An ab initio structural model of a nucleoside permease predicts functionally important residues

Permeases belonging to the equilibrative nucleoside transporter family promote uptake of nucleosides and/or nucleobases into a wide range of eukaryotes and mediate the uptake of a variety of drugs used in the treatment of cancer, heart disease, AIDS, and parasitic infections. No experimental three-dimensional structure exists for any of these permeases, and they are not present in prokaryotes, the source of many membrane proteins used in crystal structure determination. To generate a structural model for such a transporter, the LdNT1.1 nucleoside permease from the parasitic protozoan Leishmania donovani was modeled using ab initio computation. Site-directed mutations that strongly impair transport or that alter substrate specificity map to the central pore of the ab initio model, whereas mutations that have less pronounced phenotypes map to peripheral positions. The model suggests that aromatic residues present in transmembrane helices 1, 2, and 7 may interact to form an extracellular gate that closes the permeation pathway in the inward oriented conformation. Mutation of two of these three residues abrogated transport activity, consistent with the prediction of the model. The ab initio model is similar to one derived previously using threading analysis, a distinct computational approach, supporting the overall accuracy of both models. However, significant differences in helix orientation and residue position between the two models are apparent, and the mutagenesis data suggest that the ab initio model represents an improvement regarding structural details over the threading model. The putative gating interaction may also help explain differences in substrate specificity between members of this family.