A new in-silico method for determination of helical transmembrane domains based on the PepLook scan: Application to IL-2R and IL-2Rc receptor chains

Abstract

Background: Modeling of transmembrane domains (TMDs) requires correct prediction of interfacial residues for in-silico modeling and membrane insertion studies. This implies the defining of a target sequence long enough to contain interfacial residues. However, too long sequences induce artifactual polymorphism: within tested modeling methods, the longer the target sequence, the more variable the secondary structure, as though the procedure were stopped before the end of the calculation (which may in fact be unreachable). Moreover, delimitation of these TMDs can produce variable results with sequence based two-dimensional prediction methods, especially for sequences showing polymorphism. To solve this problem, we developed a new modeling procedure using the PepLook method. We scanned the sequences by modeling peptides from the target sequence with a window of 19 residues. Results: Using sequences whose NMR-structures are already known (GpA, EphA1 and Erb2-HER2), we first determined that the hydrophobic to hydrophilic accessible surface area ratio (ASAr) was the best criterion for delimiting the TMD sequence. The length of the helical structure and the Impala method further supported the determination of the TMD limits. This method was applied to the IL-2R and IL-2R TMD sequences of Homo sapiens, Rattus norvegicus, Mus musculus and Bos taurus. Conclusions: We succeeded in reducing the variation in the TMD limits to only 2 residues and in gaining structural information. © 2011 Charlois et al; licensee BioMed Central Ltd.