Structural bioinformatics prediction of membrane-binding proteins

Membrane-binding peripheral proteins play important roles in many biological processes, including cell signaling and membrane trafficking. Unlike integral membrane proteins, these proteins bind the membrane mostly in a reversible manner. Since peripheral proteins do not have canonical transmembrane segments, it is difficult to identify them from their amino acid sequences. As a first step toward genome-scale identification of membrane-binding peripheral proteins, we built a kernel-based machine learning protocol. Key features of known membrane-binding proteins, including electrostatic properties and amino acid composition, were calculated from their amino acid sequences and tertiary structures, which were then incorporated into the support vector machine to perform the classification. A data set of 40 membrane-binding proteins and 230 non-membrane-binding proteins was used to construct and validate the protocol. Cross-validation and holdout evaluation of the protocol showed that the accuracy of the prediction reached up to 93.7% and 91.6%, respectively. The protocol was applied to the prediction of membrane-binding properties of four C2 domains from novel protein kinases C. Although these C2 domains have 50% sequence identity, only one of them was predicted to bind the membrane, which was verified experimentally with surface plasmon resonance analysis. These results suggest that our protocol can be used for predicting membrane-binding properties of a wide variety of modular domains and may be further extended to genome-scale identification of membrane-binding peripheral proteins.