A ProGenGrid Service for the Protein Structure Prediction

Protein structure prediction is of high importance in medicine and biotechnology. From this point of view, an important aspect regards the function of metabolite mitochondrial carriers, a family of intrinsic proteins that mediate the flux of several metabolites from the matrix to the cytosol and vice versa, in relation to the role that such proteins cover in some mitochondrial pathologies. Along with the fast progress in the identification of novel mitochondrial carriers over the last few years, an increasing number of genes encoding mitochondrial carriers have been identified whose defects cause various inherited diseases. Sequence studies have shown that all carrier proteins have a highly conserved sequence motif, the carrier signature. To determine the possible role of this motif in the function of a carrier protein, we used the dicarboxylate carrier (DIC) of Saccharomyces cerevisiae as a model protein. In this study we model the structure of DIC, using the only carrier so far solved with atomic resolution in the PDB data bank: the ADP/ATP carrier protein of Bos taurus heart mitochondria. Here we integrated a routinely expert dependent strategy in a automatic tool that may facilitate the generation of carrier models at low resolution, good enough for serving as template models in different occasion, including site directed mutagenesis to prove and/or disprove the involvement of a computed topological structure in specific functional process. Therefore, we developed a new service, that uses applications deployed in a Grid environment, in order to automate the prediction procedure and integrate the data produced by the in vitro and in silico analysis.