Molecular Modeling and Simulations of the Conformational Changes Underlying Channel Activity in CFTR

Advisors:
Steve Harvey, Ph.D. (Georgia Tech)
Nael McCarty, Ph.D. (Emory University)
 
Committee Members:  
King Jordan, Ph.D. (Georgia Tech)
Pete Ludovice, Ph.D. (Georgia Tech)
Cheng Zhu, Ph.D. (Georgia Tech)

Mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator protein (CFTR) cause cystic fibrosis (CF), the most common life-shortening genetic disease among Caucasians. Although general features of the structure of CFTR have been predicted from homology models, the conformational changes that result in channel opening and
closing have yet to be resolved. We created new closed- and open-state homology models of CFTR, and performed targeted molecular dynamics simulations of the conformational transitions in a channel opening event. The simulations predict a conformational wave that starts at the nucleotide binding domains and ends with the formation of an open conduction pathway. Experimentally confirmed changes in side-chain interactions are observed in all major domains of the protein. We also identified lineage-specific mutations that may have led to channel activity in CFTR. Molecular modeling and simulations are used to compare the effects of these substitutions against a canonical ABC transporter, and suggest that gain of channel function in CFTR may have risen from loss of ATPase function at its nucleotide binding domains. The models and simulation add to our understanding of the mechanism of ATP-dependent gating in this disease-relevant ion channel.