ABCMdb

PMID: 18463704

Serohijos AW, Hegedus T, Riordan JR, Dokholyan NV
Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding.
PLoS Comput Biol. 2008 Feb 29;4(2):e1000008., [PubMed]

Sentences

No. Mutations Sentence Comment

46 ABCC7 p.Arg553Gln ABCC7 p.Gly550Glu ABCC7 p.Arg555Lys However, even in the presence of correcting mutants (G550E, R553Q, and R555K) [10,15-17] in our model of NBD1-DF508, we still observe a significant change in dynamics at the folding transition. Login to comment 48 ABCC7 p.Phe508Ala We also perform simulations of another mutant NBD1-F508A to serve as control. Login to comment 62 ABCC7 p.Phe508Ala Thermodynamics of NBD1-WT, NBD1-F508A, and NBD1-DF508. Login to comment 63 ABCC7 p.Phe508Ala Energy is calculated from long equilibrium simulations (106 time units) of NBD1-WT, NBD1-F508A, and NBD1-DF508 crystal structures. Login to comment 70 ABCC7 p.Phe508Ala Here, using molecular dynamics simulations of NBD1-WT, NBD1-F508A, and NBD1-DF508, we show that the deletion of Phe508 indeed alters the kinetics of NBD1 folding. Login to comment 81 ABCC7 p.Phe508Ala Folding simulations of our control structure NBD1-F508A yield a folding probability of 2664% which is intermediate to that NBD1-WTand NBD1-DF508. Login to comment 82 ABCC7 p.Phe508Ala This folding probability value is in agreement with experimental studies showing intermediate folding efficiencies and maturation levels of NBD1-F508A relative to NBD1-WT [9,11]. Login to comment 83 ABCC7 p.Phe508Ala To investigate the molecular origin of the difference in folding yields and probabilities, we map the folding pathways of NBD1-WT, NBD1-F508A, and NBD1-DF508 by identifying their metastable folding intermediate states. Login to comment 92 ABCC7 p.Phe508Ala Folding Pathways To determine the difference between the sequence of folding events of the wild type, DF508, and the F508A control, we estimate the probability of transitions between intermediate states (see Methods and Figure S3). Login to comment 93 ABCC7 p.Phe508Ala The difference in transition probabilities of NBD1-WT, NBD1-DF508, and NBD1-F508A is shown in Figure 4. Login to comment 127 ABCC7 p.Phe508Ala Crystal structures of NBD1-WT, NBD1-F508A, and NBD1DF508 are also practically identical except for the S7-H6 loop (Figure 1B) [9,10,12]. Login to comment 131 ABCC7 p.Phe508Ala U S10 S9 S8 S7 S6 S5 S4 S3 S2 S1 U S10 S9 S8 S7 S5 S4 S3 S2 S1 A B 0.65 0.85 0.64 0.94 0.79 0.1 0.91 0.13 0.15 0.15 0.13 0.11 0.2 0.15 0.76 0.19 0.1 0.57 0.58 0.14 0.69 0.1 0.64 0.93 0.14 0.91 0.9 0.1 0.15 0.84 0.25 0.15 0.23 0.31 0.16 0.9 0.15 NBD1-F508A vs. NBD1-WT NBD1-∆F508 vs. NBD1-WT Figure 4. Login to comment 147 ABCC7 p.Phe508Ala A relevant control of our simulation protocol and modeling assumptions is the folding simulation of the NBD1-F508A that yields a folding probability of 2664%, which is higher than that of NBD1DF08 but lower than that of NBD1-WT. Login to comment 167 ABCC7 p.Pro574Ser Interestingly, the P574S mutation has been observed in a CF family also possessing the DF508 mutation but without significant pulmonary or pancreatic disease. Login to comment 168 ABCC7 p.Phe494Asn The solubilizing F494N mutation, which is adjacent to Q493, has also been shown to partially correct the folding defect of CFTR-DF508 [23]. Login to comment 169 ABCC7 p.Pro574Ser The mutations P574S and F594N may promote contact formation between Q493 and P574 during NBD1DF508 folding, thus rescuing NBD1DF508 from the misfolding defect. Login to comment 170 ABCC7 p.Trp496Phe ABCC7 p.Phe508* Interestingly, Thibodeau et al. found that NBD1F508W , the only F508X mutant with a lower folding efficiency than NBD1DF508 , can be rescued by introducing the compensating mutation W496F, which is exactly in the same loop that contains Q493 and F594 [9]. Login to comment 173 ABCC7 p.Phe508Ala The nuanced effect of a mutation or deletion at position 508 is already reflected in the S7-H6 loop conformation of NBD1-WT, NBD1-F508A, and NBD1DF508 crystal structures. Login to comment 199 ABCC7 p.Phe508Ala Contacts in NBD1-WT that perturbed in the F508A and DF508 mutants. Login to comment 211 ABCC7 p.Phe508Ala Folding Simulations We perform 300 folding simulations for each NBD1-WT, NBD1-F508A, and NBD1-DF508. Login to comment 237 ABCC7 p.Phe508Ala Probability of kinetic transitions between intermediate states of NBD1-WT, NBD1-DF508, and NBD1-F508A. Login to comment 284 ABCC7 p.Gly550Glu Roxo-Rosa M, Xu Z, Schmidt A, Neto M, Cai Z, et al. (2006) Revertant mutants G550E and 4RK rescue cystic fibrosis mutants in the first nucleotide-binding domain of CFTR by different mechanisms. Login to comment