The Dynamic Conformational Cycle of the Group I Chaperonin C-Termini Revealed via Molecular Dynamics Simulation

Abstract

Chaperonins are large ring shaped oligomers that facilitate protein folding by encapsulation within a central cavity. All chaperonins possess flexible C-termini which protrude from the equatorial domain of each subunit into the central cavity. Biochemical evidence suggests that the termini play an important role in the allosteric regulation of the ATPase cycle, in substrate folding and in complex assembly and stability. Despite the tremendous wealth of structural data available for numerous orthologous chaperonins, little structural information is available regarding the residues within the C-terminus. Herein, molecular dynamics simulations are presented which localize the termini throughout the nucleotide cycle of the group I chaperonin, GroE, from Escherichia coli. The simulation results predict that the termini undergo a heretofore unappreciated conformational cycle which is coupled to the nucleotide state of the enzyme. As such, these results have profound implications for the mechanism by which GroE utilizes nucleotide and folds client proteins.

Formation of tRNA Wobble Inosine in Humans Is Disrupted by a Millennia-Old Mutation Causing Intellectual Disability

“…4A) (37). Since human tRNA-Val-AAC has m1A at position 58 (38), the formation of m1A is likely due to endogenous TRMT6/TRMT61 complexes present in cellular extracts (39). The formation of m1A provides an internal control for cellular adenosine deaminase activity since it is catalyzed by two different enzyme complexes.…”

“…The HSP60 protein forms a homooligomeric chaperonin complex consisting of a double-heptameric ring that associates with misfolded proteins in the cytoplasm and mitochondria to provide an environment for protein refolding (37, 49–51). Similar to HSP60, TRiC is a major eukaryotic cytoplasmic chaperonin that is responsible for the correct folding of endogenous client proteins that are prone to misfolding (38, 50). The interaction of chaperonin complexes with ADAT3-V144M is consistent with a change in protein conformation and misfolding induced by the V144M mutation.…”

GroEL actively stimulates folding of the endogenous substrate protein PepQ

“…It remains an open question how the C-termini are induced to release the substrate protein upon the initiation of folding. However, both experimental 39 and computational studies 61 indicate that the C-termini are coupled to the GroELS allosteric cycle, suggesting that modulation of the interaction between the C-termini and a folding intermediate might be controlled by the GroEL ATPase cycle in a manner that parallels the behaviour of the apical domains.…”

Extensive Sampling of the Cavity of the GroEL Nanomachine by Protein Substrates Probed by Paramagnetic Relaxation Enhancement

“…The paramagnetic label is located at position 19 of the C-terminal tail, and the average end-to-end distance of a 19-residue random coil is predicted to be ~44 Å, 22 more than sufficient to extend from the bottom to the rim of the cavity (35–40 Å), consistent with the results of molecular dynamics simulations. 23…”