Novel cryo-EM structure of an ADP-bound GroEL–GroES complex

Kudryavtseva, Sofia S.; Pichkur, Evgeny; Yaroshevich, Igor A.; Mamchur, Aleksandra A.; Panina, Irina; Moiseenko, Andrey; Sokolova, Olga; Muronetz, Vladimir I.

doi:10.1038/s41598-021-97657-x

Cited by 12 publications

(14 citation statements)

References 68 publications

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“…It is very probable that altering the physiological conditions may lead to a change in the steps of the functional cycle. For example, in high ADP concentration, the release of the ADP step is skipped [ 4 ]. Functional tests have indicated that the substrate-binding surface lies on the two α-helices (H and I) of the apical domain [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

Structural and Computational Study of the GroEL–Prion Protein Complex

et al. 2021

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The molecular chaperone GroEL is designed to promote protein folding and prevent aggregation. However, the interaction between GroEL and the prion protein, PrPC, could lead to pathogenic transformation of the latter to the aggregation-prone PrPSc form. Here, the molecular basis of the interactions in the GroEL–PrP complex is studied with cryo-EM and molecular dynamics approaches. The obtained cryo-EM structure shows PrP to be bound to several subunits of GroEL at the level of their apical domains. According to MD simulations, the disordered N-domain of PrP forms much more intermolecular contacts with GroEL. Upon binding to the GroEL, the N-domain of PrP begins to form short helices, while the C-domain of PrP exhibits a tendency to unfold its α2-helix. In the absence of the nucleotides in the system, these processes are manifested at the hundred nanoseconds to microsecond timescale.

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Section: Introductionmentioning

confidence: 99%

Structural and Computational Study of the GroEL–Prion Protein Complex

et al. 2021

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“…The lack of various switching reactions in the AmAc/ADP data confers an overall lack of cooperative binding of ADP; this conclusion is strengthened by the nMS data showing gaussian distribution for ADP binding at all observed ADP concentrations and by studies conducted by other researchers observing lower affinities associated with the binding of ADP. 28, 51 It has been shown that binding of ADP can cause conformational shifts in GroEL, 52 which are corroborated possibly by the entropic domination seen for GroEL-ADP5-9. However, these entropic shifts do not seem to be resultant from an allosteric transition 37 that leads to increased affinity for further ligation reactions.…”

Section: Resultsmentioning

confidence: 90%

Dissecting the Thermodynamics of ATP Binding to GroEL One Nucleotide at a Time

Walker

Sun

Gunnels

et al. 2022

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Biomolecules exist in the ever-changing environment of solution, which defines their structure, stability, dynamics, and function. Moreover, these effects are manifested in protein folding, protein-protein, and protein-ligand interactions. Thermodynamic studies, especially changes in heat capacity (DCp), are used to monitor the effects of solution temperature, concentration, ligands and/or co-solutes, but it can be challenging to relate such changes to molecular level reactions. Native mass spectrometry (nMS) has emerged as a complimentary technique to the traditional methods of structural and mechanistic characterization of biomolecules. Coupling of variable-temperature electrospray ionization (vT-ESI) to nMS affords mapping these changes to specific reactants and/or products using m/z-dispersion, whereas traditional thermodynamic measurements provide an ensemble-average of products. Here, we utilize vT-ESI-nMS to quantitate the thermodynamic contributions of stepwise binding of individual ATP or ADP ligands to GroEL-a tetradecamer chaperonin complex capable of binding up to 14 ATP molecules. We also show that small ions (viz. NH4 + ) are important contributors to the binding mechanisms of ATP and ADP to GroEL tetradecamer. The thermodynamic measurements reveal extensive enthalpy-entropy compensation (EEC) as well as increased cooperative effects for the formation of GroEL-ATP14, whereas similar cooperativity for ADP binding is absent. The thermodynamic data demonstrate that ATP binding in the cis ring (GroEL-ATP1-7) is largely entropic compared with more enthalpically driven reactions for ATP binding to the trans ring (GroEL-ATP8-14), owing to negative inter-ring cooperativity. The overall entropic effects for ATP binding to GroEL tetradecamer are attributed to conformational changes of the GroEL tetradecamer, but the magnitude of the entropy is also attributable to reorganization of GroEL-hydrating water molecules and/or expulsion of water from the GroEL cavity. This study reveals new pathways, viz. nMS, for experimental studies aimed at expanding our understanding of biologically relevant chaperonin functions.

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“…Lastly, this study represents the first directed separation of high-resolution GroEL-substrate complexes (or GroEL complexes of any kind) by single-particle cryo-EM. When applied to previous and future GroEL data sets, this focus-cleaning strategy should further remove significant heterogeneity and improve resolvability and map quality, revealing hitherto unseen, biologically relevant GroEL features and/or structures [2, 4, 6, 38, 39].…”

Section: Discussionmentioning

confidence: 99%

Three-dimensional motions of GroEL during substrate protein recognition

Stapleton

Mizobata

Miyazaki

et al. 2022

Preprint

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GroEL is a bacterial chaperonin responsible for the assisted folding of non-native and misfolded polypeptides into biologically active proteins. The adaptive nature of the recognition mechanism of chaperonins toward client polypeptides inherently lends itself to structural heterogeneity, which hampers detailed analyses of intermolecular recognition and binding. In this report, we used single-particle cryo-EM and multiple rounds of focused mask three-dimensional classification to reveal a landscape of distinct snapshots of endogenous GroEL complexed with an unfolded substrate, the water-soluble domain of human UDP glucuronosyltransferase 1A (UGT1A), at 2.7–3.5 Å resolution. We demonstrate that UGT1A occupies the GroEL ring asymmetrically, engaging with 2–3 contiguous subunits and that a subunit bound to UGT1A exhibits a wider range of conformational dynamics, consistent with AlphaFold models. These data reveal molecular motions during initial substrate capture at near-atomic detail.

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Novel cryo-EM structure of an ADP-bound GroEL–GroES complex

Cited by 12 publications

References 68 publications

Structural and Computational Study of the GroEL–Prion Protein Complex

Structural and Computational Study of the GroEL–Prion Protein Complex

Dissecting the Thermodynamics of ATP Binding to GroEL One Nucleotide at a Time

Three-dimensional motions of GroEL during substrate protein recognition

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