The transport activity of a membrane protein, bilitranslocase (T.C. # 2.A.65.1.1), which acts as a transporter of bilirubin from blood to liver cells, was experimentally determined for a large set of various endogenous compounds, drugs, purine and pyrimidine derivatives. On these grounds, the structure-activity models were developed following the OECD principles of QSAR models and their predictive ability for new chemicals was evaluated. The applicability domain of the models was estimated by Euclidean distances criteria according to the applied modeling method. The selection of the most influential structural variables was an important stage in the adopted modeling methodology. The interpretation of selected variables was performed in order to get an insight into the mechanism of transport through the cell membrane via bilitranslocase. Validation of the optimized models was performed by a previously determined validation set. The classification model was build to separate active from inactive compounds. The resulting accuracy, sensitivity, and specificity were 0.73, 0.89, and 0.64, respectively. Only active compounds were used to develop a predictive model for bilitranslocase inhibition constants. The model showed good predictive ability; Root Mean Squared error of the validation set, RMSV = 0.29 log units of Ki.
COBISS.SI-ID: 4723994
Using a combination of genomic and post-genomic approaches is rapidly altering the number of identified human influx carriers. A transmembrane protein bilitranslocase (TCDB 2.A.65) has long attracted attention because of its function as an organic anion carrier. It has also been identified as a potential membrane transporter for cellular uptake of several drugs and due to its implication in drug uptake, it is extremely important to advance the knowledge about its structure. However, at present, only the primary structure of bilitranslocase is known. In our work, transmembrane subunits of bilitranslocase were predicted by a previously developed chemometrics model and the stability of these polypeptide chains were studied by molecular dynamics (MD) simulation. Furthermore, sodium dodecyl sulfate (SDS) micelles were used as a model of cell membrane and herein we present a high-resolution 3D structure of an 18 amino acid residues long peptide corresponding to the third transmembrane part of bilitranslocase obtained by use of multidimensional NMR spectroscopy. It has been experimentally confirmed that one of the transmembrane segments of bilitranslocase has alpha helical structure with hydrophilic amino acid residues oriented towards one side, thus capable of forming a channel in the membrane.
COBISS.SI-ID: 4993562
In the first part of this paper, we present a novel graphical representation of proteins, which starts with constructing a map of a protein that is obtained from a matrix, the elements of which record the adjacencies of pairs of amino acids in the primary structure of a protein. Starting with the novel protein map, one interprets its matrix elements as vertices of a graph, which are labelled in sequential order as in the protein sequence. The nearest vertices are connected to the nearest neighbour which has a smaller label. In the second part of this paper, we describe the construction of protein binary codes that can serve as protein descriptors. This novel graphical representation of proteins is illustrated on segments of trans-membrane proteins, which are embedded in the membrane
COBISS.SI-ID: 4999194
The data about sequences and transmembrane regions were collected from PDB (Protein Data Bank). The entire studied set consists of 5800 segments. Protein sequences were represented with 20x20 matrices, where each element indicates a pair of neighbouring amino-acids. Using the couterpropagation neural network we construct the model which separates the transmembrane regions.
COBISS.SI-ID: 4344090
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.
COBISS.SI-ID: 4798234