Primary Citation PubMed: 15313620
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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
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 c... des: 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).
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, 1KP8, 1OEL, 1WE3, 1WF4).
Publication Year: 2011
Exploring a coarse-grained distributive strategy for finite-difference Poisson-Boltzmann calculations.
(2011) J Mol Model 17
PubMed: 21127924 | PubMedCentral: PMC3143316 | DOI: 10.1007/s00894-010-0904-4
These are: the 5S ribosomal RNA of the 70S ribosome (chain B of PDB id: 2J01, denoted rRNA), the p53 DNA binding domain tetramer in complex with DNA (PDB id: 2AC0, denoted p53 DBD), the GROEL heptamer... (PDB id: 1SX3, denoted GROEL), and the complete 70S ribosome (PDB id: 2J01 + 2J02, denoted the 70S ribosome).
A Mycobacterium leprae Hsp65 mutant as a candidate for mitigating lupus aggravation in mice.
(2011) PLoS One 6
PubMed: 21961033 | PubMedCentral: PMC3178518 | DOI: 10.1371/journal.pone.0024093
For comparison, the mouse Hsp60 was also modeled using the structural coordinates of the chaperonin GroEL from E. coli [PDB code 1SX3]  , which has 50% of amino acid sequence identity.
The mouse Hsp60 tridimensional model was generated based on the atomic coordinates of the Escherichia coli chaperonin GroEL [PDB code 1SX3]  , which shares 50% of sequence identity.
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