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PubMed2006

Structural variations in novel silver(I) complexes with bitopic pyrazole/n-heterocyclic carbene ligands.

The synthesis and structural characterization of several new silver complexes of L (L = a bidendate ligand of pyrazole and N-heterocyclic carbene) are described. The result shows that the choice of counterions, N-substitutions of L, and reaction conditions are crucial which lead to a variety of structural motifs, including novel metallomacrocycles [Ag2(mu-L)2]2+ with or without Ag...Ag close contact, a mononuclear [AgL2]+ complex, and a [LAg(NO3)]n coordination polymer. In particular, the nonbonding Ag...Ag distance and the overall geometry of the metallomacrocycles are controllable with different N-substitutions and counterions. All these complexes have been determined by X-ray diffraction. The solid-state aggregates are retained in solution as supported by the electrospray mass spectroscopic studies.

Journal Article↗

PubMed1997

The structural variations of epsilon-amino groups in phospholipase A2 enzymes from Naja naja atra and Bungarus multicinctus venoms.

Comparative studies on Naja naja atra phospholipase A2 (NNA-PLA2), Bungarus multicinctus phospholipase A2 (BM-PLA2), and their Lys-modified derivatives were made to assess the differences in the fine structures around the conserved Lys residues of PLA2 enzymes. It has found that the accessibility of Lys residues of PLA2 enzymes toward modified reagent, trinitrobenzene sulfonate, were not the same. Moreover, the extent of decrease in pI values of PLA2 enzymes that resulted from trinitrophenylation of lysine residues was different between NNA-PLA2 and BM-PLA2. The Lys-6 of BM-PLA2 mostly contributed to the positively charged character of the enzyme molecule, whereas the contribution of Lys-6 of NNA-PLA2 to its molecular charge was not notably different from other Lys residues. A linear relationship was observed by plotting the mobilities of PLA2 enzymes and their TNP derivatives against their pI values. However, native and Lys-modified NNA-PLA2 were not aligned with those of BM-PLA2 in the same line. Apparently the gross conformation of PLA2 enzymes was not notably perturbed by the modification of Lys residues, but the fine structure of NNA-PLA2 was not the same as that of BM-PLA2. These results indicate that the positioning of side chains of the conserved Lys residues in the two PLA2 enzymes is essentially different, and suggest that the variations in the fine structures of homologous proteins could be effectively explored by chemical modification studies and electrophoretic analysis.

Amino Acid Sequence↗

PubMed1993

Structural variations and phenotypic switching of mycoplasmal antigens.

It is becoming apparent that a high rate of variability of surface structures is a ubiquitous property among mycoplasmas. The present study demonstrates how variations in the size of the V-1 antigen (a major surface antigen of Mycoplasma pulmonis thought to be associated with virulence) are reflected by phenotypic differences (cytadherence) that may play a role in virulence of the organism. Furthermore, a similar antigen is described for the human pathogen Urea-plasma urealyticum, and data are presented on the analysis of clinical isolates that demonstrate the potential for variation in the size of this antigen in vivo. Although no direct connection of antigen variation to natural disease has yet been presented, the data further document the tremendous potential for virulence-related diversity possessed by these organisms and emphasize the importance of a valid animal model for discerning the true relationship between variation and virulence.

Animals↗

PubMed1981

Structural variation of chromosome 21 and symptoms of Down's syndrome.

The analysis of the fine structure of the chromatids permits the identification of different regions on the long arm of chromosome 21. The preponderant role of the distal third of the long arm in the syndrome of trisomy 21 is now well established. Thus, trisomy of only band 21q22 results in a state identical to that caused by complete trisomy 21. If the trisomy involves only a part of band 21q22, the intensity of the symptoms is diminished, but the appearance of the patient is still reminiscent of Down's syndrome. Monosomy for band 21q22 results in a pathologic condition in which the morphological anomalies are the inverse of those observed in trisomic patients. This syndrome, as a "contre-type" to trisomy 21, is lethal. Trisomy of the proximal long arm region of chromosome 21 (21q21 leads to 21q22) is not associated with malformations but is accompanied by mental retardation. Monosomy of the same region results in a pathologic condition, which does not have features of the contre-type of trisomy 21.

Abnormalities, Multiple↗

PubMed1996

Sequence-dependent structural variation in B-DNA.

Though fiber diffraction originally led to the belief that the structure of DNA would be a simple regular helix, X-ray crystallography of synthetic oligomers has shown that both deformability and structure depend on sequence. But the rules that determine these factors remain mysterious.

Crystallography, X-Ray↗

PubMed2003

Sensitivity analysis of narrowband photonic crystal filters and waveguides to structure variations and inaccuracy.

Photonic crystal microcavities, formed by local defects within an otherwise perfectly periodic structure, can be used as narrowband optical resonators and filters. The coupled-cavity waveguide (CCW) is a linear array of equally spaced identical microcavities. Tunneling of light between microcavities forms a guiding effect, with a central frequency and bandwidth controlled by the local defects' parameters and spacing, respectively. We employ cavity perturbation theory to investigate the sensitivity of microcavities and CCWs to random structure inaccuracies. For the microcavity, we predict a frequency shift that is due to random changes in the lattice structure and show an approximate linear dependence between the standard deviation of the structure inaccuracy and that of the resonant frequency. The effect of structural inaccuracy on the CCW devices, however, is different; it has practically no effect on the CCW performance if it is below a certain threshold but may destroy the CCW if this threshold is exceeded.

Journal Article↗

PubMed1975

Effects of structural variations in elaboration on learning by EMR and nonretarded children.

The effects of three elaboration structures (compound sentences, complex sentences, and paragraphs) on the paired-associate learning and reversal of 30 8- to 10-year-old nonretarded and 30 8- to 10-year-old EMR children were investigated. Analyses of trials-to-criterion, first trial errors, and reversal errors did not reveal any differences in the effects of the three elaboration structures. Results of the present study indicate that given constant meaning and relational factors, some forms of surface structure differneces (compound sentences vs. complex sentence vs. paragraph) are not significant in determining a child's ability to understand an elaboration or to use it in a learning situation. There was no population difference found in the analysis of first-trial errors, although small significant differences between the nonretarded and EMR children were found in the analyses of trials-to-criterion and reversal performance.

Child↗

PubMed2001

G-quadruplex DNA structures--variations on a theme.

To be functional, nucleic acids need to adopt particular three-dimensional structures. For a long time DNA was regarded as a rigid and passive molecule with the sole purpose to store genetic information, but experimental data has now accumulated that indicates the full dynamic repertoire of this macromolecule. During the last decade, four-stranded DNA structures known as G-quadruplexes, or DNA tetraplexes, have emerged as a three-dimensional structure of special interest. Motifs for the formation of G-quadruplex DNA structures are widely dispersed in eukaryotic genomes, and are abundant in regions of biological significance, for example, at telomeres, in the promoters of many important genes, and at recombination hotspots, to name but a few in man. Here I explore the plethora of G-quadruplex DNA structures, and discuss their possible biological functions as well as the proteins that interact with them.

Animals↗

PubMed2025

Recurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes.

The 17q21.31 locus in humans harbors several complex structural haplotypes including a ~970kb inversion. Different inversion haplotypes have been associated with susceptibility to microdeletions causing Koolen-de Vries syndrome and variation in fecundity and recombination rates. Here, using 210 haplotype-resolved human genome assemblies and pangenome graph-based approaches we characterize 11 distinct structural haplotypes, several of which have not been previously described. Extending our analyses to a set of haplotype-resolved great-ape genomes, we characterize the structure of an independent inversion in chimpanzees which extends an additional 650kb, encompasses 5 additional genes, and is ~2 million years younger than the human inversion. We further determine that gorillas exhibit an independent duplication of the KANSL1 gene which may predispose them to Koolen-de Vries syndrome causing microdeletions. Using short read sequencing data we characterize 17q21.31 haplotype diversity worldwide in ~5174 individuals from 107 populations finding increased frequencies of KANSL1 duplication-containing haplotypes in both European and South Asian populations as well as 8 double recombination events between inverted and non-inverted haplotypes ranging in size from 20-180kb. Finally, using 626 ancient Eurasian human genomes we show the frequency of haplotypes containing KANSL1 duplications has increased ~6-fold over the past 12 thousand years in Europe. Together, our results highlight the dynamics, complexity, and recurrent, independent evolution of a medically relevant locus across humans and great apes.

Journal Article↗

PubMed2004

Regions of minimal structural variation among members of protein domain superfamilies: application to remote homology detection and modelling using distant relationships.

Structurally conserved regions or structural templates have been identified and examined for features such as amino acid content, solvent accessibility, secondary structures, non-polar interaction, residue packing and extent of structural deviations in 179 aligned members of superfamilies involving 1208 pairs of protein domains. An analysis of these structural features shows that the retention of secondary structural conservation and similar hydrogen bonding pattern within the templates is 2.5 and 1.8 times higher, respectively, than full-length alignments suggesting that they form the minimum structural requirement of a superfamily. The identification and availability of structural templates find value in different areas of protein structure prediction and modelling such as in sensitive sequence searches, accurate sequence alignment and three-dimensional modelling on the basis of distant relationships.

Hydrogen Bonding↗

PubMed2006

Structural variations in a family of orthodialkoxyarenes organogelators.

A series of low mass organic gelators (LMOGS) 1 to 6 whose chemical structures have in common an orthodialkoxyarene feature was prepared in order to compare the shape of their fibrillar network as investigated by small-angle neutron scattering (SANS) experiments. All members of the family exhibit a pronounced tendency to bundle formation by merging isolated fibers in extended packets of average diameter >500 A. Variations of the 2D packing symmetry are observed from hexagonal to square orderings with close derivatives of the reference member 2,3-didecyloxyanthracene (DDOA). Networks in which the fraction of isolated fibers is significant enough to allow for their SANS identification are those for 6,7-dichloro-2,3-didecyloxyanthracene (Cl(2)DDOA) and 2,3-dodecyloxy-9,10-anthraquinone (5). For this latter, the monodispersity of the cross-sections (thickness=74 A) is remarkable and the rectangular shape (b/a approximately 0.12) accounts for a merging mechanism into anisotropic bundles (ribbons).

Anisotropy↗

PubMed1999

Monolayers of Some Poly(oxyethylene)-Based Surfactants at the Air-Water Interface: The Effect of Structural Variations and Salt Concentration.

The Langmuir surface balance technique has been used to study the interfacial behavior of six structurally different poly(oxyethylene) (POE)-based polymer surfactants at the air-water interface. On a pure water subphase the surfactants have collapse surface pressures dependent on the POE chain length. The surfactant monolayers collapse at well-determined surface pressures, and the lower POE chain-length surfactants collapse at higher pressures than those with high POE content. This difference vanishes as increasing amounts of salt are added to the subphase. The PiA-isotherms are smooth, which is normal for polymeric surfactants. A closer analysis of the isotherms reveals characteristic behavior that can be attributed to structural differences. Similarities in thermodynamic behavior suggest that the molecular orientation is the same despite the structural differences. A new expression for the compressibility factor is developed to explain the relationship between this parameter and surface pressure for polymeric monolayers. Copyright 1999 Academic Press.

Journal Article↗

PubMed1986

Structural variations of O-linked oligosaccharides present in leukosialin isolated from erythroid, myeloid, and T-lymphoid cell lines.

Structures of O-linked oligosaccharides of leukosialin isolated from K562 erythroid, HL-60 promyelocytic, and HSB-2 T-lymphoid cell lines were examined. Leukosialin was isolated by specific immunoprecipitation from cells which were metabolically labeled with [3H]glucosamine, and glycopeptides were isolated after Pronase digestion. O-Linked oligosaccharides were released by alkaline borohydride treatment, and the structures of purified oligosaccharides were elucidated by specific exoglycosidase digestion, Smith degradation, and methylation anaylsis. Oligosaccharides from K562 cells were found to be GalNAcOH, Gal beta 1----3GalNAcOH, NeuNAc alpha 2----6GalNAcOH, NeuNAc alpha 2----3Gal beta 1----3GalNAcOH, Gal beta 1----3(NeuNAc alpha 2----6)GalNAcOH, and NeuNAc alpha 2----3Gal beta 1----3(NeuNAc alpha 2----6)GalNAcOH. On the other hand, oligosaccharides from HL-60 and HSB-2 cells were found to be NeuNAc alpha 2----3Gal beta 1----3GalNAcOH, NeuNAc alpha 2----3Gal beta 1----4GlcNAc beta 1----6(Gal beta 1----3)GalNAcOH, Gal beta 1----4GlcNAc beta 1----6(NeuNAc alpha 2----3)Gal beta 1----3)GalNAcOH, and NeuNAc alpha 2----3Gal beta 1----4GlcNAc beta 1----6(NeuNAc alpha 2----3Gal beta 1----3)GalNAcOH. These results clearly indicate that leukosialin can be differently glycosylated with O-linked chains, and each erythroid or myeloid (and T-lymphoid) cell line expresses a characteristic set of O-linked oligosaccharides which differ in core structures as well as in sialylation.

Antigens, CD↗

PubMed1985

Effect of molecular structure variation on the disintegrant action of sodium starch glycolate.

The effect of variation in the degree of cross-linkage and extent of carboxymethylation on the disintegration and dissolution properties of sodium starch glycolate has been examined. Samples of sodium starch glycolate were evaluated for particle size distributions and bulk and tapped densities. The bulk powders were also tested for sedimentation volumes, water uptake, and bulk swelling. Direct compression formulations containing aspirin and hydrochlorothiazide and varying concentrations of the modified starches were tableted on a rotary tablet press and evaluated for weight variation, hardness, disintegration, and dissolution. The results indicate that relatively small changes in molecular structure can cause substantial modification of disintegrant properties and suggest that the specifications for one commercially available sodium starch glycolate are within optimal specifications for both cross-linkage and degree of substitution.

Aspirin↗

PubMed1986

Structural variations in the Drosophila retrotransposon, 17.6.

More than 21 members of 17.6, a Drosophila retrotransposon, were isolated and their possible structural changes were examined by restriction mapping, blot hybridization, heteroduplex analysis and nucleotide sequence determination of long terminal repeats (LTRs). At least 7 members were found to suffer with terminal or internal long deletions. No pair of LTRs having an identical nucleotide sequence was found either within an element or between elements. Although an initiation site for the presumable genome-sized transcript of 17.6, a potential substrate for reverse transcription on translocation, was identified within the left-hand LTR, our results as a whole support the notion that the majority of 17.6s have continued to reside for a long period of time at their present chromosomal loci and hence the rate of translocation of 17.6 is very low.

Animals↗

PubMed2002

DNA structural variation affects complex formation and promoter melting in ribosomal RNA transcription.

Eukaryotic ribosomal RNA promoters exhibit an unusual conservation of non-canonical DNA structure (curvature, twist angle and duplex stability) despite a lack of primary sequence conservation. This raises the possibility that rRNA transcription factors might utilize structural anomalies in their sequence recognition process. We have analyzed in detail the interaction of the polymerase I transcription factor TIF-IB from Acanthmoeba castellanii with the CORE promoter. TIF-IB interacts primarily with the minor groove of the promoter. By correlating the effects on transcription and on DNA structure of promoter point mutations, we show that the TIF-IB interaction is strongly inhibited by increases in minor groove width. This suggests that a particular DNA structure is required for interaction with the transcription factor. In addition, TIF-IB induces a small bend in the promoter upon binding. Modeling of this bend reveals that it requires an additional narrowing of the minor groove, which would favor binding to mutants with narrower grooves. We also discuss how this narrowing would induce a small destabilization of the helix upstream of the transcription start site. Telestability predicts this would result in destabilization of the sequence that melts during initiation, suggesting that TIF-IB may have a role in stimulating melting.

Acanthamoeba↗

PubMed1989

Structural variation in d(CTCTAGAG). Implications for protein-DNA interactions.

Single-crystal X-ray diffraction techniques have been used to characterize the structure of the self-complementary DNA oligomer d(CTCTAGAG). The structure was refined to an R factor of 14.7% using data to 2.15-A resolution. The tetragonal unit cell, space group P4(3)2(1)2, has dimensions a = 42.53 and c = 24.33 A. The asymmetric unit consists of a single strand or four base pairs. Two strands, related by a crystallographic dyad axis, coil about each other to form a right-handed duplex. This octamer duplex has a mean helix rotation of 32 degrees, 11.3 base pairs per turn, an average rise of 3.1 A, C3'-endo furanose conformations, a shallow minor groove, and a deep major groove. Such averaged parameters suggest classification of the octamer as a member of the A-DNA family. However, the global parameters tend to mask variations in conformational parameters observed at the level of the base pairs. In particular, the central TpA (= TpA) step displays extensive interstrand purine-purine overlap and an unusual sugar-phosphate backbone conformation. These structural features may be directly related to certain sequence-specific protein-DNA interactions involving nucleases and repressors.

Base Composition↗

PubMed2006

An MRI study of structural variations in schizophrenia using deformation field morphometry.

Magnetic resonance imaging (MRI) has an important role in investigating the changes in brain structure that are associated with schizophrenia. In this study, MRI scans of patients diagnosed with schizophrenia (37 males; 19 females; 17-42 years of age) were compared with those of an age- and sex-matched group of normal subjects (37 males; 19 females; 18-40 years of age). Based on the images of the healthy control subjects, we constructed a representative average brain template. Automated image analysis techniques were used to measure differences in the regional nonlinear deformation fields between the two groups. A deformation field, which measures the spatial transformation to deform a template of brain anatomy to each individual data, was obtained as a three-dimensional displacement vector in each voxel. There was a significantly greater magnitude of the deformation fields in the superior frontal and parietal lobes as well as in the cingulate gyrus connecting both lobes of the patients with schizophrenia than in those of healthy controls, suggesting that these cerebral regions have a significantly higher structural variability in schizophrenia.

Adolescent↗