Protein Folding: Adding a Nucleus to Guide Helix Docking Reduces Landscape Roughness

The elongated three-helix‐bundle spectrin domains R16 and R17 fold and unfold unusually slowly over a rough energy landscape, in contrast to the homologue R15, which folds fast over a much smoother, more typical landscape. R15 folds via a nucleation–condensation mechanism that guides the docking of the A and C-helices. However, in R16 and R17, the secondary structure forms first and the two helices must then dock in the correct register. Here, we use variants of R16 and R17 to demonstrate that substitution of just five key residues is sufficient to alter the folding mechanism and reduce the landscape roughness. We suggest that, by providing access to an alternative, faster, folding route over their landscape, R16 and R17 can circumvent their slow, frustrated wild-type folding mechanism.     

Genome instability: Does genetic diversity amplification drive tumorigenesis?

Recent data show that catastrophic events during one cell cycle can cause massive genome damage producing viable clones with unstable genomes. This is in contrast with the traditional view that tumorigenesis requires a long‐term process in which mutations gradually accumulate over decades. These sudden events are likely to result in a large increase in genomic diversity within a relatively short time, providing the opportunity for selective advantages to be gained by a subset of cells within a population. This genetic diversity amplification, arising from a single aberrant cell cycle, may drive a population conversion from benign to malignant. However, there is likely a period of relative genome stability during the clonal expansion of tumors – this may provide an opportunity for therapeutic intervention, especially if mechanisms that limit tolerance of aneuploidy are exploited.     

Rapid and sensitive GC/MS characterization of glycolipid released Galalpha1,3Gal-terminated oligosaccharides from small organ specimens of a single pig

Pig to human xenotransplantation is considered a possible solution to the prevailing chronic lack of human donor organs for allotransplantation. The Galalpha1,3Gal determinant is the major porcine xenogeneic epitope causing hyperacute rejection following human antibody binding and complement activation. In order to characterize the tissue distribution of Galalpha1,3Gal-containing and blood group- type glycosphingolipids in pig, acid and nonacid glycosphingolipids were isolated from the kidney, small intestine, spleen, salivary gland, liver, and heart of a single pig obtained from a semi-inbred strain homozygous at the SLA locus. Glycolipids were analyzed by thin-layer immunostaining using monoclonal antibodies, and following ceramide glycanase cleavage as permethylated oligosaccharides by gas chromatography, gas chromatography-mass spectrometry, and matrix- assisted laser desorption/ionization mass spectrometry. The kidney contained large amounts of Galalpha1,3Gal-containing penta- and hexasaccharides having carbohydrate sequences consistent with the Galalpha1,3nLc4and Galalpha1,3Lexstructures, respectively. The former structure was tentatively identified in all organs by GC/MS. The presence of extended Galalpha1,3Gal-terminated structures in the kidney and heart was suggested by antibody binding, and GC/MS indicated the presence of a Galalpha1,3nLc6structure in the heart. The kidney, spleen, and heart contained blood group H pentaglycosylceramides based on type 1 (H-5-1) and type 2 (H-5-2) chains, and H hexaglycosylceramides based on the type 4 chain (H-6-4). In the intestine H-5-1 and H-6-4 were expressed, in the salivary gland H-5-1 and H-5-2, whereas only the H-5-1 structure was identified in the liver. Blood group A structures were identified in the salivary gland and the heart by antibody binding and GC/MS, indicating an organ- specific expression of blood group AH antigens in the pig.      

Microsatellite markers flanking a stem solidness gene on chromosome 3BL in durum wheat

Sawfly (Cephus cinctus Norton) is a major insect pest of wheat (Triticum spp.). The development of durum wheat (Triticum turgidum L. var durum) with stem solidness for resistance to sawfly is a strategy to minimize loss from this insect. This study was undertaken to identify a DNA marker linked to stem solidness and sawfly cutting in durum wheat for use in marker-assisted selection. A set of 151 doubled haploid lines developed from the cross of Kyle*2/Biodur sel. (solid stemmed) and Kofa (hollow stemmed) were evaluated for stem solidness and sawfly cutting. Microsatelite primers that generated polymorphisms between the parental genotypes were tested on the whole population, and primers that followed a 1:1 ratio of parental bands were used in linkage analysis with least squares mean stem solidness scores. Three microsatellite markers, Xgwm247, Xgwm181 and Xgwm114 located on chromosome 3BL, were shown to be associated with the stem solidness locus and with sawfly cutting. The Xgwm114 marker was located on one side of the stem solidness locus with Xgwm247 and Xgwm181 on the opposing side. Recombinant inbred line populations G9580B-FE1C/AC Navigator and Golden Ball/DT379//STD65 segregating for the stem solidness trait confirmed the association between the markers and the stem solidness gene. The Golden Ball/DT379//STD65 population was also tested with the Xwmc632 microsatellite marker, which showed a polymorphism associated with stem solidness. The results also indicated the stem solidness trait was controlled by a single locus in both doubled haploid and recombinant inbred line populations. The markers should be useful in breeding programs for the identification and selection of stem solidness.     

Growing and starving Dictyostelium cells produce distinct density-sensing factors.

Prestarvation factor (PSF) and conditioned medium factor (CMF) are two autocrine factors produced by Dictyostelium cells. Although secreted at different times in the Dictyostelium life cycle (PSF by growing cells and CMF by starving cells), both factors are glycoproteins that are used by cells to measure their own density, and both are important in cell aggregation. To examine the relationship between PSF and CMF, a CMF antisense transformant was tested for the production of PSF during growth. Although this transformant produced extremely low levels of CMF, its production of PSF was essentially normal. We conclude that these two factors are not products of the same gene.     

Characterisation of chloroplast heat shock proteins in young leaves of C4 monocotyledons

In vivo radiolabeling of chloroplast proteins in grain sorghum (Sorghum bicolor L. cv. Texas 610) leaves and their separation by one-dimensional electrophoresis revealed at least 6 heat shock proteins (HSPs) between 24 and 94 kDa. of which the 24 kDa protein was the most prominent. All of these chloroplast heat shock proteins were found exclusively in the stroma. The 24 kDa heat shock protein, upon closer examination using two-dimensional electrophoresis proved to be two similarly-sized heat shock polypeptides with identical molecular masses and level of radiolahel incorporation, hut slightly different in isoeiectric points, suggesting isomers. Separation of stromal heat shock proteins synthesised in two other C₄ monocotyledons ( Punicum miliaceum L. and Umchloa panictrides L.) revealed similar putative isomers. each of 24 kDa. Several other, previously unidentified, heat shock proteins between 22 and 38 kDa were also observed in all three species. In P. miliaceum. the most prominent HSP was the pair of 24 kDa proteins, whereas in U. panicoides. it was a group of 35 to 38 kDa HSPs that was most abundant. In vivo chlorophyll fluorescence measurements showed that no sustained impairment to photosynthetic efficiency had occurred for each species after the heat stress regime. However, when cytoplasmic protein synthesis was inhibited during the high temperature treatment, a dramatic decrease was observed in photosynthetic efficiency, suggesting a possible protective role for chloroplast heat shock proteins. It was also shown that a single chloroplast HSP complex of around 380 kDa was observed in the stroma of both 5. bicolor and P. miliaceum leaves in vivo. This was in contrast to the smaller HSP complex (200–265 kDa) observed in previous studies on chloroplast heat shock proteins in C_j species.     

A shared kappa reciprocal fragment and a high frequency of secondary Jk5 rearrangements among influenza hemagglutinin specific B cell hybridomas

Ig kappa-chain gene rearrangement results in the displacement or loss of the DNA immediately 5' of Jk. This retained DNA is found on a different size fragment than in the germline (a reciprocal fragment), and contains the reciprocal joint of rearranged Vk and Jk genes, the back-to-back fusion of the heptamer/nonamer recombination signals. B cells of independent origin rarely have reciprocal fragments of the same size. However, we report that 9 of 15 B cell hybridomas of independent origin have reciprocal fragments of the same size (8-kb BamHI fragments) unrelated to their productive rearrangements. An 8-kb reciprocal fragment has also occurred on about 25% of the kappa alleles of normal splenic B cells. We find that the reciprocal fragments in two of these hybridomas contain the reciprocal joints of Jk1 genes and different Vk8 genes. In addition, we find that at least 8 of the 12 Jk4 or Jk5 expressing hybridomas have undergone double recombinations on their productive kappa alleles. The implications of these findings on the high frequency of 8-kb reciprocal rearrangements and on Vk rearrangement are discussed.     

Structural elements affecting the recognition of L-isoaspartyl residues by the L-isoaspartyl/D-aspartyl protein methyltransferase. Implications for the repair hypothesis.

We have synthesized a series of L-isoaspartyl-containing (isoD) peptides and characterized their interaction with the human erythrocyte L-isoaspartyl/D-aspartyl protein methyltransferase (EC 2.1.1.77). Our findings indicate that this enzyme interacts with 6 residues extending from the isoD-2 to isoD+3 positions in peptide substrates. Although peptides as simple as G-isoD-G are methylated with low affinity (Km = 17.8 mM), a wide variety of L-isoaspartyl-containing sequences in larger peptides are recognized with high affinity (Km less than 20 microM), the best yet discovered being VYP-isoD-HA, with a Km of 0.29 microM. Only two sequence elements have been found that can interfere with the high affinity binding of peptides of 4 or more residues, these being a prolyl residue in the isoD+1 position and negatively charged residues in the isoD+1, isoD+2, and/or isoD+3 positions. We investigated the effect of higher order structure on binding affinity using several L-isoaspartyl-containing proteins. Although conformation did, in some cases, lower the affinity of the methyltransferase for L-isoaspartyl residues, the range of kinetic constants for the methylation of these proteins was similar to that observed with the synthetic peptides. The L-isoaspartyl/D-aspartyl methyltransferase has been proposed to function in vivo to prevent the accumulation of L-isoaspartyl residues that arise spontaneously as proteins age. To examine whether such a mechanism is feasible given the wide range of substrate Km values observed in vitro, we set up a computer simulation to model the degradation and methylation reactions in aging human erythrocytes. Our results suggest that enough methyltransferase activity exists in these cells to significantly lower the expected number of L-isoaspartyl residues, even when these residues have millimolar Km values for methylation.