Primary Citation PubMed: 11779463
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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
(b) 2C7E′ is same as the PDB structure 2C7E, except for the inversion shown in step F of the allosteric cycle in Figure 1 .
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_A ( 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.
Publication Year: 2009
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.
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).
Publication Year: 2011
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