Reference : A new in-silico method for determination of helical transmembrane domains based on th...
Scientific journals : Article
Life sciences : Biochemistry, biophysics & molecular biology
http://hdl.handle.net/2268/108394
A new in-silico method for determination of helical transmembrane domains based on the PepLook scan: application to IL-2Rbeta and IL-2Rgammac receptor chains.
English
Charlois, Yan [> > > >]
Lins, Laurence mailto [Université de Liège - ULg > Chimie et bio-industries > Centre de Bio. Fond. - Section de Biophysique moléc. numér.]
Brasseur, Robert mailto [Université de Liège - ULg > Chimie et bio-industries > Centre de Bio. Fond. - Section de Biophysique moléc. numér.]
2011
BMC Structural Biology
BioMed Central
11
26
Yes (verified by ORBi)
International
1472-6807
[en] Amino Acid Sequence ; Animals ; Cattle ; Dogs ; Humans ; Hydrophobic and Hydrophilic Interactions ; Interleukin Receptor Common gamma Subunit/chemistry ; Interleukin-2 Receptor beta Subunit/chemistry ; Macaca mulatta ; Mice ; Molecular Sequence Data ; Pan troglodytes ; Protein Structure, Tertiary ; Rats ; Sequence Alignment ; Sequence Homology, Amino Acid ; Software
[en] 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-2Rbeta and IL-2Rgamma 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.
http://hdl.handle.net/2268/108394
10.1186/1472-6807-11-26

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