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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
12 gives three level superposition for GroEL: 1aon (red) and 1kp8 (green).
Figure 12 Multiple level superposition for GroEL: 1aon (red) and 1kp8 (green) .
Publication Year: 2009
IDSS: deformation invariant signatures for molecular shape comparison.
PubMed: 19463181 | PubMedCentral: PMC2694795 | DOI: 10.1186/1471-2105-10-157
(A) shows GroEL: 1kp8 (left) and 1aon (right), where 1kp8 has two separate domains and the corresponding domains of 1aon touch together.
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.
Using diffusion distances for flexible molecular shape comparison.
(2010) BMC Bioinformatics 11
PubMed: 20868474 | PubMedCentral: PMC2949899 | DOI: 10.1186/1471-2105-11-480
The four molecules are the morph deformation between two conformations of GroEL: 1AON and 1KP8.
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
MgATP coordinates for the closed holo (with nucleotide) simulation was collected from the crystal structure with PDB id 1KP8 chain A  .
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).
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
Molecular characterization of the Corynebacterium pseudotuberculosis hsp60-hsp10 operon, and evaluation of the immune response and protective efficacy induced by hsp60 DNA vaccination in mice.
(2011) BMC Res Notes 4
PubMed: 21774825 | PubMedCentral: PMC3158118 | DOI: 10.1186/1756-0500-4-243
Hsp60 from C. pseudotuberculosis (60 kDa chaperonin 1 gene, AAV48830.1); b) Hsp60 from E. coli , created with MODELLER, based on PDB related structures (1GR5, 1IOK, 1KP8, 1PCQ, 1SJP and 1WE3), as well... as on combinatorial modeling.
High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization.
(2012) BMC Syst Biol 6 Suppl 1
PubMed: 23046491 | PubMedCentral: PMC3403359 | DOI: 10.1186/1752-0509-6-S1-S18
In this section, we test our methods on subtomograms of four macromolecular complexes obtained from the Protein Data Bank (PDB id 1KP8 , 2GHO , 1W6T , 1YG6 ).
Publication Year: 2012
The structural basis of ATP as an allosteric modulator.
(2014) PLoS Comput Biol 10
PubMed: 25211773 | PubMedCentral: PMC4161293 | DOI: 10.1371/journal.pcbi.1003831
Glycogen phosphorylase Homo sapiens 1FA9 2.40 34 ATP sulfurylase Penicillium chrysogenum 1I2D 2.81 43 Chaperonin GroEL Escherichia coli 1KP8 2.00 17 Phosphofructokinase 1 Escherichia coli 1PFK 2.40 44... MutS Escherichia coli 1W7A 2.27 16 DnaA Aquifex aeolicus 2HCB 3.51 41 Uridine monophosphate kinase Bacillus anthracis 2JJX 2.82 22 Cytosolic 5’-nucleotidase II Homo sapiens 2XCW 1.90 73 ClpX Escherichia coli 3HWS 3.25 45 Ribonucleotide reductase Escherichia coli 3R1R 3.00 74 Aspartate carbamoyltransferase Escherichia coli 4AT1 2.60 75 P2X 4 ion channel Danio rerio 4DW1 2.80 19 DNA Topoisomerase II Saccharomyces cerevisiae 4GFH 4.41 42 Allosteric ATP-binding sites are less conserved than substrate ATP-binding sites To elucidate differences in the evolutionary characteristics of allosteric and substrate ATP-binding sites, we systematically explored the sequence conservation of ATP-binding sites in the ATP allosteric and substrate datasets.
Inspection of these ATP molecules reveals that seven cases adopt compact conformations (PDB: 1FA9, 1I2D, 1PFK, 3HWS, 2XCW, 3R1R, and 4DW1), while the remaining six cases adopt the extended conformations (PDB: 1W7A, 4AT1, 4GFH, 2HCB, 2JJX, and 1KP8).
PDB entry Adenine Ribose Triphosphate H-bonds Hydrophobic H-bonds H-bonds/Electrostatic 1FA9 Y75 / / R193, D227, R242, R309, R310 1I2D K527 F446, F529 / K409, D434, R437, R451, I477 1KP8 N479, A480 P33, I493 G415, D495 G32, D87, G88, T89, T90, T91 1PFK / K214 A ,Y55 B / R154 A , K213 A , R21 B , R25 B , R54 B 1W7A I597 F596, H760 / M617, G619, K620, S621, T622, E694 2HCB F88 I89 H127 G124, K125, T126, H127, D181, R277 2JJX N107 A , A110 A E111 A , I114 B R99 A , R117 A , Y126 A , R117 B , H120 B 2XCW N154, Q453 F354, I152 / R144, D145, R456, Y457 3HWS I79 L127, L317, I325 / G122, S123, G124, K125, T126, R370 3R1R E15, R16, N18 V7, I17, I22 I22 K9, E15, K21, T55, K91 4AT1 I12, K60, Y89 V91 / K94 4DW1 / R143 / N296, R298, K316 4GFH N99 I104, R77 S127, S128 S127, N129, R141, K147, K367, Q365 For example, in the P2X 4 ion channel ( Figure S4A ), residues Asn296, Arg298, and Lys316 from both the unbound (PDB: 4DW0) and ATP-bound (PDB: 4DW1) structures engage in hydrogen bonding/electrostatic interactions with the triphosphate in ATP, revealing marginal conformational changes proximal to the triphosphate in ATP.
The triphosphate part of ATP is an allosteric trigger in eight cases: (C) Cytosolic 5’-nucleotidase II (PDB: 2XCX vs. 2XCW); (D) ClpX (PDB: 3HTE vs. 3HWS); (E) Glycogen phosphorylase (PDB: 1FC0 vs. 1FA9); (F) Ribonucleotide reductase (PDB: 1R1R vs. 3R1R); (G) MutS (PDB: 1E3M vs 1W7A); (H) DnaA (PDB: 1L8Q vs. 2HCB); (I) Phosphofructokinase 1 (PDB: 2PFK vs. 1PFK); (J) Chaperonin GroEL (PDB: 1KP0 vs. 1KP8).
Publication Year: 2014
PubMed ID is not available.
Published in 2015
The crystal structure of the GroE chaperonin from Escherichia coli in the open, ATP-bound (PDBID: 1KP8) and closed (PDBID: 1AON) states.
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.
Both rings of the open state simulation, based on PDBID: 1KP8, correspond to an ATP bound ring which is competent to bind unfolded substrates.
3D alignment of a monomer from the trans-ring of PDBID: 1AON with a monomer from the ATP-bound structure, PDBID: 1KP8.
Movie depicting twenty concatenated 10 ns simulations of a GroEL holo ring (based on PDBID: 1KP8).
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.
Publication Year: 2015
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