dorsal/arxiv
View SchemaDynamics of allosteric transitions in GroEL
| Authors | Changbong Hyeon, George H. Lorimer, D. Thirumalai |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0611094 |
| URL | https://arxiv.org/abs/q-bio/0611094 |
| DOI | 10.1073/pnas.0608759103 |
| Journal | Proc. Natl. Acad. Sci. (2006) vol 103, 18939-18944 |
Abstract
The chaperonin GroEL-GroES, a machine which helps some proteins to fold, cycles through a number of allosteric states, the $T$ state, with high affinity for substrate proteins (SPs), the ATP-bound $R$ state, and the $R^{\prime\prime}$ ($GroEL-ADP-GroES$) complex. Structures are known for each of these states. Here, we use a self-organized polymer (SOP) model for the GroEL allosteric states and a general structure-based technique to simulate the dynamics of allosteric transitions in two subunits of GroEL and the heptamer. The $T \to R$ transition, in which the apical domains undergo counter-clockwise motion, is mediated by a multiple salt-bridge switch mechanism, in which a series of salt-bridges break and form. The initial event in the $R \to R^{\prime\prime}$ transition, during which GroEL rotates clockwise, involves a spectacular outside-in movement of helices K and L that results in K80-D359 salt-bridge formation. In both the transitions there is considerable heterogeneity in the transition pathways. The transition state ensembles (TSEs) connecting the $T$, $R$, and $R^{\prime\prime}$ states are broad with the the TSE for the $T \to R$ transition being more plastic than the $R\to R^{\prime\prime}$ TSE. The results suggest that GroEL functions as a force-transmitting device in which forces of about (5-30) pN may act on the SP during the reaction cycle.
{
"annotation_id": "22f30ce3-f68c-4547-8c37-74b9c747f0ac",
"date_created": "2026-03-02T18:01:35.384000Z",
"date_modified": "2026-03-02T18:01:35.384000Z",
"file_hash": "969bc1d6976572bd3949588def42fa2011d0484ba55a89f6f634d3e4af2ee6e4",
"private": false,
"record": {
"abstract": "The chaperonin GroEL-GroES, a machine which helps some proteins to fold,\ncycles through a number of allosteric states, the $T$ state, with high affinity\nfor substrate proteins (SPs), the ATP-bound $R$ state, and the\n$R^{\\prime\\prime}$ ($GroEL-ADP-GroES$) complex. Structures are known for each\nof these states. Here, we use a self-organized polymer (SOP) model for the\nGroEL allosteric states and a general structure-based technique to simulate the\ndynamics of allosteric transitions in two subunits of GroEL and the heptamer.\nThe $T \\to R$ transition, in which the apical domains undergo counter-clockwise\nmotion, is mediated by a multiple salt-bridge switch mechanism, in which a\nseries of salt-bridges break and form. The initial event in the $R \\to\nR^{\\prime\\prime}$ transition, during which GroEL rotates clockwise, involves a\nspectacular outside-in movement of helices K and L that results in K80-D359\nsalt-bridge formation. In both the transitions there is considerable\nheterogeneity in the transition pathways. The transition state ensembles (TSEs)\nconnecting the $T$, $R$, and $R^{\\prime\\prime}$ states are broad with the the\nTSE for the $T \\to R$ transition being more plastic than the $R\\to\nR^{\\prime\\prime}$ TSE. The results suggest that GroEL functions as a\nforce-transmitting device in which forces of about (5-30) pN may act on the SP\nduring the reaction cycle.",
"arxiv_id": "q-bio/0611094",
"authors": [
"Changbong Hyeon",
"George H. Lorimer",
"D. Thirumalai"
],
"categories": [
"q-bio.BM",
"physics.bio-ph"
],
"doi": "10.1073/pnas.0608759103",
"journal_ref": "Proc. Natl. Acad. Sci. (2006) vol 103, 18939-18944",
"title": "Dynamics of allosteric transitions in GroEL",
"url": "https://arxiv.org/abs/q-bio/0611094"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "6c708e10-7dc7-4125-847a-ccf646ae753f",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}