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
Results are illustrated for a ANM steps k = 1, 7 and 13 along the transition R″→T of a single subunit (subunit A in the respective PDB structures 1GRU and 1GR5... .
The end states refer to subunit A in the PDB structures 1GRU and 1GR5.
(B) 1GRU; identified with the R″/R state; it contains seven ADPs and seven ATPs bound to the cis and trans rings, respectively.
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
Optimal identification of semi-rigid domains in macromolecules from molecular dynamics simulation.
(2010) PLoS One 5
PubMed: 20498702 | PubMedCentral: PMC2869351 | DOI: 10.1371/journal.pone.0010491
A MD trajectory of the chaperone GroEL-GroES (PDB ID code, 1GRU), containing solute atoms.
Publication Year: 2010
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
ATTRACT-EM: a new method for the computational assembly of large molecular machines using cryo-EM maps.
(2012) PLoS One 7
PubMed: 23251350 | PubMedCentral: PMC3522670 | DOI: 10.1371/journal.pone.0049733
This matrix was obtained by fitting the reference structure to 1GRU, the fitted structure provided by the authors of the GroES-GroEL density map  .
Publication Year: 2012
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