red blood cell culture has always been a challenging task. Here, we report the in vitro reconstitution of the elongation module of the FAS of malaria parasite involving all four enzymes, FabB/F (β-ketoacyl-ACP synthase), FabG (β-ketoacyl-ACP reductase), FabZ (β-ketoacyl-ACP dehydratase), and FabI (enoyl-ACP reductase), and its analysis by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS). That this in vitro systems approach completely mimics the in vivo machinery is confirmed by the distribution of acyl products. Using known inhibitors of the enzymes of the elongation module, cerulenin, triclosan, NAS-21/91, and (–)-catechin gallate, we demonstrate that accumulation of intermediates resulting from the inhibition of any of the enzymes can be unambiguously followed by MALDI-TOF MS. Thus, this work not only offers a powerful tool for easier and faster throughput screening of inhibitors but also allows for the study of the biochemical properties of the FAS pathway of the malaria parasite.

Empirical torsional potential functions from protein structure data. Phi- and psi-potentials for non-glycyl amino acid residues.

The torsional potential functions Vt(phi) and Vt(psi) around single bonds N--C alpha and C alpha--C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (phi, psi)-plane with the value of Vtot(phi, psi), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in L-configuration, are Vt(phi) = 1.0 cos (phi + 60 degrees); Vt(psi) = 0.5 cos (psi + 60 degrees) - 1.0 cos (2 psi + 30 degrees) - 0.5 cos (3 psi + 30 degrees). The dipeptide energy maps Vtot(phi, psi) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line psi = 0 degrees. These functions derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

Empirical torsional potential functions from protiesn structure DATA Phi- and Psi-Potentials for Non-glycyl Amino Acid Residues

The torsional potential functions Vt(φ) and Vt(ψ) around single bonds N–Cα and Cα-C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (φ, ψ)-plane with the value of Vtot(φ, ψ), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in l-configuration, are Vt(φ) = – 1.0 cos (φ + 60°); Vt(ψ) = – 0.5 cos (ψ + 60°) – 1.0 cos (2ψ + 30°) – 0.5 cos (3ψ + 30°). The dipeptide energy maps Vtot(φ, ψ) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line ψ = 0°. These functions, derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

Analysis of the effects of amino-acid-sequence on the structure of proteins

The conformation of amino acid side chains as observed in well-determined structures of globular proteins has earlier been extensively investigated. In contrast, the structural features of the polypeptide backbone that result from the occurrence of specific amino acids along the polypeptide have not been analysed. In this article, we present the statistically significant features in the backbone geometry that appear to be a consequence of the occurrence of rotamers of different amino acid side chains by analysing 102 well-refined structures that form a random collection of proteins. It is found that the persistence of helical segments around each residue is influenced by the residue type. Several residues exert asymmetrical influence between the carboxyl and amino terminal polypeptide segments. The degree to which secondary structures depart from an average geometry also appears to depend on residue type. These departures are correlated to the corresponding Chou and Fasman parameters of amino acid residues. The frequency distribution of the side chain rotamers is influenced by polypeptide secondary structure. In turn, the rotamer conformation of side chain affects the extension of the secondary structure of the backbone. The strongest correlation is found between the occurrence of g+ conformation and helix propagation on the carboxyl side of many residues.

Electrooxidation of formic acid at platinum nanoclusters electrodeposited on PEDOT coated carbon paper electrode

Nanoclusters of Pt were electrochemically deposited on a conducting polymer, namely, poly(3,4-ethylenedioxythiophene) (PEDOT), which was also electrochemically deposited on carbon paper current collector. PEDOT facilitated uniform distribution of Pt nanoclusters, when compared with Pt electrodeposition on bare carbon paper substrate. Spectroscopy data indicated absence of any interaction between PEDOT and Pt. The electrochemically active surface area as measured from carbon monoxide adsorption followed by its oxidation was several times greater for Pt-PEDOT/C electrode in comparison with Pt/C electrode. The catalytic activity of Pt-PEDOT/C electrode for electrooxidation of formic acid was significantly greater than that of Pt/C electrode. Amperometry data suggested that the electrodes were stable for continuous oxidation of HCOOH.

Study of molecular structure and vibrational spectra of poly (beta,-1-malic acid) PMLA] using DFT approach

Poly (beta-L-malic acid) (PMLA) is a biodegradable polymer and it has various important applications in the biomedical field. In the present work the structural and spectral characteristics of PMLA have been studied by methods of infrared. Raman spectroscopy and quantum chemistry. Electrostatic potential surface, optimized geometry, harmonic vibrational frequencies, infrared intensities and activities of Raman scattering were calculated by density functional theory (DFT) using oligomeric approach employing B3LYP with complete relaxation in the potential energy surface using 6-311++G (d, p) basis set. Based on results, we have discussed the correlation between the vibrational modes and the structure of the PMLA. A complete analysis of the experimental infrared and Raman spectra has been reported on the basis of wavenumber of the vibrational bands and potential energy distribution. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The calculated infrared and the Raman spectra of the polymer based on DFT calculations show reasonable agreement with the experimental results. (c) 2012 Elsevier Ltd. All rights reserved.

Long-Term Sustained Release of Salicylic Acid from Cross-Linked Biodegradable Polyester Induces a Reduced Foreign Body Response in Mice

There has been a continuous surge toward developing new biopolymers that exhibit better in vivo biocompatibility properties in terms of demonstrating a reduced foreign body response (FBR). One approach to mitigate the undesired FBR is to develop an implant capable of releasing anti-inflammatory molecules in a sustained manner over a long time period. Implants causing inflammation are also more susceptible to infection. In this article, the in vivo biocompatibility of a novel, biodegradable salicylic acid releasing polyester (SAP) has been investigated by subcutaneous implantation in a mouse model. The tissue response to SAP was compared with that of a widely used biodegradable polymer, poly(lactic acid-co-glycolic acid) (PLGA), as a control over three time points: 2, 4, and 16 weeks postimplantation. A long-term in vitro study illustrates a continuous, linear (zero order) release of salicylic acid with a cumulative mass percent release rate of 7.34 x 10(-4) h(-1) over similar to 1.5-17 months. On the basis of physicochemical analysis, surface erosion for SAP and bulk erosion for PLGA have been confirmed as their dominant degradation modes in vivo. On the basis of the histomorphometrical analysis of inflammatory cell densities and collagen distribution as well as quantification of proinflammatory cytokine levels (TNF-alpha and IL-1 beta), a reduced foreign body response toward SAP with respect to that generated by PLGA has been unambiguously established. The favorable in vivo tissue response to SAP, as manifest from the uniform and well-vascularized encapsulation around the implant, is consistent with the decrease in inflammatory cell density and increase in angiogenesis with time. The above observations, together with the demonstration of long-term and sustained release of salicylic acid, establish the potential use of SAP for applications in improved matrices for tissue engineering and chronic wound healing.

A new load distribution strategy for linear network with communication delays

In this paper, we propose a new load distribution strategy called `send-and-receive' for scheduling divisible loads, in a linear network of processors with communication delay. This strategy is designed to optimally utilize the network resources and thereby minimizes the processing time of entire processing load. A closed-form expression for optimal size of load fractions and processing time are derived when the processing load originates at processor located in boundary and interior of the network. A condition on processor and link speed is also derived to ensure that the processors are continuously engaged in load distributions. This paper also presents a parallel implementation of `digital watermarking problem' on a personal computer-based Pentium Linear Network (PLN) topology. Experiments are carried out to study the performance of the proposed strategy and results are compared with other strategies found in literature.