2012
DOI: 10.1371/journal.pcbi.1002844
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Abstract: Investigating ligand-regulated allosteric coupling between protein domains is fundamental to understand cell-life regulation. The Hsp70 family of chaperones represents an example of proteins in which ATP binding and hydrolysis at the Nucleotide Binding Domain (NBD) modulate substrate recognition at the Substrate Binding Domain (SBD). Herein, a comparative analysis of an allosteric (Hsp70-DnaK) and a non-allosteric structural homolog (Hsp110-Sse1) of the Hsp70 family is carried out through molecular dynamics si… Show more

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Cited by 49 publications
(52 citation statements)
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“…In all simulations, they observed that when ATP was modeled into the structure of ADP-DnaK, SBDβ docked onto the NBD. This interdomain docking accompanied or followed local unfolding of the SBD helical turn (Chiappori et al, 2012), consistent with the formation of a uniform SBD helix as described above. In agreement with solution-state NMR results, the dynamics of ADP-NBD subdomain IIB were quenched in the ATP complex, and sub-domain IIB formed a stable contact with sub-domain IB.…”
Section: You Ain’t Seen Nothing Yet: Insight Into Interdomain Allostesupporting
confidence: 75%
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“…In all simulations, they observed that when ATP was modeled into the structure of ADP-DnaK, SBDβ docked onto the NBD. This interdomain docking accompanied or followed local unfolding of the SBD helical turn (Chiappori et al, 2012), consistent with the formation of a uniform SBD helix as described above. In agreement with solution-state NMR results, the dynamics of ADP-NBD subdomain IIB were quenched in the ATP complex, and sub-domain IIB formed a stable contact with sub-domain IB.…”
Section: You Ain’t Seen Nothing Yet: Insight Into Interdomain Allostesupporting
confidence: 75%
“…Molecular simulations of FL Hsp70s (human and E. coli ) played an important role in modeling the allosteric network involved in propagating nucleotide-induced structural transitions (Chiappori et al, 2012; General et al, 2014; Gołaś et al, 2012; KA, 2010; Nicolaï et al, 2010, 2013). Here, we discuss only recent simulations of the bacterial chaperone, as previous studies have been summarized (Gołaś et al, 2015; Gołaś et al, 2012)…”
Section: You Ain’t Seen Nothing Yet: Insight Into Interdomain Allostementioning
confidence: 99%
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“…Their first series of simulations was started from the SBD-closed conformation of DnaK, in which ADP was replaced with ATP, while their second series of simulations was started from an SBD-open conformation of 2KHO that was obtained by homology modeling, with bound ADP. However, both simulations resulted in similar intermediate structures, with SBD-α separated from SBD-β, but with SBD-α not docked to the NBD (Figure 2 in ref 19). …”
Section: Introductionmentioning
confidence: 92%
“…Starting from a homology model of the SBD-open conformation of bovine Hsp70, and using all-atom molecular dynamics with the GROMOS force field, Senet, Ripoll, and coworkers 16 simulated the initial stage of the dissociation of SBD-β from the NBD. Very recently, using the GROMACS 17 [with the GROMOS96 (ff43a1) 18 force field], Chiappori et al 19 carried out simulations aimed at reproducing the transitions from the SBD-closed to the SBD-open structure of DnaK, and vice versa. Their first series of simulations was started from the SBD-closed conformation of DnaK, in which ADP was replaced with ATP, while their second series of simulations was started from an SBD-open conformation of 2KHO that was obtained by homology modeling, with bound ADP.…”
Section: Introductionmentioning
confidence: 99%