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PubMed1996

Acid and base hydrolysis of lipid A from Enterobacter agglomerans as monitored by electrospray ionization mass spectrometry: pertinence to detoxification mechanisms.

Lipopolysaccharides (LPS), which are endotoxins found in the cell wall of Gram-negative bacteria, are common components of organic dusts that cause or contribute to symptoms associated with organic dust diseases. The lipid A subgroup within LPS is believed to be responsible for the toxicity. Acid and base treatments, which can be effective detoxification methods, were performed on lipid A from Enterobacter agglomerans (EA), a bacterium commonly found in field cotton. Negative-ion electrospray ionization mass spectrometry was employed to characterize the post-treatment structural changes to lipid A. Acid treatment (1% acetic acid, 100 degrees C) hydrolyzed the ester side-chains of lipid A. It was found that the ester-linked palmitoyl group was the most labile to acid hydrolysis. Hydrolysis of the palmitoyl moiety conformed to pseudo-first-order chemical reaction kinetics with a rate constant for decomposition of heptacyl-lipid A from Enterobacter agglomerans of approximately 3.3 x 10(-3) min-1. An order of lability of lipid A acyl side-chains to acid hydrolysis was also deduced: R4' (palmitoyl) > R1' (myristoyl or hydroxymyristoyl) > R3 (hydroxymyristoyl at position 3) > R1 (oxymyristoyl group at position 3') > R2' (lauroyl). Base treatment (0.05 M NaOH in 95% EtOH, 65 degrees C) was shown to be more effective at cleaving ester-linked side-chains. In addition, mass spectral evidence suggests that opening of the pyranose rings of the disaccharide backbone of lipid A and/or removal of the phosphoryl groups may be occurring during base treatment. This study sheds light on mechanistic aspects of treatment procedures leading to the detoxification of endotoxins.

Acids↗

PubMed1996

Collagen-based structures containing the peptoid residue N-isobutylglycine (Nleu): synthesis and biophysical studies of Gly-Pro-Nleu sequences by circular dichroism, ultraviolet absorbance, and optical rotation.

A peptoid residue N-isobutylglycine (Nleu) was introduced as a proline surrogate in collagen-like triple helical structures. A series of single chain and template-assembled collagen-based peptide-peptoid structures composed of Gly-Pro-Nleu sequences were prepared by solid-phase segment condensation methods. Both a synthetic route in solution and a solid phase method were employed to couple the KTA (cis,cis-1,3,5-trimethylcyclohexane-1,3,5-tricarboxylic acid, also known as the Kemp triacid) based template, KTA-(Gly-OH)3, to peptide-peptoid chains. Biophysical studies using CD, uv absorbance, and optical rotation measurements demonstrated that these compounds form triple-helical structures when the chains are longer than critical lengths. Results from melting curve measurements indicated that the Gly-Pro-Nleu sequence is comparable to the Gly-Pro-Pro sequence in stabilizing a triple-helical conformation. The KTA-based template stabilized triple-helical structures as can be seen by the increased melting temperatures as compared to equivalent single chain molecules. In addition, the template reduced the minimum chain length necessary to form a triple helix from six to only three trimer repeats.

Biophysical Phenomena↗

PubMed2000

Hydroxyl group interactions in polysaccharides: a deuterium-induced differential isotope shift 13C-NMR investigation.

The secondary isotope shift in (13)C-nmr spectra in water was used to obtain information on the interactions of hydroxyl groups with their environment in polysaccharides. Specifically, the possibility of detecting the preference of intramolecular hydrogen bonding with respect to solvation was investigated. Different aliphatic alcohols were studied in both protic and aprotic solvents in order to obtain reference systems. The polysaccharides investigated were selected so as to include both different types of glycosidic linkages and different conformational properties of the polymeric chain. In addition to polysaccharides, beta-cyclodextrin and inulin were also investigated. The experiments demonstrated that isotope shift data can advantageously contribute to the understanding of the conformational properties of polysaccharides and in particular, in setting up of constraints in molecular modeling calculations.

Alcohols↗

PubMed1999

Influence of Perfluoroarene-Arene Interactions on the Phase Behavior of Liquid Crystalline and Polymeric Materials.

A stabilization of the liquid-crystalline mesophase and thus an enlarged temperature range of the mesogenic phase is achieved by adding perfluorotriphenylene to a chiral liquid-crystalline triphenylene. This mesophase is based on 1:1 perfluoroarene-arene interactions (see picture). In a polymer with triphenylenes as mesogens in the side chains, the addition of perfluorotriphenylene led to crystallization.

Journal Article↗

PubMed1999

Nomenclature of immunoglobulin A and other proteins of the mucosal immune system. IUIS/WHO Subcommittee on IgA Nomenclature.

The predominant immunoglobulin found in exocrine secretions of humans and most other mammals is secretory IgA, a polymeric form of IgA containing an additional glycoprotein chain designated "secretory component." In this article recommended abbreviations are proposed for the following forms of human IgA and other proteins of related interest: secretory IgA, secretory IgM, secretory component, polymeric immunoglobulin receptor, polymeric IgA, monomeric IgA, IgA subclass 1, IgA subclass 2, A2 allotype marker 1, and A2 allotype marker 2.

Humans↗

PubMed1999

Possible association of fibromyalgia with a polymorphism in the serotonin transporter gene regulatory region.

OBJECTIVE: To analyze the genotypes of the promoter region of the serotonin transporter gene (5-HTT) in patients with fibromyalgia (FM). METHODS: Genomic DNA from 62 patients meeting the American College of Rheumatology 1990 criteria for FM and 110 healthy controls was analyzed by polymerase chain reaction. Additionally, the psychopathologic state of 52 of the FM patients was evaluated using the Beck Depression Inventory (BDI) and the Symptom Checklist-90-Revised (SCL-90-R). RESULTS: The 5-HTTLPR genotypes in FM patients versus controls were distributed as follows: L/L 27% versus 34%, L/S 42% versus 50%, and S/S 31% versus 16%. FM patients with the S/S genotype had higher mean scores on the BDI and the SCL-90-R compared with those in the L/L and L/S groups. CONCLUSION: A higher frequency of the S/S genotype of 5-HTT was found in FM patients compared with healthy controls. The S/S subgroup exhibited higher mean levels of depression and psychological distress. These results support the notion of altered serotonin metabolism in at least a subgroup of patients with FM.

Adult↗

PubMed1993

[Antimycobacterial 1-phenyl-1-alkylaminoalkanes].

Synthesis and testing for antimycobacterial properties (M. tuberculosis H 37 Ra, Middlebrook-7H9-broth) of 1-phenyl-1-alkylaminoalkanes, which differ from antimycobacterial N-alkylbenzylamines by an additional alkyl chain in alpha-position, is described. By variation of both alkyl chains and introduction of one or two Cl-substituents in the aromatic ring the activity increases up to an optimum within the homologous series. Overstepping optimal lipophilicity or ramification of the alkyl chains decrease activity.

Antitubercular Agents↗

PubMed2005

Adsorption of poly(ethylene glycol)-modified ribonuclease A to a poly(lactide-co-glycolide) surface.

Protein adsorption is a source of variability in the release profiles of therapeutic proteins from biodegradable microspheres. We employ optical reflectometry and total internal reflection fluorescence to explore the extent and kinetics of ribonuclease A (RNase A) adsorption to spin-cast films of poly(lactide-co-glycolide) (PLG) and, in particular, to determine how covalent grafting of polyethylene glycol (PEG) to RNase A affects adsorption. Adsorption kinetics on PLG surfaces are surface-limited for RNase A but transport-limited for unconjugated PEG homopolymers and for PEG-modified RNase A, indicating that PEG anchors the conjugates to the surface during the transport-limited regime. PEG modification of RNase A decreases the total number of adsorbed molecules per unit area but increases the areal surface coverage because the grafted PEG chains exclude additional surface area. Total internal reflection fluorescence-based exchange measurements show that there is no exchange between adsorbed and solution-phase protein molecules. This indicates an unusually tenacious adsorption. Streaming current measurements indicate that the zeta potential of the PLG surface becomes increasingly negative as the film is exposed to water for several weeks, as expected. Aging of the PLG surface results in increased adsorption of unmodified RNase A but decreased adsorption of unconjugated PEG homopolymers and of PEG-RNase A conjugates, relative to the extent of adsorption on freshly prepared PLG surfaces. Adsorption results correlate well with an increase in the rate, total extent and preservation of bioactivity of RNase A released from PLG microspheres for the PEG-modified version of RNase A.

Adsorption↗

PubMed1989

Thermospray mass spectroscopy/high performance liquid chromatographic identification of the metabolites formed from arteether using a rat liver microsome preparation.

Thermospray LC/MS methods with internal standardization were developed for the quantification of the antimalarial arteether and six of its metabolites at the 1-10 micrograms/ml level in liver microsome preparations without the use of solvent extraction. The thermospray mass spectra of arteether and most of its metabolites exhibited strong [M + NH4]+ and [M - OR]+ peaks arising from the molecular ion adduct and the loss of the alkoxy or hydroxy group of the side chain. In addition to the six metabolites for which authentic reference standards were available, three additional metabolites were detected. The major metabolites of arteether were found to be dihydroartemisinin, deoxydihydroartemisinin, 3-hydroxydeoxydihydroartemisinin, two isomers of hydroxyarteether, and 3-hydroxydeoxyarteether. Deoxyartheether was not found at significant concentrations in the microsome preparation.

Animals↗

PubMed2003

Mechanism of hydroxyl radical-induced breakdown of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-d).

Oxidative transformations by the hydroxyl radical are significant in advanced oxidation processes for the breakdown of organic pollutants, yet mechanistic details of the reactions are lacking. A combination of experimental and computational methods has been employed in this study to elucidate the reactivity of the hydroxyl radical with the widely used herbicide 2,4-D (2,4-dichlorophenoxyacetic acid). The experimental data on the reactivity of the hydroxyl radical in the degradation of the herbicide 2,4-D were obtained from gamma-radiolysis experiments with both (18)O-labeled and unlabeled water. These were complemented by computational studies of the (.)OH attack on 2,4-D and 2,4-DCP (2,4-dichlorophenol) in the gas phase and in solution. These studies firmly established the kinetically controlled attack ipso to the ether functionality as the main reaction pathway of (.)OH and 2,4-D, followed by homolytic elimination of the ether side chain. In addition, the majority of the early intermediates in the reaction between the hydroxyl radical and 2,4-DCP, the major intermediate, were identified experimentally. While the hydroxyl radical attacks 2,4-D by (.)OH-addition/elimination on the aromatic ring, the oxidative breakdown of 2,4-DCP occurs through (.)OH addition followed by either elimination of chlorine or formation of the ensuing dichlorophenoxyl radical.

2,4-Dichlorophenoxyacetic Acid↗

PubMed2004

Odd-even chain length-dependent order in pH-switchable self-assembled layers.

The reversible self-assembly of a series of bipolar amphiphiles, alpha,omega-bis(3- or 4-amidinophenoxy)alkanes (chain length n = 5-12), on mercaptoalkanoic acid-functionalized gold surfaces (chain length n = 10, 11, 14, 15) has been studied by in-situ ellipsometry, IR reflection absorption spectroscopy (IRAS), and atomic force microscopy (AFM). The layer order, amphiphile orientation, and tendency to form bilayers depends on the position of the amidine substituent, the alkyl chain length of both the amidine amphiphile and the underlying acid self-assembled monolayer (SAM), and whether the amidine alkyl chain contained an even or odd number of methylene groups. Thus, para-substituted bisbenzamidines containing more than six methylene groups (n>6) and with an odd number (n = 7, 9, 11) tended to form bilayered structures, whereas those containing an even number formed monolayers when adsorbed on SAMs of the long-chain acids (n = 14, 15). This behavior also correlated with the average tilt angle of the benzene moieties of the amphiphiles, as estimated by IRAS. The odd-numbered chains gave lower tilt angles than the even-numbered ones, and a possible model that accounts for these results is proposed. IRAS also revealed a higher order of the odd-numbered chains and an increasing hydrogen-bonding contribution with increasing chain length. Additional evidence for the proposed bilayered assemblies and their reversibility was obtained by AFM. Images obtained from the assembly of decamidine on a SAM of mercaptohexadecanoic acid in a pH 9 borate buffer revealed domains of similar size to that of the underlying acid SAM (20-30 nm), but less densely packed. By acidifying the solution, the second layer was destabilized and a very smooth layer with few defects appeared. Further acidification to pH 3 also destabilized the first layer.

Journal Article↗

PubMed1979

Differences in the expression of histocompatibility antigens on mouse lymphocytes and tumor cells: immunochemical studies.

Immunochemical studies have shown that labeled, detergent-solubilized extracts of SL2 (H-2d) lymphoma cells contain components reactive with several anti-H-2 alloantisera of restricted specificity. Anti-H-2k and anti-H-2ja as well as anti-H-2d sera precipitated labeled polypeptides of a molecular weight similar to that of H-2 heavy chains. In addition, all antisera tested precipitated a component of 70000 daltons molecular weight, which is antigenically related to gp 69/71 of Friend murine leukemia virus. Reactions with antisera directed against haplotypes other than H-2d could be blocked by addition of unlabeled, detergent-solubilized extracts of H-2d lymphocytes, or by H-2 antigens against which the antiserum was directed. Sequential immunoprecipitations initially using antisera against the K, D, or L region gene products to remove individual known H-2d antigens have made possible the identification of some molecules responsible for these reactions. The results show that antisera against haplotypes other than H-2d which react with SL2 cells, cross-react with normal H-2d antigens. Quantitative absortion of these antisera with intact or solubilized cells has shown that lymphocytes and tumor cells differ in their expression of some H-2 determinants. The antibodies bind only weakly to intact H-2d lymphocytes, but strongly to the corresponding detergent-solubilized antigens. These results do not, therefore, support the derepression hypothesis put forward earlier.

Animals↗

PubMed1990

Microheterogeneity of human interleukin 6 synthesized by transfected NIH/3T3 cells: comparison with human monocytes, fibroblasts and endothelial cells.

A cDNA containing the entire coding region of human interleukin 6 (IL 6) was stably expressed in murine NIH/3T3 fibroblasts using a bovine papilloma virus-based expression vector with a metallothionein promoter. Expression of IL 6 in transfected cells was highly inducible by heavy metals like cadmium as measured at mRNA and protein levels. Cadmium-stimulated transfected NIH/3T3 cells synthesized and exported biologically active IL 6 (1.7 x 10(4) U/10(6) cells/24 h). IL 6 from the culture medium of transfected NIH/3T3 cells exhibited at least eight bands on Western blots after sodium dodecyl sulfate-polyacrylamide gel electrophoresis, indicating that human IL 6 expressed in NIH/3T3 cells shows a complex glycosylation pattern. Using glycosidases and the N-glycosylation inhibitor tunicamycin it was possible to discriminate between five species carrying N-linked carbohydrate side chains and two species carrying only O-linked side chains. In addition, a substantial amount of unglycosylated IL 5 was observed. IL 6 from transfected NIH/3T3 cells differed markedly in its glycosylation pattern from those of stimulated human monocytes, fibroblasts and endothelial cells.

Animals↗

PubMed2005

Hydrodynamic radius ladders of proteins.

We introduce hydrodynamic radius ladders of proteins as a new tool to isolate and measure the role of hydrodynamic size on transport properties of proteins. Radius ladders are collections of derivatives of a protein that differ incrementally in number of polyethylene glycol (PEG) chains grafted to their surface. The addition of these chains causes the hydrodynamic size of the protein to increase. Capillary electrophoresis (CE) separates these derivatives into individual peaks or "rungs" of a ladder composed of proteins that have the same number of PEG chains, and provides a way to measure the values of hydrodynamic radius of proteins that constitute the rungs of the ladder. We demonstrate the utility of this approach by measuring the partitioning of radius ladders into polymer hydrogels. The combination of radius ladders and CE produces a large amount of internally consistent data on hydrodynamic size. This technique will have applicability to the study of the role of hydrodynamic size on transport.

Electrophoresis, Capillary↗

PubMed2005

Characterisation of poly(N-isopropylacrylamide) by asymmetrical flow field-flow fractionation, dynamic light scattering, and size exclusion chromatography.

Asymmetrical flow field-flow fractionation (AsFIFFF) was used to determine the hydrodynamic particle sizes, molar masses, and phase transition behaviour of various poly(N-isopropylacrylamide) (PNIPAM) samples synthesised by reversible addition--fragmentation chain transfer (RAFT) and conventional free radical polymerisation processes. The results were compared with corresponding data obtained by dynamic light scattering (DLS) and size exclusion chromatography (SEC). Agreement between the three methods was good except at higher molar masses, where the molar mass averages obtained by SEC were much lower than those obtained by AsFIFFF and light scattering. The aggregation of the polymers, which are thermally sensitive, was studied by DLS and AsFIFFF at various temperatures. In deionised water there was an abrupt change in the particle size due to phase separation at approximately equal to 32-35 degrees C. The critical temperatures determined by AsFIFFF were 3-5 degrees C higher than those obtained by DLS.

Acrylic Resins↗

PubMed2005

Highly branched stimuli responsive poly[(N-isopropyl acrylamide)-co-(1,2-propandiol-3-methacrylate)]s with protein binding functionality.

Highly branched poly(NIPAM) have been prepared using the technique of reversible addition-fragmentation chain transfer (RAFT) polymerisation using a chain transfer agent that allows the incorporation of imidazole functionality in the polymer chain-ends. The lower critical solution temperature (LCST) of the polymers can be controlled by the amount of hydrophobe and GMA incorporated during copolymerisation procedures. These thermally responsive "smart" polymers were used to purify a His-tagged BRCA-1 protein fragment by affinity precipitation. [Diagram: see text]

Acrylic Resins↗

PubMed2006

Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching.

The formation of disulphide bridges between cysteines plays an important role in protein folding, structure, function, and evolution. Here, we develop new methods for predicting disulphide bridges in proteins. We first build a large curated data set of proteins containing disulphide bridges to extract relevant statistics. We then use kernel methods to predict whether a given protein chain contains intrachain disulphide bridges or not, and recursive neural networks to predict the bonding probabilities of each pair of cysteines in the chain. These probabilities in turn lead to an accurate estimation of the total number of disulphide bridges and to a weighted graph matching problem that can be addressed efficiently to infer the global disulphide bridge connectivity pattern. This approach can be applied both in situations where the bonded state of each cysteine is known, or in ab initio mode where the state is unknown. Furthermore, it can easily cope with chains containing an arbitrary number of disulphide bridges, overcoming one of the major limitations of previous approaches. It can classify individual cysteine residues as bonded or nonbonded with 87% specificity and 89% sensitivity. The estimate for the total number of bridges in each chain is correct 71% of the times, and within one from the true value over 94% of the times. The prediction of the overall disulphide connectivity pattern is exact in about 51% of the chains. In addition to using profiles in the input to leverage evolutionary information, including true (but not predicted) secondary structure and solvent accessibility information yields small but noticeable improvements. Finally, once the system is trained, predictions can be computed rapidly on a proteomic or protein-engineering scale. The disulphide bridge prediction server (DIpro), software, and datasets are available through www.igb.uci.edu/servers/psss.html.

Amino Acid Sequence↗

PubMed2000

Isolation and characterization of glycophorin from nucleated (chicken) erythrocytes.

A sialoglycoprotein fraction was isolated from chicken erythrocytes by two methods based on the phenol extraction or chloroform/2-propanol extraction of differently prepared erythrocyte membranes. Both preparations gave in SDS-PAGE two major PAS-stained bands (GP2 and GP3), which migrated as 60- and 33-kDa species, respectively, compared to reference proteins, or as 44- and 23-kDa molecules, compared to human glycophorins. Some less abundant slower migrating PAS-stained components, antigenically related to GP2 and GP3, also were detected. No evidence for the presence of antigenically distinct glycoproteins of leukosialin type was obtained. Interconversion in SDS-PAGE, similar carbohydrate composition, and similar antigenic properties of GP2 and GP3 indicated that they are a dimer and monomer, respectively, of the same glycoprotein which shows properties that allow it to be classified as a glycophorin. Lectin binding studies and methylation analysis of beta-elimination products of chicken glycophorin preparation showed the presence of O-glycans and N-glycans. The major O-glycans include sialylated Galbeta1-3GalNAc units and more complex GlcNAc-containing chains. Among the N-glycans, there are complex-type biantennary structures with a bisecting GlcNAc residue, accompanied by chains with additional antennas linked to alpha-mannose residues. A characteristic feature of the chicken glycophorin is a relatively high proportion of N-glycans to O-glycans, compared to the glycophorin A from human erythrocytes.

Animals↗