Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 2

Citations in PubMed

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PDB ID Mentions in PubMed Central

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NMR structure of the human prion protein with the pathological Q212P mutation reveals unique structural features.

(2010) PLoS One 5

PubMed: 20661422 | PubMedCentral: PMC2908606 | DOI: 10.1371/journal.pone.0011715

(C) Structural details of α 3 helix in the family of 20 lowest energy structures from Met205 to Arg220 in the Q212P mutant (left, pdb id 2KUN) and WT HuPrP C (right, pdb id 1QM1) [25&#... 0005d; .

(A) HuPrP(90–231, M129, Q212P) (pdb id 2KUN, this work).

pdb id Angle (°) Distance (Å) HuPrP(90–231, M129, Q212P) 2KUN 33.1 8.4 HuPrP(90-231, M129) 1QM1 [25] 50.9 7.0 Elk PrP C 1XYW [34] 47.9 7.7 Bank vole PrP C 2K56 [33] 45.6 8.0 Tammar wallaby PrP C 2KFL [32] 52.6 6.9 a Calculated with Chimera system [59] .

Publication Year: 2010


The landscape of the prion protein's structural response to mutation revealed by principal component analysis of multiple NMR ensembles.

(2012) PLoS Comput Biol 8

PubMed: 22912570 | PubMedCentral: PMC3415401 | DOI: 10.1371/journal.pcbi.1002646

DATASET DESCRIPTION # PDBs # Models Subdomain Contribution to each PC PC1 PC2 PC3 Human (hPrP) NMR ensembles of wildtype, variant, and mutant PrPs 11 230 S2-H2 loop, C-terminus H3 N-terminus &... S1, H2-H3 loop S1-H1 loop & H1 Wildtype hPrP 4 non-pathogenic hPrP 4 80 All subdomains H2-H3 loop, C-terminus H3 N-terminus, S1-H1 loop Mutant hPrP 7 Variant and mutant PrP structures 7 150 S2-H2 loop, C-terminus H3 N-terminus, H2-H3 loop S1-H1 loop Wildtype hPrP+CJD Mutant 8 WT & Variant hPrP structures+the CJD Mutant structure (E200K), (PDB 1FO7) 9 190 S2-H2 loop, H2-H3 loop, C-terminus H3 - N-terminus, S1-H1 loop & H1 Wildtype hPrP+FFI Mutant 8 WT & Variant hPrP structures+the FFI Mutant structure (D178N), (PDB 2K1D) 9 180 S2-H2 loop, C-terminus H3 N-terminus S1-H1 loop & H1, H2-H3 loop Wildtype hPrP+GSS Mutant 8 WT & Variant hPrP structures+the GSS Mutant structure (Q212P), (PDB 2KUN) 9 180 S2-H2 loop, C-terminus H3 N-terminus, S1-H1 loop & H1, H2-H3 loop - WT PrP with chicken 16 PrP species, including chicken (chPrP), both TSE-susceptible & TSE-non-susceptible 21 420 H2-H3 loop H1, S2-H2 loop - WT PrP without chicken 15 PrP species, excluding the conformational outlier chPrP 20 400 H2-H3 loop H1, S2-H2 loop - Mammalian PrPs 13 WT PrP Species, excluding chicken, turtle, frog 18 360 C-terminus H3 S1-H1 loop & H1, S2-H2 loop, H2-H3 loop N-terminus TSE-non-susceptible Mammals Subgroup of mammalian PrPs (n = 5 species, including Sheep R168), excluding chicken, turtle, frog 5 95 C-terminus H3, N-terminus S1-H1 loop & H1, S2-H2 loop H2-H3 loop TSE-susceptible Mammals Subgroup of mammalian PrPs (n = 9, including Sheep H168) 9 265 N-terminus, S2-H2 loop, H2-H3 loop, C-terminus H3 S1-H1 loop H1 Mouse (mPrP) 3 non-pathogenic and 11 mutant PrP structures 14 280 C-terminus H3 - - Mouse (mPrP) without 2KFM & 2L1K Removal of conformational outliers 2KFM and 2L1K to determine influence on variation in S2-H2 12 240 C-terminus H3 - - Discussion Delineating and Ranking Important PrP Conformational Subdomains We have conducted exhaustive PCA analyses on a large set of PrP globular structures, as well as several subsets representing particular species of interest (human and mouse), or groupings which hold biological significance (TSE susceptibility or non-susceptibility); from these analyses we identified five conformationally variable subdomains in PrP undergoing varying levels of correlated movements in all datasets, and which are thought to be significant for the PrP conformational conversion process that underlies prion disease.

For each of the remaining three clusters, each cluster is composed of the models of the NMR ensemble representing the PDB structure of each of the human TSE diseases of GSS (red oval) [PDB 2KUN] [26] , FFI (blue oval) [PDB 2K1D], and CJD (green oval) [PDB 1FO7] [27] ( Figure 1A, 1B ).

( B ) CJD mutant (PDB 1FO7) and WT+V, ( C ) FFI mutant (PDB 2K1D) and WT+V, ( D ) GSS mutant (PDB 2KUN) and WT+V.

The 11 PDB files of hPrP include: [ 1E1G , 1E1P , 1E1U , 1FO7 , 1H0L , 1HJN , 1QLZ , 1QM1 , 1QM3 , 2K1D , 2KUN ] The 14 PDB files of mPrP include: [ 1XYX , 2K5O , 2KFM , 2KFO , 2KU5 , 2KU6 , 1Y15 , 1Y16 , 2L1D , 2L1E , 2L1H , 2L1K , 2L39 , 2L40 ] The 21 PDB files of WT PrP include (species in parenthesis): [ 1XYX ] (mouse); [ 1DWZ , 1DX1 ] (bovine); [ 1HJN , 1QLZ , 1QM1 , 1QM3 ] (human); [ 1Y2S , 1XYU ] (sheep); [ 1B10 ] (hamster); [ 1XYJ ] (cat); [ 1XYQ ] (pig); [ 1XYW ] (elk); [ 2K56 ] (bank vole); [ 1XYK ] (dog); [ 2KU4 ] (horse); [ 2FJ3 ] (rabbit); [ 1U3M ] (chicken); [ 1U5L ] (turtle); [ 1XU0 ] (frog); [ 2KFL ] (wallaby) NMR Ensembles For each of the datasets studied, an analysis was performed all models of the PDB NMR Ensembles, as well as the subset of representative models for each ensemble, identified using EBI OLDERADO [39] .

Publication Year: 2012