Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR

Most proteins are highly flexible and can adopt conformations that deviate from the energetically most favorable ground state. Structural information on these lowly populated, alternative conformations is often lacking, despite the functional importance of these states. Here, we study the pathway by which the Dcp1:Dcp2 mRNA decapping complex exchanges between an autoinhibited closed and an open conformation. We make use of methyl Carr–Purcell–Meiboom–Gill (CPMG) NMR relaxation dispersion (RD) experiments that report on the population of the sparsely populated open conformation as well as on the exchange rate between the two conformations. To obtain volumetric information on the open conformation as well as on the transition state structure we made use of RD measurements at elevated pressures. We found that the open Dcp1:Dcp2 conformation has a lower molecular volume than the closed conformation and that the transition state is close in volume to the closed state. In the presence of ATP the volume change upon opening of the complex increases and the volume of the transition state lies in-between the volumes of the closed and open state. These findings show that ATP has an effect on the volume changes that are associated with the opening-closing pathway of the complex. Our results highlight the strength of pressure dependent NMR methods to obtain insights into structural features of protein conformations that are not directly observable. As our work makes use of methyl groups as NMR probes we conclude that the applied methodology is also applicable to high molecular weight complexes.     

Elevated serum α-fetoprotein level of nude mice bearing hepatoma cells by treatment with monoclonal antibodies to α-fetoprotein

This study was carried out to clarify the reason for elevation of serum α-fetoprotein (AFP) level of nude mice bearing hepatoma cells after treatment with monoclonal antibodies (MoAbs) to AFP. MoAbs to AFP showed no effect on the cumulative amounts of AFP secreted from human hepatoma cell line, HuH-7, in vitro. However, the treatment of nude mice bearing HuH-7N cells (HuH-7 xenograft) with MoAbs to AFP led to elevation of the serum AFP level in spite of the fact that the growth curve of HuH-7N cells was similar to that for PBS treatment. This apparent elevation of the serum AFP level is thought to be due to the slow elimination of AFP-MoAb immune complexes with little lattice structure from circulation, but not the enhancement of AFP secretion of HuH-7N cells. Thus, when using a MoAb alone or MoAb-drug conjugate, the serum AFP level should only be cautiously used as a tumor marker for evaluating the targeting immunotherapy.     

Evaluation of somatic embryos of interior spruce. Characterization and developmental regulation of storage proteins

Storage proteins of interior spruce ( Picea glauca engelmanii complex) somatic embryos were compared to those of zygotic embryos by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblotting. Somatic embryos contain the same storage proteins as zygotic embryos based on similarities of molecular weight, isoelectric variants, solubility characteristics and disulfide linkages. Storage protein levels varied among different somatic embryo genotypes; however, all genotypes tested accumulated significant amounts of storage proteins. Zygotic and somatic embryos display a similar developmental accumulation of storage proteins. The 22, 24, 33 and 35 kDa proteins appear in early stage embryos, while the 41 kDa protein begins to accumulate during mid cotyledon development. The 22, 24 and 41 kDa proteins accumulate continuously during cotyledon development in somatic embryos cultured on abscisic acid. In contrast, zygotic embryos display a more rapid and transient accumulation of these proteins.     

GENETIC DIFFERENTIATION OF POLISH POPULATIONS OF SOREX ARANEUS L. III. INTERCHROMOSOMAL RECOMBINATION IN A HYBRID ZONE

Two parapatric chromosomal races of the common shrew (Sorex araneus) in Poland differ in their complement of metacentric arm combinations: hk, io, gr, nm (race IV), and hi, ko, gm, np (race II). In hybrids, these eight race-diagnostic metacentrics form two randomly segregating complexes. The first complex (C₁) occurs in the form of a ring configuration ok/kh/hi/io, or a chain o/ok/kh/hi/i (when there is Robertsonian polymorphism of the element io). The second complex (C₂) always takes the form of a six-element chain configuration r/rg/gm/mn/np/p. The C₂ complex may be shortened to five or even four elements, when acrocentrics g, m and n are present. In the contact zone we found shrews of pure races (race II or IV), as well as hybrids with C₁ or C₂ complexes, and recombinants hi, ko, gr, nm. Complex heterozygotes are likely to suffer reduced fertility due to malsegregation at meiosis. However, the C₁ hybrids with ring configurations occur with a high frequency throughout the contact zone. This suggest that their fitness is only slightly lowered relative to pure race individuals, in contrast to the hybrids with C₁ or C₂ chain configurations, which presumably have a more heavily reduced fertility. On the other hand, at the center of the zone there is a high proportion of recombinants, which, being chromosomal homozygotes, should display normal meiotic segregation. Furthermore, the high frequencies of recombinants within the contact zone should facilitate gene flow between the races. The occurrence of recombinants plays a similar role as the appearance of the maximum frequencies of acrocentric homozygotes described in several contact zones of S. araneus.     

LIGHT-HARVESTING PIGMENT-PROTEIN COMPLEXES OF THE ULVOPHYCEAE (CHLOROPHYTA):CHARACTERIZATION AND PHYLOGENETIC SIGNIFICANCE1

Photosystem II light-harvesting complexes were isolated from a number of ulvophycean algae. Some of these light-harvesting complexes displayed unusual features, most notably a high apparent molecular weight (ca. 58,000) when isolated by lithium doderyl sulfate polyarrylamide gel electrophoresis. Other ulvophycean light-harvesting complexes had a low-molecular weight (ca. 30,000). The distribution of the high-molecular weight complex was limited to certain members of the Caulerpales and Blastophysa rhizopus (Siphanocladales). Within the Caulerpales, there were also spectral differences between the high-molecular weight and low-molecular weight light-harvesting complex types. The differences in light-harvesting complexes in the Ulvophyceae suggest that there are two lines of evolution in the Caulerpales and that Blastophysa may be an intermediate between the Siphon-ocladales and the Caulerpales.     

Structure, biosynthesis, and function of asparagine-linked glycans on plant glycoproteins

In plants, glycoproteins with asparagine-linked glycans (oligosaccharides) are found in vacuoles, in the extracellular space or matrix, and associated with the endo-membrane system (endoplasmic reticulum, Golgi apparatus, plasma membrane, tonoplast). These glycans are of the high-mannose type, with a structure identical to that found in other organisms (mammals, yeast), or of the complex type with a β1–2 linked xylosyl residue not found in mammalian complex glycans. Asparagine-linked glycans play multiple roles by modifying the physicochemical properties of the polypeptides to which they are attached.     

Occurrence of Verticillium fungicola var. fungicola on Agaricus bitorquis Mushroom Crops in Spain

Diseased fruit bodies of Agaricus bitorquis, with similar symptoms to those caused by dry bubble on Agaricus bisporus, were observed in some Spanish crops during summer 1999. Isolates of Verticillium fungicola from A. bitorquis and A. bisporus were submitted to different temperatures and to prochloraz–Mn sensitivity tests. All the isolates collected from A. bitorquis and A. bisporus were identified as V. fungicola var. fungicola. Artificial infections of A. bisporus and A. bitorquis with V. fungicola var. fungicola are also described in the present study. The appearance of natural infections of V. fungicola var. fungicola in A. bitorquis crops could well be due to the growing temperatures used in Spain, which are considerably below those used in other countries.     

A comparison of carbon/energy and complex nitrogen sources for bacterial sulphate-reduction: potential applications to bioprecipitation of toxic metals as sulphides

Detailed nutrient requirements were determined to maximise efficacy of a sulphate-reducing bacterial mixed culture for biotechnological removal of sulphate, acidity and toxic metals from waste waters. In batch culture, lactate produced the greatest biomass, while ethanol was more effective in stimulating sulphide production and acetate was less effective. The presence of additional bicarbonate and H₂ only marginally stimulated sulphide production. The sulphide output per unit of biomass was greatest using ethanol as substrate. In continuous culture, ethanol and lactate were used directly as efficient substrates for sulphate reduction while acetate yielded only slow growth. Glucose was utilised following fermentation to organic acids and therefore had a deleterious effect on pH. Ethanol was selected as the most efficient substrate due to cost and efficient yield of sulphide. On ethanol, the presence of additional carbon sources had no effect on growth or sulphate reduction in batch culture but the presence of complex nitrogen sources (yeast extract or cornsteep) stimulated both. Cornsteep showed the strongest effect and was also preferred on cost grounds. In continuous culture, cornsteep significantly improved the yield of sulphate reduced per unit of ethanol consumed. These results suggest that the most efficient nutrient regime for bioremediation using sulphate-reducing bacteria required both ethanol as carbon source and cornsteep as a complex nitrogen source.     

中国尖音库蚊复合组杂交的研究

本文对分布在我国的尖音库蚊复合组的尖音库蚊,致倦库蚊和淡色库蚊进行杂交研究,结果表明致倦库蚊与尖音库蚊及淡色库蚊以及两者尖交可以产生能育的Ｆ１代,它们之间没有传统意义上的生殖隔离,致倦库蚊应为尖音库蚊是的一个亚种,而不是如国外有些学者认为的独立种,另外,杂种Ｆ２代成活率很低,这有可能是尖音库蚊（广义）种下分化在遗传学上的反映。