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PubMed2007

Structure and properties of a truely apo form of AraC dimerization domain.

The arabinose-binding pockets of wild type AraC dimerization domains crystallized in the absence of arabinose are occupied with the side chains of Y31 from neighboring domains. This interaction leads to aggregation at high solution concentrations and prevents determination of the structure of truely apo AraC. In this work we found that the aggregation does not significantly occur at physiological concentrations of AraC. We also found that the Y31V mutation eliminates the self-association, but does not affect regulation properties of the protein. At the same time, the mutation allows crystallization of the dimerization domain of the protein with only solvent in the arabinose-binding pocket. Using a distance difference method suitable for detecting and displaying even minor structural variation among large groups of similar structures, we find that there is no significant structural change in the core of monomers of the AraC dimerization domain resulting from arabinose, fucose, or tyrosine occupancy of the ligand-binding pocket. A slight change is observed in the relative orientation of monomers in the dimeric form of the domain upon the binding of arabinose but its significance cannot yet be assessed.

AraC Transcription Factor↗
PubMed1991

Analysis of local helix geometry in three B-DNA decamers and eight dodecamers.

Local variations in B-DNA helix structure are compared among three decamers and eight dodecamers, which contain examples of all ten base-pair step types. All pairwise combinations of helix parameters are compared by linear regression analysis, in a search for internal relationships as well as correlations with base sequence. The primary conclusions are: (1) Three-center hydrogen bonds between base-pairs occur frequently in the major groove at C-C, C-A, A-A and A-C steps, but are less convincing at C-C and C-T steps in the minor groove. The requirements for large base-pair propeller are (1) that the base-pair should be A.T rather than G.C, and (2) that it be involved in a major groove three-center hydrogen bond with the following base-pair. Either condition alone is insufficient. Hence, a large propeller is expected at the leading base-pair of A-A and A-C steps, but not at A-T, T-A, C-A or C-C steps. (2) A systematic and quantitative linkage exists between helix variables twist, rise, cup and roll, of such strength that the rise between base-pairs can hardly be described as an independent variable at all. Two typical patterns of behavior are observed at steps from one base-pair to the next: high twist profile (HTP), characterized by high twist, low rise, positive cup and negative roll, and low twist profile (LTP), marked by low twist, high rise; negative cup and positive roll. Examples of HTP are steps G-C, G-A and Y-C-A-R, where Y is pyrimidine and R is purine. Examples of LTP steps are C-G, G-G, A-G and C-A steps other than Y-C-A-R. (3) The minor groove is especially narrow across the two base-pairs of the following steps: A-T, T-A, A-A and G-A. (4) In general, base step geometry cannot be correlated solely with the bases that define the step in question; the two flanking steps also must be taken into account. Hence, local helix structure must be studied in the context, not of two base-pairs: A-B, but of four: x-A-B-y. Calladine's rules, although too simple in detail, were correct in defining the length of sequence over which a given perturbation is expressed. Whereas ten different two-base steps are possible, allowing for the identity of complementary sequences, there are 136 different four-base steps. Only 33 of these 136 four-base steps are represented in the decamer and dodecamer structures solved to date, and hence it is premature to try to set up detailed structural algorithms. (5) The sugar-phosphate backbone chains of B-DNA place strong limits on sequence-induced structural variation, damping down most variables within four or five base-pairs, and preventing purine-purine anti-anti mismatches from causing bulges in the double helix. Hence, although short-range sequence-induced deformations (or deformability) are observed, long-range deformations propagated down the helix are not to be expected.

Base Composition↗
PubMed1987

Synthesis and antitumor activity of tropolone derivatives. 6. Structure-activity relationships of antitumor-active tropolone and 8-hydroxyquinoline derivatives.

The bis derivative 6 of 8-hydroxyquinoline, which, like tropolones, readily forms a chelate, was synthesized and found to have high potency (dose = 12.5 mg/kg, T/C % = 164) against leukemia P388 in mice approximately equivalent to that of the bistropolone 1b. 8-Hydroxyquinoline analogues with broad structural variation were synthesized and their structure-activity relationships followed the same pattern as in the tropolone series. In addition, the bistropolones 1a-e were tested for their ability to bind to tubulin and found to have no such property. The results of this study suggested that bistropolone and bis(8-hydroxyquinoline) derivatives must form a chelate with the metal necessary for the enzyme, such as ribonucleotide reductase, which catalyzes the DNA biosynthetic pathways.

Animals↗
PubMed1997

Solution structure of reduced microsomal rat cytochrome b5.

The solution structure of the major form of the reduced soluble fragment of rat microsomal cytochrome b5 has been solved through 1H-NMR spectroscopy. The protein contains 98 amino acids. Proton assignment was available for residues 1-94, except 90 [Guiles, R. D., Basus, V. J., Kuntz, I. D. & Waskell, L. (1992) Biochemistry 31, 11,365-11,375] and has been confirmed. From 1722 NOEs, of which 1203 were found to be meaningful, a family of 40 energy-minimized structures has been obtained with average backbone rmsd (for residues 5-89) of 0.078 +/- 0.018 nm and average target function of 0.0045 nm2, no distance violations being larger than 0.029 nm. The structure has been compared with the X-ray structure of the oxidized rat mitochondrial isoenzyme and with that of the highly similar bovine microsomal isoenzyme in the oxidized form. The analysis of the elements of secondary structure is instructive in terms of their stability and of their occurrence in related structures, and of the capability of NMR and X-ray spectroscopy to observe them. Some detailed structural variations are noticed among the solved structures of the various isoenzymes and between solid and solution. The structural features in solution of the residues proposed to be involved in protein-protein recognition are found to be largely conserved with respect to the solid state.

Amino Acid Sequence↗
PubMed2005

The HS:1 serostrain of Campylobacter jejuni has a complex teichoic acid-like capsular polysaccharide with nonstoichiometric fructofuranose branches and O-methyl phosphoramidate groups.

Recently, the CPS biosynthetic loci for several strains of Campylobacter jejuni were sequenced and revealed evidence for multiple mechanisms of structural variation. In this study, the CPS structure for the HS:1 serostrain of C. jejuni was determined using mass spectrometry and NMR at 600 MHz equipped with an ultra-sensitive cryogenically cooled probe. Analysis of CPS purified using a mild enzymatic method revealed a teichoic acid-like [-4)-alpha-d-Galp-(1-2)-(R)-Gro-(1-P](n), repeating unit, where Gro is glycerol. Two branches at C-2 and C-3 of galactose were identified as beta-d-fructofuranoses substituted at C-3 with CH(3)OP(O)(NH(2))(OR) groups. Structural heterogeneity was due to nonstoichiometric glycosylation at C-3 of galactose and variable phosphoramidate groups. Identical structural features were found for cell-bound CPS on intact cells using proton homonuclear and (31)P heteronuclear two-dimensional HR-MAS NMR at 500 MHz. In contrast, spectroscopic data acquired for hot water/phenol purified CPS was complicated by the hydrolysis and subsequent loss of labile groups during extraction. Collectively, the results of this study established the importance of using sensitive isolation techniques and HR-MAS NMR to examine CPS structures in vivo when labile groups are present. This study uncovered how incorporation of variable O-methyl phosphoramidate groups on nonstoichiometric fructose branches is used in C. jejuni HS:1 as a strategy to produce a highly complex polysaccharide from its small CPS biosynthetic locus and a limited number of sugars.

Campylobacter jejuni↗
PubMed1962

Cross-tolerances of dieldrin-resistant flies and mosquitos to various cyclodiene insecticides.

Nineteen cyclodiene insecticides incorporating major and minor structural variations of the chlorinated bridged bicycloheptene structure were evaluated against susceptible and dieldrin-resistant houseflies, and against larvae and adults of susceptible Culex pipiens quinquefasciatus Say and dieldrin-resistant Anopheles albimanus Wied. Determinations of LD(50) or LC(50) values demonstrated cross-resistance to all of the cyclodienes studied. This cross-resistance was very marked for most compounds, but was least in all cases for octachloro-endomethano-tetrahydrophthalan (Telodrin), which was also very toxic to the susceptible insects.

Animals↗
PubMed2025

Comparative Analysis of Mammalian Adaptive Immune Loci Revealed Spectacular Divergence and Common Genetic Patterns.

Adaptive immune responses are mediated by the production of adaptive immune receptors, antibodies, and T-cell receptors, which bind antigens, thus causing their neutralization. Unlike other proteins, adaptive immune receptors are not fully encoded in the germline genome and result from a complex of somatic processes collectively called V(D)J recombination affecting germline immunoglobulin (IG) and T-cell receptor (TR) loci consisting of template genes. While various existing studies report extreme diversity of antibodies and T-cell receptors, little is known about the diversity of germline IG and TR loci. To overcome this gap, the first comparative analysis of full-length sequences of IG/TR loci across 46 mammalian species from 13 taxonomic orders was performed. First, germline gene counts were shown to correlate in immunoglobulin heavy chain immunoglobulin heavy chain (IGH)/immunoglobulin lambda (IGL) loci and T-cell receptor alpha (TRA)/T-cell receptor beta (TRB) and anticorrelate in immunoglobulin kappa (IGK)/IGL, possibly indicating coevolution between corresponding chains. Second, structures of IG/TR loci were analyzed, and it was shown that IG/TR loci formed by long arrays of high multiplicity repeats are more common for species that have experienced population bottlenecks. Finally, haplotypes of IG/TR loci with little or no sequence similarity within a species were found, suggesting that they may have a limited potential for homologous recombination. These results demonstrate that IG/TR loci are rapidly evolving genomic regions whose structural variation is shaped by the population history of the species and open new perspectives for immunogenomics studies.

Animals↗
PubMed1999

Nuclear chromatin variations in human spermatozoa undergoing swim-up and cryopreservation evaluated by the flow cytometric sperm chromatin structure assay.

The sperm chromatin structure assay (SCSA) is a flow cytometric (FCM) technique which exploits the metachromatic properties of Acridine Orange to monitor the susceptibility of sperm chromatin DNA to in-situ acid denaturation. SCSA was used to study the chromatin structure variations of human spermatozoa in semen, both before and after swim-up and after cryopreservation. Semen samples were provided by 19 healthy normozoospermic subjects attending pre-marriage checks. Each sample was divided into three aliquots: the first aliquot was evaluated without further treatment, the second underwent swim-up, and the third was stored according to standard cryopreservation techniques in liquid nitrogen at -196 degrees C. Samples were also analysed by light and fluorescence microscopy (after Acridine Orange staining to evaluate the number of green fluorescent sperm heads), and by computer-assisted semen analysis. The results showed that post-rise spermatozoa represent a subpopulation characterized by a general improvement of the morphological (reduction of the percentage of abnormal forms and heads, increase of the green head sperm percentage) and kinetic parameters. This subpopulation also exhibited improved chromatin structure properties, confirming that these cells have the best structural and functional characteristics, indicative of optimal fertilizing ability. On the other hand, overall sperm quality deteriorates after cryopreservation. When thawed spermatozoa underwent an additional swim-up round, a general improvement of nuclear maturity was seen in the post-rise spermatozoa.

Adult↗
PubMed2006

Physicochemical properties and structures of room-temperature ionic liquids. 3. Variation of cationic structures.

A series of room-temperature ionic liquids (RTILs) were prepared with different cationic structures, 1-butyl-3-methylimidazolium ([bmim]), 1-butylpyridinium ([bpy]), N-butyl-N-methylpyrrolidinium, ([bmpro]), and N-butyl-N,N,N-trimethylammonium ([(n-C(4)H(9))(CH(3))(3)N]) combined with an anion, bis(trifluoromethane sulfonyl)imide ([(CF(3)SO(2))(2)N]), and the thermal property, density, self-diffusion coefficients of the cation and anion, viscosity, and ionic conductivity were measured over a wide temperature range. The self-diffusion coefficient, viscosity, ionic conductivity, and molar conductivity follow the Vogel-Fulcher-Tamman equation for temperature dependencies, and the best-fit parameters have been estimated, together with the linear fitting parameters for the density. The relative cationic and anionic self-diffusion coefficients for the RTILs, independently determined by the pulsed-field-gradient spin-echo NMR method, appear to be influenced by the shape of the cationic structure. A definite order of the summation of the cationic and anionic diffusion coefficients for the RTILs: [bmim][(CF(3)SO(2))(2)N] > [bpy][(CF(3)SO(2))(2)N] > [bmpro][(CF(3)SO(2))(2)N] > [(n-C(4)H(9))(CH(3))(3)N][(CF(3)SO(2))(2)N], has been observed, which coincides with the reverse order to the viscosity data. The ratio of molar conductivity obtained from the impedance measurements to that calculated by the ionic diffusivity using the Nernst-Einstein equation quantifies the active ions contributing to ionic conduction in the diffusion components and follows the order: [bmpro][(CF(3)SO(2))(2)N] > [(n-C(4)H(9))(CH(3))(3)N][(CF(3)SO(2))(2)N] > [bpy][(CF(3)SO(2))(2)N] > [bmim][(CF(3)SO(2))(2)N] at 30 degrees C.

Journal Article↗
PubMed1991

Quantitative structure-activity relationships of heterocyclic amine mutagens formed during the cooking of food.

The major protein-rich foods, particularly muscle meats, contain part-per-billion quantities of potent mutagens formed by frying or broiling to a well-done state. Related mutagens are formed by pyrolysis of amino acids or proteins and in heated model systems. The thermic mutagens so far identified are heterocyclic aromatic amines of aminoimidazo-azaarene (AIA) and aminocarboline classes. The chemicals require activation by enzymes to form metabolites reactive with nucleic acids. These thermic mutagens, and numerous synthetic congeners, exhibit an enormous range of potency as frameshift mutagens in the Ames/Salmonella assay. However, structural variations are nominal within the two classes. Structural parameters that appeared relevant to determining potency were selected for 38 AIAs and 23 amino-carbolines. For the AIA class these were: the number of fused rings, the number of heteroatoms in Rings 2 and 3, methyl substitution on imidazo ring nitrogen atoms, and methyl substitution on ring carbon atoms. For the amino-carboline class the structural parameters were: the position of the pyridine-type nitrogen atom in Ring 1, the substitution position of the exocyclic amino group on Ring 1, and methyl substitution on ring carbon atoms. These structural parameters may influence mutagenic potency in the following ways. 1) Electronic or steric effects may determine the reactivity and stability of the ultimate mutagenic metabolite. Optimal balance of reactivity and lifetime of this transient intermediate may be required for access to and reaction with nuclear DNA to cause mutations. 2) Substitution on the rings may block detoxication reactions. The structural parameters identified should prove useful in predicting the mutagenicity of untested compounds of these types.

Amines↗
PubMed1992

Substructure of the flagellar basal body of Salmonella typhimurium.

The Salmonella typhimurium basal body, a part of the flagellar rotary motor, consists of four rings (denoted M, S, P and L) and a coaxial rod. Using low-dose electron microscopy and image averaging methods on negatively stained and frozen-hydrated preparations, we examined whole basal body complexes and subcomplexes obtained by dissociation in acid. Dissociation occurs in steps, allowing us to obtain images of substructures lacking the M ring, lacking the M and S rings, and lacking the M and S rings and the proximal portion of the rod. We obtained images of the L and P ring subcomplex. The existence of a subcomplex missing only the M ring suggests either that the S and M rings derive from two different proteins, or that the M ring is a labile domain of a single protein, which makes up both rings. At the 25 to 30 A resolution of our averaged images, the L, P and S rings appear cylindrically symmetric. Images of the M ring show variability that may be due to differences in angular orientation of the grid, but equally could be due to structural variations. Three-dimensional reconstructions of these structures from the averaged images reveal the internal structure and spatial organization of these components.

Flagella↗
PubMed1998

An Octahedral Template Based on a New Molecular Turn: Synthesis and Structure of a Model Complex and a Reactive, Diphenolic Ligand and Its Metal Complexes.

The design and synthesis of a new family of tridentate Schiff base ligands for use in octahedral molecular templates has been successfully demonstrated. As anticipated, two molecules of the ligand, 2,6-pyridinedicarboxaldhydebis(p-hydroxyphenylimine), coordinate equatorially to six-coordinate octahedral metal ions to give orthogonally oriented molecular turns around the anchoring metal ion. This new template offers the advantages that (1) syntheses of the ligand and its complexes are straightforward, giving high yields in simple, one-pot reactions, and (2) structural variations are easily accomplished. X-ray structural analysis has shown that the ligand will only function as a turn when its spatial organization is controlled by coordination to a metal ion. Upon chelation, the phenolic groups are directed across and beyond the metal ion center, and, unlike earlier ligands of this general type which lacked reactive moieties, substitution reactions may be carried out at the free phenolic groups of the octahedral complex. These reactions remain to be optimized in order to achieve the long-term goal of proving their value as synthons for interlocked molecules.

Journal Article↗
PubMed1990

Variable antigens of Ureaplasma urealyticum containing both serovar-specific and serovar-cross-reactive epitopes.

Currently there are 14 recognized serovars of Ureaplasma urealyticum, and it has been postulated that only certain ones may be associated with disease and that lack of serovar-specific antibody may be an important risk factor. Unfortunately, ureaplasma antigens important in the human immune response and disease pathogenesis are poorly defined. By using sera from ureaplasma-infected patients and antiureaplasma monoclonal antibodies, the present study has demonstrated, for serovars 3, 8, and 10, antigens which (i) are species specific, (ii) contain both serovar-specific and cross-reactive epitope(s), (iii) are produced not only in vitro but also in vivo, (iv) undergo a high rate of structural variation in vitro, (v) are present and structurally variable on invasive ureaplasma isolates (i.e., those from placenta, lung, and cerebrospinal fluid), and (vi) are among the predominant antigens recognized during infections in humans. Furthermore, we have shown that monoclonal antibodies to these antigens can inhibit the growth of the organisms in vitro, indicating the potential for these antigens to be important for host defense.

Antibodies, Monoclonal↗
PubMed2001

Tacrine-huperzine A hybrids (huprines): a new class of highly potent and selective acetylcholinesterase inhibitors of interest for the treatment of Alzheimer's disease.

Tacrine-huperzine A hybrids (huprines) are a new class of very potent and selective acetylcholinesterase (AChE) inhibitors. Huprines were designed from tacrine and (-)-huperzine A through a conjunctive approach. They combine the 4-aminoquinoline substructure of tacrine with the carbobicyclic substructure of (-)-huperzine A. Structural variations on several parts of a lead structure have allowed to complete a structure-activity relationship exploration of this new structural family and have led to several huprines more active than other known AChE inhibitors.

Alkaloids↗
PubMedDate not supplied

Morphologic variations in bacteria under stress conditions: near-field optical studies.

The morphologic and structural variations suffered by cells of a population of Pseudomonas aeruginosa ATCC 27853 under stress conditions were investigated by using scanning near-field optical microscopy. The analysis of the images, supported by microbiological data, showed that the bacteria evolved from the initial distribution of rod-shaped cells of standard size to a population with structural and morphologic modifications. The detection of variations in the optical reflectivity over a subwavelength scale (< or = 100 nm), combined with the concurrently acquired topographical signal, allowed the visualisation of rod-shaped bacteria going towards a lytic process and entire "U"-shaped cells. In the latter cells, which derived from a morphology refolding of rod bacteria, cellular matter seemed to rearrange itself to attain a coccoid stress resistant form, responsible for the residual viability of the population.

Biomass↗
PubMed1996

A comparative study of perichondrial tissue in mammalian cartilages.

The general organization, cellular and extracellular components, and structural variation of perichondrium have been studied in different mammalian cartilages by polarized light and transmission electron microscopy. The overall structure is that of a dense connective tissue composed of variable numbers of thin, stratified, closely-packed lamellae, themselves composed of closely-matted collagen fibres running in the plane of the cartilage surface, but oriented at various angles to each other. Variations mainly concern the arrangement of the fibre bundles in the transition zones between perichondrial and cartilage matrices, and between perichondrium and surrounding tissues. Perichondrial cells have the characteristics of fibrocytes. A cambial layer of undifferentiated stem cells was never observed. A layer of 'perichondrial lining cells' with distinctive ultrastructural characteristics was observed in some cartilage units, which separates the perichondrium from the surrounding loose connective tissue. The ultrastructural results demonstrate that the cartilage and perichondrial extracellular matrices are distinct, and what have been designated perichondrial 'transition' and 'proliferative' zones are in fact parts of the most superficial cartilage layer. Variations in perichondrial structure appear to correlate with diversity of cartilage function and we conclude that each cartilage unit plus perichondrium forms a tightly-integrated entity, best regarded as a unitary organ within the skeletal system.

Adult↗
PubMed2003

Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its implications.

Single-stranded DNA-binding protein (SSB) is an essential protein necessary for the functioning of the DNA replication, repair and recombination machineries. Here we report the structure of the DNA-binding domain of Mycobacterium tuberculosis SSB (MtuSSB) in four different crystals distributed in two forms. The structure of one of the forms was solved by a combination of isomorphous replacement and anomalous scattering. This structure was used to determine the structure of the other form by molecular replacement. The polypeptide chain in the structure exhibits the oligonucleotide binding fold. The globular core of the molecule in different subunits in the two forms and those in Escherichia coli SSB (EcoSSB) and human mitochondrial SSB (HMtSSB) have similar structure, although the three loops exhibit considerable structural variation. However, the tetrameric MtuSSB has an as yet unobserved quaternary association. This quaternary structure with a unique dimeric interface lends the oligomeric protein greater stability, which may be of significance to the functioning of the protein under conditions of stress. Also, as a result of the variation in the quaternary structure the path adopted by the DNA to wrap around MtuSSB is expected to be different from that of EcoSSB.

Amino Acid Sequence↗