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PubMed1996

Structural features of the pectic polysaccharides isolated from retted hemp bast fibres.

Pectic polysaccharides were solubilized from retted hemp bast fibre bundles, by sequential extraction with water and ammonium oxalate at 100 degrees C. The polysaccharides isolated from the extracts were de-esterified and fractionated by anion exchange chromatography, yielding five fractions from boiling water extract and five fractions from oxalate characterized by chemicals methods, 1H and 13C NMR, as extract. Five of these fractions were characterized by chemicals methods, 1H and 13C NMR, as polysaccharides containing galacturonic acid, rhamnose and galactose units in variable ratios. Their chemical structure comprises a disaccharide repeating unit-->2)-alpha-L-Rhap-(1-->4)-alpha-GalpA-(1-->backbone, with short side chains attached to the rhamnosyl residues. The beta-D-Galactose residues are attached to O-4 of the rhamnosyl residues, but the amount of L-rhamnosyl residues that are 2,4-linked can vary from 36 to 75%, from one fraction to another. A fraction corresponding to a mixture of oligosaccharides with an average dp of 13, with ten galacturonic acid, two rhamnose and one galactose units was also isolated.

Cannabis↗
PubMed1998

[Structural features of the rat adrenal cortex with inherited stress-induced arterial hypertension in the early period of postnatal ontogenesis].

Comparative morphometric examination of adrenal cortex was carried out in 3 wks HNCAI rats with inherited stress induced arterial hypertension and normotensive Wistar rats. Relative adrenal mass, volume of cortex and its glomerular zone in HNCAI rats exceeds appropriate values in Wistar rats. Increase of adrenocorticocytes due to hyperplasia of their ultrastructural components was found. In hypertensive rats adrenocorticocyte numerical density increase due to their hyperplasia was found in adrenal fasciculate zone in contrast to glomerular one. These structural organization peculiarities in 3 wks hypertensive rat adrenal cortex reflect their elevated functional activity and may determine genetically programmed increased organism responsiveness to stress that consequently provides the grounds for the hypertensive status formation in this rat line.

Adrenal Cortex↗
PubMed1990

Immunological and structural features of the protein core of human polymorphic epithelial mucin.

The protein core of high mol. wt polymorphic epithelial mucin (PEM--approximately 400 kDa glycoprotein) which is associated with breast carcinomas, consists of a repeating 20 amino acid peptide motif [Gendler et al. (1988) J. biol. Chem. 263, 12,820-12,823]. Monoclonal antibodies C595 (anti-urinary mucin) and NCRC-11 (anti-breast carcinoma cells), and other antibodies against human milk fat globule membranes, were found to recognize determinants present within this 20 amino acid peptide. A model of the peptide was developed based on hydropathicity and structure prediction calculations and these indicated that the repeated structure is dominated by a hydrophilic domain of seven amino acids, extending into two flanking beta turns. NMR analysis of the 20 amino acid peptide was undertaken to probe the secondary structure. Epitope mapping experiments involving solid phase synthesis of overlapping heptapeptides in the repeat unit identified the minimum structures for antibody binding as Arg-Pro-Ala-Pro and Arg-Pro-Ala for the C595 and NCRC-11 antibodies, respectively. These determinants were found within the predicted hydrophilic turn region domain of the peptide. The epitopes for six other PEM-reactive monoclonal antibodies were also determined to reside within the predicted hydrophilic turn domain. This evidence is in accord with the disposition of this region of the PEM peptide core being at the exterior of the glycoprotein where it would be accessible to antibody recognition and binding events.

Amino Acid Sequence↗
PubMed2001

Structural features of a snake venom thrombin-like enzyme: thrombin and trypsin on a single catalytic platform?

The Lachesis muta thrombin-like enzyme (LM-TL) is a single chain serine protease that shares 38% sequence identity with the serine protease domain of thrombin and also displays similar fibrinogen-clotting activity. In addition, the 228 amino acid residue LM-TL is 52% identical to trypsin, and cleaves chromogenic substrates with similar specificity. Herein we report a three-dimensional (3D) model validated experimentally for LM-TL based on these two homologous proteins of known 3D structure. Spatial modeling of LM-TL reveals a serine protease with a chymotrypsin fold presenting a hydrophobic pocket on its surface, involved in substrate recognition, and an important 90's loop, involved in restricting the LM-TL catalytic site cleft. Docking analysis showed that LM-TL would not form a stable complex with basic pancreatic trypsin inhibitor and wild-type ecotin since its 90's loop would restrict the access to the catalytic site. LM-TL formed acceptable interactions with fibrinopeptide A and a variant of ecotin; ecotin-TSRR/R in which both the primary and secondary binding sites are mutated Val81Thr, Thr83Ser, Met84Arg, Met85Arg and Asp70Arg. Furthermore, analysis of the primary structures of LM-TL and of the seven snake venom thrombin-like enzymes (SVTLEs) family reveals a subgroup formed by LM-TL, crotalase, and bilineobin, both closely related to thrombin. Therefore, LM-TL provides an initial point to compare SVTLEs with their counterparts, e.g. the mammalian serine proteases, and a basis for the localization of important residues within the little known SVTLEs family.

Amino Acid Sequence↗
PubMed2006

Structural features of the modulated BiCu2(P(1-x)V(x))O6 solid solution; 4-D treatment of x = 0.87 compound and magnetic spin-gap to gapless transition in new Cu2+ two-leg ladder systems.

The BiCu(2)(P(1-x)V(x))O(6) system shows the appearance of various phenomena that progressively change as a function of the average (P/V)O(4) groups size. Then, from x = 0 to x approximately 0.7, a solid solution exists with respect to the basic orthorhombic unit cell of BiCu(2)PO(6). For greater x values (0.7 < x <0.96), structural modulations with incommensurate q vector that slightly change versus x appear. The 4-D treatment of single-crystal XRD data of the modulated phase corresponding to x = 0.87 at 100 K (orthorhombic, a = 12.379(3)Angstrom, b = 5.2344(9) Angstrom, c = 7.8270(14) Angstrom, q = 0.268(3) b*, super space group: Xbmm(0gamma0) s00, X stands for the nonprimitive centering vector (1/2,0,1/2,1/2), R(obs)(overall) = 5.27%, R(obs)(fundamental) = 4.48%, R(obs)(satellite) = 6.58%) has evidenced strong positional modulated effects within the [BiCu(2)O(2)](3+) ribbons while three XO(4) configurations compete along the x(4) fourth dimension. There is no P/V segregation along x(4) in good agreement with steric-only origins of the modulation. Finally for 0.96 < x <1, two phases coexist, i.e., BiCu(2)VO(6) (X = 1) and a modulated phase of the previous domain.The BiCu(2)VO(6) crystal structure shows a unit cell tripling associated with monoclinic symmetry lowering. The VO(4) orientations between two ribbons proceed with respect to the interribbon distance. Then the full system shows flexible interactions between modulated Bi/M/O-based ribbons and surrounding tetrahedral groups, depending on the average XO(4) size. Furthermore, between two ribbons the Cu(2+) arrangement forms magnetically isolated zigzag copper two-leg ladders. Our preliminary results show a spin-gap behavior likely due to the existence of true S = (1)/(2) Heisenberg two-leg ladders. Modulated compositions are gapless, in good agreement with band-broadening toward a continuum in the magnetic excitation spectrum. The continuous distribution of Cu-Cu distances along the rungs and legs of the ladders should be mainly responsible for this magnetic change.

Journal Article↗
PubMed1997

Structural features of the binding site for ribosomal protein S8 in Escherichia coli 16S rRNA defined using NMR spectroscopy.

Ribosomal protein S8 of Escherichia coli plays a key role in 30S ribosomal subunit assembly through its interaction with 16S rRNA. S8 also participates in the translational regulation of ribosomal protein expression through its interaction with spc operon mRNA. The binding site for protein S8 within the 16S rRNA encompasses nucleotides G588 to G604 and C634 to C651 and is composed of two base paired helical regions that flank a phylogenetically conserved core element containing nine residues. We have investigated the structure of the rRNA binding site for S8 both in the free state and in the presence of protein using NMR spectroscopy. The integrity of the two helical segments has been verified, and the presence of G597 x C643 and A596 x U644 base pairs within the conserved core, predicted from comparative analysis, have been confirmed. In addition, we have identified a base triple within the core that is composed of residues A595 x (A596 x U644). The NMR data suggest that S8-RNA interaction is accomplished without significant changes in the RNA. Nonetheless, S8 binding promotes formation of the U598 x A640 base pair and appears to stabilize the G597 x C643 and A596 x U644 base pairs.

Amino Acid Sequence↗
PubMed1999

The nature of lignin from steam explosion/ enzymatic hydrolysis of softwood: structural features and possible uses: scientific note.

Effective utilization of the lignin by-product is a prerequisite to the commercial viability of ethanol production from softwood wastes using a steam explosion (SE)/enzymatic hydrolysis (EH)/fermentation process. Changes in the chemical composition of Douglas fir wood on SO2-catalyzed SE followed by EH were assessed using conventional analytical methods and new halogen-probe techniques. A significant solubilization of hemicelluloses was observed in the SE stage, the severity of which affected subsequent fermentation of cellulose and sorption of enzymes. SE of softwood resulted in dramatic changes in the chemical structure of lignin in the residual material involving chemical reactions via the benzyl cation. This leads to a more condensed lignin with partly blocked alpha-reaction centres. Possible uses for this lignin are discussed.

Journal Article↗
PubMed2006

Structural features of the L-argininamide-binding DNA aptamer studied with ESI-FTMS.

The 24-mer DNA aptamer of Harada and Frankel (Harada, K.; Frankel, A. D. EMBO J. 1995, 14, 5798-5811) that binds L-argininamide (L-Arm) was studied by electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). This DNA folds into a stem and loop such that the loop is able to engulf L-Arm. As controls, two derivatives of the same base composition, one with the same stem but a scrambled loop and the other with no ability to form a secondary structure, were studied. The two DNAs that could fold into stem-loop structures showed a more negatively charged distribution of ions than the linear control. This tendency was preserved in the presence of ligand; complexes expected to have more secondary structure had ions with more negative charges. Distinct species corresponding to no, one, and two bound L-Arm molecules were observed for each DNA. The fractional peak intensities were fit to a straightforward binding model and binding constants were obtained. Thus, ESI-FTMS can provide both qualitative and quantitative data regarding the structure of DNA and its interactions with noncovalent ligands.

Aptamers, Nucleotide↗
PubMed2000

Molecular pathology and structural features of enteroviral replication. Toward understanding the pathogenesis of viral heart disease.

Enteroviruses of the Picornaviridae and primarily coxsackieviruses of group B (CVB) can be detected in humans and various experimental murine models of acute myocarditis and chronic heart muscle diseases indicating enterovirus persistence in the myocardium. Persistent myocardial infection is characterized by restricted viral replication and gene expression in myocytes capable of sustaining chronic inflammation. Viral cytotoxicity was found to be crucial for organ pathology both during acute and persistent infection. In-situ hybridization experiments at the cellular and subcellular level have demonstrated that virus replication is associated with severe structural changes of the cardiomyocyte cytoarchitecture at any stage of the disease. In tissue culture experiments and transgenic mice, it was shown that restricted replication and gene expression of the virus are capable of inducing myocytopathic effects. Investigations at the molecular level revealed that interference of coxsackievirus replication with the cellular metabolism is mediated by cleavage of host cell proteins by virus-encoded proteinases. Notably, there is also evidence that enteroviruses are able to activate specific cellular signal transduction pathways in the course of infection, thus promoting enteroviral replication. In summary, these data indicate that mutual influences of virus replication and subsequent modifications of the host cell metabolism are crucial for cardiac injury and dysfunction during acute and chronic disease.

Animals↗
PubMed1996

Structural features of an arabinan fragment isolated from the water-soluble fraction of dehulled rapeseed.

A water-soluble polysaccharide fraction was prepared from dehulled rapeseed meal (winter rapeseed variety Casino). Further purification yielded two major fractions having a high content of arabinose and galactose residues, with Ara/Gal ratios of 5.4 (G1) and 1.8 (G2). The Ara/Gal ratio of the high molecular weight fraction G1 was stable over the whole gel filtration peak, indicating that the arabinose and galactose residues are part of the same polysaccharide. The high molecular weight fraction G1 was studied further by methylation analysis and several NMR techniques. Structural studies showed G1 to consist mainly of arabian fragments, which have terminal alpha-L-arabinofuranosyl groups with anomeric carbons bound (1-->5) (A) or (1-->2) (B), and 2,5-substituted arabinosyl residues with anomeric carbons bound (1-->5) (D) or (1-->2) (C) to adjacent arabinosyl residues. The A:B:C:D ratios were 2:1:1:1 according to results from NMR and methylation analysis.

Arabinose↗
PubMed1993

Crystallographic analyses of an active HIV-1 ribonuclease H domain show structural features that distinguish it from the inactive form.

. An active recombinant preparation of the carboxy-terminal ribonuclease H (RNase H) domain of HIV-I reverse transcriptase has produced crystals of several different forms, including a trigonal prism form (P3(1); a = b = 52.03, c = 113.9 A with two molecules per asymmetric unit) and a hexagonal tablet form (P6(2)22 or P6(4)22; a = b = 93.5, c = 74.1 A with one molecule per asymmetric unit). The former appears to be isomorphous with crystals of a similar, but inactive, version of the enzyme that was used for a prior crystal structure determination [Davies, Hostomska, Hostomsky, Jordan & Matthews (1991). Science, 252, 88-95]. We have also obtained a structure solution for this crystal form and have refined it with 2.8 A resolution data (R = 0.216). We report here details of our crystallization studies and some initial structural results that verify that the preparation of active HIV-1 RNase H yields a protein that is not just enzymatically, but also structurally, distinguishable from the inactive form. Evidence suggests that region 538-542, which may be involved in the catalytic site and which is disordered in both molecules in the prior structure determination, is ordered in the crystal structure of the active enzyme, although the ordering may include more than one conformation for this loop. It should also be noted that, in the crystal structure of the trigonal form, RNase H monomers associate to form noncrystallographic twofold-symmetric dimers by fusing five-stranded mixed beta sheets into a single ten-stranded dimerwide sheet, an assembly that was not remarked upon by previous investigators.

Journal Article↗
PubMed1998

Existence and localization of a protein in zebra finch brain with similar structural features as the large subunit of the splicing factor U2AF.

From brains of the adult male zebra finch, we purified a peptide that has a homologous sequence of the large subunit of human U2AF. U2AF is a non-small-nuclear ribonucleoprotein (snRNP) splicing factor required for pre-spliceosome assembly. U2AF consists of a large and a small subunit, whereas only a large subunit is required for in vitro splicing. To show that U2AF large-subunit-like protein exists in the brain of zebra finches, we conducted immunoblot analysis on brain extract, using antiserum against an isolated peptide with primary structures similar to the U2AF large subunit (ppU2AFls). The immunoblot analysis showed that a protein with a molecular weight of about 60 kd reacted with the anti-ppU2AFls-antibody to a putative peptide of the U2AF large subunit. To examine the localization of this protein in the brain, we also conducted immunohistochemical analysis with the anti-peptide. An intense immunoreaction was restricted within the cellular nucleus throughout the brain, suggesting that this protein may contribute to the pre-spliceosome assembly in almost all of the regions of the brain.

Amino Acid Sequence↗
PubMed1997

Functional evaluation of the structural features of proteases and their substrate in fibrin surface degradation.

A new model has been introduced to characterize the action of a fluid phase enzyme on a solid phase substrate. This approach is applied to evaluate the kinetics of fibrin dissolution with several proteases. The model predicts the rate constants for the formation and dissociation of the protease-fibrin complex, the apparent order of the association reaction between the enzyme and the substrate, as well as a global catalytic constant (kcat) for the dissolution process. These kinetic parameters show a strong dependence on the nature of the applied protease and on the structure of the polymerized substrate. The kinetic data for trypsin, PMN-elastase, and three plasminogen-derived proteases with identical catalytic domain, but with a varied N-terminal structure, are compared. The absence of kringle5 in des-kringle1-5-plasmin (microplasmin) is related to a markedly lower kcat (0.008 s-1) compared with plasmin and des-kringle1-4plasmin (miniplasmin) (0.039 s-1). The essentially identical kinetic parameters for miniplasmin and plasmin with the exception of kdiss, which is higher for miniplasmin (81.8 s-1 versus 57.6 s-1), suggest that the first four kringle domains are needed to retain the enzyme in the enzyme-fibrin complex. Trypsin, a protease of similar primary specificity to plasmin, but with a different catalytic domain, shows basically the same kcat as plasmin, but its affinity to fibrin is markedly lower compared with plasmin and even microplasmin. The latter suggests that in addition to the kringle domains, the structure of the catalytic domain in plasmin also contributes to its specificity for fibrin. The thinner and extensively branched fibers of fibrin are more efficiently dissolved than the fibers with greater diameter and lower number of branching points. When the polymer is stabilized through covalent cross-linking, the kcat for plasmin and miniplasmin is 2-4-fold higher than on non-cross-linked fibrin, but the decrease in the association rate constant for the formation of enzyme-substrate complex explains the relative proteolytic resistance of the cross-linked fibrin. Thus, the functional evaluation of the discrete steps of the fibrinolytic process reveals new aspects of the interactions between proteases and their polymer substrate.

Aminocaproic Acid↗
PubMed1988

Signal peptidases recognize a structural feature at the cleavage site of secretory proteins.

The cloning of the gene for staphylococcal nuclease A in the pIN-III-OmpA secretion vector results in a hybrid protein which is processed by signal peptidase I, yielding an active form of the nuclease that is secreted across the cytoplasmic membrane (Takahara, M., Hibler, D., Barr, P. J., Gerlt, J. A., and Inouye, M. (1985) J. Biol. Chem. 260, 2670-2674). Using oligonucleotide-directed site-specific mutagenesis, we have constructed a set of mutants at the cleavage site area of the precursor hybrid protein designed to alter progressively the predicted secondary structure of the cleavage site. Our results show that processing becomes increasingly defective as the turn probability decreases. These results are consistent with the structural requirement that we found for the processing of lipoprotein by signal peptidase II (Inouye, S., Duffaud, G., and Inouye, M. (1986) J. Biol. Chem. 261, 10970-10975). We conclude that secretory precursor proteins have a distinct secondary structural requirement at their cleavage site for processing by signal peptidase I, as well as by signal peptidase II.

Amino Acid Sequence↗
PubMed2001

A correlation between differential structural features and the degree of endopeptidase activity of type A botulinum neurotoxin in aqueous solution.

Botulinum neurotoxin type A is one of the most toxic substances known to man (LD(50) for mouse 0.1 ng/kg). It is also an effective therapeutic drug against involuntary muscle disorders and for pain management. BoNT/A is a Zn(2+) endopeptidase which selectively cleaves SNAP-25 (synaptosomal-associated protein of 25 kDa), a critical component of the exocytotic machinery. Based on nucleotide sequence, BoNT/A is a 145 kDa protein, which appears as a 145 kDa protein band on sodium dodecyl sulfate--polyacrylamide gel electrophoresis. We have examined the structure of BoNT/A in aqueous solution, and found the structure in aqueous solution differs dramatically from that resolved by X-ray crystallography, both at secondary and at quaternary levels. In terms of secondary structure, BoNT/A in aqueous solution has about 47% beta-sheet structure as revealed by infrared spectroscopy, while X-ray crystallography revealed only 17% beta-sheet structure. In terms of quaternary structure, the estimated molecular mass of the native BoNT/A in aqueous solution ranged between 230 and 314 kDa, based on results from different chemical and biophysical techniques (native gel electrophoresis, chemical cross-linking, size exclusion chromatography, and fluorescence anisotropy). These results indicate that BoNT/A exists as a dimer in aqueous solution, which contrasts with the reported monomeric structure of BoNT/A based on X-ray crystallography. The dimeric form of BoNT/A can self-dissociate into the monomeric form at a concentration lower than 50 nM. This concentration-dependent structural change has a significant impact on the endopeptidase activity of BoNT/A: the catalytic efficiency of the monomeric BoNT/A is about 4-fold higher than that of its dimeric form. This difference implies a sterically restricted catalytic site of BoNT/A in the dimeric form of BoNT/A.

Botulinum Toxins, Type A↗
PubMed1999

Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence.

Nucleosomes, the fundamental building blocks of chromatin, play an architectural role in ensuring the integrity of the genome and act as a regulator of transcription. Intrinsic properties of the underlying DNA sequence, such as flexibility and intrinsic bending, direct the formation of nucleosomes. We have earlier identified genomic nucleosome-positioning sequences with increased in vitro ability for nucleosome formation. One group of sequences bearing a 10-base pair consensus repeat sequence of TATAAACGCC had the highest reported nucleosome affinity from genomic material. Here, we report the intrinsic physical properties of this sequence and the structural details of the nucleosome it forms, as analyzed by footprinting techniques. The minor groove is buried toward the histone octamer at the AA steps and facing outwards at the CC steps. By cyclization kinetics, the overall helical repeat of the free DNA sequence was found to be 10.5 base pairs/turn. Our experiments also showed that this sequence is highly flexible, having a J-factor 25-fold higher than that of random sequence DNA. In addition, the data suggest that twist flexibility is an important determinant for translational nucleosome positioning, particularly over the dyad region.

Animals↗
PubMed1984

Morphologic features, structure, and adherence to bovine turbinate cells of three haemophilus somnus variants.

Three colony variants (translucent, small opaque, and large opaque) of Haemophilus somnus recovered during infection studies of chicken embryos were examined using electron microscopy. Ruthenium red-strained H somnus preparations revealed no capsule in any variants. Pili were not seen on phosphotungstate-negative stained preparations. The translucent variant was thin-walled and had an irregular, pleomorphic rod shape. The small opaque variant had a thicker cell wall and an even rod shape. The large opaque variant had the thickest, most rigid wall of the 3, with uniform rod morphologic features. When each of the 3 variants was allowed to contact bovine epithelial turbinate cells, the translucent and small opaque were significantly (P less than 0.01) more adherent than was the large opaque variant.

Animals↗