ABCMdb

ABCC7 p.Phe508Ala

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Publications

PMID: 16697012 [PubMed] Ramaen O et al: "Structure of the human multidrug resistance protein 1 nucleotide binding domain 1 bound to Mg2+/ATP reveals a non-productive catalytic site."

No. Sentence Comment

63 Structure based sequence alignment of MRP1-NBD1 with MRP1-NBD2, h-CFTR-NBD1 (pdb code 1xmi, F508A F429S H667R mutant), BtuCD (pdb code 1l7v), TAP1 (pdb code 1jj7), MJ0796 (pdb code 1l2t, E171Q mutant), MJ1267 (pdb code 1g9x, N31C mutant), HisP (pdb code 1b0u) and HlyB-NBD (pdb code 1mt0). Login to comment

PMID: 15528182 [PubMed] Lewis HA et al: "Impact of the deltaF508 mutation in first nucleotide-binding domain of human cystic fibrosis transmembrane conductance regulator on domain folding and structure."

No. Sentence Comment

40 Crystallization and Data Collection-Crystallization leads at 4 °C from hNBD1-2b-F508A at 6-17 mg/ml 4 °C were optimized using microseeding. Login to comment
46 Structure Determination and Refinement-Structures were determined by molecular replacement using mNBD1 (for hNBD1-2b-F508A) or hNBD1-2b-F508A (for hNBD1-7a-⌬F508) as the search model with the program MolRep (16) and manually rebuilt using the program XtalView (17) over several cycles of refinement with CNX (18) and/or Refmac (16). Login to comment
48 The refined model of hNBD1-2b-F508A includes residues 388-411 and 429-671 in molecule A; 389-413, 429-532, 539-541, and 547-671 in molecule B; 389-415 and 429-671 in molecule C; 388-410 and 426-672 in molecule D; 389-411 and 429-671 in molecule E; 1 ATP/ TABLE I Human NBD1 proteins Thermodynamic values are listed for those proteins analyzed in equilibrium denaturation experiments. Login to comment
76 Recombinant proteins harboring the F508A mutation gave higher yields than the equivalent proteins with phenylalanine at position 508, whereas constructs with the ⌬F508 mutation consistently gave lower yields. Login to comment
82 Crystal Structure of hNBD1 Shows That Regulatory Protein Segments Adopt Multiple Conformations Altering Access to the Active Site-High-resolution diffraction data were obtained for hNBD1-2b-F508A, containing two solubilizing mutations (F429S and H667R) in addition to the F508A substitution (Table II). Login to comment
85 With the exception of the RI and RE segments, the structure of hNBD1-2b-F508A closely matches that of mNBD1. Login to comment
86 Least squares superposition of the remainder of the F1-type core and ABCbeta subdomains yields a 0.46-Å root mean square deviation (rmsd) for 127 C-␣ atoms, only slightly exceeding the 0.39-Å rmsd observed after superposition of the different molecules within the asymmetric unit of the crystal structure of hNBD1- 2b-F508A. Login to comment
91 We concluded that these differences re- TABLE II Statistics of structure determination and refinement hNBD1-2b-F508A hNBD1-7a-⌬F508 Data collection Resolution range 2.25-27.3 Å 2.25-26.7 Å Space Group C2221 P43212 a 144.46 Å 59.79 Å b 154.02 Å 59.79 Å c 136.09 Å 144.40 Å Completeness (overall/outer shell) 99.9%/99.9% 99.8%/99.8% Rsym (overall/outer shell)a 8.5%/40.7% 8.3%/41.7% I/␴(I) (overall/outershell) 4.3/1.2 7.5/1.6 Refinement Resolution range 2.25-27.3 Å 2.30-25.0 Å Rfree (overall/outer shell)b 26.5%/31.0% 28.0%/32.1% R (overall/outer shell)c 21.2%/28.0% 22.0%/22.1% Waters 704 135 rmsd bond lengths 0.006 Å 0.010 Å rmsd angles 1.0° 1.3° Average B-factorsd 32.5 34.9 Core Ramachandran 92.9% 93.1% Allowed Ramachandran 6.7% 6.4% Disallowed Ramachandran 0.2% 0.0% a Rsym ϭ ⌺hkl⌺i͉Ii(hkl-)͗(I(hkl)͉͘/⌺hkl⌺iIi(hkl), where Ii is the intensity of the observation and ͗I͘ is the mean intensity of the reflection. Login to comment
98 Although the conformation of the regulatory segments observed in the crystal structure of hNBD1-2b-F508A would preclude formation of a canonical ATP-sandwich complex with NBD2 because of a steric overlap at the interface, their dramatic change in conformation compared with the crystal structure of mNBD1 confirms our prediction that these segments of NBD1 are conformationally dynamic. Login to comment
101 It shows only minor differences compared with hNBD1-2b-F508A except in the immediate vicinity of the deletion of Phe-508 (Fig. 2) and at the regulatory seg- FIG. 1. Login to comment
109 Regions with conformational differences are shown in cyan for hNBD1-2b-F508A (molecule E), blue for hNBD1-7a-⌬F508, and gold for mNBD1 (molecule B). Login to comment
113 Superposition of the F1-type core and ABCbeta subdomains with those in hNBD1-2b-F508A gives an rmsd of 0.51 Å for 127 C-␣ atoms, similar to the deviations observed between the different protomers in that structure. Login to comment
114 The ABC␣ subdomain is rotated by 6° relative to its position in hNBD1-2b-F508A but is largely conserved in structure, exhibiting an rmsd of 0.87Å for the superposition of 49 C-␣ atoms. Login to comment
116 However, the position of ␣-helix 9b in the RE is very similar in the structures of hNBD1-7a-⌬F508 and mNBD1 (and different from the position observed in the structure of hNBD1-2b-F508A), suggesting that this may represent a preferred conformation of the dynamically flexible RE. Login to comment
119 A, stereo image of conformation of Phe-508 loop region in mNBD1 (gold), hNBD1-2b-F508A (cyan), and hNBD1-7a-⌬F508 (blue). Login to comment
120 B and C, worm diagrams of hNBD1-2b-F508A (B) and hNBD1-7a-⌬F508 (C). Login to comment
125 D and E, surface properties of hNBD1-2b-F508A (D) and hNBD1-7a-⌬F508 (E) in same orientations as in B and C. Login to comment
126 Residues 507-510 in hNBD1-2b-F508A structure have been replaced with those from the mNBD1 structure to provide an image representative of the wild-type human protein. Login to comment
133 The superposition of the three available NBD1 crystal structures (mNBD1, hNBD1-2b-F508A, and hNBD1-7a-⌬F508) based on least squares alignment of ␣-helices 3 and 4 demonstrates that the conformation is extremely similar even in the immediate vicinity of the deletion, consistent with the quantitatively similar folding parameters observed either in the absence or presence of the ⌬F508 mutation. Login to comment

PMID: 15619636 [PubMed] Thibodeau PH et al: "Side chain and backbone contributions of Phe508 to CFTR folding."

No. Sentence Comment

33 The F508A,F508M,F508P,F508D,F508Q,F508R and F508S mutant proteins were more similar to the wild type than the ∆F508 protein in their temperature-dependence of refolding (Fig. 1b,c). Login to comment
43 The missense mutant proteins F508A, F508M,F508P,F508D,F508Q,F508R and F508S had similar ∆Gunfolding and m-values, 3.4-3.8 kcal mol-1 and 1.5-1.7 kcal mol-1 M-1 denaturant, respectively, highlighting the fact that changes in the bulk or chemical properties of the substituted side chain had little effect on the native-state stabilities of these domains as measured by denaturation with GuHCl (Table 1). Login to comment
46 How does the isolated NBD accommodate such Temperature (ºC) 4 10 16 22 Fractionalyield 0.0 0.5 1.0 Temperature (ºC) 4 10 16 22 Temperature (ºC) 4 10 16 22 Wild type ∆F508 Wild type ∆F508 ̄ F508A ̄ F508M F508P F508W ͷ F508W W496F Wild type ∆F508 F508Q F508R F508D F508S a b c Figure 1 NBD1 folding efficiency as a function of folding temperature. Login to comment
53 Table 1 Stability of wild-type and mutant NBD proteins Protein ∆Gunfolding ∆∆Gunfolding m-value (kcal mol-1) (kcal mol-1) (kcal mol-1 M-1) Wild type 3.7 ± 0.1 0 1.7 ∆F508 3.6 ± 0.1 0.1 1.7 F508A 3.6 ± 0.2 0.1 1.6 F508M 3.5 ± 0.1 0.1 1.6 F508P 3.5 ± 0.3 0.2 1.6 F508D 3.6 ± 0.1 0.1 1.6 F508Q 3.5 ± 0.2 0.2 1.6 F508R 3.4 ± 0.3 0.3 1.6 F508S 3.8 ± 0.2 -0.1 1.6 considerable changes in amino acid character at position 508 when this position is critical to the proper biogenesis of the full-length protein, and what are the underlying structural changes associated with these substitutions? Login to comment
91 Band C levels in F508A, F508G, F508L and F508V as well as the polar amino acid substitutions F508S, F508T, F508N and F508Q were evident, but substantially reduced relative to wild-type band C levels. Login to comment
113 W ild type ∆∆F508 F508 F508D F508K F508E F508R F508H F508S F508T F508N F508Q C B Charged Polar F508A F508C F508I F508L ∆F508 F508 W ild type C B F508W F508Y F508G F508P Hydrophobic F508M F508V ̅̆ ̆ ̅ Figure 3 Maturation of full-length CFTR mutants. Login to comment
148 Note added in proof: Crystal structures of the human F508A missense NBD1 (with solublizing mutations F429S and H667R) and the corrected ∆F508 NBD1 (with three known suppressor mutations G550E, R553Q and R555K, and the solublizing mutations F409L, F429S, F433L and H667R) have been reported51. Login to comment
150 The in vivo yield of soluble ∆F508 protein is decreased relative to both the wild-type and F508A proteins with both solublizing and suppressor mutations, consistent with a decrease in the efficiency of domain folding as described in this study. Login to comment

PMID: 16966475 [PubMed] Zhou Z et al: "The two ATP binding sites of cystic fibrosis transmembrane conductance regulator (CFTR) play distinct roles in gating kinetics and energetics."

No. Sentence Comment

61 The crystal structure of human F508A NBD1-ATP complexes (pdb code: 1xmi, chain A) was used as a template. Login to comment
81 (A) Interactions between ATP and key amino acids in the NBD1 binding pocket, adopted from the monomeric crystal structure of the human F508A NBD1-ATP complexes (pdb code: 1xmi, chain A) (left). Login to comment

PMID: 17036051 [PubMed] Mense M et al: "In vivo phosphorylation of CFTR promotes formation of a nucleotide-binding domain heterodimer."

No. Sentence Comment

41 Introduction of target cysteines for crosslinking studies On the basis of crystal structures of nucleotide-bound prokaryotic NBD homodimers and of monomeric NBD1 F508A from human CFTR, we made a homology model of the anticipated CFTR NBD1-NBD2 complex (Figure 3; see Materials and methods). Login to comment
55 NNBD1 NBD2 A462 S605 S1347 S459 S434 D1336 V1379 A1374 S549 S1248 Figure 3 Homology model of a head-to-tail CFTR NBD1-NBD2 heterodimer, based on crystal structures of human CFTR NBD1 F508A and of ATPor AMPPNP-bound NBDs of other ABC proteins (Materials and methods). Login to comment
220 Structural alignments were created including only ATP- (or AMPPNP-) bound NBD structures (HisP, PDB ID 1B0U (Hung et al, 1998); MJ0796, 1L2T (Smith et al, 2002); MalK, 1Q12 (Chen et al, 2003); GlcV, 1OXV (Verdon et al, 2003) and HlyB, 1XEF (Zaitseva et al, 2005), as well as human CFTR NBD1 F508A, 1XMI (Lewis et al, 2005). Login to comment

PMID: 18080175 [PubMed] Mendoza JL et al: "Building an understanding of cystic fibrosis on the foundation of ABC transporter structures."

No. Sentence Comment

67 In contrast to the large number of sequences available for the NBD align- Table 1 ABC transporter structures in the research collaboratory for structural bioinformatics (RCSB) database Release Date PDB Protein Resolution Species NBD Structures Jun-05 1Z47 CysA 1.9 Alicyclobacillus acidocaldarius Sep-03 1OXX GlcV G144A 1.45 Sulfolobus solfataricus Jun-03 1OXT GlcV nucleotide free 2.1 Sulfolobus solfataricus Jun-03 1OXU GlcV w/ ADP 2.1 Sulfolobus solfataricus Jun-03 1OXV GlcV w/ AMP.PNP 2.1 Sulfolobus solfataricus Jun-03 1OXS GlcV w/ iodide ions 1.65 Sulfolobus solfataricus Nov-99 1B0U HisP w/ ATP 1.5 Salmonella typimurium Jun-03 1MT0 HlyB (467-707) 2.6 Escherichia coli Aug-06 2FFB HlyB E631Q w/ ADP 1.9 Escherichia coli Aug-06 2FGK HlyB E631Q w/ ATP 2.7 Escherichia coli Aug-06 2FFA HlyB H662A w/ ADP 1.7 Escherichia coli Aug-06 2FGJ HlyB H662A w/ ATP 2.6 Escherichia coli Jun-05 1XEF HlyB w/ ATP 2.5 Escherichia coli Aug-06 2FF7 HlyB w/ADP 1.6 Escherichia coli Dec-03 1MV5 LmrA w/ ADP, ATP 3.1 Lactococcus lactis Dec-00 1G29 MalK 1.9 Thermococcus litoralis Sep-03 1Q1E MalK 2.9 Escherichia coli Dec-04 1VCI MalK w/ ATP 2.9 Pyrococcus horikoshii Aug-07 2QRR metN 1.71 Vibrio parahaemolyticus Aug-07 2QSW metN C-terminal domain 1.5 Enterococcus faecalis Jul-02 1L2T MJ0796 E171Q Dimeric Structure 1.9 Methanococcus jannaschii Jul-01 1F3O MJ0796 w/ ADP 2.7 Methanococcus jannaschii Nov-01 1GAJ MJ1267 2.5 Methanococcus jannaschii Jul-01 1G6H MJ1267 w/ ADP 1.6 Methanococcus jannaschii Feb-03 1G9X MJ1267 w/ ADP 2.6 Methanococcus jannaschii May-06 2CBZ MRP1-NBD1 1.5 Homo sapiens Nov-04 1V43 Multi-sugar transporter 2.2 Pyrococcus horikoshii Aug-04 1SGW Putative 1.7 Pyrococcus furiosus Apr-07 2P0S Putative 1.6 Porphyromonas gingivalis Sep-07 2IHY Putative 1.9 Staphylococcus aureus Jan-06 2D3W SufC 2.5 Escherichia coli Oct-06 2IXE Tap1 D645N w/ ATP 2 Rattus norvegicus Oct-06 2IXF Tap1 D645Q, Q678H w/ ATP 2 Rattus norvegicus Oct-06 2IXG Tap1 S621A, G622V, D645N w/ ATP 2.7 Homo sapiens Sep-01 1JJ7 Tap1 w/ ADP 2.4 Homo sapiens Aug-02 1JI0 Thermatoga w/ ATP 2 Sulfolobus solfataricus Nov-04 1VPL TM0544 2.1 Thermotoga maritima CFTR NBD Structures Nov-04 1XMJ Human CFTR dF508 NBD1 2.3 Homo sapiens Nov-05 2BBT Human CFTR dF508 NBD1 w/ two solublizing mutations 2.3 Homo sapiens Nov-05 2BBS Human CFTR dF508 NBD1 w/ 3M 2.05 Homo sapiens Nov-05 2BBO Human CFTR NBD1 2.55 Homo sapiens Nov-04 1XMI Human CFTR NBD1-F508A w/ ATP 2.25 Homo sapiens Dec-04 1XFA Murine CFTR-F508R 3.1 Mus musculus Dec-04 1XF9 Murine CFTR-F508S 2.7 Mus musculus Dec-03 1R0W Murine CFTR NBD1 2.2 Mus musculus Dec-03 1R0Z Murine CFTR NBD1 - phosphorylated w/ ATP 2.35 Mus musculus J Bioenerg Biomembr (2007) 39:499-505 501501 ments in Pfam, only 6,419 transmembrane sequences are in the MSA of ABC transporter TMDs, PF00664 (Sonnhammer et al. 1997). Login to comment

PMID: 18463704 [PubMed] Serohijos AW et al: "Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding."

No. Sentence Comment

48 We also perform simulations of another mutant NBD1-F508A to serve as control. Login to comment
62 Thermodynamics of NBD1-WT, NBD1-F508A, and NBD1-DF508. Login to comment
63 Energy is calculated from long equilibrium simulations (106 time units) of NBD1-WT, NBD1-F508A, and NBD1-DF508 crystal structures. Login to comment
70 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 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 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 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 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 The difference in transition probabilities of NBD1-WT, NBD1-DF508, and NBD1-F508A is shown in Figure 4. Login to comment
127 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 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 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
173 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 Contacts in NBD1-WT that perturbed in the F508A and DF508 mutants. Login to comment
211 Folding Simulations We perform 300 folding simulations for each NBD1-WT, NBD1-F508A, and NBD1-DF508. Login to comment
237 Probability of kinetic transitions between intermediate states of NBD1-WT, NBD1-DF508, and NBD1-F508A. Login to comment

PMID: 19403599 [PubMed] Aleksandrov AA et al: "Relationship between nucleotide binding and ion channel gating in cystic fibrosis transmembrane conductance regulator."

No. Sentence Comment

136 All mutants have nearly the same mean open time of 220 ms while mean closed times varied from 230 ms for the wild-type CFTR to 7.8 s for F508A. Login to comment

PMID: 19927121 [PubMed] Kanelis V et al: "NMR evidence for differential phosphorylation-dependent interactions in WT and DeltaF508 CFTR."

No. Sentence Comment

96 This surface changes when the RE adopts an alternate conformation and contacts only helices H6 and H7, as observed in the crystal structure of human NBD1-RE F508A (Lewis et al, 2004, 2005). Login to comment
179 The crystal structure of the human F508A NBD1-RE (Lewis et al, 2005), in which the RI is not bound to the NBD core, was also used as a template. Login to comment
191 This interface is occluded in crystal structures of the murine WT and human DF508 NBD1-RE in which the RI is bound to the NBD core, but is exposed in the human F508A NBD1-RE structure (Lewis et al, 2004, 2005). Login to comment
234 Notably, a 1801 rotation in position of the RE and RI between the murine WT and human F508A crystal structures (Lewis et al, 2004, 2005) (Supplementary Figure 1b) also indicates significant conformational flexibility of the phospho-regulatory elements of CFTR. Login to comment
310 The crystal structures of Sav1866 (PDB code 2HYD) and the human CFTR F508A NBD1-RE (PDB code 1XMI), excluding residues Gln634-Asp673, were used as templates. Login to comment

PMID: 19944699 [PubMed] Lewis HA et al: "Structure and dynamics of NBD1 from CFTR characterized using crystallography and hydrogen/deuterium exchange mass spectrometry."

No. Sentence Comment

114 Taking this possibility into account, the available structures can be clustered into three maximally independent groups-the four hNBD1 structures from crystals grown in high-molecular-weight PEG precipitants at pH ~7.5-9.0 (1XMJ, 2BBO, 2BBS, and 2BBT), the single hNBD1-F508A structure from a crystal grown in a low-molecular-weight PEG precipitant at pH ~4.5 (1XMI), and the nine mNBD1 structures from crystals grown using 3.5 M sodium acetate as the precipitant at pH 7.5. Login to comment
132 Bright green and magenta represent human F508 and F508A structures, respectively, shades of red/orange represent human ΔF508 human structures, and shades of blue/cyan represent murine structures (F508, F508S, or F508R). Login to comment
156 Other than these variations in domain orientation and loop conformation, no significant structural variations are observed elsewhere even in the most divergent structures in the ensemble (PDB IDs 1XMI and 1R0Z, containing hNBD1-2b-F508A and mNBD1, respectively). Login to comment

PMID: 20150177 [PubMed] Atwell S et al: "Structures of a minimal human CFTR first nucleotide-binding domain as a monomer, head-to-tail homodimer, and pathogenic mutant."

No. Sentence Comment

207 A similar analysis has been conducted comparing a human DF508 NBD1 with a human F508A NBD1 with different sets of solubilizing mutations (Lewis et al., 2005). Login to comment

PMID: 20667826 [PubMed] Thibodeau PH et al: "The cystic fibrosis-causing mutation deltaF508 affects multiple steps in cystic fibrosis transmembrane conductance regulator biogenesis."

No. Sentence Comment

115 Consistent with this result, the introduction of the -3M mutations onto F508A and F508C had little effect on protein maturation. Login to comment

PMID: 20976528 [PubMed] Kalid O et al: "Small molecule correctors of F508del-CFTR discovered by structure-based virtual screening."

No. Sentence Comment

255 Solubilizing mutations and the F508A mutation present in 1XMI were mutated back to the wild-type sequence using Prime [48]. Login to comment

PMID: 21594796 [PubMed] Serohijos AW et al: "Molecular modeling tools and approaches for CFTR and cystic fibrosis."

No. Sentence Comment

112 We used the following structures for wild type and mutant NBD1s: wild type (PDB ID: 2BBO), F508del (PDB ID: 1XMJ), and F508A (PDB ID: 1XMI) (see Note 2). Login to comment
113 The F508A mutant has been shown to exhibit intermediate folding defects compared to F508del (7), and thus is an interesting control for the folding simulations. Login to comment
124 Simulation Protocol Using the simplified models described above, in our previous studies, we performed folding simulations for each NBD1-WT, NBD1-F508del, and NBD1-F508A. Login to comment
135 (c) Contacts in NBD1-WT that perturbed in the F508A and F508del mutants. Login to comment
150 We found that at the given tmax, wild type exhibited higher folding probability than the F508del, and F508A folding probability is intermediate to that of wild type and F508del. Login to comment

PMID: 17531517 [PubMed] Warner DJ et al: "Modelling the restoration of wild-type dynamic behaviour in DeltaF508-CFTR NBD1 by 8-cyclopentyl-1,3-dipropylxanthine."

No. Sentence Comment

55 Following completion of the work presented here, crystal structures for human CFTR DF508 and F508A NBD1 domains were reported and made available [22] (PDB codes 1XMI and 1XMJ). Login to comment

PMID: 24735712 [PubMed] Odolczyk N et al: "Molecular modelling approaches for cystic fibrosis transmembrane conductance regulator studies."

No. Sentence Comment

1804 The calculations were performed on simplified bead protein models of three NBD1 variants as follows: WT-NBD1, F508-NBD1 and F508A-NBD1. Login to comment