On the design of optimally inserted transmembrane helices

Resum

The great majority of helical membrane proteins are inserted co-translationally into the ER membrane through a continuous ribosome-translocon channel. The efficiency of membrane insertion depends on transmembrane (TM) helix amino acid composition, the helix length and the position of the amino acids within the helix. Recent advances in high-resolution structure determination of membrane proteins enable now the analysis of the main features of amino acids in transmembrane (TM) segments in comparison with amino acids in water-soluble helices. In this Thesis, we introduced a large-scale analysis of amino acid propensities using a data set of 170 structures of integral membrane proteins obtained from MPTopo database and 930 structures of water-soluble helical proteins obtained from the Protein Data Bank. We also examined the distribution of residues along the TM helices included in our database. Next, we conducted a computational analysis of the composition and location of amino acid residues in this database to obtain an extensive set of designed polypeptide segments with naturally occurring amino acid distributions. Finally, using an in vitro translation system in the presence of biological membranes, we experimentally validated our predictions by analyzing its membrane integration capacity. Coupled with known strategies to control membrane protein topology, the findings of this Thesis may pave the way to de novo membrane protein design.