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Background  Membrane proteins compose up to 30% of coding sequences within genomes. However, their structure determination is lagging behind compared with soluble proteins due to the experimental difficulties. Therefore, it is important to develop reliable computational methods to predict structures of membrane proteins.    Results  We present a method for prediction of the TM helix orientation, which is an essential step in  ab initio  modeling of membrane proteins. Our method is based on a canonical model of the heptad repeat originally developed for coiled coils. We identify the helical surface patches that interface with lipid molecules at an accuracy of about 88% from the sequence information alone, using an empirical scoring function LIPS ( LIP id-facing  S urface), which combines lipophilicity and conservation of residues in the helix. We test and discuss results of prediction of helix-lipid interfaces on 162 transmembrane helices from 18 polytopic membrane proteins and present predicted orientations of TM helices in TRPV1 channel. We also apply our method to two structures of homologous cytochrome b 6 f complexes and find discrepancy in the assignment of TM helices from subunits PetG, PetN and PetL. The results of LIPS calculations and analysis of packing and H-bonding interactions support the helix assignment found in the cytochrome b 6 f structure from green alga but not the assignment of TM helices in the cyanobacterium b 6 f structure.    Conclusion  LIPS calculations can be used for the prediction of helix orientation in  ab initio  modeling of polytopic membrane proteins. We also show with the example of two cytochrome b 6 f structures that our method can identify questionable helix assignments in membrane proteins. The LIPS server is available online at   .

Prediction of transmembrane helix orientation in polytopic membrane proteins.