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51.
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Jožica Dolenc John H. Missimer Michel O. Steinmetz Wilfred F. van Gunsteren 《Journal of biomolecular NMR》2010,47(3):221-235
The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus
of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16–31,
encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement
protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 ϕ torsional-angle restraints,
the resulting set of 20 NMR model structures exhibits regular α-helical structure. However, the set slightly violates some
measured NOE bounds and does not reproduce all 15 measured 3J(HN-HCα)-coupling constants, indicating that different conformers of GCN4p16–31 might be present in solution. With the aim to resolve
structures compatible with all NOE upper distance bounds and 3J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics
(MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged
NOE distance and 3J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the
simulated ensembles show that the conformational variability of GCN4p16–31 in solution admitted by the available set of 187
measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16–31 in solution
differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model
structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle
restraints that have little basis in the primary, i.e. measured NMR data. 相似文献
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Maize Brittle stalk2 encodes a COBRA-like protein expressed in early organ development but required for tissue flexibility at maturity 总被引:5,自引:0,他引:5
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Sindhu A Langewisch T Olek A Multani DS McCann MC Vermerris W Carpita NC Johal G 《Plant physiology》2007,145(4):1444-1459
The maize (Zea mays) brittle stalk2 (bk2) is a recessive mutant, the aerial parts of which are easily broken. The bk2 phenotype is developmentally regulated and appears 4 weeks after planting, at about the fifth-leaf stage. Before this time, mutants are indistinguishable from wild-type siblings. Afterward, all organs of the bk2 mutants turn brittle, even the preexisting ones, and they remain brittle throughout the life of the plant. Leaf tension assays and bend tests of the internodes show that the brittle phenotype does not result from loss of tensile strength but from loss in flexibility that causes the tissues to snap instead of bend. The Bk2 gene was cloned by a combination of transposon tagging and a candidate gene approach and found to encode a COBRA-like protein similar to rice (Oryza sativa) BC1 and Arabidopsis (Arabidopsis thaliana) COBRA-LIKE4. The outer periphery of the stalk has fewer vascular bundles, and the sclerids underlying the epidermis possess thinner secondary walls. Relative cellulose content is not strictly correlated with the brittle phenotype. Cellulose content in mature zones of bk2 mature stems is lowered by 40% but is about the same as wild type in developing stems. Although relative cellulose content is lowered in leaves after the onset of the brittle phenotype, total wall mass as a proportion of dry mass is either unchanged or slightly increased, indicating a compensatory increase in noncellulosic carbohydrate mass. Fourier transform infrared spectra indicated an increase in phenolic ester content in the walls of bk2 leaves and stems. Total content of lignin is unaffected in bk2 juvenile leaves before or after appearance of the brittle phenotype, but bk2 mature and developing stems are markedly enriched in lignin compared to wild-type stems. Despite increased lignin in bk2 stems, loss of staining with phloroglucinol and ultraviolet autofluorescence is observed in vascular bundles and sclerid layers. Consistent with the infrared analyses, levels of saponifiable hydroxycinnamates are elevated in bk2 leaves and stems. As Bk2 is highly expressed during early development, well before the onset of the brittle phenotype, we propose that Bk2 functions in a patterning of lignin-cellulosic interactions that maintain organ flexibility rather than having a direct role in cellulose biosynthesis. 相似文献
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Setiadi AF David MD Seipp RP Hartikainen JA Gopaul R Jefferies WA 《Molecular and cellular biology》2007,27(22):7886-7894
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McGinley CM Jacquot C van der Donk WA 《Bioorganic & medicinal chemistry letters》2007,17(14):4049-4052
The mechanism by which prostaglandin synthase converts arachidonic acid to prostaglandin G(2), creating five new chiral centers in the process, is still incompletely understood. The first radical intermediate has been characterized by EPR spectroscopy but subsequent proposed intermediates have not succumbed to detection. We report the synthesis of 7-thiaarachidonic acid designed to stabilize one of the proposed radical intermediates, which may allow its detection. 相似文献
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Qi Zhang James R. Doroghazi Xiling Zhao Mark C. Walker Wilfred A. van der Donk 《Applied and environmental microbiology》2015,81(13):4339-4350
Lanthionine-containing peptides (lanthipeptides) are a rapidly growing family of polycyclic peptide natural products belonging to the large class of ribosomally synthesized and posttranslationally modified peptides (RiPPs). Lanthipeptides are widely distributed in taxonomically distant species, and their currently known biosynthetic systems and biological activities are diverse. Building on the recent natural product gene cluster family (GCF) project, we report here large-scale analysis of lanthipeptide-like biosynthetic gene clusters from Actinobacteria. Our analysis suggests that lanthipeptide biosynthetic pathways, and by extrapolation the natural products themselves, are much more diverse than currently appreciated and contain many different posttranslational modifications. Furthermore, lanthionine synthetases are much more diverse in sequence and domain topology than currently characterized systems, and they are used by the biosynthetic machineries for natural products other than lanthipeptides. The gene cluster families described here significantly expand the chemical diversity and biosynthetic repertoire of lanthionine-related natural products. Biosynthesis of these novel natural products likely involves unusual and unprecedented biochemistries, as illustrated by several examples discussed in this study. In addition, class IV lanthipeptide gene clusters are shown not to be silent, setting the stage to investigate their biological activities. 相似文献
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