An algorithm has been developed to improve the success rate in the prediction of the secondary structure of proteins by taking into account the predicted class of the proteins. This method has been called the 'double prediction method' and consists of a first prediction of the secondary structure from a new algorithm which uses parameters of the type described by Chou and Fasman, and the prediction of the class of the proteins from their amino acid composition. These two independent predictions allow one to optimize the parameters calculated over the secondary structure database to provide the final prediction of secondary structure. This method has been tested on 59 proteins in the database (i.e. 10,322 residues) and yields 72% success in class prediction, 61.3% of residues correctly predicted for three states (helix, sheet and coil) and a good agreement between observed and predicted contents in secondary structure.

No abstract

Several cell surface eukaryotic proteins have a glycosylphosphatidylinositol (GPI) modification at the C-terminal end that serves as an anchor to the plasma membrane and could be responsible for the presence of GPI proteins in rafts, a type of functionally important membrane microdomain enriched in sphingolipids and cholesterol. In order to understand better how GPI proteins partition into rafts, the insertion of the GPI-anchored alkaline phosphatase (AP) was studied in real-time using atomic force microscopy. Supported phospholipid bilayers made of a mixture of sphingomyelindioleoylphosphatidylcholine containing cholesterol (Chl+) or not (Chl-) were used to mimic the fluid-ordered lipid phase separation in biological membranes. Spontaneous insertion of AP through its GPI anchor was observed inside both Chl+ and Chl-lipid ordered domains, but AP insertion was markedly increased by the presence of cholesterol.