Improved NMR spectra of a protein–DNA complex through rational mutagenesis and the application of a sensitivity optimized isotope-filtered NOESY experiment

The NMR spectra of the complex between the DNA-binding domain of the Dead ringer protein (DRI-DBD, Gly262-Gly398) and its DNA binding site (DRI-DBD:DNA, 26 kDa) have been optimized by biochemical and spectroscopic means. First, we demonstrate the utility of a modified 2D [F1,F2] ¹³C-filtered NOESY experiment that employs a ¹J_HC versus chemical shift optimized adiabatic ¹³C inversion pulse [Zwahlen, C. et al. (1997) J. Am. Chem. Soc., 119, 6711–6721]. The new sequence is shown to be more sensitive than previously published pulse schemes (up to 40% in favorable cases) and its utility is demonstrated using two protein–DNA complexes. Second, we demonstrate that the targeted replacement of an interfacial aromatic residue in the DRI-DBD:DNA complex substantially reduces line broadening within its NMR spectra. The spectral changes are dramatic, salvaging a protein–DNA complex that was originally ill suited for structural analysis by NMR. This biochemical approach is not a general method, but may prove useful in the spectral optimization of other protein complexes that suffer from interfacial line broadening caused by dynamic changes in proximal aromatic rings.     

Interchange of DNA-binding modes in the deformed and ultrabithorax homeodomains: a structural role for the N-terminal arm

The deformed (Dfd) and ultrabithorax (Ubx) homeoproteins regulate developmental gene expression in Drosophila melanogaster by binding to specific DNA sequences within its genome. DNA binding is largely accomplished via a highly conserved helix-turn-helix DNA-binding domain that is known as a homeodomain (HD). Despite nearly identical DNA recognition helices and similar target DNA sequence preferences, the in vivo functions of the two proteins are quite different. We have previously revealed differences between the two HDs in their interactions with DNA. In an effort to define the individual roles of the HD N-terminal arm and recognition helix in sequence-specific binding, we have characterized the structural details of two Dfd/Ubx chimeric HDs in complex with both the Dfd and Ubx-optimal-binding site sequences. We utilized hydroxyl radical cleavage of DNA to assess the positioning of the proteins on the binding sites. The effects of missing nucleosides and purine methylation on HD binding were also analyzed. Our results show that both the Dfd and Ubx HDs have similar DNA-binding modes when in complex with the Ubx-optimal site. There are subtle but reproducible differences in these modes that are completely interchanged when the Dfd N-terminal arm is replaced with the corresponding region of the Ubx HD. In contrast, we showed previously that the Dfd-optimal site sequence elicits a very different binding mode for the Ubx HD, while the Dfd HD maintains a mode similar to that elicited by the Ubx-optimal site. Our current methylation interference studies suggest that this alternate binding mode involves interaction of the Ubx N-terminal arm with the minor groove on the opposite face of DNA relative to the major groove that is occupied by the recognition helix. As judged by hydroxyl radical footprinting and the missing nucleoside experiment, it appears that interaction of the Ubx recognition helix with the DNA major groove is reduced. Replacing the Dfd N-terminal arm with that of Ubx does not elicit a complete interchange of the DNA-binding mode. Although the position of the chimera relative to DNA, as judged by hydroxyl radical footprinting, is similar to that of the Dfd HD, the missing nucleoside and methylation interference patterns resemble those of the Ubx HD. Repositioning of amino acid side-chains without wholesale structural alteration in the polypeptide appears to occur as a function of N-terminal arm identity and DNA-binding site sequence. Complete interchange of binding modes was achieved only by replacement of the Dfd N-terminal arm and the recognition helix plus 13 carboxyl-terminal residues with the corresponding residues of Ubx. The position of the N-terminal arm in the DNA minor groove appears to differ in a manner that depends on the two base-pair differences between the Dfd and Ubx-optimal-binding sites. Thus, N-terminal arm position dictates the binding mode and the interaction of the recognition helix with nucleosides in the major groove.     

Determination of residual dipolar couplings in homonuclear MOCCA-SIAM experiments

In solutions with partial molecular alignment, anisotropic magnetic interactions such as the chemical shift anisotropy, the electric quadrupole interaction, and the magnetic dipole-dipole interaction are no longer averaged out to zero in contrast to isotropic solutions. The resulting residual anisotropic magnetic interactions are increasingly used in biological NMR studies for the determination of 3D structures of proteins and other biomolecules. In the present paper we propose a new approach allowing the measurement of residual H^N-H dipolar couplings of non-isotope enriched proteins based on the application of the MOCCA-SIAM experiment. This experiment allows the measurement of homonuclear coupling constants with an accuracy of ca. ±0.2 Hz and is therefore particularly well suited to determine residual dipolar couplings at relatively low degrees of molecular orientation. The agreement between experimentally determined residual H^N-H couplings and calculated values is demonstrated for BPTI.     

A unified parametric regression model for recapture studies with random removals in continuous time

Conditional likelihood based on counting processes are combined with a Horvitz-Thompson estimator to yield a population size estimator that is more efficient than the existing ones. Random removals are allowed in the recapturing process. Simulation studies are shown to assess the performance of the proposed estimators. Examples on a bird banding and a small mammal recapturing study are given.     

Stable carbon and nitrogen isotope signatures of decomposing tropical macrophytes

The Pantanal of Mato Grosso, Brazil, is a large, seasonal wetland, which exhibits high macrophyte productivity at the beginning of the rainy season, when the floodplain becomes flooded. During inundation, from December through May, there is rapid turnover of decomposing macrophyte litter, which is subsequently colonized and consumed by various organisms. In this paper, the variation in the carbon and nitrogen isotope signatures of decomposing macrophytes and detritus was determined to provide an isotopic baseline for the elucidation of higher trophic levels. Seven abundant macrophyte species, Cyperaceae sp., Pontederia lanceolata, Cabomba furcata, Salvinia auriculata, Eichhornia crassipes, Nymphaea amazonum and Paspalum repens, were exposed in mesocosm decomposition experiments lasting 21 or 100 days. Stable isotope ratios of carbon and nitrogen and the atomic C/N ratios were determined for decomposing plant material, particulate organic matter (POM), the microbial film, and aquatic invertebrate larvae. The ¹³C values for the macrophytes did not change during decomposition. However, the variability of ¹⁵N was high (range of ± 6 ) due to microbial activity. There was no consistent difference in the isotopic signatures of macrophytes and POM. C/N ratios decreased from 17 to 50 in macrophytes, to 7 to 12 in POM. The isotopic signatures and C/N ratios of the microbial film were the same as those of POM. We concluded that heterotrophic processes did not fractionate stable carbon isotopes but caused an increase in the variability of stable nitrogen ratios and a change in the C/N ratios in our experimental system. Therefore, it was not possible to distinguish fresh and senescent material or even POM when used as a food source. The ¹³C values of the aquatic larvae were closely coupled to those of the carbon source provided.     

Analysis of metabolic and physiological responses to gnd knockout in Escherichia coli by using C-13 tracer experiment and enzyme activity measurement

The physiological and metabolic responses to gnd knockout in Escherichia coli K-12 was quantitatively investigated by using the (13)C tracer experiment (GC-MS/NMR) together with the enzyme activity analysis. It was shown that the general response to the gene knockout was the local flux rerouting via Entner-Doudoroff pathway and the direction reversing via non-oxidative pentose phosphate pathway (PPP). The mutant was found to direct higher flux to phosphoglucose isomerase reaction as compared to the wild-type, but the respiratory metabolism was comparable in both strains. The anaplerotic pathway catalyzed by malic enzyme was identified in the mutant, which was accompanied with an up-regulation of phosphoenolpyruvate carboxylase and down-regulation of phosphoenolpyruvate carboxykinase. The presented results provide first evidence that compensatory mechanism existed in PPP and anaplerotic pathway in response to the gnd deletion.     

敦煌壁画色变中微生物因素的研究──Ⅰ.色变壁画的微生物类群及优势菌的检测

通过对敦煌莫高窟6个洞窟中的51个典型变色颜料样品的微生物检测,发现其中的细菌有6个属,优势菌为芽孢杆菌属和产碱菌属;霉菌有5个属,优势菌为青霉属。将分离得到的菌种,通过模拟试验证明,枝孢霉、黑曲霉和2种特殊细菌对壁画红色颜料变色和胶结材料的老化均起着重要作用。     

Rapid data collection and assessment of the biology of Acanthurus nigrofuscus at Woleai Atoll, Micronesia

Traditional community fishing methods commonly employed in the tropical Pacific were used to generate information on the fishery biology of Acanthurus nigrofuscus at Woleai Atoll, Micronesia, over a short time period. A simple depletion model was used to estimate the biomass of A. nigrofuscus at four back reef lagoon sites at Woleai, using two different fishing methods; spear fishing and drive-in-net fishing. The mean biomass and density of A. nigrofuscus on the lagoon reefs was 8000 g ha ⁻¹ and 183 fish ha ⁻¹ respectively, with a total estimated standing stock for the lagoon of 91 500 fish or a biomass of 4·0 t. The size frequencies of fish caught by spear fishing were biased towards larger sized individuals, while those from drive-in-net fishing were thought to be more representative of the true population size frequencies. Variation in the density and biomass of A. nigrofuscus at the four reef sites was thought to be due to the length of time between episodes of community fishing at each reef site. The sex ratio (male: female) of A. nigrofuscus was significantly different from unity (1: 0·47) and males grew larger than females. Sexually mature fish were present in all size classes above the minimum capture length and spawning activity was greatest during the period of the full moon.