A novel Asn344 deletion in the core domain of coagulation factor XIII A subunit: its effects on protein structure and function

We re-evaluated three schemes of liver organization: the classic lobule, the portal lobule, and Rappaport's liver acinus. The lobular angioarchitecture of normal rat liver and the three-dimensional structure of pseudolubules found in rat livers with fibrosis induced by swine serum were compared with the classic lobule of the pig. Normal and fibrotic rat livers and pig livers were perfused, injected with either India ink or 0.75% OsO4 through the portal and/or hepatic vein, and immersionfixed. Whole lobes and hand-cut thick sections were made transparent with a solution of benzyl benzoate and methyl salicylate. The angioarchitecture of normal rat liver differs from pig liver. In the former, terminal portal branches and central veins interdigitate, and in the latter, numerous terminal portal branches that arise from interlobular portal veins establish a vascular basket surrounding one central vein and forming classic lobule. The structure of liver acinus is never found in the pig liver. The terminal portal branch, together with the terminal hepatic artery and bile duct, are present inside each pseudolobule of fibrotic rat livers. Blood from the terminal portal branch flows through inlet venules into radiating sinusoids, and, at the periphery converges into newly formed septal and angular outlet venules; these venules terminate in fibrotic central veins located at each corner. Pseudolobules are not rugby ball-like as Rappaport's liver acini are but are polyhedron in shape. The rat pseudolobules are comparable with the portal lobule; its structure and microcirculation are the reverse of the pig classic lobule. Rat pseudolobules are different from liver acini, as shown by the following: 1) their three-dimensional shape is different; and 2) they have a reverse relationship to classic lobules while acini are defined to subdivide classic lobules. In normal and fibrotic rat livers, the liver unit is the portal lobule with a terminal portal branch as the axial branch and central veins at the periphery. The co-existence of liver acini and classic lobules is doubtful.     

An analysis of simultaneous variation in protein structures

The simultaneous substitution of pairs of buried amino acid side chains during divergent evolution has been examined in a set of protein families with known crystal structures. A weak signal is found that shows that amino acid pairs near in space in the folded structure preferentially undergo substitution in a compensatory way. Three different physicochemical types of covariation 'signals' were then examined separately, with consideration given to the evolutionary distance at which different types of compensation occur. Where the compensatory covariation tends towards retaining the combined residue volumes, the signal is significant only at very low evolutionary distances. Where the covariation compensates for changes in the hydrogen bonding, the signal is strongest at intermediate evolutionary distances. Covariations that compensate for charge variations appeared with equal strength at all the evolutionary distances examined. A recipe is suggested for using the weak covariation signal to assemble the predicted secondary structural elements, where the evolutionary distance, covariation type and weighting are considered together with the tertiary structural context (interior or surface) of the residues being examined.      

A homology model for the human theta-class glutathione transferase T1-1

A manual threading approach is used to model the human glutathione transferase T1-1 based on the coordinates of the related Theta class enzyme T2-2. The low level of sequence identity (about 20%), found in the C-terminal extension in conjunction with a relative deletion of about five residues makes this a challenging modeling problem. The C-terminal extension contributes to the active site of the molecule and is thus of particular interest for understanding the molecular mechanism of the enzyme. Manual docking of known substrates and non-substrates has implicated potential candidates for the T1-1 catalytic residues involved in the dehalogenation and epoxide-ring opening activities. These include the conserved Theta class residues Arg 107, Trp 115, and the conserved GSTT1 subclass residue His 176. Also, the residue at position 234 is implicated in the modulation of T1-1 activity with different substrates between species.     

Easy adaptation of protein structure to sequence

An investigation into the conservation of coarse, medium andfine grain structural properties has been performed over a dataset of 175 protein tertiary structures in 34 different families,each characterized by a common core fold and a library of conservedsites formed for each family. It is shown that, while the conservationof coarse and medium grain properties correlates to the structuraldeviation between the proteins, fine grain properties are poorlyconserved except in functional sites. This flexibility in finegrain properties suggests that folding can be viewed as an optimizationprocess whereby side chains have freedom to position themselvesas best as possible given environmental conformationa] constraintsand that given a basic framework, the local structure is ableto adapt easily to sequence variation. The conserved cores ofthe 34 families are used to estimate a minimal core size of35% of the fold, consistent with buried residue considerations.Finally, conservation in side chain l torsion angles is combinedwith structural deviation, sequence deviation and resolutionto suggest a set of example structure pairs suitable for testingautomatic homology modelling programs     

A roadmap for HLA-A, HLA-B, and HLA-C peptide binding specificities

The characteristics of the circadian rhythm of locomotor activity in the crayfish Procambarus clarkii during ontogeny under constant darkness and light-dark (LD 12:12) conditions were studied in 132 juvenile crayfish, aged 10-140 days, divided in four groups. All animals were individually monitored with a motor activity recording system. Activity was quantitatively and qualitatively analyzed. All ages showed a circadian rhythm, although the probability of its appearance increased with age. Period values oscillated between 25.0 h in group I (2-4-week-old animals) and 24.3 h in group IV (16-20-week-old animals with more than 6 molts), but always with a high standard deviation. Groups II (5-10-week-old animals) and IV showed a statistically significant bimodal nonrandom synchrony of phases. The activity/ rest relationship diminishes as development progresses and is most uniform in group IV. We discuss the possibility that the pacemaker system responsible for this rhythm might be present from the moment of eclosion, but the coupling strength of this system with the effectors might change along development. The results presented in this work seem to indicate that the central pacemakers responsible for the activity and the ERG rhythm are not the same.     

Human theta class glutathione transferase: the crystal structure reveals a sulfate-binding pocket within a buried active site

Depressive illness has been reported to interfere with effortful processing, which requires conscious attention. The aim of this study was to evaluate divided attention in depressed patients, as a function of the degree of difficulty of the task performed. Tasks designed to measure unimodal and bimodal reaction times were presented to 10 patients with major depression and 10 normal control subjects. Performance was evaluated both before treatment when the patients were depressed and after treatment when they had recovered. Unlike the unimodal trials, the bimodal reaction time tasks were designed to evaluate decision-making under conditions in which attention was divided between two perceptual channels. Reaction times were measured under two different conditions in order to assess the extent of the response delay induced by divided attention, modality shifting, and decision processing. During simple response tasks, the depressed patients displayed significantly greater lengthening of reaction times when their attention was divided between two perceptual channels. This cross-modal delay effect occurred both for stimuli of the same modality and when shifting between modalities. The cross-modal delay effect was evident only for the choice tests in both the depressed and the recovered patients, but only the recovered patients were as accurate as the control subjects. These results suggest that the need for decision processing in depressed patients results in a failure to allocate the mental resources required to complete interchannel shifting, when attention is divided between two perceptual channels. These data are consistent with the hypothesis that attentional regulation is impaired in major depression.     

Anti-MUC1 antibodies react directly with MUC1 peptides presented by class I H2 and HLA molecules

Codon usage bias, the preferential use of particular codons within each codon family, is characteristic of synonymous base composition in many species, including Drosophila, yeast, and many bacteria. Preferential usage of particular codons in these species is maintained by natural selection acting largely at the level of translation. In Drosophila, as in bacteria, the rate of synonymous substitution per site is negatively correlated with the degree of codon usage bias, indicating stronger selection on codon usage in genes with high codon bias than in genes with low codon bias. Surprisingly, in these organisms, as well as in mammals, the rate of synonymous substitution is also positively correlated with the rate of nonsynonymous substitution. To investigate this correlation, we carried out a phylogenetic analysis of substitutions in 22 genes between two species of Drosophila, Drosophila pseudoobscura and D. subobscura, in codons that differ by one replacement and one synonymous change. We provide evidence for a relative excess of double substitutions in the same species lineage that cannot be explained by the simultaneous mutation of two adjacent bases. The synonymous changes in these codons also cannot be explained by a shift to a more preferred codon following a replacement substitution. We, therefore, interpret the excess of double codon substitutions within a lineage as being the result of relaxed constraints on both kinds of substitutions in particular codons.