Structure Elucidation of Transmembrane Proteins using Public-Available Databases and Experimental Data on Competitive Inhibition

We present an approach towards structure elucidation of bilitranslocase, the membrane protein which transports bilirubin from blood to liver cells. The sequence and secondary structure information of transmembrane segments of proteins with known 3D structure is exploited to predict the transmembrane domains of structurally unresolved target protein. With the help of known structures the transmembrane domains are encoded in such a way that it is possible to group and classify them with respect to their specific sub-structural characteristics and to build a model for prediction of transmembrane segments. We have shown that the model for prediction of transmembrane segments proposed four transmembrane alpha helices, each containing around 20 amino acids. This result is partially confirmed with experimental studies using particular antibodies corresponding to parts of amino acid sequences of bilitranslocase. In order to shed light on the bilitranslocase transport mechanism, we also tested a set of non-congeneric compounds for their competitive inhibition constants in the investigated protein-substrate system. The information about chemical structure of small molecules that either pass or block the transmembrane path enabled by bilitranslocase helps us to build a hypothesis about the transport mechanism of the studied biological system.