Alternative splicing and protein function

Background  

Alternative splicing is a major mechanism of generating protein diversity in higher eukaryotes. Although at least half, and probably more, of mammalian genes are alternatively spliced, it was not clear, whether the frequency of alternative splicing is the same in different functional categories. The problem is obscured by uneven coverage of genes by ESTs and a large number of artifacts in the EST data.     

Copolymerizations of epsilon-caprolactone and glycolide-a comparison of tin(II)octanoate and bismuth(III)subsalicylate as initiators

Copolymerizations of epsilon-caprolactone (epsilonCL) and glycolide (GL) were conducted in bulk at 120 degrees C with variation of the reaction time. Either Sn(II) 2-ethylhexanoate (SnOct(2)) or bismuth(III)subsalicylate (BiSS) were used as initiators combined with tetra(ethylene glycol) as co-initiator. The resulting copolyesters were analyzed by (1)H and (13)C NMR spectroscopy with regard to the total molar composition and to the sequence of the comonomers. Furthermore, two series of copolymerizations (either Sn- or Bi-initiated) were performed at constant time with variation of the temperature. It was found that BiSS favors alternating sequences more than SnOct(2). Time-conversion curves and MALDI-TOF mass spectrometry of homopolymerization suggest that SnOct(2) is the more efficient transesterification catalyst. A hypothetical reaction mechanism is discussed.     

Analysing six types of protein-protein interfaces

Non-covalent residue side-chain interactions occur in many different types of proteins and facilitate many biological functions. Are these differences manifested in the sequence compositions and/or the residue-residue contact preferences of the interfaces? Previous studies analysed small data sets and gave contradictory answers. Here, we introduced a new data-mining method that yielded the largest high-resolution data set of interactions analysed. We introduced an information theory-based analysis method. On the basis of sequence features, we were able to differentiate six types of protein interfaces, each corresponding to a different functional or structural association between residues. Particularly, we found significant differences in amino acid composition and residue-residue preferences between interactions of residues within the same structural domain and between different domains, between permanent and transient interfaces, and between interactions associating homo-oligomers and hetero-oligomers. The differences between the six types were so substantial that, using amino acid composition alone, we could predict statistically to which of the six types of interfaces a pool of 1000 residues belongs at 63-100% accuracy. All interfaces differed significantly from the background of all residues in SWISS-PROT, from the group of surface residues, and from internal residues that were not involved in non-trivial interactions. Overall, our results suggest that the interface type could be predicted from sequence and that interface-type specific mean-field potentials may be adequate for certain applications.     

Enzyme function less conserved than anticipated

The level of sequence similarity that implies similarity in protein structure is well established. Recently, many groups proposed thresholds for similarity in sequence implying similarity in enzymatic function. All previous results suggest the strong conservation of enzymatic function above levels of 50% pairwise sequence identity. Here, I argue that all groups substantially overestimated the conservation of enzyme function because their data sets were either too biased, or too small. An unbiased analysis suggested that less than 30% of the pair fragments above 50% sequence identity have entirely identical EC numbers. Another surprising finding was that even BLAST E-values below 10(-50) did not suffice to automatically transfer enzyme function without errors. As expected, most misclassifications originated from similarities in relatively short regions and/or from transferring annotations for different domains. Both problems cannot be corrected easily by adjusting the thresholds for automatic transfer of genome annotations. A score relating sequence identity to alignment length (distance from HSSP-threshold) outperformed statistical BLAST scores for high sequence similarity. In particular, the distance score allowed error-free transfer of enzyme function for the 10% most similar enzyme pairs. The results illustrated how difficult it is to assess the conservation of protein function and to guarantee error-free genome annotations, in general: sets with millions of pair comparisons might not suffice to arrive at statistically significant conclusions. In practice, the revised detailed estimates for the sequence conservation of enzyme function may provide important benchmarks for everyday sequence analysis and for more cautious automatic genome annotations.     

Evaluation of the protective effect of oestradiol against toxicity induced by 6-hydroxydopamine and 1-methyl-4-phenylpyridinium ion (Mpp+) towards dopaminergic mesencephalic neurones in primary culture

Recent findings suggest that gonadal steroid hormones are neuroprotective and may provide clinical benefits in delaying the development of Parkinson's disease. In this report we investigated the ability of oestradiol to protect mesencephalic dopaminergic neurones cultured in serum-free or serum-supplemented medium from toxicity induced by 6-hydroxydopamine or 1-methyl-4-phenylpyridinium ion (MPP+). The efficiency of both toxins and oestradiol was evaluated by tyrosine hydroxylase (TH) immunocytochemistry, [3H]dopamine ([3H]DA) uptake, length of dopaminergic processes and lactate dehydrogenase (LDH) release measurement. In cultures grown in serum-supplemented medium, a 2-h pre-treatment with high concentrations (10-100 microM) of 17beta-oestradiol or 17alpha-oestradiol, the stereoisomer with weak oestrogenic activity, protected both dopaminergic and non-dopaminergic neurones from toxicity induced by 6-hydroxydopamine (6-OHDA; 40 or 100 microM) and by the high MPP+ concentrations (50 microM) necessary to obtain significant neuronal death under those culture conditions. At these concentrations, MPP+ was no longer selective for dopaminergic neurones but affected all cells present in the culture. In contrast, the hormonal treatments did not protect against selective degeneration of dopaminergic neurones induced by lower MPP+ concentrations (below 10 microM), related to inhibition of complex I of respiratory chain. In cultures grown in serum-free medium, oestradiol concentrations higher than 1 microM induced neuronal degeneration and no protection against 6-OHDA or MPP+ toxicity was observed at lower concentrations of the steroid. The neuroprotective effects of 17alpha- or 17beta-oestradiol evidenced in this model might be due to the antioxidant properties of these compounds. However, other non-genomic effects of the steroids cannot be excluded.     

Expression and localization of the multidrug resistance-associated protein 3 in rat small and large intestine

Multidrug resistance-associated protein 3 (MRP3; symbol ABCC3), has been shown to mediate ATP-dependent transport of organic anions including 17beta-glucuronosyl estradiol, glucuronosyl bilirubin, monovalent, and sulfated bile salts. MRP3 mRNA expression was reported in rat intestine suggesting a role of MRP3 in the intestinal transport. We examined the expression and localization of MRP3 in rat small and large intestine by RT-PCR, immunofluorescence, and immunoblot analysis. MRP3 was identified in all intestinal segments by RT-PCR. MRP3 expression was low in duodenum and jejunum but markedly increased in ileum and colon. With the use of a rat MRP3 specific antibody, MRP3 was localized to the basolateral domains of enterocytes. Immunofluorescence analysis and immunoblot analysis confirmed a strong expression of rat MRP3 in ileum and colon. In contrast, MRP2 was predominantly expressed in the proximal segments of rat small intestine. Our findings demonstrate a high expression of rat MRP3 in ileum and colon and provide evidence for an involvement of MRP3 in the ATP-dependent transport of organic anions, including bile salts from the enterocyte into blood.     

The PredictProtein server

PredictProtein (PP, http://cubic.bioc.columbia.edu/pp/) is an internet service for sequence analysis and the prediction of aspects of protein structure and function. Users submit protein sequence or alignments; the server returns a multiple sequence alignment, PROSITE sequence motifs, low-complexity regions (SEG), ProDom domain assignments, nuclear localisation signals, regions lacking regular structure and predictions of secondary structure, solvent accessibility, globular regions, transmembrane helices, coiled-coil regions, structural switch regions and disulfide-bonds. Upon request, fold recognition by prediction-based threading is available. For all services, users can submit their query either by electronic mail or interactively from World Wide Web.     

Target space for structural genomics revisited

MOTIVATION: Structural genomics eventually aims at determining structures for all proteins. However, in the beginning experimentalists are likely to focus on globular proteins to achieve a rapid basic coverage of protein sequence space. How many proteins will structural genomics have to target? How many proteins will be excluded since we already have structural information for these or since they are not globular? We have to answer these questions in the context of our target selection for the North-East Structural Genomics Consortium (NESG). RESULTS: We estimated that structural information is available for about 6-38% of all proteins; 6% if we require high accuracy in comparative modelling, 38% if we are satisfied with having a rough idea about the fold. Excluding all regions that are not globular, we found that structural genomics may have to target about 48% of all proteins. This corresponded to a similar percentage of residues of the entire proteomes (52%). We explored a number of different strategies to cluster protein space in order to find the number of families representing these 48% of structurally unknown proteins. For the subset of all entirely sequenced eukaryotes, we found over 18 000 fragment clusters each of which may be a suitable target for structural genomics. AVAILABILITY: All data are available from the authors, most results are summarized at: http://cubic.bioc.columbia.edu/genomes/RES/2002_bioinformatics/