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Cystic Fibrosis (CF) is caused by mutations to the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) chloride channel. CFTR is composed of two membrane spanning domains, two cytosolic nucleotide-binding domains (NBD1 and NBD2) and a largely unstructured R-domain. Multiple CF-causing mutations reside in the NBDs and some are known to compromise the stability of these domains. The ability to predict the effect of mutations on the stability of the cytosolic domains of CFTR and to shed light on the mechanisms by which they exert their effect is therefore important in CF research. With this in mind, we have predicted the effect on domain stability of 59 mutations in NBD1 and NBD2 using 15 different algorithms and evaluated their performances via comparison to experimental data using several metrics including the correct classification rate (CCR), and the squared Pearson correlation ([Formula: see text]) and Spearman’s correlation ([Formula: see text]) calculated between the experimental [Formula: see text] values and the computationally predicted [Formula: see text] values. Overall, the best results were obtained with FoldX and Rosetta. For NBD1 (35 mutations), FoldX provided [Formula: see text] and [Formula: see text] values of 0.64 and –0.71, respectively, with an 86% correct classification rate (CCR). For NBD2 (24 mutations), FoldX [Formula: see text] , [Formula: see text] , and CCR were 0.51, –0.73 and 75%, respectively. Application of the Rosetta high-resolution protocol (Rosetta_hrp) to NBD1 yielded [Formula: see text] , [Formula: see text] and CCR of 0.64, –0.75, and 69%, respectively, and for NBD2, [Formula: see text] , [Formula: see text] and CCR of 0.29, –0.27 and 50%, respectively. The corresponding numbers for the Rosetta’s low-resolution protocol (Rosetta_lrp) were [Formula: see text] = 0.47, [Formula: see text] = −0.69, CCR= 69% for NBD1 and [Formula: see text] = 0.27, [Formula: see text] = −0.24, CCR = 63% for NBD2. For NBD1, both algorithms suggest that destabilizing mutations suffer from destabilizing vdW clashes whereas stabilizing mutations benefit from favourable H-bond interactions. Two triple consensus approaches based on FoldX, Rosetta_lpr and Rosetta_hpr were attempted using either majority voting or all voting. The all voting consensus outperformed the individual predictors, albeit on a smaller data set. In summary, our results suggest that the effect of mutations on the stability of CFTR’s NBDs could be largely predicted. Since NBDs are common to all ABC transporters, these results may find usage in predicting the effect and mechanism of action of multiple disease-causing mutations in other proteins. |
