The secondary structures of the 5'-untranslated region (5'-UTR) of five different tymoviruses have been determined by structure probing, computer prediction and sequence comparison, Despite large... Show moreThe secondary structures of the 5'-untranslated region (5'-UTR) of five different tymoviruses have been determined by structure probing, computer prediction and sequence comparison, Despite large sequence differences, there are remarkable similarities in the secondary structure, In all viruses two or four hairpins are found, most of which contain a symmetrical internal loop consisting of adjacent C-C or C-A mismatches, Since it is known that such mismatches can be protonated and protonated cytosines play an important role in RNA-protein interactions in tymoviral virions, the influence of pH on the conformation of the internal loop was studied, UV melting experiments and 1-dimensional proton NMR at varying pH values and salt concentrations confirm that the hairpins can be protonated under relatively mild conditions, The hairpin found in the 5'-UTR of erysimum latent virus, which has an asymmetrical internal loop consisting of cytosines and uridines, shows comparable behaviour, It is concluded that all tymoviral RNAs contain protonatable hairpins in the 5'-UTR, Binding experiments with empty viral capsids, however, do not yet establish a role in capsid protein binding. Show less
Meskers, S.C.J.; Ubbink, M.; Canters, G.W.; Dekkers, H.P.J.M. 1996
To examine the function of the central pseudoknot in 16S rRNA, we have studied Escherichia coli 30S subunits with the A(18) mutation in this structure element, Previously, this mutation, which... Show moreTo examine the function of the central pseudoknot in 16S rRNA, we have studied Escherichia coli 30S subunits with the A(18) mutation in this structure element, Previously, this mutation, which changes the central base pair of helix 2, C-18-G(917) to an A(18)xG(917) mismatch, was shown to inhibit translation in vivo and a defect in initiation was suggested, Here, we find that the mutant 30S particles are impaired in forming 70S tight couples and predominantly accumulate as free 30S subunits, Formation of a 30S initiation complex, as measured by toeprinting, was almost as efficient for mutant 30S subunits, derived from the tight couple fraction, as for the wild-type control, However, the A(18) mutation has a profound effect on the overall stability of the subunit, The mutant ribosomes were inactivated by affinity chromatography and high salt treatment, due to easy loss of ribosomal proteins, Accordingly, the particles could be reactivated by partial in vitro reconstitution with 30S ribosomal proteins, Mutant 30S subunits from the free subunit fraction were already inactive upon isolation, but could also be reactivated by reconstitution, Apparently, the inactivity in initiation of these mutant 30S subunits is, at least in part, also due to the lack of essential ribosomal proteins, We conclude that disruption of helix 2 of the central pseudoknot by itself does not affect the formation of a 30S initiation complex, We suggest that the in vivo translational defect of the mutant ribosomes is caused by their inability to form 70S initiation complexes. Show less
The RNA of all tymoviruses, a group of ssRNA plant viruses, has a base composition that is different from that of most other viruses. The excess of cytosines (35-42%) and the low number of... Show moreThe RNA of all tymoviruses, a group of ssRNA plant viruses, has a base composition that is different from that of most other viruses. The excess of cytosines (35-42%) and the low number of guanosines (15-17%) must impel an RNA structure with a relatively low amount of base pairing and a high incidence of unpaired cytosines. These unpaired cytosines probably function in RNA-protein interactions. To gain insight into the way the RNA is positioned inside the virion, the secondary structure has been determined of a part of TYMV RNA, including the so-called tymobox, the coat protein gene, and the 3' untranslated region, by structure probing, sequence comparison, and computer predictions. Conservation of secondary structure elements in tymoviruses is not high and does not parallel the conservation of the primary structure. A combination of structure prediction and probing experiments, however, results in a model consisting of structured domains of 100-200 nucleotides interspersed by long unpaired cytosine-rich regions. The latter may interact with the coat protein inside the virion. The structure of some functionally interesting regions of the 3' part of TYMV RNA is also discussed. (C) 1996 Academic Press, Inc. Show less
Penetration enhancers mediate trans-dermal drug delivery. The penetration enhancer dodecyl-azacycloheptanone (Azone(R)) was characterized in situ with H-2 NMR on human stratum corneum treated with... Show morePenetration enhancers mediate trans-dermal drug delivery. The penetration enhancer dodecyl-azacycloheptanone (Azone(R)) was characterized in situ with H-2 NMR on human stratum corneum treated with either uniformly deuterated Azone(R) or penetration enhancer with only the entire chain deuterated, in both cases in propylene glycol. The H-2 NMR spectrum at ambient temperature constitutes a single narrow line only 180 Hz wide. This contrasts with the complex lineshapes 1-25 kHz wide commonly observed for methylene deuterons of lipids in a bilayer gel phase, Hence there is no evidence for differences in orientational behaviour between different deuterons at ambient temperature. The narrow line translates into a low overall order parameter S-CD < 0.0008, for all deuterons, revealing rapid motion of the entire enhancer with correlation times tau(c) much less than 6 x 10(-6) s, in all possible directions. At temperatures of about 150 K a H-2 NMR pattern characteristic for a random isotropic powder was observed on samples of stacked stratum corneum sheets at different orientations with respect to the magnetic field. This provides strong evidence for random isotropic freezing of the Azone(R) molecules upon cooling. The H-2 NMR data suggest than incubation with Azone(R) in propylene glycol provokes dynamic structural disorder of the intercellular lamellar lipid structure throughout the stratum corneum and possibly even the creation of fluid domains involving the intercellular lipids, which may be essential for the penetration enhancing effect. Show less
Rossum, B.J. van; Boender, G.J.; Groot, H.J.M. de 1996
Nominal Zn1-xMnxAl2O4 (0 less than or equal to x < 1) solid solutions have been prepared from nitrates hi air at 1423 K. MnAl2O4 was prepared in a flow of 5% H-2/N-2 at 1273 K. All the oxides... Show moreNominal Zn1-xMnxAl2O4 (0 less than or equal to x < 1) solid solutions have been prepared from nitrates hi air at 1423 K. MnAl2O4 was prepared in a flow of 5% H-2/N-2 at 1273 K. All the oxides exhibit the spinel structure with an almost linear variation of the lattice constant with x (a = 0.80946 + 0.01182x + 0.00497x(2) [nm]). With the exception of ZnAl2O4, upon preparation the samples eliminate 0.17x of ct-alumina, which is compensated by oxidation of some manganese to Mn3+. For charge balance the average valence of Mn should then be 2.11. However, chemical analysis of the sample with x = 0.5 shows that there is further oxidation up Mn-2.82+, which implies that cation vacancies phi must be present in the lattice. The above-mentioned chemical analysis, combined with an analysis of the line intensities of the X-ray pattern (Rietveld method, X-ray pattern simulation) and MAS-NMR results (which rule out the presence of Al3+ in tetrahedral positions), leads to the formula (Zn(0.53)(2+)Mn(0.09)(2+)Mn(0.31)(3+)phi 0.07)[Mn(0.10)(3+)Al(1.84)(3+)phi(0.05)]O-4, where parentheses and square brackets denote tetrahedral and octahedral sites, respectively. Intensity analysis combined with X-ray pattern simulations (without chemical analysis) proves that in all the samples [Mn3+] = 0.17x +/- 0.01. Assuming that the same oxidation level of Mn exists in all the series, the general formula of the studied solutions should be close to (Zn(1-x)(2+)Mn(0.20x)(2+)Mn(0.63)(3+)phi(0.17x))[Mn(0.17x)(3+)Al(2-0.34)(3+)phi(0.17x)]O-4. (C) 1996 Academic Press, Inc. Show less
The reaction products from the radically initiated grafting of specifically C-13-enriched maleic anhydride ([2,3-C-13(2)]MA) Onto polyethene, isotactic polypropene and ethene-propene copolymers in... Show moreThe reaction products from the radically initiated grafting of specifically C-13-enriched maleic anhydride ([2,3-C-13(2)]MA) Onto polyethene, isotactic polypropene and ethene-propene copolymers in the melt and in solution are investigated using noise-decoupled and 1D inadequate C-13 NMR spectroscopy. The sites of attachment and the structures of the grafts depend oil (co)polymer composition. In random EPM, MA attaches to methylene and methine carbons in the backbone. In alternating EPM, MA attaches solely to polymer methines, indicating that (CH2)(m) seguences with m > 3 are needed for MA attachment to backbone methylene carbons. In the copolymers and in IPP, grafts are single succinic anhydride rings; in HDPE and LDPE short MA oligomers are also present. In polyolefins containing polypropene sequences, chain scission can yield structures in which the anhydride ring is attached to the chain terminus via a fully substituted double bond. Show less
A Car-Paninello ab initio molecular dynamics calculation is presented of all-trans and 11-cis retinals. The minimum energy configurations of the two isomers have been determined by a simulated... Show moreA Car-Paninello ab initio molecular dynamics calculation is presented of all-trans and 11-cis retinals. The minimum energy configurations of the two isomers have been determined by a simulated annealing procedure. The backbone conjugation is properly described within the local density approximation. The vibrational frequencies have been determined from the molecular dynamics trajectories. The theoretical results show an excellent agreement with experiment and provide grounds for an analysis of the retinal vibrations in terms of localized modes. Show less
