dorsal/arxiv
View SchemaUnbiased simulation of structural transitions in calmodulin
| Authors | Daniel M. Zuckerman |
|---|---|
| Categories | |
| ArXiv ID | physics/0302103 |
| URL | https://arxiv.org/abs/physics/0302103 |
Abstract
We introduce an approach for performing "very long" computer simulations of the dynamics of simplified, folded proteins. Using an alpha-carbon protein model and a fine grid to mimic continuum computations at increased speed, we perform unbiased simulations which exhibit many large-scale conformational transitions at low cost. In the case of the 72-residue N-terminal domain of calmodulin, the approach yields structural transitions between the calcium-free and calcium-bound structures at a rate of roughly one per day on a single Intel processor. Stable intermediates can be clearly characterized. The model employs Go-like interactions to stabilize two (or more) experimentally-determined structures. The approach is trivially parallelizable and readily generalizes to more complex potentials at minimal cost.
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"date_created": "2026-03-02T18:00:43.430000Z",
"date_modified": "2026-03-02T18:00:43.430000Z",
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"abstract": "We introduce an approach for performing \"very long\" computer simulations of\nthe dynamics of simplified, folded proteins. Using an alpha-carbon protein\nmodel and a fine grid to mimic continuum computations at increased speed, we\nperform unbiased simulations which exhibit many large-scale conformational\ntransitions at low cost. In the case of the 72-residue N-terminal domain of\ncalmodulin, the approach yields structural transitions between the calcium-free\nand calcium-bound structures at a rate of roughly one per day on a single Intel\nprocessor. Stable intermediates can be clearly characterized. The model employs\nGo-like interactions to stabilize two (or more) experimentally-determined\nstructures. The approach is trivially parallelizable and readily generalizes to\nmore complex potentials at minimal cost.",
"arxiv_id": "physics/0302103",
"authors": [
"Daniel M. Zuckerman"
],
"categories": [
"physics.bio-ph",
"physics.chem-ph",
"physics.comp-ph",
"q-bio"
],
"title": "Unbiased simulation of structural transitions in calmodulin",
"url": "https://arxiv.org/abs/physics/0302103"
},
"schema_id": "dorsal/arxiv",
"source": {
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"type": "Model",
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