Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Structure variation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5Linked to original sources
PubMed1984

Natural structural variation in enzymes as a tool in the study of mechanism exemplified by a comparison of the catalytic-site structure and characteristics of cathepsin B and papain. pH-dependent kinetics of the reactions of cathepsin B from bovine spleen and from rat liver with a thiol-specific two-protonic-state probe (2,2'-dipyridyl disulphide) and with a specific synthetic substrate (N-alpha-benzyloxycarbonyl-L-arginyl-L-arginine 2-naphthylamide).

Cathepsin B (EC 3.4.22.1) from bovine spleen and the analogous enzyme from rat liver were investigated at 25 degrees C at I0.1 in acidic media by kinetic study of (a) the reactions of their catalytic-site thiol groups towards the two-protonic-state reactivity probe 2,2'-dipyridyl disulphide and (b) their catalysis of the hydrolysis of N-alpha-benzyloxycarbonyl-L-arginyl-L-arginine 2-naphthylamide. Reactivity-probe kinetics showed that nucleophilic character is generated in the sulphur atom of cathepsin B by protonic dissociation with pKa 3.4, presumably to form an S-/ImH+ ion-pair. Substrate-catalysis kinetics showed that ion-pair formation is not sufficient to generate catalytic competence in cathepsin B, because catalytic activity is not generated as the pH is raised across pKa 3.4 but rather as it is raised across pKa 5-6 (5.1 for kcat; 5.6 for kcat./Km for the bovine spleen enzyme and 5.8 for kcat./Km for the rat liver enzyme). The implications of these results and of known structural differences between the catalytic sites of the rat liver enzyme and papain (EC 3.4.22.2) for the mechanism of cysteine-proteinase-catalysed hydrolysis are discussed.

2,2'-Dipyridyl↗
PubMed1988

Ribosomal gene structure, variation and inheritance in maize and its ancestors.

We have examined the structure of nuclear genes coding for ribosomal RNAs in maize and its wild relatives, the teosintes and Tripsacum. Digestion of the rDNA (genes coding for 18S, 5.8S and 26S RNAs) with 15 restriction endonucleases (with six base pair recognition sites) yields essentially a single map for the approximately 10,000 repeat units within an individual plant or species. Both length and site variation were detected among species and were concentrated in the intergenic spacer region of the rDNA repeat unit. This result is in agreement with patterns of rDNA change observed among wheat and its relatives (Triticeae), and among vertebrate species. Digestion of these nuclear DNAs with BamHI and subsequent hybridization with a 5S RNA gene-specific probe allowed determination of the size of the 5S gene repeat unit in maize, teosintes, and Tripsacum. Groupings in the genus Zea were characterized by distinct repeat unit types five Tripsacum species examined shared a 260 base pair major repeat unit type. Additionally, several other restriction endonuclease cleavage patterns differentiated among the 5S DNAs within the genus Zea. The rDNA and 5S DNA restriction site variation among the species can be interpreted phylogenetically and agrees with biochemical, karyotypic, and morphological evidence that places maize closest to the Mexican teosintes. For both gene arrays, contributions from each parental genome can be detected by restriction enzyme analysis of progeny from crosses between maize and two distantly related teosintes, Zea luxurians or Zea diploperennis, but certain teosinte arrays were underrepresented in some of the hybrids.

Blotting, Southern↗
PubMed1994

Different types of structural variation in STRs: HumFES/FPS, HumVWA and HumD21S11.

Alleles of the STR systems HumFES/FPS, HumVWA and HumD21S11 were sequenced and analyzed. Sequence data revealed 3 different systems concerning the complexity of their sequence structure. HumFES/FPS belongs to the STR polymorphism with a simple repeat structure. Only 2 subtypes were found with a base substitution in the 5'-flanking region and no variation in the repeat region. In the STR system HumVWA the sequence structure of the repeat region is more complex, because 2 tetranucleotide units TCTA and TCTG were present. Additionally allele 14 revealed a completely different sequence structure leading to a different electrophoretic mobility. The repeat region of HumD21S11 is compound in structure. The possibility of variation at 3 positions leads to the occurrence of microheterogeneities in fragments of apparent length. In the upper allele range alleles arise with an additional incomplete TA-repeat.

Alleles↗
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↗
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↗
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↗
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↗
PubMed1995

Hematopoietic growth factor receptors: structure variations and alternatives of receptor complex formation in normal hematopoiesis and in hematopoietic disorders.

Receptors of most hematopoietic growth factors are structurally related and grouped in the hematopoietin or cytokine receptor superfamily. In this paper, we will first review the general principles of hematopoietin receptor complex formation and cytoplasmic signaling. Subsequently, the significance of defective hematopoietic growth factor receptors for the development of hematological diseases will be discussed.

Amino Acid Sequence↗
PubMed1990

Structural variation in the antithrombin III binding site region and its occurrence in heparin from different sources.

A tetrasaccharide possessing a biosynthetically permissible structural variability in and adjacent to the antithrombin III (ATIII) binding site has been isolated from heparin lyase depolymerized bovine lung heparin by using strong anion-exchange high-pressure liquid chromatography (SAX-HPLC). On the basis of two-dimensional 500-MHz 1H NMR experiments, including phase-sensitive correlated spectroscopy (COSY) and rotating frame nuclear Overhauser enhancement spectroscopy (ROESY), and fast-atom bombardment mass spectrometry (FAB-MS), the primary structure of this tetrasaccharide was unambiguously established as delta UAp2S (1----4)-alpha-D-GlcNp2S6S(1----4)-beta-D-GlcAp(1----4)-alph a-D-GlcNp2S3S6S (where delta UA represents 4-deoxy-alpha-L-threo-hex-4-enopyranosyluronic acid). The 1H NMR ROESY experiment proved to be particularly valuable in offering sequence information. Heparins from a variety of species and tissue sources were examined by oligosaccharide mapping using SAX-HPLC and gradient polyacrylamide gel electrophoresis. Two of these heparins are used as anticoagulants; they are porcine intestinal mucosal heparin and bovine lung heparin. The predominant ATIII-binding site in porcine heparin contained an N-acetylated glucosamine residue. We now report the structure of the predominant ATIII-binding site in bovine heparin as----4)-alpha-D-GlcNp2S6S(1----4)-beta-D-GlcAp(1----4)-alph a-D- GlcNp2S3S6S(1----4)-alpha-L-IdoAp2S(1----4)-alpha-D-GlcNp 2S6S(1----. This study shows the presence of one or both types of ATIII-binding-site variants in all of the heparins that were examined.

Animals↗
PubMedDate not supplied

Species and structural variations affecting pyrethroid neurotoxicity.

Pyrethroids provide fascinating patterns and examples of species selectivity resulting from variations in nerve sensitivity and detoxification rates. Three classification systems are useful in considering pyrethroids: origin, structure, stability and use relative to the natural pyrethrin I; lethal and sublethal or knockdown agents; Types I and II symptoms and nerve action. Pyrethroid-detoxifying esterases and oxidases contribute importantly to the species and strain specificity and provide an opportunity to use inhibitors as synergists for improved effectiveness. Pyrethroids are potent and selective neuropharmacological agents inducing repetitive discharges or conduction block in a variety of sensory and motor nerves and in the CNS. Small structural modifications in the pyrethroid often change the type of action as well as the potency and species specificity. Pyrethroid resistance in selected strains of insect pests may involve a modified and pyrethroid-insensitive target site.

Animals↗