dorsal/arxiv
View SchemaFolding pathways of a helix-turn-helix model protein
| Authors | D. Hoffmann, E. W. Knapp |
|---|---|
| Categories | |
| ArXiv ID | physics/9706018 |
| URL | https://arxiv.org/abs/physics/9706018 |
Abstract
A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a beta-strand conformation or two different loop conformations of the protein glutamine synthetase, six trajectories are generated using the so-called window move in dihedral angle space. This move changes conformations locally and leads to realistic, quasi-continuously evolving trajectories. Four of the six trajectories end in stable native-like conformations. Their folding pathways show a fast initial development of a helix-bend-helix motif, followed by a dynamic behaviour predicted by the diffusion-collision model of Karplus and Weaver. The phenomenology of the pathways is consistent with experimental results.
{
"annotation_id": "a5fabf06-7e35-4bf6-b3de-e0a0636501d0",
"date_created": "2026-03-02T18:01:20.658000Z",
"date_modified": "2026-03-02T18:01:20.658000Z",
"file_hash": "f0d5b286ea55377b444c09c8ea3cb25bbde966c3ba8d1fac25a02df372ce1244",
"private": false,
"record": {
"abstract": "A small model polypeptide represented in atomic detail is folded using Monte\nCarlo dynamics. The polypeptide is designed to have a native conformation\nsimilar to the central part of the helix-turn-helix protein ROP. Starting from\na beta-strand conformation or two different loop conformations of the protein\nglutamine synthetase, six trajectories are generated using the so-called window\nmove in dihedral angle space. This move changes conformations locally and leads\nto realistic, quasi-continuously evolving trajectories. Four of the six\ntrajectories end in stable native-like conformations. Their folding pathways\nshow a fast initial development of a helix-bend-helix motif, followed by a\ndynamic behaviour predicted by the diffusion-collision model of Karplus and\nWeaver. The phenomenology of the pathways is consistent with experimental\nresults.",
"arxiv_id": "physics/9706018",
"authors": [
"D. Hoffmann",
"E. W. Knapp"
],
"categories": [
"physics.bio-ph",
"cond-mat.soft",
"physics.chem-ph",
"q-bio"
],
"title": "Folding pathways of a helix-turn-helix model protein",
"url": "https://arxiv.org/abs/physics/9706018"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "ba3f84cd-1313-41fb-9035-9fb702657c9d",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}