Membrane proteomics: Use of additive main effects with multiplicative interaction model to classify plasma membrane proteins according to their solubility and electrophoretic properties

Recent efforts at the proteomic level were employed to describe the protein equipment of the plasma membrane of the model plant Arabidopsis thaliana. These studies had revealed that the plasma membrane is rich in extrinsic pr oteins but came up against two major problems: (i) few hydrophobic proteins were recovered in two-dimensional electrophoresis gels, and (ii) many plas ma membrane proteins had no known function or were unknown in the database despite extensive sequencing of the Arabidopsis genome. In this paper, seve ral methods expected to enrich a membrane sample in hydrophobic proteins we re compared. The optimization of solubilization procedures revealed that th e detergent to be used depends on the lipid content of the sample. The corr esponding proteomes were compared with the statistical model AMMI (additive main effects with multiplicative interaction) that aimed at regrouping pro teins according to their solubility and electrophoretic properties. Distinc t groups emerged from this analysis and the identification of proteins in e ach group allowed us to assign specific features to several of them. For in stance, two of these groups regrouped very hydrophobic proteins, one group contained V-ATPase subunits, another group contained proteins with one tran smembrane domain as well as proteins known to interact with membrane protei ns. This study provides methodological tools to study particular classes of plasma membrane proteins and should be applicable to other cellular membra nes.