Genome scale-annotation of membrane proteins and more..

First of all why membrane proteins?: a very large set of yet-to be-characterized proteins mediating all the relevant life-related functions both in prokaryotes and eukaryotes. Estimates are suggesting that in whole genomes the content of this protein type may vary from 10% to 40% of the whole protein content, depending on the organism type. What do we know: 1) some 2% of the PDB data base contain membrane proteins known at the atomic level (crystallization for this type of membrane proteins is yet a very difficult process given the fact that these proteins expose two different chemico-physical surfaces to the environment: water and lipid-like); 2) membrane proteins structures are of two types: all-alfa or beta-barrel membrane proteins. Most of membrane proteins consist of bundles of transmembrane helices. Some of membrane proteins are located in the outer membrane of mitochondria and chloroplasts, or in the outer membrane of gram-negative bacteria; in this case they are endowed with a very well conserved architecture known as transmembrane beta barrel; 3) some 1D experimentally characterized sets of membrane proteins in relation to their topology with respect to the membrane phase (where the N and C termini are located). What can we do: we can take advantage of the available information for annotating membrane proteins. Also we can model them depending on their type and we can also investigate in humans how their folding/misfolding is related to diseases.