100ps Molecular Dynamic Simulation of d(TATCACC)2

Abstract

A heptanucleotide sequence d(TATCACC)2 from OR3 region of bacteriophage X is considered sufficient for the recognition of Cro protein. We present here results on molecular dynamic simulations on this sequence for 100 ps in 0.02 ps interval. The simulations are done using computer program GROMOS. The conformational results are averaged over each ps. The IUPAC torsional parameters for 100 conformations are illustrated using a wheal and a dial systems. Several other stereochemical parameters such as H-bonding lengths and angles, sugar puckers, helix twist and roll angles as also distances between opposite strand phosphorus are depicted graphically. We find that there is rupture of terminal H-bonds. The bases are tilted and shifted away from the helix axis giving rise to bifurcated H-bonds. H- bonds are seen even in between different base pairs. The role of these dynamic structural changes in the recognition of OR3 operator by Cro protein is discussed in the paper.     

The chemical compound ‘Heatin’ stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases

Temperature passively affects biological processes involved in plant growth. Therefore, it is challenging to study the dedicated temperature signalling pathways that orchestrate thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf-cooling capacity. We screened a chemical library for compounds that restored hypocotyl elongation in the pif4-2–deficient mutant background at warm temperature conditions in Arabidopsis thaliana to identify modulators of thermomorphogenesis. The small aromatic compound ‘Heatin’, containing 1-iminomethyl-2-naphthol as a pharmacophore, was selected as an enhancer of elongation growth. We show that ARABIDOPSIS ALDEHYDE OXIDASES redundantly contribute to Heatin-mediated hypocotyl elongation. Following a chemical proteomics approach, the members of the NITRILASE1-subfamily of auxin biosynthesis enzymes were identified among the molecular targets of Heatin. Our data reveal that nitrilases are involved in promotion of hypocotyl elongation in response to high temperature and Heatin-mediated hypocotyl elongation requires the NITRILASE1-subfamily members, NIT1 and NIT2. Heatin inhibits NIT1-subfamily enzymatic activity in vitro and the application of Heatin accordingly results in the accumulation of NIT1-subfamily substrate indole-3-acetonitrile in vivo. However, levels of the NIT1-subfamily product, bioactive auxin (indole-3-acetic acid), were also significantly increased. It is likely that the stimulation of hypocotyl elongation by Heatin might be independent of its observed interaction with NITRILASE1-subfamily members. However, nitrilases may contribute to the Heatin response by stimulating indole-3-acetic acid biosynthesis in an indirect way. Heatin and its functional analogues present novel chemical entities for studying auxin biology.     

Dimerization of Cadherin-11 involves multi-site coupled unfolding and strand swapping

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Antifungal Biphenyl Derivatives from Sorbus pohuashanensis Leaves Infected by Alternaria tenuissi and Their Effect against Crop Pathogens

Eight natural biphenyl-type phytoalexins exhibiting antifungal effect were isolated from the leaves of Sorbus pohuashanensis, which invaded by Alternaria tenuissi, and their growth inhibition rate towards A. tenuissi were 50.3 %, 54.0 %, 66.4 %, 58.8 %, 48.5 %, 51.0 %, 33.3 %, and 37.0 %, respectively. In vivo activity assay verified the protective effect of these natural biphenyls on tobacco leaves. The observation of mycelial morphology revealed that these compounds possessed adverse effects on mycelial growth of A. tenuissi. Subsequently, the most potent active compounds, 3′,4′,5′-trimethoxy[1,1′-biphenyl]-4-ol ( 3 ) and 3,4,4′,5-tetramethoxy-1,1′-biphenyl ( 4 ), were conducted to the further antifungal evaluation and showed significant activity against the other four crop pathogens, Fusarium graminearum, Helminthosporium maydis, Sclerotinia sclerotiorum, and Exserohilum turcicum. Further, the structure-activity relationships and biosynthesis of these compounds were speculated in this work.     

Chemically-Synthesized Gene Encoding Modified Human Superoxpde Dismutase: Its Construction,Expression and Properties of the Product

The gene encoding modified human superoxide dismutax (h-SOD) with 153 amino acid residues was constructed by chemical synthesis using the phosphoramidite method. The gene was designed so as to use bacterial codons for expression in prokaryotes and to introduce several unique restriction sites for further mutagenesis by the cassette exchange method. The distance between Shine-Dalgarno sequence and initiation codon was adjusted to maximum expression by using synthesized oligonucleotide. In addition, Cys 6 of h-SOD was changed to Ala to improve instability of native h-SOD.

Synthesized structural gene of h-SOD was expressed in E. coli after induction of isopropyl β-D-thiogalactoside by inserting the gene into the expression vector pKK223–3 having tac promoter. The gene that has 10 base pairs between Shine-Dalgarno sequence and initiation codøn showed the most efficient expression. The gene produced three active SOD isomers as revealed by chromatofocusing.

The main isomer was purified to homogeneity and characterized. The h-SOD-Ala⁶ showed similar properties to those of native h-SOD with respect to molecular weight, subunit structure, absorption spectrum. but the modified SOD was more resistant to heat denaturation than was native h-SOD; half-denaturing temperature was shifted by 10°C. Thus. the exchange of Cys 6 to Ala of h-SOD increased a stability of the enzyme.     

Flight behaviour of Encarsia formosa in response to plant and host stimuli

The flight behaviour of Encarsia formosa Gahan (Hymenoptera: Aphelinidae), a parasitoid of Trialeurodes vaporariorum (Westwood) (Homoptera: Aleyrodidae) has been studied in response to the following natural components: bean plant (Phaseolus vulgaris L.) infested with T. vaporariorum (PHC, plant host complex), host damaged bean plant from which whiteflies were removed (HDP, host damaged plant), T. vaporariorum third instar larvae (H, host), uninfested bean plant (P, plant) and T. vaporariorum empty pupal cases (EPC, empty pupal cases). A combination of chemical and visual stimuli is necessary in host location from a distance by E. formosa and seems to deeply affect the dispersal of this parasitoid. The presence of host (PHC, H) or of its parts (EPC) led to a substantial increase of oriented flights suggesting the occurrence of host derived chemicals. At a closer range, a combination of visual and chemical stimuli deriving from all the components of the plant host complex elicited the transition flying-landing and the following landing on the source.     

Geographic variation of flavonoids in Phlox carolina

Non-anthocyanin flavonoid expression was determined among 64 continuous range and nine disjunct range populations of Phlox carolina. The species contains four flavone nuclei and a total of 25 derivatives, most of which are $\text{C-}\text{glycosides}$. Nearly all populations express unique flavone patterns. Using a qualitative similarity index of minimum biosynthetic step distance (MBSD), the average population contains only ca. 50% of the overall substitutional diversity. The separate ranges are distinctive in the % occurrence of most compounds but only weakly divergent in comparative mean MBSD. Proximity and MBSD are significantly correlated overall but local variability is extensive and no discrete racism is apparent. Within the continuous range 18 compounds are distributed in independent but overlapping gradients and 13 of these extend consistently through the disjunct range. The patch-work continuum of flavone variation is the apparent consequence of dissection and contraction of a historically more widespread distribution. Other general aspects of the variation patterns are discussed.     

Chemical composition of fresh and composted urban waste

Chemical, spectroscopic (IR and NMR), and molecular characteristics of humus extracted from urban waste before and after compositing are reported. The main differences are in the contents of acidic groups and straight aliphatic chains which diminish in the composted material. In comparing humus characteristics of composted urban waste and soils, the only real difference was found in the elution curves on Sephadex G-100, where the ratio of 100,000 and 1,300 peaks was higher in the compost than in the soil curve. The finding suggests that this ratio is a parameter that could enable us, even if in a semiquantitative manner, to follow the humification process of the compost when its addition to the soil is not less than the autochthonous organic matter content.Research work supported by CNR, Italy, Special grant I.P.R.A.-Sub-project 1. Paper N. 1531.     

Mechanisms of host discrimination and intraspecific competition in the aphid parasitoid Ephedrus cerasicola

The aphid parasitoid Ephedrus cerasicola Starý (Hymenoptera: Aphidiidae) discriminates between parasitized and unparasitized aphid hosts (Myzus persicae (Sulzer), Homoptera: Aphididae) in two different ways. By antennal contact with the parasitized host, it can detect an external marking pheromone which is effective only for a few hours. The behaviour of the parasitoid also indicated that it responded to an internal marker, probably by means of chemoreceptors on the ovipositor. The parasitoid behaviour was studied in encounters with parasitized hosts 0–10 min, 2–3 h, 6–7 h and 23–24 h after the first parasitization. Aphids were superparasitized within 1 h or after 24 h, and aphids in each experiment were later dissected at two different times. It is suggested that the supernumerary offspring were eliminated by chemical means, whether the time between the two ovipositions was 0–1 h or 24 h.

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Résumé Le parasitoïde de puceron, E. cerasicola Starý (Hym.: Aphidiidae) sélectionne les pucerons, Myzus persicae (Sulzer), parasités ou non, de deux façons différentes. Il peut percevoir une phéromone externe de marquage perceptible seulement pendant quelques heures par contact antennaire. Son comportement montre qu'il réagit aussi à un marquage interne, probablement par des chémorécepteurs de sa tarière. Le comportement du parasitoïde a été étudié en le mettant en contact avec des hôtes parasités depuis 0–10 min, 2–3 h, 6–7 h et 23–24 h. Les pucerons ont été surparasités pendant la première heure ou après 24 heures. Les pucerons de toutes les expériences ont été disséqués à deux moments différents. Ceci a conduit à estimer que les descendants en surnombre ont été éliminés chimiquement quand la période entre deux pontes successives était inférieure à 1 h ou supérieure à 24 h.