Analysis and predication of structural motifs in the glycolytic enzymes

Protein crystallography has determined the three-dimensional structures of 10 of the 13 enzymes of the glycolytic pathway. Diagrams and details of these enzyme structures are given in the paper. Most of the enzyme domains are variations and extensions of a many (4--9)-stranded, predominantly or totally parallel, beta-sheet that is shielded from solvent by alpha-helices (i.e. alpha/beta structures). There are strong structural similarities between the domains of some, but not all, of the enzymes. In particular the dinucleotide binding fold of lactate dehydrogenase and the beta-barrel of triose phosphate isomerase are found in other domains. General rules governing the topology and packing of alpha-helices against a beta-sheet provide a basis for the combinatorial prediction of the tertiary fold of glycolytic domains from their amino acid sequence and observed secondary structure. The predication algorithm demonstrates that there are severe restrictions on the number of possible structures. However, these restrictions do not fully explain some of the remarkable structural similarities between different enzymes that probably result from evolution from a common ancestor.     

On the conformation of proteins: The handedness of the β-strand-α-helix-β-strand unit

The β-strand-α-helix-β-strand unit consists of two parallel, but not necessarily adjacent, β-strands which lie in a β-pleated sheet and are connected by one or more α-helices. This unit, which occurs in 17 functionally different globular proteins, may adopt a right- or a left-handed conformation. An analysis of the distribution shows that 57 out of the 58 units are right-handed. If the unit had no right-handed preference, the probability of observing such a distribution by chance is 10^?16. This may be explained in terms of the twist of the β-sheet which is shown to favour a right-handed unit, as otherwise steric hindrance occurs in the loop regions. We show that the right-handed strand-helix-strand unit determines the sense of the super-secondary structure found in the dehydrogenases and of related folds found in other structures. The evolutionary relationships between proteins containing this unit are re-evaluated in terms of this preference. The high probability that the unit will fold with a right-handed conformation has implications for the prediction of tertiary structure.     

Hippocampal 8-[3H]Hydroxy-2-(Di-n-Propylamino)Tetralin Binding Site Densities, Serotonin Receptor (5-HT1A) Messenger Ribonucleic Acid Abundance, and Serotonin Levels Parallel the Activity of the Hypothalamopituitary-Adrenal Axis in Rat

We have previously demonstrated that susceptibility of the Lewis rat to inflammatory disease, compared with the relatively resistant Fischer F344/N rat, is related to a hyporesponsive hypothalamopituitary-adrenal axis to inflammatory and other stress mediators. Because serotonin (5-HT) and the 5-HT1A receptor are important stimulators of this axis, we have investigated the levels of 8-[3H]-hydroxy-2,3-(di-n-propylamino)tetralin binding sites, 5-HT1A mRNA, 5-HT, and 5-hydroxyindoleacetic acid in various brain regions of Lewis, outbred Harlan Sprague Dawley, and Fischer F344/N rats. Lewis rats expressed significantly fewer hippocampal and frontal cortical 8-[3H]-hydroxy-2,3-(di-n-propylamino)tetralin binding sites and less 5-HT1A mRNA than Harlan Sprague Dawley and Fischer F344/N rats. Adrenalectomy increased the number of 8-[3H]hydroxy-2,3-(di-n-propylamino)tetralin binding sites and 5-HT1A mRNA expression in the hippocampus of all three strains. Levels of hippocampal 5-HT in Fischer F344/N rats were significantly greater than levels detected in the same regions from Lewis and Harlan Sprague Dawley rats. Hypothalamic 5-HT and 5-hydroxyindoleacetic acid levels in Harlan Sprague Dawley rats were higher than the same area from the other two strains. Adrenalectomy increased the levels of 5-hydroxyindoleacetic acid in the hypothalamus of all three strains. We conclude that hippocampal 5-HT1A receptor densities and 5-HT levels in the rat parallel the activity and responsiveness of the hypothalamopituitary-adrenal axis.     

Molecular dynamics of calmodulin as monitored by fluorescence anisotropy

Static and dynamic measurements of fluorescence anisotropy have been made for calmodulin, employing both the intrinsic fluorescence of Tyr-99 and Tyr-138 and the fluorescence of dansyl and fluorescein groups attached to Tyr-99, as well as AEDANS groups attached to methionines. All approaches indicate the presence of a significant internal mobility involving the probe for calmodulin in the absence of Ca²⁺. This is diminished in the presence of Ca²⁺.²     

Nematode Postembryonic Cell Lineages

The complete postembryonic ceil lineages of the free-living nentatodes Caenorhabditis elegans and Panagrellus redivivus are known. Postembryonic cell divisions lead to substantial increases in the number of cells and, in most cases, in the number of types of cells in the neuronal, muscular, hypodermal, and digestive systems. The patterns of postembyronic cell divisions are essentially invariant and generate a fixed number of progeny cells of strictly specified fates. Cell fates depend upon both lineage history and cell-cell interactions: lineage limits the developmental potential of each cell and, for certain cells, cell-cell interactions specify which of a small number of alternative potential fates is acquired. Relatively simple differences in cell lineage account for some of the striking differences in gross morphology both between sexes and between species. Genetic studies indicate that these cell lineage differences reflect one or a few relatively simple mutational events. Interspecific differences in cell lineage are likely to be good indicators of evolutionary distance and may be helpful in defining taxonomic relationships. Both the techniques utilized in, and the information acquired from, studies of cell lineages in C. elegans and P. redivivus may prove useful to other hematologists.     

Distribution of bacterial growth activity in flow-chamber biofilms.

In microbial communities such as those found in biofilms, individual organisms most often display heterogeneous behavior with respect to their metabolic activity, growth status, gene expression pattern, etc. In that context, a novel reporter system for monitoring of cellular growth activity has been designed. It comprises a transposon cassette carrying fusions between the growth rate-regulated Escherichia coli rrnBP1 promoter and different variant gfp genes. It is shown that the P1 promoter is regulated in the same way in E. coli and Pseudomonas putida, making it useful for monitoring of growth activity in organisms outside the group of enteric bacteria. Construction of fusions to genes encoding unstable Gfp proteins opened up the possibility of the monitoring of rates of rRNA synthesis and, in this way, allowing on-line determination of the distribution of growth activity in a complex community. With the use of these reporter tools, it is demonstrated that individual cells of a toluene-degrading P. putida strain growing in a benzyl alcohol-supplemented biofilm have different levels of growth activity which develop as the biofilm gets older. Cells that eventually grow very slowly or not at all may be stimulated to restart growth if provided with a more easily metabolizable carbon source. Thus, the dynamics of biofilm growth activity has been tracked to the level of individual cells, cell clusters, and microcolonies.     

On the marine sister groups of the freshwater crabs (Crustacea: Decapoda: Brachyura)

Freshwater crab sister group relationships with marine eubrachyuran families were investigated. A morphology-based cladistic analysis was conducted on representatives of the freshwater crab families Deckeniidae, Gecarcinucidae, Parathelphusidae, Potamidae, Potamonautidae, Pseudothelphusidae, and Trichodactylidae using a disparate assemblage of marine heterotreme and thoracotreme brachyurans as possible sister groups. The monophyly of the freshwater crabs sensu lato is falsified. The family Trichodactylidae and the marine portunid subfamily Carcininae form basal groups within the superfamily Portunoidea. The monophyly of the Pseudothelphusidae and the Paleotropical freshwater crab families is supported, and this clade is the sister group of the Thoracotremata (Gecarcinidae, Grapsidae s.l., and Ocypodoidea). The origin, groundplan, and diversification of freshwater crabs are discussed in the context of previously published scenarios of their evolution.     

Sensory processing by neural circuits in Caenorhabditis elegans

The anatomical and developmental constancy of Caenorhabditis elegans belies the complexity of its numerically small nervous system. Indeed, there is an increased appreciation of C. elegans as an organism to study systems level questions. Many recent studies focus on the circuits that control locomotion, egg-laying, and male mating behaviors and their modulation by multiple sensory stimuli.     

Clustering of protein domains in the human genome

We present a systematic study of the clustering of genes within the human genome based on homology inferred from both sequence and structural similarity. The 3D-Genomics automated proteome annotation pipeline () was utilised to infer homology for each protein domain in the genome, for the 26 superfamilies most highly represented in the Structural Classification Of Proteins (SCOP) database. This approach enabled us to identify homologues that could not be detected by sequence-based methods alone. For each superfamily, we investigated the distribution, both within and among chromosomes, of genes encoding at least one domain within the superfamily. The results indicate a diversity of clustering behaviours: some superfamilies showed no evidence of any clustering, and others displayed significant clustering either within or among chromosomes, or both. Removal of tandem repeats reduced the levels of clustering observed, but some superfamilies still displayed highly significant clustering. Thus, our study suggests that either the process of gene duplication, or the evolution of the resulting clusters, differs between structural superfamilies.     

The BRCA1 C-terminal domain: structure and function

The BRCA1 C-terminal region contains a duplicated globular domain termed BRCT that is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions with DNA strand breaks. The sequence and functional diversity of the BRCT superfamily suggests that BRCT domains are evolutionarily convenient interaction modules.