Issues in high-throughput comparative modelling: a case study using the ubiquitin E2 conjugating enzymes

Sequences of the ubiquitin-conjugating enzyme (UBC or E2) family were used as a test set to investigate issues associated with the high-throughput comparative modelling of protein structures. A semi-automatic method was initially developed with particular emphasis on producing models of a quality suitable for structural comparison. Structural and sequence features of the E2 family were used to improve the sequence alignment and the quality of the structural templates. Initially, failure to correct for subtle structural inconsistencies between templates lead to problems in the comparative analysis of the UBC electrostatic potentials. Modelling of known UBC structures using Modeller 4.0 showed that multiple templates produced, on average, no better models than the use of just one template, as judged by the root-mean-squared deviation between the comparative model and crystal structure backbones. Using four different quality-checking methods, for a given target sequence, it was not possible to distinguish the model most similar to the experimental structure. The UBC models were thus finally modelled using only the crystal structure template with the highest sequence identity to the target to be modelled, and producing only one model solution. Quality checking was used to reject models with obvious structural anomalies (e.g., bad side-chain packing). The resulting models have been used for a comparison of UBC structural features and of their electrostatic potentials. The work was extended through the development of a fully automated pipeline that identifies E2 sequences in the sequence databases, aligns and models them, and calculates the associated electrostatic potential.     

Bystander activation involving T lymphocytes in herpetic stromal keratitis

Herpes simplex virus infection of mouse corneas can lead to the development of an immunopathological lesion, termed herpetic stromal keratitis (HSK). Such lesions also occur in TCR-transgenic mice backcrossed to SCID (TgSCID) that are unable to mount detectable HSV-specific immune responses. The present study demonstrates that lesion expression in such mice depends on continuous viral replication, whereas in immunocompetent mice, lesions occurred even if virus replication was terminated at 4 days after infection. The continuous replication in TgSCID mice was considered necessary to produce an activating stimulus to CD4(+) T cells that invade the cornea. Lesions in TgSCID were resistant to control by cyclosporin A, but were inhibited by treatment with rapamycin. This result was interpreted to indicate that T cell activation involved a non-TCR-mediated cytokine-driven bystander mechanism. Bystander activation was also shown to play a role in HSK lesions in immunocompetent mice. Accordingly, in immunocompetent DO11.10 mice, lesions were dominated by KJ1.26(+) OVA-specific CD4(+) T cells that were unreactive with HSV. In addition, KJ1.26(+) HSV nonimmune cells parked in ocularly infected BALB/c mice were demonstrable in HSK lesions. These results provide insight for the choice of new strategies to manage HSK, an important cause of human blindness.     

Pyridoxal phosphate binding sites are similar in human heme-dependent and yeast heme-independent cystathionine beta-synthases. Evidence from 31P NMR and pulsed EPR spectroscopy that heme and PLP cofactors are not proximal in the human enzyme

Two classes of cystathionine beta-synthases have been identified in eukaryotes, the heme-independent enzyme found in yeast and the heme-dependent form found in mammals. Both classes of enzymes catalyze a pyridoxal phosphate (PLP)-dependent condensation of serine and homocysteine to produce cystathionine. The role of the heme in the human enzyme and its location relative to the PLP in the active site are unknown. (31)P NMR spectroscopy revealed that spin-lattice relaxation rates of the phosphorus nucleus in PLP are similar in both the paramagnetic ferric (T(1) = 6.34 +/- 0.01 s) and the diamagnetic ferrous (T(1) = 5.04 +/- 0.06 s) enzyme, suggesting that the two cofactors are not proximal to each other. This is also supported by pulsed EPR studies that do not provide any evidence for strong or weak coupling between the phosphorus nucleus and the ferric iron. However, the (31)P signal in the reduced enzyme moved from 5.4 to 2.2 ppm, and the line width decreased from 73 to 16 Hz, providing the first structural evidence for transmission to the active site of an oxidation state change in the heme pocket. These results are consistent with a regulatory role for the heme as suggested by previous biochemical studies from our laboratory. The (31)P chemical shifts of the resting forms of the yeast and human enzymes are similar, suggesting that despite the difference in their heme content, the microenvironment of the PLP is similar in the two enzymes. The addition of the substrate, serine, resulted in an upfield shift of the phosphorus resonance in both enzymes, signaling formation of reaction intermediates. The resting enzyme spectra were recovered following addition of excess homocysteine, indicating that both enzymes retained catalytic activity during the course of the NMR experiment.     

Molecular dissection of diheme cytochrome C gene from soil isolate of a Gram negative, facultative chemolithotrophic sulfur oxidizer

A gram negative chemolithotrophic bacterium (RPI) with facultative mode of nutrition was isolated from the soil. Enzymological studies confirmed presence of Thiosulphate oxidase, sulphite oxidase and Rhodanese, all of which play role in sulfur metabolism pathway. A set of degenerate oligonucleotide primer pairs was used for thermal amplification of a major part of the coding region of the Cytochrome c gene locus of this bacterium. Nucleotide and translated amino acid sequence revealed the gene to be a diheme Cytochrome c, different from the monoheme Cytochrome c observed in Chloribium limicola, a photosynthetic green sulfur bacterium. Significant homology at the nucleotide level could be detected only with Pseudoaminobacter salicylatoxidans. On the contrary, significant homology at the amino acid level was observed with Bradyrhizobium japonicum, Silicobacter pomeroyi apart from P. salicylatoxidans. This is possibly because of codon degeneracy observed within the diverse members of chemolithotrophs. Greater homology at amino acid level with P. salicylatoxidans and B. japonicum compared to that with P. denitrificans hint at possibly grouping of RP1 with the Rhizobium-Agrobacterium sub group of alpha Proteobacteria.     

The conserved RNA recognition motif 3 of U2 snRNA auxiliary factor (U2AF 65) is essential in vivo but dispensable for activity in vitro

The general splicing factor U2AF(65) recognizes the polypyrimidine tract (Py tract) that precedes 3' splice sites and has three RNA recognition motifs (RRMs). The C-terminal RRM (RRM3), which is highly conserved, has been proposed to contribute to Py-tract binding and establish protein-protein contacts with splicing factors mBBP/SF1 and SAP155. Unexpectedly, we find that the human RRM3 domain is dispensable for U2AF(65) activity in vitro. However, it has an essential function in Schizosaccharomyces pombe distinct from binding to the Py tract or to mBBP/SF1 and SAP155. First, deletion of RRM3 from the human protein has no effect on Py-tract binding. Second, RRM123 and RRM12 select similar sequences from a random pool of RNA. Third, deletion of RRM3 has no effect on the splicing activity of U2AF(65) in vitro. However, deletion of the RRM3 domain of S. pombe U2AF(59) abolishes U2AF function in vivo. In addition, certain amino acid substitutions on the four-stranded beta-sheet surface of RRM3 compromise U2AF function in vivo without affecting binding to mBBP/SF1 or SAP155 in vitro. We propose that RRM3 has an unrecognized function that is possibly relevant for the splicing of only a subset of cellular introns. We discuss the implications of these observations on previous models of U2AF function.     

Thyroidal regulation of different isoforms of NaKATPase in the primary cultures of neurons derived from fetal rat brain

The developmental profile of the different isoforms of NaKATPase have been investigated using primary cultures of isolated neurons initiated from 17 day old fetal rat brain. Northern blot analysis showed that the expression of three alpha isoforms (alpha(1), alpha(2) and alpha(3)) and two beta isoforms (beta(1) and beta(2)) increased progressively and reached a peak between 12 to 16 days of culture. Comparison of the mRNA levels of these isoforms in the cells maintained in thyroid hormone deficient (TH def) and thyroid hormone supplemented (TH sup) media for 6-12 days, revealed for the first time that in the neurons three alpha and two beta isoforms of NaKATPase are sensitive to TH. Furthermore immunocytochemical staining of these cells with isoform specific NaKATPase antibodies showed that the uniform distribution of alpha(2), alpha(3) and beta(2) isoforms in the neuronal processes require the presence of TH. These results establish neurons as the target cells for the regulation of NaKATPase by TH in the developing brain.     

WISP-2: a serum-inducible gene differentially expressed in human normal breast epithelial cells and in MCF-7 breast tumor cells

WISP-2 is a Wnt-1-induced signaling protein identified as a member of CCN growth factor family. A role for this molecule during tumorigenesis is suspected but remains unproven. Here we show that WISP-2 expression was undetectable, or minimally detectable, in nontransformed human mammary epithelial cells, but was overexpressed in MCF-7 cells. Expression of WISP-2 in MCF-7 cells was modulated by serum and correlated with the serum-induced MCF-7 tumor cell proliferation, suggesting that WISP-2 is serum responsive and may be a positive regulator of tumor cell proliferation.     

Optimization of some additives to improve protease production under SSF

In a locally isolated Rhizopus oryzae strain highest-production of protease (388.54/g wheat bran) was observed in presence of Tween-80 and dioctyl sodium sulfosuccinate individually at 40mg/g wheat bran concentration. Under solid state fermentation biotin (0.0025mg/g wheat bran); Ca2+ (0.05mg/g wheat bran) and 1-Naphthyl acetic acid (0.01mg/g wheat bran) also showed some inducing effect on the synthesis of the enzyme protease by solid state fermentation.