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PubMed2000

Elucidation of the structural features of heparan sulfate important for interaction with the Hep-2 domain of fibronectin.

The interaction of fibronectin with cell surface heparan sulfate proteoglycans is important biologically in inducing reorganization of the cytoskeleton and the assembly of focal adhesions. The major heparan sulfate-binding site in fibronectin, which is also implicated in these morphological events, is the COOH-terminal Hep-2 domain. We describe the first extensive study of the structural determinants required for the interaction between heparan sulfate/heparin and Hep-2. It is clear that, in heparan sulfate, there is a very prominent role for N-sulfate groups, as opposed to a relatively small apparent contribution from carboxyl groups. Furthermore, a minimal octasaccharide binding sequence appeared to contain at least two 2-O-sulfated iduronate residues, but no 6-O-sulfate groups. However, affinity was enhanced by the presence of 6-O-sulfates, and the interaction with Hep-2 also increased progressively with oligosaccharide size up to a maximum length of a tetradecasaccharide. This overall specificity is compatible with recent information on the structure of Hep-2 (Sharma, A., Askari, J. A., Humphries, M. J., Jones, E. Y., and Stuart, D. I. (1999) EMBO J. 18, 1468-1479) in which two separate, positively charged clusters, involving up to 11 basic amino acid residues (mostly arginines with their preferential ability to co-ordinate sulfate groups), could form a single extended binding site.

3T3 Cells↗
PubMed2002

Structural features of two distinct molecular complexes of copper(II) cationic porphyrin and deoxyribonucleotides.

The associations of the water-soluble cationic copper(II)-5,10,15,20-meso-tetrakis(4-N-methylpyridyl) porphyrin (CuP) with d(pT)9 oligothymidylate and its building blocks deoxythymidine (dT) and deoxythymidine 5'-monophosphate (dTMP) were investigated by spectrophotometric titration [absorption, nanosecond transient resonance Raman (ns-RR) and picosecond time-resolved resonance Raman (ps-TR3) spectroscopies] to elucidate the structural requirements for the CuP exciplex formation in molecular complexes with unchained mononucleotides. In the d(pT)9 a factor analysis and global fit of the CuP absorption spectra revealed the formation of a single spectral species attributable to a 1 : 1 CuP. d(pT)9 complex throughout a wide range of d(pT)9/CuP ratios (0-10). Using ps-TR3 spectroscopy, the CuP. d(pT)9 complex was shown to be fully responsible for exciplex formation. In contrast, CuP mixed with dTMP ([dTMP]/[CuP] < 3000) yielded two spectroscopically distinct types of molecular complexes with 1 : 1 (CuP. dTMP) and 1 : 2 (CuP. (dTMP)2) (or even higher for [dTMP]/[CuP] > 3000) stoichiometry, the latter being spectroscopically identical to the CuP. d(pT)9 and providing a microenvironment favorable for exciplex formation to the same extent as the oligothymidylate. On the other hand, the 1 : 1 CuP. dTMP complex (prevailing for [dTMP]/[CuP] < 100) yielded no exciplex features. Similar behavior was observed for the CuP complexed with dT. To explain the difference in the ability of the CuP. dTMP and CuP. (dTMP)2 species to form the exciplex, two types of molecular complexes were suggested and discussed, differing in the orientation of the thymine planes with respect to the porphyrin macrocycle.

Cations↗
PubMed1993

Structural features of the 26 S proteasome complex.

Proteasomes play a key role in the degradation of abnormal proteins, of short-lived regulatory proteins and in antigen processing. Evidence is accumulating that the 20 S proteasome represents the proteolytic core of the 26 S protease complex (26 S proteasome) which contains several additional subunits implicated in regulation and substrate recognition. Using electron microscopy and digital image analysis we obtained first insights into the structure of this complex which has an estimated molecular weight of approximately 2000 kDa. Two highly asymmetric masses which presumably contain the regulatory subunits of the 26 S complex are attached to both ends of the dimeric 20 S proteasome clearly reflecting its C2 symmetry. The structural uniformity of the complex, i.e. the absence of significant inter-image variations, has important implications for the structure of the latter: It indicates that, in spite of their sequence similarities, the various alpha-type and beta-type subunits of the 20 S proteasome are not promiscuous but occupy precisely defined positions.

Animals↗
PubMed1993

Regulated activity of the distal promoter-like element of the human corticotropin-releasing hormone gene and secondary structural features of its corresponding transcripts.

Corticotropin-releasing hormone (CRH) plays a major role in the coordination of the stress response. Its gene is expressed in multiple brain regions, the peripheral sympathetic system and the placenta, as well as in peripheral inflammatory sites where CRH acts as a pro-inflammatory cytokine. The human (h) CRH gene, in addition to its primary promoter (TATA box I), has a second distal promoter-like structure (TATA box II) and a functional cyclic adenosine monophosphate-responsive element, all of which are preserved in the rat and ovine genes. To examine the functionality of TATA II, we positioned a 881-bp-long segment of the 5' flanking region of the hCRH gene containing TATA II, but lacking TATA I, upstream from a chloramphenicol acetyltransferase (CAT) reporter gene cloned in a pUC vector. We transfected COS-7 cells with this construct and examined responsiveness of CAT activity to potential stimulants and inhibitors. Phorbol ester (TPA) and forskolin had mild but clear stimulatory effects on CAT expression (approximately 1.5- and approximately 1.3-fold, respectively), with a combined effect of approximately 1.9-fold. Dexamethasone (DEX) inhibited TPA-stimulated CAT activity by approximately 2.6-fold. In contrast, in the presence of a co-transfected glucocorticoid receptor cDNA expression plasmid, DEX augmented TPA-stimulated CAT expression by approximately 3.1-fold. The predicted secondary structures of the primary transcripts employing the distal and proximal promoters had significant differences, which could affect their stability and translatability.2

Base Sequence↗
PubMed1989

Prostate. III--A structural feature characteristic of the rat prostate 5 alpha-reductase active site.

To aid in the design of new inhibitors of steroidal 5 alpha-reductase for treatment of prostate cancer, we have studied the topography of the 5 alpha-reductase active site (5 alpha-R) and of the related androgen (RA) and progesterone (RP) receptors in the region complementary to C.6 of progesterone. To this end we have determined the total structures of 17 alpha-acetoxy-6-methylene-4-pregnene-3,20-dione (VII; R = H) and of 17 beta-hydroxy-6,6-ethylene-4-androsten-3-one (VIa) by X-ray crystal structure analysis and, using these data, have developed Newman projections of the 6 alpha-Me, 6 beta-Me, 6-methylene and 6,6-ethylene derivatives of progesterone. From them we have developed a Newman projection of a composite model formed from steroids (V), (VI), (VIIIa) and (VIIIb). This is shown in Fig. 4 and illustrates the relative conformations of these substituents around C.6. From there we proceeded to receptor-binding studies. Our results led to the conclusion that androgen receptor, (RA), takes up preferred but different conformations when bound to testosterone (T) and to 17 beta-hydroxy-5 alpha-androstan-3-one (5 alpha-dihydrotestosterone, DHT), respectively, and that the resulting steroid-receptor complexes bind preferentially to different chromatin acceptor sites. We have therefore used the convention RT and RDHT in place of RA as appropriate. Working on the assumption that binding affinities reflect spatial contours, we have developed comparative silhouettes for the 5 alpha-R, RP and RDHT protein binding sites complementary to C.6 of the steroidal ligand. These data show that the 5 alpha-reductase active site is characterized by a hydrophobic pocket which specifically accommodates a 6-methylenic moiety and partially accommodates a 6 beta-methyl group. RDHT, in contrast, shows much less specificity and largely accommodates all the above substituents. Progesterone receptor differs in failing to accommodate 6,6-ethylene and 6 beta-methyl, with minimal accommodation of 6-methylene. It possesses a hydrophobic pocket skewed towards the alpha-face of the steroid, thereby allowing optimal binding of the 6 alpha-methyl substituent to the receptor. 6-Methylene-4-pregnene-3,20-dione (V) fails to bind significantly to androgen and progesterone receptors thereby supporting the postulate that its antiprostatic activity stems primarily from 5 alpha-reductase inhibition.

3-Oxo-5-alpha-Steroid 4-Dehydrogenase↗
PubMed1989

Host-range related structural features of the acidic extracellular polysaccharides of Rhizobium trifolii and Rhizobium leguminosarum.

Proton nuclear magnetic resonance (1H NMR) and fast atom bombardment mass spectrometric analyses were performed on enzymatically derived oligosaccharides from the acidic excreted polysaccharides (EPS) from representative bacterial strains of the pea-nodulating symbiont, Rhizobium leguminosarum (128C53, 128C63, and 300) and the clover-nodulating symbiont, Rhizobium trifolii (NA-30, ANU843, 0403, TA-1, LPR5035, USDA20.102, and 4S). The results revealed structural similarities and differences between EPS of these two species. Octasaccharide units containing galactose, glucuronic acid, alpha-L-threo-hex-4-enopyranosyluronic acid, and glucose in a molar ratio of 1:1:1:5 were obtained from the EPS of the three R. leguminosarum strains and had the same primary glycosyl sequence and location of pyruvate, acetate, and 3-hydroxybutyrate substituents. About 80% of the galactose residues were acylated with 3-hydroxybutyrate, and there were two acetyl groups per repeating unit distributed between the 2 glucose residues of the main chain-derived sequence of the octasaccharides. In contrast, the R. trifolii strains had varied EPS structures, each of which differed from the common R. leguminosarum EPS structure. The EPS from one group of R. trifolii strains (0403 and LPR5035) most closely resembled the R. leguminosarum EPS but differed in that a lower number of galactose and glucose residues were substituted by 3-hydroxybutyryl and acetyl groups, respectively. The EPS from a second group of R. trifolii strains (ANU843, TA-1, and NA-30) was even more different than the R. leguminosarum EPS. These R. trifolii octasaccharides bore a single acetyl group on O-3 of the glucuronic acid residue. In addition, the level of acylation by 3-hydroxybutyryl groups was 50% of that present in the R. leguminosarum EPS. The remaining two strains of R. trifolii (USDA20.102 and 4S) had very different patterns of acylation to each other and to all of the other strains. The EPS from strain USDA20.102 practically lacked 3-hydroxybutyryl groups and had a unique degree and pattern of acetylation. The oligomers from the EPS of R. trifolii strain 4S completely lacked 3-hydroxybutyryl groups and galactose. The latter EPS contained only one O-1-carboxyethylidene group and had a different degree and pattern of acetylation. Interestingly, these two latter strains differ from the other R. trifolii strains in nodulation rates on rare clover species in the Trifolium cross-inoculation group. Thus, we define several groups of R. trifolii based upon their EPS structures and establish their similarities and distinct differences with the EPS of R. leguminosarum.(ABSTRACT TRUNCATED AT 400 WORDS)

Gas Chromatography-Mass Spectrometry↗
PubMed2006

Cadmium-induced alterations of the structural features of pectins in flax hypocotyl.

In the course of our studies on the putative role of pectins in the control of cell growth, we have investigated the effect of cadmium on their composition, remodelling and distribution within the epidermis and fibre tissues of flax hypocotyl (Linum usitatissimum L.). Cadmium-stressed seedlings showed a significant inhibition of growth whereas the hypocotyl volume did not significantly change, due to the swelling of most tissues. The structural alterations consisted of significant increase of the thickness of all cell walls and the marked collapse of the sub-epidermal layer. The pectic epitopes recognized by the anti-PGA/RGI and JIM5 antibodies increased in the outer parts of the epidermis (external tangential wall and junctions) and fibres (primary wall and junctions). Concomitantly, there was a remarkable decrease of JIM7 antibody labelling and consequently an increase of the ratio JIM5/JIM7. Conversely, the ratio JIM7/JIM5 increased in the wall domains closest to the plasmalemma, which would expel the cadmium ions from the cytoplasm. The hydrolysis of cell walls revealed a cadmium-induced increase of uronic acid in the pectic matrix. Sequential extractions showed a remodelling of both homogalacturonan and rhamnogalacturonan I. In fractions enriched in primary walls, the main part of the pectins became cross-linked and could be extracted only with alkali. In fractions enriched in secondary walls, the homogalacturonan moieties were found more abundantly in the calcium-chelator extract while the rhamnogacturonan level increased in the boiling water extract.

Cadmium↗
PubMed1998

Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits.

Molecular medicine began with Pauling's seminal work, which recognized sickle-cell anemia as a molecular disease, and with Ingram's demonstration of a specific chemical difference between the hemoglobins of normal and sickled human red blood cells. During the four decades that followed, investigations have focused on the gene--how mutations specifically alter DNA and how these changes affect the structure and expression of encoded proteins. Recently, however, the advances of the human genome project and the completion of total genome sequences for yeast and many bacterial species, have enabled investigators to view genetic information in the context of the entire genome. As a result, we recognize that the mechanisms for some genetic diseases are best understood at a genomic level. The evolution of the mammalian genome has resulted in the duplication of genes, gene segments and repeat gene clusters. This genome architecture provides substrates for homologous recombination between nonsyntenic regions of chromosomes. Such events can result in DNA rearrangements that cause disease.

Chromosome Aberrations↗
PubMed2004

High-pressure cryoimmobilization of murine skin reveals novel structural features and prevents extraction artifacts.

Cryoimmobilization by high-pressure freezing (HPF) and subsequent freeze substitution has been proven as an effective method to preserve tissues. Here, we demonstrate for the first time that a comprehensive morphological and ultrastructural preservation of mouse skin throughout all its layers can be achieved in this way. Using conditions limiting tissue-extraction during freeze substitution, we could prevent the massive interdigitation of cell membranes, the loss of tubular structures of the Golgi complex, the aggregation of keratin to electron-dense bundles, the formation of round-shaped keratohyalin aggregates, the dispersion of locally organized ribosomes, the excessive aggregation of material at hemidesmosomal plaques, the massive extraction of material from the basement membrane and the adjacent dermal region, and the dissociation of components of the dermal matrix. Taken together, HPF in combination with freeze substitution emerges as a highly sensitive tool for morphological and ultrastructural analysis.

Animals↗
PubMed1987

Structural features of the terminal loop region of frog retinal rod outer segment disk membranes: III. Implications of the terminal loop complex for disk morphogenesis, membrane fusion, and cell surface interactions.

The perimeter of rod outer segment (ROS) disks displays a two-dimensional lattice of components referred to as the terminal loop complex (Corless, Fetter, Zampighi, Costello, and Wall-Buford: J. Comp. Neurol. 257:9-23, '87b). We take the view that this pattern of structural organization reflects the mechanism(s) whereby the disk perimeter is defined and constructed. Herein we develop and partially evaluate a generalized template mechanism of disk perimeter development, to account for the structure and the axial alignment of both marginal and incisural domains. Components of the terminal loop complex are conceived as the morphogens that determine the location and guide the differentiation of the disk perimeter. Briefly, we postulate that transmembranous components of the terminal loop complex are present within the reflection of plasmalemma that forms the base of the rod outer segment. These components interact with the cytoplasmic template provided by the perimeter lattice present along the lower surface of the most basal disk, thereby propagating the lattice and creating an extracellular template. The latter is then available to interact with corresponding elements distributed within the apical surface of the adjacent disk precursor evagination. The progressive interaction and alignment of these extracellular domains form the scaffolding that guides the restructuring of the plasmalemma, to form the mature disk margin topology. Successive repetitions of this process are seen to produce an axial stacking of disks whose perimeters are aligned and ensheathed by a two-dimensional net.

Animals↗
PubMed1991

Conformational analysis of the amino termini (5 residues) of human glycophorin AM and AN: differentiation of the structural features of the TN and T antigenic determinants in relation to their specificity.

The N-terminus of glycophorin A, the main transmembrane erythrocyte glycoprotein responsible for the MN blood-group specificity, has been modelled. As the minimum size of the protein recognised by the antiglycophorin A antibodies is the N-terminal glycopentapeptide, attention was focused on the TN and T antigenic determinants of this size in order to determine wether differences in 3D structure exist and how a specific response with different antibodies is induced.

Amino Acid Sequence↗
PubMedDate not supplied

Determination of the structural features of (+)-CC-1065 that are responsible for bending and winding of DNA.

Analysis of the anomalous migration in electrophoretic mobilities of (+)-CC-1065-modified oligomers following ligation reveals that (+)-CC-1065 induces DNA bending and winding of the helix. (+)-CC-1065 is a potent antitumor antibiotic produced by Streptomyces zelensis. This drug selectively bonds covalently to N3 of adenine and lies in the minor groove of DNA, reacting in a highly sequence-selective manner. Structurally, (+)-CC-1065 consists of three subunits: two identical pyrroloindole units (subunits B and C) and a third subunit containing the DNA-reactive cyclopropane ring (subunit A). While the bonding reaction is the main determinant of DNA sequence selectivity of (+)-CC-1065, binding interactions between the inside edge substituents of the B and C subunits and the floor of the minor groove of DNA can modulate or fine tune this sequence selectivity, [Hurley, L. H., Lee, C.-S., McGovern, J. P., Mitchell, M. A., Warpehoski, M. A., Kelly, R. C., & Aristoff, P. A. (1988) Biochemistry 27, 3886-3892]. The A subunit of (+)-CC-1065 is responsible for the bending of DNA, and close van der Waals contacts between the inside edge of (+)-CC-1065 and the floor of the minor groove of DNA cause winding equivalent to about 1 base pair per alkylation site and stiffening of DNA. The magnitude of DNA bending induced by (+)-CC-1065 and related compounds is about 14-19 degrees, which is equivalent to that produced by an adenine-thymine tract of about 5-6 base pairs in length. Experiments using oligomers containing both an adenine tract and a unique (+)-CC-1065 bonding site approximately one helix turn apart demonstrate that the directionality of drug-induced bending is in toward the minor groove and the locus of bending is about 2-3 base pairs to the 5'-side of the covalently modified adenine. A circularization efficiency assay shows that the optimum size of circles produced by (+)-CC-1065 and related drugs is between 168 and 180 base pairs. These results are discussed in relation to the molecular basis of the DNA sequence selectivity of (+)-CC-1065, and the (+)-CC-1065-induced DNA bending is compared with the intrinsic bending associated with adenine tracts. Since (+)-CC-1065 induces effects on local DNA structure that appear similar to those produced naturally by adenine tracts and certain DNA binding proteins, the relevance of this phenomenon to biological effects of (+)-CC-1065 and related drugs is considered.

Antibiotics, Antineoplastic↗
PubMed1999

Structural features of a gene encoding the vacuolar H+-ATPase c subunit from a marine red alga, Porphyra yezoensis.

We report the nucleotide sequence of a gene encoding the c ('16 kDa') subunit of the vacuolar-type H+-ATPase (V-ATPase) from a marine red alga, Porphyra yezoensis. A cDNA clone was isolated from a leafy gametophyte cDNA library and analyzed for the sequence. The genomic DNA sequence was directly determined by nested PCR. The structural gene contained four introns within a coding sequence of 483 base pairs which encodes a polypeptide of 161-amino acids with four hydrophobic transmembrane-spanning regions. Comparison of the deduced amino acid sequences showed higher similarity to the land plant Oryza sativa (69.1%) than to the Ulvophyceae Acetabularia acetabulum (64.1%). The mRNA was detected both in the leafy gametophytes and filamentous sporophytes.

Amino Acid Sequence↗
PubMed1999

Structural features and hypoglycemic activity of a polysaccharide (CS-F10) from the cultured mycelium of Cordyceps sinensis.

A polysaccharide (CS-F10) purified from a hot water extract of the cultured mycelium of Cordyceps sinensis was composed of galactose, glucose and mannose in a molar ratio of 43:33:24; its molecular weight was estimated to be about 15000. The results of chemical and spectroscopic investigations suggest that CS-F10 has a comb-type structure, and has alpha-D-glucopyranosyl residues on the terminal of the side-chains and characteristic sugar residues of C. sinensis i.e., 1,5-linked beta-D-galactofuranosyl residues. CS-F10 significantly lowered the plasma glucose level in normal, streptozotocin (STZ)-induced diabetic and epinephrine-induced hyperglycemic mice after intraperitoneal administration (50 mg/kg). Administration of CS-F10 to STZ-induced diabetic mice significantly increased the activity of hepatic glucokinase. A significant reduction in the hepatic glucose output was observed following the infusion of CS-F10 using the perfused rat liver. CS-F10 also significantly decreased protein content of facilitative glucose transporter isoform 2 (GLUT2) from rat liver following i.p. administration. These effects presumably contribute to the hypoglycemic activity.

Animals↗
PubMed2003

Structural features of N-glycans linked to glycoproteins from oil palm pollen, an allergenic pollen*.

The pollen of oil palm (Elaeis guineensis Jacq.) is a strong allergen and causes severe pollinosis in Malaysia and Singapore. In the previous study (Biosci. Biotechnol. Biochem., 64, 820-827 (2002)), from the oil palm pollens, we purified an antigenic glycoprotein (Ela g Bd 31 K), which is recognized by IgE from palm pollinosis patients. In this report, we describe the structural analysis of sugar chains linked to palm pollen glycoproteins to confirm the ubiquitous occurrence of antigenic N-glycans in the allergenic pollen. N-Glycans liberated from the pollen glycoprotein mixture by hydrazinolysis were labeled with 2-aminopyridine followed by purification with a combination of size-fractionation HPLC and reversed-phase HPLC. The structures of the PA-sugar chains were analyzed by a combination of two-dimensional sugar chain mapping, electrospray ionization mass spectrometry (ESI-MS), and tandem MS analysis, as well as exoglycosidase digestions. The antigenic N-glycan bearing alpha1-3 fucose and/or beta1-2 xylose residues accounts for 36.9% of total N-glycans: GlcNAc2Man3Xyl1Fuc1GlcNAc2 (24.6%), GlcNAc2Man3Xyl1GlcNAc2 (4.4%), Man3Xyl1Fuc1-GlcNAc2 (1.1%), GlcNAc1Man3Xyl1Fuc1GlcNAc2 (5.6%), and GlcNAc1Man3Xyl1GlcNAc2 (1.2%). The remaining 63.1% of the total N-glycans belong to the high-mannose type structure: Man9GlcNAc2 (5.8%), Man8GlcNAc2 (32.1%), Man7GlcNAc2 (19.9%), Man6GlcNAc2 (5.3%).

Allergens↗