Molecular Dynamics Simulations of CFTR Gating and Conductance

Abstract

The crystal structure of CFTR, the chloride ion channel defective in cystic fibrosis, has not yet been solved. Here we present two new homology models of human CFTR based on template structures from related ABC transporters. The first is based on the bacterial transporter Sav1866 and is representative of the open channel state of CFTR. Unlike previous Sav1866-based homology models of CFTR, our model incorporates several key structural features expected from experiment, including the proper positioning of pore-lining residues and important salt bridges. The second is based on the crystal structure of murine P-glycoprotein and models the closed state of CFTR. We performed targeted molecular dynamics simulations using these two models as end states, in order to gain insight into the conformational changes that CFTR undergoes during its gating cycle. Our simulations reveal that CFTR gating involves a conformational wave that is initiated at the nucleotide-binding domains, and propagates through interactions in the intracellular loops to the membrane-spanning domains. Analysis of our simulations also led to a better understanding of the relative motions of the twelve transmembrane helices in CFTR, and how they alter pore structure during gating. Our MD simulations allowed identification of key inter-residue interactions that stabilize the end states as well as transient interactions that may exist in the intermediate stages in gating. Charting the progression of these interactions provides a timeline of events likely to occur during gating, and may prove invaluable in furthering our understanding of structure-function relationships in CFTR. Finally, we report on preliminary simulations of chloride ion conduction in the open CFTR channel, which reveal key interactions of pore-lining residues with passing ions, as well as identifying the putative narrow region in the pore that may form a selectivity filter in this channel. (NIH-2R56DK056481-07)