Small Structural Variations Research Articles

Differential effects of monoclonal antibodies on activating transcription factor-1 and cAMP response element binding protein interactions with DNA.

Activating transcription factor-1 (ATF1) and cAMP response element binding protein (CREB) have been implicated in cAMP-, calcium-, and virus-induced transcriptional alterations. Although CREB and ATF1 share extensive homology, they appear to mediate distinct cellular functions. We investigated the effect on DNA binding and in vitro transcription of four monoclonal antibodies (mAb) that bound to domains in either the regulatory region (mAb 1 and 3) or unique regions near the DNA-binding domains (mAb 4 and 5) of ATF1.mAb 1 and 3 supershifted both ATF1 and CREB in a DNA binding assay but did not affect in vitro transcription. mAb 4 prevented ATF1-DNA binding while supershifting CREB.DNA complexes and inhibited in vitro transcription by 95% from the CRE-containing murine proliferating cell nuclear antigen promoter. mAb 5 reacted specifically with ATF1 and did not prevent DNA binding or affect in vitro transcription. The mAb 4 epitope was located within ATF1 amino acid residues 205-219, including the first 3 basic residues in the putative DNA-binding domain. Secondary structural analysis predicted that this region comprises a transition site from alpha-helix to a turn-like conformation in ATF1. The transition to turn-like motifs is predicted to occur in CREB after 5 additional residues, with a correspondingly longer alpha-helical domain. Although regulatory domains distinct from DNA binding regions are thought to account for most of the differences in activity of members of the CREB subfamily, our results suggest that small structural variations adjacent to DNA binding regions may also contribute to the distinct functional activities of ATF1 and CREB.

HPLC Enantioseparation Of Dl-and Tripeptides on Cyclodextrin Bonded Stationary Phases After Derivatization with 6-Aminoquinolyl-N-hydroxysuccinimidyl Carbamate (AQC)

Abstract Enantiomeric separations were performed on a number of di- and tripeptides after their pre-column derivatization with the fluorescence derizatizing agent 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC). It has been demonstrated that the choice of a suitable cyclodextrin bonded phase in conjunction with nonaqueous polar mobile phases offers an effective means to resolve chiral peptides. It was found that the strength of interaction between the cyclodextrin and the solute, and therefore the retention and stereoselectivity, is extremely sensitive to small structural variations of the analyte.

Wing quivering of black-capped chickadees with nestlings: invitation or appeasement?

Discrimination between conspecifics is important in mediating social interactions between several individuals in a network environment. In great tits, Parus major, females readily distinguish between the songs of their mate and those of a stranger. The high degree of song sharing among neighbouring males, however, raises the question of whether females are also able to perceive differences between songs shared by their mate and a neighbour. The great tit is a socially monogamous, hole-nesting species with biparental care. Pair bond maintenance and coordination of the pair's reproductive efforts are important, and the female's ability to recognize her mate's song should therefore be adaptive. In a neighbour–mate discrimination playback experiment, we presented 13 incubating great tit females situated inside nestboxes with a song of their mate and the same song type from a neighbour. Each female was tested in two trials with the opposite order of stimulus presentation. Eleven females responded to the song of their mate in both trials, while two females responded to those of their mate in one trial and a neighbour in the other. Thus, great tit females are able to perceive subtle individual differences between their mate's song and a neighbour's rendition of the same song type despite being inside nestboxes, which are known to alter the received song structure and intensity. We suggest that this female discrimination ability inside nest holes is mediated by a high perceptual sensitivity towards small variations in song structure that should be adaptive to this hole-nesting bird species.

Integument and epidermal sensory structures of Myzostoma cirriferum (Myzostomida)

The fine structure of the integument of Myzostoma cirriferum is described with special attention to the integument sensory areas. Hypotheses about the function and a functional model of these are proposed. The integument consists of an external pseudostratified epithelium with cuticle (the epidermis) covering a parenchymo-muscular layer (the dermis). The dermis includes two types of cells: muscular fibers of the double obliquely striated type and parenchymal cells. Differences occur in the epidermis, which consists either of a large non-innervated myoepithelial area (viz. the regular epidermis). or of several rather localized sensory-secretory areas associated with discrete nerve proceses (viz. the sensory epidermis). The regular epidermis is made up of three types of cell: covering cells, ciliated cells and myoepithelial cells. The sensory epidermis shows small or marked structural variations from the regular epidermis. Small variations occur in the cirri, the buccal papilla, the body margin, the parapodia and the parapodial folds where nerve processes insinuate between epidermal cells. They are thought to be mechanoreceptor sites that could give information on the structural variations of the host's integument and participate in the recognition of individuals of the same species. The sensory epidermis differs markedly from the regular eidermis in the four pairs of lateral organs. Each lateral organ consists of a villous and ciliated dome-like central part, surrounded by a peripheral fold. The epidermis of the fold's inner part (viz. the part facing the central dome) is made up of secretory cells, while that of the fold's outer part is similar to the regular epidermis. The epidermis of the dome includes vacuolar cells, sensory cells and a different type of secretory cell. Lateral organs are presumed to be both chemoreceptors and mechanoreceptors. They could allow the myzostomids to recognize the host's integument and prevent them from shifting on the surrounding inhospitable substrate.

On intramolecular dyotropy: structural effects on reaction rates, crystal structure–molecular mechanics correlations and primary deuterium kinetic isotope effects. (Parameters for intramolecular recognition)

Previous attempts to prepare the pentacyclic triene 17 for comparison of the rate of intramolecular dyotropy with the kinetics of similar irreversible rearrangements of norbornene ring-substituted analogues had given only dyotropomer 18 with an estimated minimum ratio K1(17)/K1(5)∼ 2 × 105 at 36 °C. In the following it is shown that the steric proximity, dCH, of transferring H atoms to receptor sp2 carbons in the reaction zone cavity together with M M-calculated π-energy differences between dyotropomers can rationalise the large rate enhancement observed for the triene 17 compared with 5 and its analogues. For a series of compounds modelled on 5, in which dCH variations are quite small, observed differences in dyotropic rate are identified as arising from the interplay of molecular geometry changes and small changes in π-energy at the receptor alkene site occasioned by proximate polar groups, the electronic changes associated with aromatisation of the appended donor-site ring remaining essentially constant across the series. When the electronic energy changes associated with dyotropy for a pair of analogous structures are very closely similar, a rate-spread of ca. 104 can be identified with a change in dCH of 0.1–0.17 A. Similar kinetic effects concomitant on small parallel structural variations, virtually identical in relative-rate terms to those in the triene series, are seen in the irreversible dyotropy of a series of analogous pyrazolines modelled on compound 36 and may be likewise rationalised. Kinetic comparisons for a group of aryl-ring substituted analogues of pyrazoline 36 reveal quite modest substituent effects, consistent with reactant-like transition-states for these quantitative, exothermic rearrangements. Inter-series comparison of alicyclic trienes with pyrazolines indicate that when dCH values are essentially identical in representative examples, a rate-differential of 102–103 between the two series can be identified principally with the differing electronic requirements for triene and (slower) pyrazoline rearrangements. Primary deuterium kinetic isotope effects (K12H/K12D, dln[K12H/K12D]/dt and especially A2H/A2D) reveal strong evidence for non-classical behaviour especially for pyrazoline 38.

16] Enzyme probes in Vitro

This chapter discusses the structure of DNA structure using enzymatic probes. The most widely used enzymatic probes for DNA structure in vitro are endonucleases with little or no sequence specificity, such as the family of zinc-dependent single-strand-specific endonucleases that comprise S1 nuclease, P1 nuclease, mung bean nuclease, and others. In general, double-stranded DNA is cleaved by these enzymes at low rates, whereas single strands are digested rapidly. If structural transitions in the DNA lead to unpairing of complementary bases, the nuclease then cuts at this site. Because this provides a positive signal for a structural transition, nucleases have been extensively used to monitor conformational parameters in nucleic acids. S1 nuclease from Aspergillus oryzae has been widely used to probe structural transitions in DNA. It has a pH optimum in the acidic range (pH 5 and below), which makes it a good probe for the investigation of protonated structures but restricts its use under physiological conditions. P1 nuclease from Penicillium citrium acts in many ways similarly to S1 nuclease. An important difference is its ability to cut DNA well at neutral pH values, although its pH optimum is acidic. The products of P1 nuclease action are oligonucleotides with 5´-phosphates. Mung bean nuclease is related to the S1 and P1 nucleases. The enzyme is highly sensitive to small variations in DNA structure and converts single-stranded DNA to mono- or oligo-nucleotides with 5´-phosphates.

Structural changes that accompany the reduced catalytic efficiency of two semisynthetic ribonuclease analogs.

The structures of two catalytically defective semi-synthetic RNases obtained by replacing aspartic acid 121 with asparagine or alanine have been determined and refined at a resolution of 2.0 A (R = 0.186 and 0.172, respectively). When these structures are compared with the refined 1.8-A structure (R = 0.204) of the fully active aspartic acid-containing enzyme (Martin, P.D., Doscher, M.S., and Edwards, B. F. P. (1987) J. Biol. Chem. 262, 15930-15938), numerous and widespread changes, much greater in number and magnitude than the small structural variations noted previously between the semisynthetic complex and RNase A, are found to have occurred. These changes include the movement of the loop containing residues 65-72 away from the active site, a more or less generalized relocation of crystallographically bound water molecules, and a number of rearrangements in the hydrogen bonding network at the active site. Most changes are far removed from the immediate site of the modifications and are distributed essentially throughout the molecule. The details of many of these changes are unique to each analog. In the asparagine analog, a destabilization in the positioning of active site residue His-119 also appears to have occurred.

Two Closely Related Wheat Storage Proteins Follow a Markedly Different Subcellular Route in Xenopus laevis Oocytes.

[alpha]-Gliadins and [gamma]-gliadins are two closely related wheat storage proteins that evolved from a common ancestral gene. However, synthesis of [alpha]-gliadins and [gamma]-gliadins in Xenopus laevis oocytes revealed striking differences in their subcellular routing. The major portion of [alpha]-gliadin accumulated inside the oocyte, whereas most of the [gamma]-gliadin was secreted. Disruption of the Golgi apparatus by monensin revealed that the major part of secretion of [gamma]-gliadin is Golgi mediated. The difference in the subcellular route between [alpha]-gliadin and [gamma]-gliadin may be attributed to differential transport from the endoplasmic reticulum to the Golgi apparatus, a process that is generally the rate-limiting step in protein secretion. Coinjection of the two mRNAs had no effect on their routing, indicating no interaction between them. Our results support the hypothesis that subcellular transport of gliadins in wheat endosperm occurs in two separate routes; one is Golgi mediated, and the other is not. We also show that the subcellular transport may be markedly affected by small structural variations within closely related storage proteins.

Structural perfection of InGaAs/InP strained-layer superlattices grown by gas source molecular-beam epitaxy: A high-resolution x-ray diffraction study

High-resolution x-ray diffraction (HRXRD) studies have been carried out to determine the structural perfection and periodicity for a number of high-quality InGaAs/InP strained-layer superlattices grown by gas source molecular-beam epitaxy. X-ray scans were carried out with a compact four-crystal monochromator resulting in a resolution of one molecular layer (∼3 Å), which enables one to observe very small variations in the periodic structure. Sharp and strong higher-order satellite reflections in the XRD profiles were observed indicating smooth interfaces with well-defined modulated structures. Excellent computer simulated fits of the x-ray satellite pattern could be generated based on a kinematical XRD step model which assumes ideally sharp interfaces. Our results demonstrate that HRXRD in conjunction with the kinematical step model provides a powerful tool to evaluate the structural perfection of InGaAs/InP strained-layer superlattices.

The migration anomaly of DNA fragments in polyacrylamide gels allows the detection of small sequence‐specific DNA structure variations

Curved DNA fragments have a reduced electrophoretic mobility in polyacrylamide gels. The retardation in gels is extremely sensitive to small structural variations which influence the DNA helix axis. This gel assay can also be used to detect very small structural variations in DNA sequences which are not curved: The noncurved sequences of interest can be combined with curved stretches in phase with the helix turn. Using such sequence constructions, even subtle influences on the DNA helix axis can be detected. Experiments of this kind allow the determination of a relative order of sequence-specific DNA twist and wedge angles.

Surface wave amplitude anomalies: is reciprocity valid?

Surface wave amplitude anomalies are studied using Global Digital Seismograph Network (GDSN) records of some recent circum-Pacific events (e.g., 1983 Costa Rica, 1983 Akita-oki, 1982 Ometepec and 1983 Peru-Ecuador). Some event-station pairs can be effectively used to interchange the source and receiver on a given path, and thus provide information on an approximately reciprocal path. At certain stations, amplitude asymmetries of R 3 to R 2 are significant. Band-pass filtered records show that such asymmetries are frequency dependent. As these anomalies are primarily caused by focusing and defocusing effects, we have done ray tracing experiments using the phase velocity model of Tanimoto in an attempt to account for the observed anomalies. While anomalies such as those at TATO and MAJO for the Costa Rica event or at COL for the Akita-oki event are well predicted by the ray tracing, others are not. At station HON, where the ray tracing experiment failed to predict any asymmetry, we studied surface wave propagation on nearly reciprocal paths in some detail using records of smaller events. The results indicate that actual propagation in the heterogeneous Earth considerably varies between closely spaced, but not exactly reciprocal paths. Such sensitivity to source and receiver placement is not predicted by smooth Earth structures. This suggests that there must be substantial small scale structural variations. The length scale of these variations is presumably on the order of the wavelengths of 100–250 s surface waves (400–1000 km). There is an unexpectedly large vertical component associated with the overtone phase X 3 at some stations. In the radial component of these records we identify two group arrivals around the X 3 phase; the first one directly propagated from the source and the second one, which has a prominent vertical component, may be due to modal conversion through the path.

Structural Perfection of in GaAs/InP Superlattices Grown by Gas Source Molecular Beam Epitaxy: A High-Resolution X-Ray Diffraction Study

ABSTRACTHigh-resolution X-ray diffraction (HRXRD) studies have been cardied out to determine the structural perfection and periodicity for a number of high-quality InGaAsfInP superlattices grown by gas source molecular beam epitaxy. X-ray scans were carried out with a compact four-crystal monochromator resulting in a resolution of one molecular layer (∼3,Å), which enables one to observe very small variations in the periodic structure. Sharp and strong higher-order satellite reflections in the XRD profiles were observed indicating smooth interfaces with well-defined modulated structures. Excellent computer simulated fits of the X-ray satellite pattern could be generated based on a kinematical XRD step model which assumes ideally sharp interfaces, and periodic structural parameters such as the strain in the well could be extracted. Our results3 demonstrate that HRXRD in conjunction with the kinematical step model is a very sensitive method to assess periodic structural modifications in superlattices as a result of the precise growth conditions in the gas source MBE system.

Cell cycle variations in chromatin structure detected by DNase I

We have recently developed a reproducible method for the use of DNase I as a sensitive probe of chromatin structure (Prentice, D A & Gurley, L R, Biochim biophys acta 740 (1983) 134) [12] and have used this probe to investigate chromatin structure during the interphase of the cell cycle. Chinese hamster cells (line CHO) were synchronized by: (1) mitotic detachment, to obtain M-phase cells; (2) isoleucine deprivation, to obtain G1-phase cells; and (3) sequential use of isoleucine deprivation followed by release into the presence of hydroxyurea, to obtain cells blocked at the start of S phase. The cells were released from the various blocking schemes and nuclei were isolated and digested with DNase I at various times. The digestion kinetics were monitored to detect possible changes in chromatin condensation through the cell cycle. The chromatin was much more accessible to DNase I in G1 phase than in S or G2 phase, with only small variations in structure detected in late G1 and very early S phase. From early S phase up to mitosis, the chromatin became increasingly condensed and inaccessible to DNase I action. These results support the concept of a chromatin condensation cycle during interphase as well as during mitosis.

Beam-propagation analysis of stripe-geometry semiconductor lasers: Threshold behavior

The axial and lateral variations of the optical mode and carrier-density profiles of a gain-guided double-heterostructure stripe-geometry semiconductor laser are analyzed theoretically using a beam-propagation method based on the fast Fourier transform technique. The numerical results near the laser threshold indicate that the characteristic length lc, over which the lateral mode adjusts itself to small axial variations in the laser structure, is typically in the range 50 μm≲lc≲100 μm.

Species differences determine azido phencyclidine labeling pattern in desensitized nicotinic acetylcholine receptors

Acetylcholine receptor enriched membranes from Torpedo ocellata , Torpedo marmorata and Torpedo californica were studied using [ 3H] azido-phencyclidine (AZ-PCP). [ 3H]-PCP binding to receptors from all three species revealed marked similarities. Photoaffinity labeling by [ 3H]-AZ-PCP resulted in the tagging of mainly α, β and δ subunits in all species. When carbamylcholine was added, it enhanced the labeling of β subunits in T. ocellata , δ in T. marmorata and α in T. californica , suggesting species differences in the photolabeling pattern. Multiple homologous binding sites for PCP between the receptor subunits would allow small variations in receptor structure to be manifested in labeling by AZ-PCP, with no differences in binding and functional properties of the receptors.

Metabolic Activation of Xenobiotics: Ethylene Dibromide and Structural Analogs

A large number of compounds which can enter living organisms are relatively harmless as such, but are transformed by the body into reactive agents. The structure of such a compound is the factor determining its disposition in the organism. Its physicochemical characteristics determine the overall fate in terms of absorption, distribution and excretion, while the chemical structure is the decisive factor in its biotransformation. Whether formation of reactive intermediates occurs depends on what points of attack it has to offer to the different enzyme systems. The extent to which alkylation of cellular macromolecules by reactive intermediates occurs in turn depends on the balance of activating and detoxifying enzymes in the particular cell and on the reactivity of the intermediates towards critical targets in the cell macro-molecules. Many chemicals undergo several concurrent metabolic pathways. The ratio between these pathways may be a decisive factor determining the extent of adverse effects caused by these chemicals. Small variations in structure may have a drastic effect on the activation and detoxification by competing enzyme systems. These concepts are elucidated using the examples of ethy-lene dibromide and some structural analogs. Apart from the parent compound itself, two alkylating species may be responsible for the toxic effects of these compounds. Bromo-acetaldehyde is formed by oxidation, catalyzed by cyto-chrome P-450, followed by spontaneous loss of hydrogen bromide; S-2-bromoethylglutathione results from replacement of a bromine atom by glutathione, catalyzed by the glutathione transferases. The latter intermediate possesses a reactivity comparable to sulfur mustard. Results indicate that the reactive glutathione conjugate is responsible for the mutagenic and possibly also the carcinogenic effect of ethy-lene dibromide. However, in vivo, oxidation is quantitatively much more important as a primary process.

Elasticity of pyroxenes: Effects of composition versus crystal structure

The variation of elastic moduli among five pyroxenes exhibiting three crystal structures is generally small. The variations that do exist are related to structural differences. C11 is most sensitive to compositional changes on the basis of a mechanical structural analog. Its small variation among these pyroxenes suggests that the compositional range reflected by these samples (enstatite, bronzite, diopside) does not affect the elastic moduli. C33 is most sensitive to structural perturbations. The large variation of C33 (20%) implies that the small variations in crystal structure dominate the variations in elastic moduli.

Plasma polymerization. IV. A systematic investigation of the inductively coupled RF plasma polymerization of pentafluorobenzene.

AbstractThe composition and gross structural features of plasma polymer films prepared by inductively coupled RF plasmas excited in pentafluorobenzene were investigated by ESCA as a function of the operating parameters. The rate of film deposition is dependent on the W/FM parameter and on site of deposition. The polymer formed in the glow region shows only small variations in structure as a function of power and pressure. Polymer films deposited in the regions away from the site of primary excitation typically have a higher fluorine content than those formed in the coil region; the stoichiometry for the latter is comparable to that of the starting material.

Asymmetric hydrogenation in the presence of bicyclic chiral phosphines

Both enantiomers of trans-2,3-diphenylphosphinomethyl-norbornene-(5), prepared by two independent synthetic routes, were used as ligands in the asymmetric hydrogenation of α-acetamidocinnamic acid in the presence of rhodium(I). Small variations in the ligand structure have a remarkable influence on the activity of the catalytic system.

Small scale auroral absorption events associated with substorms

WE describe the first results obtained from a new facility designed to study auroral absorption events exhibiting small scale spatial structure and rapid temporal variations. The absorption is measured by means of a modern solid-state riometer with high time resolution1 and the spatial resolution is obtained using a narrow-beam antenna with 64 elements. The most striking observations made so far involve intense, short-lived ‘spikes’ of absorption associated with the onsets of auroral substorms. These spikes, which seem to be of small spatial scale, are probably related to the sudden ionospheric absorption (SIA or SAI) events reported by previous workers2–5 and perhaps to the ‘spikes’ of intense energetic electron precipitation observed from polar-orbiting satellites6–11. Five such spikes were observed during November and December 1975.