We have presented anew protein–prot

We have presented anew protein–protein docking approach to model heterodimeric structures based on
the conformations of the monomeric units. The conventional modeling method relies on superimposing
two monomeric structures onto the crystal structure of a homologous protein dimer. The resulting
structure may exhibit severe backbone clashes at the dimeric interface depending on the backbone
dissimilarity between the target and template proteins. Our method overcomes the backbone clashing
problem and requires noa prioriknowledge of the dimeric structure of a homologous protein. Here we
used human Cystic Fibrosis Transmembrane conductance Regulator (CFTR), a chloride channel whose
dysfunction causes cystic fibrosis, for illustration. The two intracellular nucleotide-binding domains
(NBDs) of CFTR control the opening and closing of the channel. Yet, the structure of the CFTR’s NBD1–
NBD2 complex has not been experimentally determined. Thus, correct modeling of this heterodimeric
structure is valuable for understanding CFTR functions and would have potential applications for drug
design for cystic fibrosis treatment. Based on the crystal structure of human CFTR’s NBD1, we
constructed a model of the NBD1–NBD2 complex. The constructed model is consistent with the dimeric
mode observed in the crystal structures of other ABC transporters. To verify our structural model, an ATP
substrate was docked into the nucleotide-binding site. The predicted binding mode shows consistency
with related crystallographic findings and CFTR functional studies. Finally, genistein, an agent that
enhances CFTR activity, though the mechanism for such enhancement is unclear, was docked to the
model. Our predictions agreed with genistein’s bell-shaped dose–response relationship. Potential
mutagenesis experiments were proposed for understanding the potentiation mechanism of genistein
and for providing insightful information for drug design targeting at CFTR. The method used in this study
can be applied to modeling studies of other dimeric protein structures