Primary Citation PubMed: 9285585
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Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES.
(2006) Mol Syst Biol 2
PubMed: 16820777 | PubMedCentral: PMC1681507 | DOI: 10.1038/msb4100075
( A ) Space-filling model from the crystal structure determined by Xu et al (1997) (Protein Data Bank (PDB): 1AON).
Publication Year: 2006
PMG: online generation of high-quality molecular pictures and storyboarded animations.
(2007) Nucleic Acids Res 35
PubMed: 17478496 | PubMedCentral: PMC1933120 | DOI: 10.1093/nar/gkm277
(C ) Large protein assembly animation: This example depicts the oligomerization of the chaperonin Groel–Groes complex, PDB code 1AON (starting position = left image, final position = right ima... e).
Publication Year: 2007
Multi-scale simulations provide supporting evidence for the hypothesis of intramolecular protein translocation in GroEL/GroES complexes.
(2008) PLoS Comput Biol 4
PubMed: 18463703 | PubMedCentral: PMC2265519 | DOI: 10.1371/journal.pcbi.1000006
To obtain a full-atomistic model, the program MODELLER  has been used to generate a starting configuration of the chains missing in the X-ray structure (PDB code: 1AON) of the GroE... /GroES complex loaded with ADP.
Publication Year: 2008
Amyloid oligomer conformation in a group of natively folded proteins.
(2008) PLoS One 3
PubMed: 18800165 | PubMedCentral: PMC2528939 | DOI: 10.1371/journal.pone.0003235
Because the aligned site in 1aon was hidden from view at the viewing angle we used for the other structures, only 1aon is shown from a different angle from other molecules.
(A) GroEL [1aon].
FitEM2EM--tools for low resolution study of macromolecular assembly and dynamics.
PubMed: 18974836 | PubMedCentral: PMC2572833 | DOI: 10.1371/journal.pone.0003594
In the first test, the coordinates of the trans ring of GroEL  from PDB  entry 1AON were used to calculate an electron density map at 10 Å resolution (t... e resolution of the docking partner).
Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model.
(2008) Biophys J 95
PubMed: 18708469 | PubMedCentral: PMC2576401 | DOI: 10.1529/biophysj.108.137125
Because an accuracy evaluation of fitting is feasible by comparison with the crystal atomic structure registered in the PDB ( 42 ) (PDB code: 1aon), other researchers have also tested their methods us... ng this complex ( 18 , 22 ).
( B ) Atomic model of the complex (PDB code: 1aon) fitted into the 3D density map.
FIGURE 7 Correlation coefficient between the simulated low-resolution density map for the 21-subunit heterocomplex structure (PDB code: 1aon) and its GMM.
For a 21-subunit heterocomplex, GroEL/ES ( 42 ) (PDB code: 1aon), the same types of correlation coefficient plot are shown in Fig. 7 , and density maps are shown in Fig. 8 .
For our fitting calculation, we picked up three types of subunit from the complex atomic structure (1aon): the cis ring form of GroEL (chain A), the trans ring form of GroEL(chain H), and the GroES (chain O).
Using least median of squares for structural superposition of flexible proteins.
(2009) BMC Bioinformatics 10
PubMed: 19159484 | PubMedCentral: PMC2639377 | DOI: 10.1186/1471-2105-10-29
Figure 12 Multiple level superposition for GroEL: 1aon (red) and 1kp8 (green) .
12 gives three level superposition for GroEL: 1aon (red) and 1kp8 (green).
Publication Year: 2009
Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.
(2009) PLoS Comput Biol 5
PubMed: 19381265 | PubMedCentral: PMC2664929 | DOI: 10.1371/journal.pcbi.1000360
A. Single GroEL subunit (*) RMSD (Å) 1GR5_A (T) 2C7E_A (R) 2C7C_A (R′) 1GRU_A (R″) 1GR5_A ( T ) – 5.21 12.06 12.33 2C7E_A ( R ) 5.21 – 12.23 12.35 2C7C_... ( R′ ) 12.06 12.23 – 1.50 1GRU_A ( R″ ) 12.33 12.35 1.50 – B. Intact GroEL RMSD (Å) 1GR5 (T/T) 2C7E (R/T) 2C7C (R′/T) 1AON (R″/T) 1GRU (R″/R) 1GR5 ( T/T ) – 6.72 12.09 11.48 12.19 2C7E ( R/T ) 6.72 – 10.85 10.65 11.03 2C7C ( R′T ) 12.09 10.85 – 3.17 2.65 1AON ( R″/T ) 11.48 10.65 3.17 – 2.67 1GRU ( R″/R ) 12.19 11.03 2.65 2.67 – (*) based on α-carbons.
The PDB ids for the structures T/T, R/T, R″/R, R′/T and R″/T are 1GR5, 2C7E and 1GRU  , 2C7C  and 1AON  , respectively.
Chaperonin structure: the large multi-subunit protein complex.
(2009) Int J Mol Sci 10
PubMed: 19399224 | PubMedCentral: PMC2672005 | DOI: 10.3390/ijms10030844
Data The 1AON – the structure of the object under consideration has been taken from the PDB (deposit 1AON) [ 15 ].
ProteinShader: illustrative rendering of macromolecules.
(2009) BMC Struct Biol 9
PubMed: 19331660 | PubMedCentral: PMC2672931 | DOI: 10.1186/1472-6807-9-19
Overall, the 46-fold increase in number of residues from the smallest to the largest test protein ( 1AQB to 1AON ) results in very close to a 46-fold decrease in frames per second (from 153 to 3.2 fra... es per second for Phong lighting (Plain) and from 86.7 to 1.9 frames per second for Halftoning).
PDB ID Residues Atoms Protein 1AQB 175 1574 retinol-binding protein 1BL8 388 2824 potassium channel 6ADH 748 5669 alcohol dehydrogenase 13PK 1660 12508 phosphoglycerate kinase 1E79 3315 25248 F1 ATPase inhibited by DCCD 1AON 8015 59674 GroEL-GroES-(ADP)7 chaperonin complex The performance tests graphed in Figures 10 to 12 were made on a Macintosh 2.16 GHz Intel Core 2 Duo with 2 GB of RAM and an ATI Radeon X1600 graphics card with 256 MB VRAM.
IDSS: deformation invariant signatures for molecular shape comparison.
PubMed: 19463181 | PubMedCentral: PMC2694795 | DOI: 10.1186/1471-2105-10-157
Here the input shape is the volumetric data with the simulated 8 Å resolution density map for GroEL (PDB code: 1aon ).
(A) shows GroEL: 1kp8 (left) and 1aon (right), where 1kp8 has two separate domains and the corresponding domains of 1aon touch together.
Figure 4 Illustration of computing the inner distance for the protein (PDB code: 1aon ).
In Figure 10(A) , two molecules are two conformations of GroEL (PDB code: 1kp8 and 1aon ), where the intermediate domain of 1kp8 swings down towards the equatorial domain and the central channel so that the surfaces of two domains intersect in 1aon.
GroEL-assisted protein folding: does it occur within the chaperonin inner cavity?
PubMed: 19564940 | PubMedCentral: PMC2695268 | DOI: 10.3390/ijms10052066
The figure was plotted using the SwissPdb Viewer [ 109 ] and POV-Ray ( www.povray.org ) freeware and files 1OEL [ 20 , 21 ] and 1AON [ 32 ] which are available in PDB.
Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES.
PubMed: 19798437 | PubMedCentral: PMC2741606 | DOI: 10.1371/journal.pcbi.1000526
Responses are calculated using (A) the T state conformation (pdb 1oel), (B) the R state conformation (2c7e), and (C) the R″ state conformation (1aon) of the chaperon complex structures.
MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures.
(2010) Bioinformatics 26
PubMed: 20529921 | PubMedCentral: PMC2881380 | DOI: 10.1093/bioinformatics/btq195
The map and the Cα backbone structure of a closed conformation GroEL ring (PDB ID: 1aon) were compared using MOTIF-EM ( Fig. 10 , left, top block).
Publication Year: 2010
A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps.
PubMed: 20529915 | PubMedCentral: PMC2881386 | DOI: 10.1093/bioinformatics/btq201
For the fitting, we used seven identical copies of one of the apo-GroEL components taken from an x-ray crystal structure of GroEL-GroES (PDB id: 1AON).
Robust probabilistic superposition and comparison of protein structures.
(2010) BMC Bioinformatics 11
PubMed: 20594332 | PubMedCentral: PMC2912885 | DOI: 10.1186/1471-2105-11-363
Table 1 Marginal likelihood of different models Protein PDB IDs Student t K Laplace Gauss GroEL 1AON - 1OEL -4328.57 -4307.22 -5132.84 -5722.35 DNA Pol 1IH7 - 1IG9 -5574.80 -5750.12 -6340.01 -8011.05 ... AN 1RRP - 1BYU -1124.86 -1176.53 -1795.92 -2286.10 Topo II 1BGW - 1BJT -4496.17 -4553.50 -7210.74 -8042.00 Pneumolysin 2BK2 - 2BK1 -2692.73 -2465.09 -5195.85 -5491.90 ER 3ERD - 3ERT -538.11 -622.69 -1290.81 -1980.96 RNA Pol 1QLN - 1MSW -5296.61 -5455.79 -8471.69 -10168.07 Adenylate Kinase 1AKE - 4AKE -1499.73 -1502.75 -1685.11 -2000.35 Myosin 1B7T - 1DFK -4819.91 -5046.02 -6380.11 -7701.83 Synthetic data Student t -9179.46 -9253.48 -12465.97 -13951.94 Synthetic data Gauss -5108.73 -5112.43 -5077.97 -5115.98 Logarithm of the marginal likelihood P ( M | D ) of the different displacement models obtained for nine structure pairs undergoing domain movements.
Pooled distribution of local structural differences in all three spatial directions between the bound and unbound state of GroEL (1AON and 1OEL) is shown as grey histogram.
Cartoon representation of the superposition of the bound and unbound state of GroEL (1AON (grey) and 1OEL (colored)) using a Gaussian model (A, D), a Student t (B, E) model and a K distribution (C, F).
Using diffusion distances for flexible molecular shape comparison.
PubMed: 20868474 | PubMedCentral: PMC2949899 | DOI: 10.1186/1471-2105-11-480
Here the input shape is the volumetric data with the simulated 8 Å resolution density map for GroEL (PDB code: 1AON ).
The four molecules are the morph deformation between two conformations of GroEL: 1AON and 1KP8.
Conformational sampling and nucleotide-dependent transitions of the GroEL subunit probed by unbiased molecular dynamics simulations.
(2011) PLoS Comput Biol 7
PubMed: 21423709 | PubMedCentral: PMC3053311 | DOI: 10.1371/journal.pcbi.1002004
A total of 21 crystal structures (287 GroEL subunits) were kept for further analysis (PDB-codes: 1PCQ, 1PF9, 1SVT, 3C9V, 1AON, 1GRU, 1MNF, 1XCK, 2C7D, 2NWC, 3E76, 2EU1, 1SS8, 1SX3, 1J4Z, 1KPO, 2C7E, 1... P8, 1OEL, 1WE3, 1WF4).
Contact matrices were calculated for 28 closed (T) apo subunits (PDB code: 1XCK, 1SS8, 1OEL), 28 closed (T) ATP bound subunits (PDB code: 1KP8, 1SX3) and 28 open (R″) ADP bound subunits (PDB codes: 1AON, 1SVT, 1SX4, and 1PF9), and 6000 snapshots obtained from the last 50 ns of the 12 independent MD simulations on the closed GroEL subunit (6 apo and 6 holo).
Publication Year: 2011
A chaperonin subunit with unique structures is essential for folding of a specific substrate.
(2011) PLoS Biol 9
PubMed: 21483722 | PubMedCentral: PMC3071376 | DOI: 10.1371/journal.pbio.1001040
Homology Modeling The structure model of the Cpn60β4 protein was obtained by homology modeling using the SWISS-MODEL server ( http://swissmodel.expasy.org/ )  , and the cry... tal structure of E. coli GroEL (PDB 1AON, Chain A) was used as a modeling template.
The structure model of E. coli GroEL (PDB 1AON, Chain A) was used as a modeling template.
Heat shock proteins in association with heat tolerance in grasses.
(2011) Int J Proteomics 2011
PubMed: 22084689 | PubMedCentral: PMC3200123 | DOI: 10.1155/2011/529648
(a) The overall structure of GroEL/GroES complex reported by Xu et al. (PDB ID: 1AON) [ 42 ].
3DMolNavi: a web-based retrieval and navigation tool for flexible molecular shape comparison.
(2012) BMC Bioinformatics 13
PubMed: 22583488 | PubMedCentral: PMC3430558 | DOI: 10.1186/1471-2105-13-95
Figure 1 illustrates the flowchart of flexible molecular shape comparison and similarity measure based on the computed IDSS histograms, where two different molecules (PDB codes: 1aon-A, 1irk-A) have a... low similarity score equal to 0.6535.
An example is given for calculating the similarity measure between two different molecules (PDB codes: 1aon-A, 1irk-A), where the similarity score is equal to 0.6535.
Publication Year: 2012
Identification of elements that dictate the specificity of mitochondrial Hsp60 for its co-chaperonin.
(2012) PLoS One 7
PubMed: 23226518 | PubMedCentral: PMC3514286 | DOI: 10.1371/journal.pone.0050318
Y360, a neighbor of D359, interacts with the A383-L183-F281 cluster in which A383 and L183 are located on the adjacent subunit (PDB entry 1AON).
(B–C) 3D-structure models of GroEL subunit in the down (B) and up (C) conformations (Protein Data Bank entry 1AON)  .
ATTRACT-EM: a new method for the computational assembly of large molecular machines using cryo-EM maps.
PubMed: 23251350 | PubMedCentral: PMC3522670 | DOI: 10.1371/journal.pone.0049733
System The method was tested on the GroES-GroEL complex (PDB code 1AON  ).
The assembly has been crystallized as a whole (PDB code 1AON  ), providing a reference state to which assembled models can be compared.
During fitting, seven copies of chains A, O and/or N were assembled into the electron density: generated models were compared to a reference structure, which was built by fitting coordinates of each of the three chains seven times onto the coordinates of 1AON using PyMol  .
Since there are minor differences between the intra-ring components, there is a minor RMSD of 0.4 Å (C-alpha RMSD) between the reference structure and 1AON.
Unfortunately, the components of GroES and GroEL have not been crystallized in monomeric forms, making it still necessary to use the bound coordinates from 1AON.
Coevolution analyses illuminate the dependencies between amino acid sites in the chaperonin system GroES-L.
(2013) BMC Evol Biol 13
PubMed: 23875653 | PubMedCentral: PMC3728108 | DOI: 10.1186/1471-2148-13-156
We downloaded the sequences for the crystallized cpn10 and cpn60 proteins of Escherichia coli (PDB ID: 1AON, MMDB ID: 47936) from the NCBI site ( http://www.ncbi.nlm.nih.gov/sites/structure ) to map t... e coevolving amino acidic sites detected using CAPS in the protein structure.
In these networks, amino acid sites are represented using the three-letter amino acid codes followed by the position of the amino acid in the three-dimensional structure of the GroESL protein complex (PDB ID: 1AON, MMDB ID: 47936).
The coevolution network between GroES and GroEL (a) is represented by inter-connected circles, each of which contains the three-leter code of the amino acid and the position in the crystal structure of GroESL (PDB ID: 1AON, MMDB ID: 47936).
We used the numbering of sites according to the structure of GroEL from Escherichia coli (PDB ID: 1AON, MMDB ID: 47936).
We used amino acid numberings according to the position of the site in the crystal structure of GroEL from Escherichia coli (PDB ID: 1AON, MMDB ID: 47936).
All amino acid sites numbering and composition are referred throughout the text to the numbering in the crystal structure of GroESL from E. coli (1AON.
Figure 6 Distribution of groups of coevolving sites within the three domains of crystal structure of GroEL (1AON.
Publication Year: 2013
MORPH-PRO: a novel algorithm and web server for protein morphing.
(2013) Algorithms Mol Biol 8
PubMed: 23844614 | PubMedCentral: PMC3738870 | DOI: 10.1186/1748-7188-8-19
Two GroEL proteins (PDB codes: 1GRL and 1AON) exhibit a simple morph on 515 aligned residues, changing from a closed conformation to an open conformation.
The role of Cdc42 and Gic1 in the regulation of septin filament formation and dissociation.
(2013) Elife 2
PubMed: 24286829 | PubMedCentral: PMC3840788 | DOI: 10.7554/eLife.01085
The idealized model of a septin-Gic1-Cdc42-GppNHp complex ( Figure 20B–C ) was obtained by fitting several copies of the crystal structure of the mammalian septin trimer (PDBid: 2QAG ) into th... density of septin filaments and placing of GROEL/GROES (PDBid: 1AON ) into the density corresponding to Gic1-Cdc42-GppNHp cross-bridges in one of our reconstructions ( Figure 20A ).
( B ) Model of a septin-Gic1-Cdc42-GppNHp complex obtained by fitting the crystal structure of the mammalian septin trimer (PDBid: 2QAG , gold) and GROEL/GROES (PDBid: 1AON , green) into ( A ), shown in three different orientations.
Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods.
(2013) BMC Struct Biol 13 Suppl 1
PubMed: 24564964 | PubMedCentral: PMC3953241 | DOI: 10.1186/1472-6807-13-S1-S2
Table 3 Proteins used in the experiments Protein Residues PDB ID init PDB ID goal C α RMSD ADK 214 4ake 1ake 6.51 LAO 238 2lao 1laf 3.73 DAP 320 1dap 3dap 3.78 NS3 436 3kqk 3kql 2.75 DDT 535 1... dt 1mdt 10.96 GroEL 547 1aon 1oel 10.49 ATP 573 1m8p 1i2d 3.78 LTF 691 1cb6 1bka 4.75 IBS 876 1ukl 1qgk 6.17 HKC 917 1hkc 1hkb 3.00 Figure 4 The ten proteins used in the experiment .
B-cell epitopes in GroEL of Francisella tularensis.
(2014) PLoS One 9
PubMed: 24968190 | PubMedCentral: PMC4072690 | DOI: 10.1371/journal.pone.0099847
The FtGroEL SchuS4 sequence (NC_006570 REGION: 1764262.1765896  ), which has 74% sequence identity to EcGroEL with no gaps or deletions ( http://blast.ncbi.nlm.nih.gov/Blast.cgi ), was threaded on... o the GroES-bound chain and non-GroES-bound chain of the 1AON structure, representing each conformation of EcGroEL observed in the crystal structure.
To create the seven-member GroES ring, the FtGroES model was superposed onto the other chains of EcGroES in the 1AON structure.
The FtGroEL model was built based on the bullet-shaped structure of the EcGroEL/EcGroES/ADP complex (Protein Data Bank http://www.rcsb.org/pdb/home/home.do code 1AON).
Publication Year: 2014
PubMed ID is not available.
Published in 2014
GroEL and GroES in the crystal structure of the GroEL–GroES complex (PDB code: 1AON) 6 are represented by space-filling (in gray) and ball-and-stick (in magenta) models, respectively.
YASARA View - molecular graphics for all devices - from smartphones to workstations.
(2014) Bioinformatics 30
PubMed: 24996895 | PubMedCentral: PMC4184264 | DOI: 10.1093/bioinformatics/btu426
Low-resolution depth map of PDB file 1CRN to calculate shadows ( D ), balls and sticks of 1CRN ( E ) and space-filling display of PDB file 1AON ( F ) In practice, many different images of atoms are ne... ded, as atoms can have different colors and sizes.
Xu Z , Horwich AL , Sigler PB , 1997 , Crystal structure of the asymmetric chaperonin complex groel/groes/(ADP)7 , 1AON ; http://dx.doi.org/10.2210/pdb1AON/pdb , Publicly available at the RCSB Protein... Data Bank.
Published in 2015
In this study, the open, ATP-bound (PDB ID: 1KP8)[ 36 ] and closed ADP-bound (PDB ID: 1AON)[ 7 ] structures of GroE were simulated in implicit solvent for a total of 190 ns each.
The open state simulation was based on PDBID:1KP8 while the closed state simulation was based on PDBID:1AON.
3D alignment of a monomer from the trans-ring of PDBID: 1AON with a monomer from the ATP-bound structure, PDBID: 1KP8.
The closed state simulation based on PDBID: 1AON contained two types of chaperonin rings.
Materials and Methods The open, ATP-bound (PDB ID: 1KP8)[ 36 ] and closed ADP-bound (PDB ID: 1AON)[ 7 ] structures of GroE were simulated in implicit solvent for a total of 190 ns each.
Movie depicting twenty concatenated 10 ns simulations of the GroEL/ES complex (based on PDBID: 1AON).
The crystal structure of the GroE chaperonin from Escherichia coli in the open, ATP-bound (PDBID: 1KP8) and closed (PDBID: 1AON) states.
Movie depicting twenty concatenated 10 ns simulations of GroEL/ES in the closed state (based on PDBID: 1AON).
Publication Year: 2015
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