Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier.
BACKGROUND
Membrane proteins are estimated to represent about 25% of open reading frames in fully sequenced genomes. However, the experimental study of proteins remains difficult. Considerable efforts have thus been made to develop prediction methods. Most of these were conceived to detect transmembrane helices in polytopic proteins. Alternatively, a membrane protein can be monotopic and anchored via an amphipathic helix inserted in a parallel way to the membrane interface, so-called in-plane membrane (IPM) anchors. This type of membrane anchor is still poorly understood and no suitable prediction method is currently available.


RESULTS
We report here the "AmphipaSeeK" method developed to predict IPM anchors. It uses a set of 21 reported examples of IPM anchored proteins. The method is based on a pattern recognition Support Vector Machine with a dedicated kernel.


CONCLUSIONS
AmphipaSeeK was shown to be highly specific, in contrast with classically used methods (e.g. hydrophobic moment). Additionally, it has been able to retrieve IPM anchors in naively tested sets of transmembrane proteins (e.g. PagP). AmphipaSeek and the list of the 21 IPM anchored proteins is available on NPS@, our protein sequence analysis server.
Sapay
Nicolas
N
Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS-Univ, Lyon 1 - IFR128 BioSciences Lyon-Gerland, F-69367 Lyon Cedex 07, France. n.sapay@ibcp.fr
Guermeur
Yann
Y
Deléage
Gilbert
G
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008565:Membrane Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D010363:Pattern Recognition, Automated / Q000379:methods*; D017433:Protein Structure, Secondary; D015203:Reproducibility of Results; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods
D008565:Membrane Proteins