Molecular dynamics simulation study on the structural instability of the most common cystic fibrosis-associated mutant ΔF508-CFTR

Abstract

Cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel that belongs to the ATP binding cassette protein superfamily. Deletion of phenylalanine at position 508 (ΔF508) is the most common CF-associated mutation and is present in nearly 90% of CF patients. Currently, atomistic level studies are insufficient for understanding the mechanism by which the deletion of a single amino acid causes greatly reduced folding as well as trafficking and gating defects. To clarify this mechanism, we first constructed an atomic model of the inward-facing ΔF508-CFTR and performed allatom molecular dynamics (MD) simulations of the protein in a membrane environment. All of the computational methodologies used are based on those developed in our previous study for wild-type CFTR. Two important findings were obtained. First, consistent with several previous computational results, the deletion of F508 causes a disruption of a hydrophobic cluster located at the interface between the nucleotide binding domain 1 (NBD1) and intracellular loop 4 (ICL4). This exerts unfavorable influences on the correlated motion between ICLs and transmembrane domains (TMDs), likely resulting in gating defects. Second, the F508 deletion affected the NBD1–NBD2 interface via allosteric communication originating from the correlated motion between NBDs and ICLs. As a result, several unusual inter-residue interactions are caused at the NBD1–NBD2 interface. In other words, their correct dimerization is impaired. This study provided insight into the atomic-level details of structural and dynamics changes caused by the ΔF508 mutation and thus provides good insight for drug design.

F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis

“…Other studies using cross‐linking experiments and simulation, show that F508 interacts with ICL4 and the equivalent residues in NBD2 are important to interact with ICL2 . Therefore, other consequence of F508del is the interference with the interactions between the NBDs and the transmembrane domains.…”

“…13,14,81 Nevertheless, our results show that dimer dynamics before and after ATP hydrolysis are different in the mutant, affecting the ABP inter- Other studies using cross-linking experiments and simulation, show that F508 interacts with ICL4 and the equivalent residues in NBD2 are important to interact with ICL2. 22,[83][84][85] Therefore, other consequence of F508del is the interference with the interactions between the NBDs and the transmembrane domains. Still, our simulations show that F508del affects the pre-and post-hydrolysis behavior of the NBD dimer, regardless of the presence of the transmembrane domains.…”

Identification and selection of healthy spermatozoa in heterozygous carriers of the Phe508del-variant of the CFTR-gene in assisted reproduction

“…Phe508del is most common among population living in Central and Northern Europe and in the Basque countries 4 – 6 , whereas other pathogenic variants may occur in other ethnicities as well 7 . The pathogenic variant Phe508del represents a deletion of 3 base pairs resulting in the loss of codon 508 encoding phenylalanine and in consequence in altered phosphoregulation of the CFTR-protein resulting in the increased retention of p.Phe508del in the endocytoplasmic reticulum, in rapid degradation at the cell surface and in reduced recycling of p.Phe508del to the cell surface 8 . Abnormal CFTR, such as p.Phe508del, disturbs the intracellular transport of both chloride (Cl − ) and bicarbonate (HCO3 − ) into epithelial cells disrupting the outward flow of water producing thickened mucus, which impairs function of lungs and digestive organs potentially becoming infected repeatedly.…”

Exploring the effect of N308D mutation on protein tyrosine phosphatase‐2 cause gain‐of‐function activity by a molecular dynamics study

“…[12][13][14] However, the details of the increase of catalytic activity in the mutant SHP2-N308D are still unknown. 18,19 In terms of mutations proteins, MD has been used to study nonactive site mutations disturb the loop dynamics, dimerization, viral budding, and egress of VP40 of the Ebola virus, 19 and to study on the structural instability of the most common cystic fibrosis-associated mutant ΔF508-CFTR, 18 and to use the restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two-component signaling systems. 15 Molecular dynamics (MD) simulations provide indepth details regarding the motions of individual atoms of biological macromolecules in an appropriate time scale.…”