Disease-relevant mutations alter amino acid co-evolution networks in the second nucleotide binding domain of CFTR.

Klaus Brusgaard,Robert T. Youker,Gabrianne Ivey

doi:10.1371/journal.pone.0227668

Abstract

Cystic Fibrosis (CF) is an inherited disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel. Mutations in CFTR cause impaired chloride ion transport in the epithelial tissues of patients leading to cardiopulmonary decline and pancreatic insufficiency in the most severely affected patients. CFTR is composed of twelve membrane-spanning domains, two nucleotide-binding domains (NBDs), and a regulatory domain. The most common mutation in CFTR is a deletion of phenylalanine at position 508 (ΔF508) in NBD1. Previous research has primarily concentrated on the structure and dynamics of the NBD1 domain; However numerous pathological mutations have also been found in the lesser-studied NBD2 domain. We have investigated the amino acid co-evolved network of interactions in NBD2, and the changes that occur in that network upon the introduction of CF and CF-related mutations (S1251N(T), S1235R, D1270N, N1303K(T)). Extensive coupling between the α- and β-subdomains were identified with residues in, or near Walker A, Walker B, H-loop and C-loop motifs. Alterations in the predicted residue network varied from moderate for the S1251T perturbation to more severe for N1303T. The S1235R and D1270N networks varied greatly compared to the wildtype, but these CF mutations only affect ion transport preference and do not severely disrupt CFTR function, suggesting dynamic flexibility in the network of interactions in NBD2. Our results also suggest that inappropriate interactions between the β-subdomain and Q-loop could be detrimental. We also identified mutations predicted to stabilize the NBD2 residue network upon introduction of the CF and CF-related mutations, and these predicted mutations are scored as benign by the MUTPRED2 algorithm. Our results suggest the level of disruption of the co-evolution predictions of the amino acid networks in NBD2 does not have a straightforward correlation with the severity of the CF phenotypes observed.

Highlights

Cystic fibrosis (CF) is one of the most common autosomal recessive genetic disorders among Caucasians and results from a mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) [1,2]
We performed coevolution analyses to test whether the predicted network of coupled residues in NBD2 of CFTR is disrupted by known CF causing and CF-associated mutations
Homo sapiens CFTR was used as the query sequence for PSI-BLAST of the nonredundant protein database with a 20,000-maximum target parameter, and sub-alignments were performed in Clustal Omega to obtain the NBD2 sequences

Summary

Introduction

Cystic fibrosis (CF) is one of the most common autosomal recessive genetic disorders among Caucasians and results from a mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) [1,2]. Phosphorylation of the R domain and ATP-dependent “head-to-tail” heterodimerization of the NBDs controls ion channel gating [4,5]. The most common mutation in CF patients is a deletion of a single phenylalanine at position 508 in NBD1 (ΔF508) [6]. As opposed to ΔF508, the S1235R and N1303K mutants are not rescued by low temperature [16]. This suggests NBD2 dynamics are not necessarily identical to NBD1, but less is known about the allosteric control of NBD2

Methods

Results

Discussion

Conclusion