XB-ART-48769
PLoS One
2013 Jan 01;88:e73476. doi: 10.1371/journal.pone.0073476.
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Ordered disorder of the astrocytic dystrophin-associated protein complex in the norm and pathology.
Na I
,
Redmon D
,
Kopa M
,
Qin Y
,
Xue B
,
Uversky VN
.
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The abundance and potential functional roles of intrinsically disordered regions in aquaporin-4, Kir4.1, a dystrophin isoforms Dp71, α-1 syntrophin, and α-dystrobrevin; i.e., proteins constituting the functional core of the astrocytic dystrophin-associated protein complex (DAPC), are analyzed by a wealth of computational tools. The correlation between protein intrinsic disorder, single nucleotide polymorphisms (SNPs) and protein function is also studied together with the peculiarities of structural and functional conservation of these proteins. Our study revealed that the DAPC members are typical hybrid proteins that contain both ordered and intrinsically disordered regions. Both ordered and disordered regions are important for the stabilization of this complex. Many disordered binding regions of these five proteins are highly conserved among vertebrates. Conserved eukaryotic linear motifs and molecular recognition features found in the disordered regions of five protein constituting DAPC likely enhance protein-protein interactions that are required for the cellular functions of this complex. Curiously, the disorder-based binding regions are rarely affected by SNPs suggesting that these regions are crucial for the biological functions of their corresponding proteins.
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Species referenced: Xenopus laevis
Genes referenced: dmd.2 kcnj10 nos1
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Figure 2. Abundance of intrinsic disorder in proteins from six vertebrate DAPCs.A. AQP-4; B. Kir4.1; C. Dp71; D. α-1 syntrophin; and E. α-dystrobrevin. PONDR-FIT scores are shown for corresponding proteins from Homo sapiens (black lines), Mus musculus (red lines), Gallus gallus (green lines), Anolis carolinensis (yellow lines), Xenopus laevis (blue lines), and Brachydanio rerio (pink lines). Disorder profiles were manually aligned by visual inspection to ensure matching of the most characteristic features. The number of gaps introduced in affected proteins during these visual alignments was kept to a minimum. Plot F represents a PONDR-FIT plot for human α-1 syntrophin. Domain structure of this protein is also indicated in relation to the disorder profile. Pink shadow around PONDR-FIT curve represents distribution of errors in the evaluation of the PONDR-FIT scores. |
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Figure 3. Mean disorder scores evaluated for five DAPC proteins from six vertebrate species: Homo sapiens (black bars), Mus musculus (red bars), Gallus gallus (green bars), Anolis carolinensis (yellow bars), Xenopus laevis (blue bars), and Brachydanio rerio (pink bars).Error bars represent the corresponding standard errors. |
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Figure 4. Structural information on some members of the dystrophin-associated protein complex: A. Crystal structure of the human AQP-4 fragment (PDB ID: 3GD8, residues 32â254); B. Crystal structure of the human dystrophin fragment (PDB ID: 1EG3, residues 3046â3306).C. NMR solution structure of the mouse α-1 syntrophin fragment (PDB ID: 1Z87, residues 2â264 that correspond to the PHNâPDZâPHC module). D. NMR solution structure of the mouse α-1 syntrophin fragment (PDB ID: 2ADZ, residues 2â80/165â264 that correspond to the PHN-âLâ-PHC construct). Ten representative members of the conformational ensemble are shown by chains of different color. E. Crystal structure of a complex (PDB ID: 1QAV) between the PDZ domain of mouse α-1 syntrophin (residues 77â164, shown as a colored chain) and the Neuronal nitric oxide synthase, nNOS (shown as gray surface). F. NMR solution structure of the fragment of human α-dystrobrevin (PDB ID: 2E5R, residues 237â292 that correspond to the ZZ-domain). Ten representative members of the conformational ensemble are shown by chains of different color. |
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Figure 5. Sequence conservation of the PDZ-binding motifs in AQP-4 (A) and Kir4.1 (B), and of the α-1 syntrophin PDZ-domain (C).Sequence conservation of the α-1 syntrophin SU domain (D) and of the α-1 syntrophin binding domain of Dp71 (E). In each plot, the position of the corresponding binding motifs and functional domains are highlighted as a colored rectangle. |
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Figure 6. Analysis of sequence conservation of the inter-subunit interaction sites in the DAPC.In each plot, the position of the corresponding binding motifs and functional domains are highlighted as a colored rectangle. A. Conservation of the α-dystrobrevin-interacting site of α-1 syntrophin. B. Multi-domain sequence conservation analysis of α-dystrobrevin (conservation of the domains interacting with α-1 syntrophin and Dp71). C. Conservation of the α-dystrobrevin-interacting domain of Dp71. D. Multi-domain sequence conservation analysis of Dp71 (conservation of the domains interacting with the α-1 syntrophin SU-domain and α-dystrobrevin). |
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Figure 7. Frequencies of disease-related mutations in Kir4.1. |
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Figure 8. Distribution of SNPs affecting polar and non-polar residues in AQP-4 (A), KCNJ-10 (Kir4.1, B), α1-syntrophin (C), Dp71 (D), and α-dystrobrevin (E). |
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Figure 9. Scatter plots showing SNP distributions within the amino acid sequences of AQP-4 (A), Kir4.1 (B), α1-syntrophin (C), Dp71 (D), and α-dystrobrevin (E).SNPs happening in known binding regions are indicated by different colors that match colors in corresponding tables (see Tables 9-11). |
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Figure 10. Analyzing the effect of SNPs on the fraction of disordered residues in a target protein: AQP-4 (A), Kir4.1 (B), Dp71 (C), α1-syntrophin (D), and α-dystrobrevin (E).For a given protein, faction of disordered residues was determined as a relative content of residues with the disorder score above the 0.5 threshold. Note that numbers on the X-axis correspond to the identification numbers of SNPs and not to their positions within the protein sequence. |
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Figure 11. Correlation between the per-residue disorder scores of the wild type proteins and SNP-produced variants of AQP-4 (A), Kir4.1 (B), α1-syntrophin (C), Dp71 (D), and α-dystrobrevin (E).These graphs are generated by plotting the per-residue disorder scores of SNP-produced variants versus the per-residue disorder scores of corresponding wild type proteins. Each line in these plots corresponds to the pre-residue disorder scores correlation evaluated for one SNP-produced variant. |
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Figure 1. Schematic representation of the astrocytic DAPC analyzed in this study.The major focus of our work was dystrophin (Dp71) and the Dp71-associated proteins AQP-4, Kir4.1, α-1 syntrophin (α-Snt), and α-dystrobrevin. |
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