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PubMed2000

Structural effects on polyether cationization by alkali metal ions in matrix-assisted laser desorption/ionization

Structural effects on polyether cationization in matrix-assisted laser desorption/ionization (MALDI) are investigated using three different polyethers: PEG (polyethylene glycol), PPG (polypropylene glycol), and PTHF (polytetrahydrofuran). This study was performed using equimolar cesium and lithium chlorides as the cationizing agent. It was observed that the polyether structure variation led to a substantial change in polyether selectivity for alkali metal ion complexation. Moreover, it was found that like PEG, PPG displays a different selectivity for Cs+ and Li+ with different matrices. Discussion of these results and their implication in MALDI are given.

Journal Article↗

PubMed2003

Automated reconstruction of three-dimensional neuronal morphology from laser scanning microscopy images.

Experimental and theoretical studies demonstrate that both global dendritic branching topology and fine spine geometry are crucial determinants of neuronal function, its plasticity and pathology. Importantly, simulation studies indicate that the interaction between local and global morphologic properties is pivotal in determining dendritic information processing and the induction of synapse-specific plasticity. The ability to reconstruct and quantify dendritic processes at high resolution is therefore an essential prerequisite to understanding the structural determinants of neuronal function. Existing methods of digitizing 3D neuronal structure use interactive manual computer tracing from 2D microscopy images. This method is time-consuming, subjective and lacks precision. In particular, fine details of dendritic varicosities, continuous dendritic taper, and spine morphology cannot be captured by these systems. We describe a technique for automated reconstruction of 3D neuronal morphology from multiple stacks of tiled confocal and multiphoton laser scanning microscopy (CLSM and MPLSM) images. The system is capable of representing both global and local structural variations, including gross dendritic branching topology, dendritic varicosities, and fine spine morphology with sufficient resolution for accurate 3D morphometric analyses and realistic biophysical compartment modeling. Our system provides a much needed tool for automated digitization and reconstruction of 3D neuronal morphology that reliably captures detail on spatial scales spanning several orders of magnitude, that avoids the subjective errors that arise during manual tracing with existing digitization systems, and that runs on a standard desktop workstation.

Animals↗

PubMed1998

Evaluating precursor-directed biosynthesis towards novel erythromycins through in vitro studies on a bimodular polyketide synthase.

BACKGROUND: Modular polyketide synthases (PKSs) catalyse the biosynthesis of complex polyketides using a different set of enzymes for each successive cycle of chain extension. Directed biosynthesis starting from synthetic diketides is a potentially valuable route to novel polyketides. We have used a purified bimodular derivative of the erythromycin-producing polyketide synthase (DEBS 1-TE) to study chain extension starting from a variety of diketide analogues and, in some cases, from the alternative acyl-CoA thioester substrates. RESULTS: Chain initiation in vitro by DEBS 1-TE module 2 using a synthetic diketide analogue as a substrate was tolerant of significant structural variation in the starter unit of the synthetic diketide, but other changes completely abolished activity. Interestingly, a racemic beta-keto diketide was found to be reduced in situ on the PKS and utilised in place of its more complex hydroxy analogue as a substrate for chain extension. The presence of a diketide analogue strongly inhibited chain initiation via the loading module. Significantly higher concentrations of diketide N-acetylcysteamine analogues than their corresponding acyl-CoA thioesters are required to achieve comparable yields of triketide lactones. CONCLUSIONS: Although a broad range of variation in the starter residue is acceptable, the substrate specificity of module 2 of a typical modular PKS in vitro is relatively intolerant of changes at C-2 and C-3. This will restrict the usefulness of approaches to synthesise novel erythromycins using synthetic diketides in vivo. The use of synthetic beta-keto diketides in vivo deserves to be explored.

Catalysis↗

PubMed2000

Structural basis of peptide binding and presentation by the type I diabetes-associated MHC class II molecule of NOD mice.

We have determined the crystal structure of I-Ag7, an integral component in murine type I diabetes development. Several features distinguish I-Ag7 from other non-autoimmune-associated MHC class II molecules, including novel peptide and heterodimer pairing interactions. The binding groove of I-Ag7 is unusual at both terminal ends, with a potentially solvent-exposed channel at the base of the P1 pocket and a widened entrance to the P9 pocket. Peptide binding studies with variants of the hen egg lysozyme I-Ag7 epitope HEL(11-25) support a comprehensive structure-based I-Ag7 binding motif. Residues critical for T cell recognition were investigated with a panel of HEL(11-25)-restricted clones, which uncovered P1 anchor-dependent structural variations. These results establish a framework for future experiments directed at understanding the role of I-Ag7 in autoimmunity.

Amino Acid Sequence↗

PubMed1995

Angle of the articular eminence in patients with temporomandibular joint dysfunction and asymptomatic volunteers.

OBJECTIVE: The purpose of this study was to compare structural variations of the temporomandibular joint anatomy between symptomatic patients with temporomandibular joint dysfunction and asymptomatic controls. STUDY DESIGN: There were 74 symptomatic patients with temporomandibular joint dysfunction, 29 asymptomatic volunteers with normal joints, and 6 asymptomatic volunteers with disk displacement with reduction included in this study. All subjects had bilateral high resolution magnetic resonance imaging scans performed in the sagittal (closed and opened) and coronal (closed) positions. All subjects had right and left full profile laminagraphs, one in the centric occlusal position, and one with the incisors edge to edge. RESULTS: Student-Newman-Keuls tests demonstrated no significant angular or linear differences for depth of the articular fossa, angle of the articular eminence, horizontal and vertical overlap of the incisor teeth, and linear condylar translation. CONCLUSION: This study concludes that there are no significant differences in angular and linear measurements in the articular fossa of asymptomatic volunteers and symptomatic subjects with temporomandibular joint dysfunction.

Adult↗

PubMed1990

Monoclonal antibodies directed against human Rh antigens in tests with the red cells of nonhuman primates.

Monoclonal antibodies against Rh related antigens on human red cells often crossreact with the red cells of the highest subhuman primate species. Depending on specificity of antibody, the species tested, and technique used, these reactions can be either species-specific or type specific. In tests with chimpanzee red cells, some of the latter type reactions have specificities related to the R antigen of the R-C-E-F blood group system of chimpanzee; specificities of some others seem to be unrelated to any known chimpanzee blood groups. Monoclonal anti-D reagents that give uniformly positive reactions with human D-positive (common and rare types) red cells, display wide individual differences in tests with chimpanzee blood. This indicates that there are minute structural variations of antibody molecules from one monoclonal anti-D antibodies apparently have no bearing on recognition of the D combining site on the human red cells, but come into play when in contact with chimpanzee rbcs. Some of the monoclonal antibodies directed against Rh and LW molecules are distinguished by unusually strong reactions with the red cells of the Old World monkeys (macaques and baboons), which is in contrast with negative or weak reactions of the same antibodies with the red cells of anthropoid apes and human bloods. One may recall, that polyclonal anti-Rh sera do not react with the blood of rhesus monkeys, the phenomenon that was the source of controversy surrounding the discovery of the rhesus factor of the human blood.

Animals↗

PubMed1998

Combinatorial biosynthesis of erythromycin and complex polyketides.

Modular polyketide synthases that produce many clinically important natural products such as erythromycins and lovastatins have been engineered in many ways to produce novel natural products. The structural variations have included alterations to the substituents on the macrolide ring, including the starter acid residue, using either semi-synthetic methodology or genetic engineering. It is now also possible to produce shorter polyketide chains that are released either as lactone rings (6-, 8-, 12- and 14-membered rings) or linear products. The strategies for engineering polyketide synthases to produce specific natural products are now well established. Several of the macrolides produced recently have been elaborated to produce novel antibiotics.

Drug Design↗

PubMed2000

Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations.

We describe a novel method for analysis of marker genotype data from admixed populations, based on a hybrid of Bayesian and frequentist approaches in which the posterior distribution is generated by Markov chain simulation and score tests are obtained from the missing-data likelihood. We analysed data on unrelated individuals from eight African-American populations, genotyped at ten marker loci of which two (FY and AT3) are linked (22 cM apart). Linkage between these two loci was detected by testing for association of ancestry conditional on parental admixture. The strength of this association was consistent with European gene flow into the African-American population between five and nine generations ago. To mimic the mapping of an unknown gene in an 'affecteds- only' analysis, a binary trait was constructed from the genotype at the AT3 locus and a score test was shown to detect linkage of this 'trait' with the FY locus. Mis-specification of the ancestry-specific allele frequencies - the probabilities of each allelic state given the ancestry of the allele - was detected at three of the ten marker loci. The methods described here have wide application to the analysis of data from admixed populations, allowing the effects of linkage and population structure (variation of admixture between individuals) to be distinguished. With more markers and a more complex statistical model, genes underlying ethnic differences in disease risk could be mapped by this approach.

Bayes Theorem↗

PubMed2003

Ion flotation of cadmium(II) and zinc(II) in the presence of proton-ionizable lariat ethers.

Competitive flotation of Cd(II) and Zn(II) from very dilute aqueous solutions by proton-ionizable lariat ethers in the presence of nonylphenol nona(ethylene glycol) ether as a nonionic foaming agent is reported. Influences of structural variation within the collector (identity of the pendent acidic group and lipophilicity), concentration of the collector, and pH of the aqueous solution are assessed. A monoethyl lariat ether phosphonic acid collector is found to exhibit high Cd(II)/Zn(II) flotation selectivity under certain conditions.

Journal Article↗

PubMed2005

Detection of peroxidase/H2O2-mediated oxidation with enhanced yellow fluorescent protein.

The ability to sense oxidative stress in live cells and organisms would have far-reaching implications for biotechnology, drug discovery, and potentially medical imaging. We hypothesized that tyrosine-containing fluorescent proteins could be used as switches for sensing oxidative stress, based on their sensitivity to environmental and structural variations. We therefore tested purified EGFP, EYFP, ECFP, and DsRed proteins against the heme-peroxidase/H(2)O(2) reaction. We found that peroxidase-mediated oxidation resulted in up to 99.5% quenching of EYFP fluorescence (but not that of other fluorescent proteins) in a dose-dependent manner. Western blotting revealed inter- and intramolecular cross-linking. The observed detection limit for hydrogen peroxide was approximately 100 nM, well below the extracellular levels previously reported to occur in mammalian tissue during signaling. Combined expression of EYFP (quenchable) and ECFP or EGFP (nonquenchable) is expected to allow sensitive monitoring of oxidative stress.

Bacterial Proteins↗

PubMed2004

Importance and reduction of the sidewall-induced band-broadening effect in pressure-driven microfabricated columns.

The influence of the detailed design of the sidewall region upon the over-all band-broadening in microfabricated packed-bed or collocated monolithic support structure (COMOSS) columns has been investigated using computational fluid dynamics (CFD) simulation techniques. It is shown that, under unretained solute conditions, very small structural variations of the order of only 5% of the particle diameter can give rise to a 4-fold increase of the band-broadening. A comprehensive study has been made to quantify this effect as a function of the fluid velocity, the particle diameter, the channel widths, and of course, the sidewall region design. Because the sidewall effect can be fully attributed to a mismatch between the flow rates in the column center and in the sidewall region, it is fortunately also quite straightforward to avoid it. A very simple design, yielding band-broadening values identical to that of a hypothetical sidewall-less column for all possible values of the flow velocity, the particle diameter, or the channel width is proposed.

Biotechnology↗

PubMed1995

Oligosaccharide behavior of complex natural glycosphingolipids in multicomponent model membranes.

Wideline 2H NMR of model membranes was used to consider the molecular consequences of factors often suggested as modulators of complex glycosphingolipid oligosaccharide arrangement and motional characteristics at cell surfaces. GM1, asialo-GM1, and globoside were studied as examples of plasma membrane recognition sites. The experimental approach involved substitution of deuterons (D) for protons at specific locations within the carbohydrate chains. Deuterated glycolipids were then dispersed at 7-10 mol% in unsonicated bilayers of 1-palmitoyl-2-oleoylphosphatidylcholine. Factors tested for their significance to carbohydrate chain conformation and dynamics included glycolipid natural alkyl and acyl chain variability, membrane fluidity, and the presence of cholesterol and a charged sugar residue (neuraminic acid). Effects of Ca2+ and membrane-associated protein were briefly considered. Two distinct strategies were employed in substituting deuterons for selected protons of carbohydrate residues. Neither approach necessitated alteration of the glycolipid natural fatty acid composition. (i) Protons of the exocyclic hydroxymethyl group on the terminal Gal residue of GM1 and asialo-GM1, and on the terminal N-acetylgalactosamine (GalNAc) residue of globoside, were replaced with deuterium (producing -CDHOH) by an enzymatic oxidation/reduction cycle. This represents the first application of such an approach to deuteration of complex neutral glycolipids. Spectral results were compared to those obtained for the similarly-deuterated monoglycosyl lipid, galactosylceramide (GalCer), with natural fatty acid composition. Efficacy of this labeling method may in principle be influenced by structural variations within a given glycolipid family. Also, asymmetric rotation of the deuterated group made it less attractive than the second method for relating spectral features to receptor geometry. (ii) A general synthetic, nonenzymatic method was investigated for replacing amino sugar N-acetyl groups with deuterated acetate (-COCD3). The acetate group of the GalNAc residue of globoside, GM1, and asialo-GM1, as well as that on neuraminic acid in GM1, was replaced with -COCD3. This second method afforded better signal-to-noise--an important consideration for 2H NMR. The NMR technique employed had the potential for detecting changes of as little as 10% in oligosaccharide orientation or motional order. Each glycolipid demonstrated clear evidence of preferred average oligosaccharide conformations in all (fluid) membrane environments examined. The most striking observation was that, in fluid matrices, conformation and motional order of the complex oligosaccharide chains were only modestly influenced by factors tested, including natural variation in the glycolipid hydrocarbon chains, membrane fluidity, temperature, and the presence of cholesterol or the N-acetylneuraminic acid (NeuAc) residue on GM1.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Sugars↗

PubMed1992

Rates of spontaneous exchange of synthetic radiolabeled sterols between lipid vesicles.

14C-labeled sterols with structural variation in the polar function [3 alpha-OH, 3-O(CH2)2O-(CH2)2O(CH2)2OH, 3 alpha-NH2, 3 beta-NH2, and 3-OC(O)CHN = N] and at the 7 position (7-oxo, 7 alpha-OH, and 7 beta-OH) were synthesized and incorporated into unilamellar vesicles for studies of the rates of transfer to an excess of acceptor vesicles. Cholesterol, cholestanol, and epicholesterol underwent full exchange in a single kinetic pool, and 90% of the 3 alpha-triethoxycholesterol was exchangeable in one pool. Biphasic kinetics with full exchangeability were observed for cholesterylamines, which bear a positive charge at the 3 position; the slow phase reflects the high activation energy for inner-to-outer leaflet movement of the charged lipid. Biphasic kinetics were also found for cholesteryl diazoacetate, indicating that this photoaffinity probe and cholesterol have different mechanisms of transfer. Sterols that are more hydrophilic than cholesterol as estimated by reversed-phase high-performance chromatography (elution with acetonitrile-2-propanol, 4:1 v/v, with varying proportions of water) gave faster exchange rates than cholesterol, whereas sterols that are more hydrophobic gave slower exchange rates. However, the rates of [14C]sterol desorption from the lipid-water interface are not correlated with the relative sterol hydrophobicity as estimated by the logarithm of the capacity factors using acetonitrile-2-propanol-water as the mobile phase. These studies suggest that the interaction of sterols with phospholipids provides the principal physical-chemical basis for determining the rates of spontaneous exchange of sterols between bilayers.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed1991

Mechanism of colchicine binding to tubulin. Tolerance of substituents in ring C' of biphenyl analogues.

The limits of structural variation of the substituent in position 4' of ring C' of biphenyl colchicine analogues (ring C in colchicine) were probed by the synthesis of a number of analogues and the examination of their binding to tubulin and its consequences. Binding was found to require the location in three-dimensional space of the oxygen in the 4'-substituent at a locus not far distant from those of the colchicine ring C oxygens. All those analogues that bind to the colchicine site of tubulin induced the GTPase activity and inhibited microtubule assembly, those containing a carbonyl group substoichiometrically and the others stoichiometrically. A similar relation was found for the induction of the abnormal polymerization of the colchicine analogue-tubulin complex, with methoxy-containing compounds requiring a higher temperature to induce the polymerization. A concerted analysis of the binding thermodynamics of colchicine and its various analogues has shown full consistency with the previously proposed two-step binding pathway that involves two nonidentical binding moieties in the ligand [Andreu, J. M., & Timasheff, S. N. (1982) Biochemistry 21, 534-543]. Comparison of the binding parameters of colchicine, its des(ring B) analogue (MTC), and ring A and C compounds individually with the thermodynamic parameters deduced for the first steps of the bindings of colchicine and MTC [Engelborghs, Y., & Fitzgerald, T. J. (1987) J. Biol. Chem. 262, 5204-5209] have led to the conclusion that binding can occur by two pathways leading to the identical product. In the first pathway, ring A binds first; this is followed by a rate-determining thermodynamically indifferent reaction (protein conformation change), and finally a rapid binding of ring C. In the second pathway, the events are the same except that the order of binding of the rings is reversed. Colchicine, due to the steric hindrance of ring B, can follow only the second pathway. For MTC, both kinetic pathways are open and binding may be initiated by random first contact of either ring A or ring C.

Animals↗

PubMed1985

Calcium binding of arterial tropomyosin: involvement in the thin filament regulation of smooth muscle.

Bovine aortic tropomyosin has been isolated by DEAE-Sepharose chromatography following isoelectric precipitation and ammonium sulfate fractionation. A single polypeptide [Mr 36 000 on a sodium dodecyl sulfate (SDS)-polyacrylamide gel] was obtained under different electrophoretic conditions. The amino acid composition of bovine tropomyosin was very similar to that of rabbit skeletal muscle; the amino-terminal residue is blocked. The molecular weight of the native tropomyosin (76 000), which is twice that calculated from the SDS-polyacrylamide gel, suggests that the molecule is a dimer. The diffusion coefficient of 3.4 X 10(-7) cm2 s-1 and the frictional coefficient of 1.7 indicate that the molecule is asymmetric. Comparative high-pressure liquid chromatography peptide mapping of rabbit skeletal and bovine aortic tropomyosins shows primary structure variation. Bovine aortic tropomyosin binds calcium under physiological conditions of pH and ionic strength (22 mol of Ca2+/mol of tropomyosin with a Kd of 1.4 mM). Such a property is not shared by skeletal tropomyosin. In low Mg2+ concentration, both skeletal and aortic actin activations of the skeletal myosin ATPase activity are calcium independent. Addition of aortic tropomyosin to a hybrid actomyosin (aortic actin, skeletal myosin) yields an enhancement of the actin activation of the myosin ATPase activity, but the addition of skeletal tropomyosin yields a decrease of this activity. However, both the enhancement and decrease are calcium dependent. Addition of skeletal or aortic tropomyosin to an actomyosin system, where both actin and myosin come from skeletal muscle, yields only an enhancement of the actin activation of the myosin ATPase activity.(ABSTRACT TRUNCATED AT 250 WORDS)

Actin Cytoskeleton↗

PubMed1987

Structural elucidation of the Brucella melitensis M antigen by high-resolution NMR at 500 MHz.

The Brucella M antigen from the species type strain Brucella melitensis 16M has been identified as a component of the cell wall lipopolysaccharide (LPS). O polysaccharide liberated from this LPS by mild acid hydrolysis exhibited M activity in serological tests and was shown to be a homopolymer of 4-formamido-4,6-dideoxy-alpha-D-mannopyranosyl residues arranged in an oligosaccharide repeating unit as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the native lipopolysaccharide. Structural analysis of the O polysaccharide by NMR methods was difficult due to apparent microheterogeneity of the repeating unit, which was in fact caused by the presence of rotational isomers of the N-formyl moiety. This problem was resolved by chemical modification of the polysaccharide to its amino and N-acetyl derivatives, the 500-MHz 1H and 125-MHz 13C NMR spectra of which could be analyzed in terms of a unique structure through application of pH-dependent beta-shifts and two-dimensional techniques that included COSY, relayed COSY, and NOESY experiments together with heteronuclear C/H shift correlation spectroscopy. On the basis of these experiments and supported by methylation and periodate oxidation data, the structure of the M polysaccharide was determined as a linear polymer of unbranched pentasaccharide repeating units consisting of four 1,2-linked and one 1,3-linked 4,6-dideoxy-4-formamido-alpha-D-mannopyranosyl residues. The marked structural similarity of the M antigen and the A antigen, which is known to be a 1,2-linked homopolysaccharide of 4,6-dideoxy-4-formamido-alpha-D-mannopyranosyl units, accounts for cross-serological reactions of the two and the long-standing confusion surrounding the nature of their antigenic determinants. Structural and serological considerations in conjuction with the sodium dodecyl sulfate banding pattern of Brucella A LPS suggest that its biosynthesis differs appreciably from that of the M antigen, which appears to be synthesized by regulated assembly of preformed oligosaccharide repeating units. Temperature, lysogenic phage may be responsible for such biosynthetic and structural variations.

Antigens, Bacterial↗

PubMed1990

Coupling of tertiary and quaternary changes in human hemoglobin: a 1D and 2D NMR study of hemoglobin Saint Mandé (beta N102Y).

Hemoglobin Saint Mandé (beta N102Y) is a low-affinity mutant with the substitution site situated in the quaternary-sensitive alpha 1 beta 2 interface. In adult hemoglobin the Asn102 beta contributes to the stability of the liganded (R) state, forming a hydrogen bond with Asp94 alpha. The quaternary and tertiary perturbations subsequent to the Tyr for Asn substitution in monocarboxylated hemoglobin Saint Mandé have been investigated by one- and two-dimensional nuclear magnetic resonance (NMR) spectroscopy. Analysis of the one-dimensional NMR spectra of the liganded and unliganded samples in 1H2O provides evidence that both R and T quaternary structures of Hb Saint Mandé are different from the corresponding ones in HbA. In the monocarboxylated form of the mutant hemoglobin, at acid pH, we have observed the disappearance of an R-type hydrogen bond and the appearance of a new one whose proton resonates like a deoxy T marker. Using two-dimensional NMR methods and on the basis of previous results on the monocarboxylated HbA, we have obtained a significant number of resonance assignments in the spectra of monocarboxylated Hb Saint Mandé at pH 5.6 in the presence or absence of a strong allosteric effector, inositol hexaphosphate. This enabled us to characterize the tertiary conformational changes (relative to the liganded normal hemoglobin) triggered by the quaternary-state modification. The observed structural variations are confined within the heme pocket regions but concern both the alpha and beta subunits. Most of them, localized in the C, F, G, and FG segments, could result directly from the side-chain substitution, while others, such as Leu141 beta, could be explained only by long-range interactions.

Hemoglobins↗

PubMed1981

Protein influences on porphyrin structure in cytochrome c: evidence from Raman difference spectroscopy.

To probe the details of protein heme interactions, we have developed a Raman difference spectroscopic technique, which allows reliable detection of very small, approximately equal to 0.01 cm-1, frequency differences. When this technique is applied to heme proteins, structural differences in the protein which perturb the porphyrin macrocycle may be examined by obtaining Raman difference data on the porphyrin vibrational modes which are strongly enhanced in the Raman spectrum produced with visible laser excitation. We report here Raman difference spectroscopic data on cytochromes c from 24 species. The differences in the Raman spectrum of the porphyrin between the cytochromes c of any two species are small, confirming that all of the cytochromes we have examined have the same "cytochrome fold". However, many small (0.02-2 cm-1) but systematic differences were detected which indicate structural differences among these proteins. These differences could be classified into three different groups and interpreted in terms of different types of structural variations resulting from specific differences in the amino acid sequences. First, direct interactions between near-heme residues and the porphyrin influence the electron density in the pi orbitals of the porphyrin macrocycle. Second, variation in the residue at position 92, far removed from the heme, affects the frequency of the core-size marker line at 1584 cm-1. Third, the conformation near cysteine 14 affects the shape of the Raman mode which is sensitive to the pyrrole ring substituents (approximately 1313 cm-1). From these data we conclude that there are several ways in which the protein amino acid sequence may regulate the oxidation-reduction potential and several ways in which the sequence can modify the binding site between cytochrome c and its redox partners.

Animals↗