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Abstract: Despite several genomes have been largely or completely sequenced, we are still far from a 'whole proteome' functional characterization. Thousands of 'hypothetical proteins', 'unique' (i.e. not homologous to any other) gene products, and even partially characterized proteins hide unknown, possibly important functions. In the absence of experimental confirmation, sequence analysis alone never demonstrates a function, and simple homology search is even unable to infer function from sequence for about a third of the gene products in any of the sequenced genomes. On the other hand, a 'brute-force' experimental characterization of whole proteomes would be too expensive and time-consuming. In order to find an alternative to shotgun characterization of gene products with unknown function, we are following a "molecular bioinformatics" approach, combining step-by-step in silico analyses with in vitro and in vivo prediction-driven experiments. This allowed to unravel molecular mechanisms underlying function of rolB plant oncogene (F. Filippini et al., Nature 379:499-500, 1996; V. Rossi et al., ms. in preparation) and of bifunctional phospholipase-chitinase EP3 (R. Picco et al., ms. in preparation); further, work is in progress about characterization of the unique N-terminal domain of SYBL1 (M. D'Esposito et al., Nature Genetics, 227-230, 1996), the molecular significance of MeCP2 mutations in Rett syndrome patients, to attempt a genotype-phenotype correlation (Vacca et al et al. , ms. in preparation) and about comparative analysis of mammalian and plant adaptins and protein tyrosine kinases. Using comparative analysis of mammalian and plant genomes we are searching for evolutionarily conserved "sequence function tags" - such as motifs and even weak homology regions - in order to get suggestions for a 'targetted' experimental approach to the demonstration of function or for the identification of homologous elements. This approach is finally aimed to unravel possibly the deregulation of important functions underlying a genetic diseases or fundamental genes involved in plant and mammalian developmental control.

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Abstract: In eukaryotic cells, SNARE proteins of the vesicle or target membrane (v- or t-SNAREs) play a central role in the control of membrane fusion and protein and lipid traffic. SNAREs’ coiled-coil domains (CCDs) have probably evolved from a common ancestor with a hydrophobic heptad register, interrupted by a conserved polar residue at the ionic “zero” layer. Depending on the nature of such residue, SNAREs have been reclassified as either Q- or R-SNAREs. R-SNAREs consist of two subfamilies: (i) short VAMPs or brevins (from the latin word “brevis” = short), and (ii) long VAMPs or longins, sharing a conserved N-terminal Longin Domain. Distinct amino acid patches are likely to determine specificity of SNARE pairing by reducing structural integrity when mismatched SNAREs interact. When considering pairing of the Q- and R-SNARE CCDs, an asymmetric ‘‘complementarity’’ is found in layers -3, -2, and +6, where bulky side chains are packed together with smaller ones, possibly enforcing the correct register between the CCDs of the fusion complex. Sequence variation in the SNARE domains, by altering local charges at the interaction layers, is likely to mediate a fine modulation of the interaction specificity and/or kinetics, regulating intramolecular binding as well as binding to a growing family of SNARE-interacting factors. Although the structure of the SNARE complex is evolutionarily conserved, biological specificity is probably mediated mainly by accessory proteins recognizing different CCD surface patterns of charges, polar and nonpolar side chains different between the endosomal and neuronal complexes. Recently, it has been reported that the interaction among acidic surface residues from the SNAREs and basic residues over the concave surface of α-SNAP is crucial to the disassembly of the complex.