PROTEIN INTERACTIONS AND DISEASE PHENOTYPES IN THE ABC TRANSPORTER SUPERFAMILY

LIBUSHA KELLY, RACHEL KARCHIN, ANDREJ SALI
2006 Biocomputing 2007  
ABC transporter proteins couple the energy of ATP binding and hydrolysis to substrate transport across a membrane. In humans, clinical studies have implicated mutations in 19 of the 48 known ABC transporters in diseases such as cystic fibrosis and adrenoleukodystrophy. Although divergent in sequence space, the overall topology of these proteins, consisting of two transmembrane domains and two ATP-binding cassettes, is likely to be conserved across diverse organisms. We examine known
more » ... orter domain interfaces using crystallographic structures of isolated and complexed domains in ABC transporter proteins and find that the nucleotide binding domain interfaces are better conserved than interfaces at the transmembrane domains. We then apply this analysis to identify known disease-associated point and deletion mutants for which disruption of domain-domain interfaces might indicate the mechanism of disease. Finally, we suggest a possible interaction site based on conservation of sequence and disease-association of point mutants. * Corresponding author libusha@salilab.org Pacific Symposium on Biocomputing 12:51-63 (2007) proper function. One such example is the vitamin B12 transporter BtuCD in E. coli, in which the two BtuC proteins and two BtuD proteins associate for transport [3] . Because there are no complete, high-resolution structures of eukaryotic ABC transporters, it is not known how similar their structures and mechanisms are to those of their bacterial and archaeal homologs. However, the striking sequence conservation of domains (e.g., the motif conservation and sequence identity between NBDs of diverse organisms) suggests that, despite differences in gene organization, human ABC transporters are likely to have a quarternary structure similar to those observed in bacteria and archaea [5] . Four crystal structures of NBD dimers (PDB IDs 1L2T, 1XEF, 1L7V and 1Q12) all have a structurally similar NBD/NBD interface, with the Walker A phosphate binding loop of one NBD appearing directly across the interface from the highly conserved 'signature' motif of the opposite NBD [6, 7, 3, 8] . The Cα RMSD (computed with MODELLER's salign feature [17] ) between the structures is between 1.7 and 2.7 Å, further demonstrating that the NBD/NBD interface is well conserved among different ABC transporters. An unanswered question about ABC transporter associations is whether the "two NBD / two TMD" model can also include higher-order oligomeric states [9, 10] . ABC transporters are also known to interact with a number of other membrane and soluble proteins. The sulfonylurea transporters (ABCC8 and 9) interact with inwardly rectifying (Kir) potassium channels to form ATPsensitive potassium channels that modulate the electrical activity in cells [11] . The CFTR protein is known to interact with PDZ domains and likely has other binding partners, including adrenergic receptors [12] . Because of the lack of high-resolution structural data, the nature of these interactions at the amino acid residue level is not known. Point mutations at interfaces can affect the function of ABC transporters in several ways. First, the mutant might destabilize domain folding or association during folding and prevent proper maturation of the protein. A medically relevant example is the deletion mutant ΔF508 in CFTR that is the most common cause of cystic fibrosis. This mutation leads to an immature, lower molecular weight form of the protein that is retained in the endoplasmic reticulum and degraded, which leads to a lack of functional transporters localized to the membrane [2]. Second, the mutant might interfere with the function of an intact transporter by affecting ATP binding and hydrolysis. Third, the mutant might affect allosteric interactions between the domains that are required for substrate binding and transport. Given the importance of intra-and inter-protein interactions in the ABC transporters, coupled with the large body of data on disease-associated
doi:10.1142/9789812772435_0006 fatcat:my5ag4vlxnfvzeti6y4526bwsi