dorsal/arxiv
View SchemaThree-body Interactions Improve the Prediction of Rate and Mechanism in Protein Folding Models
| Authors | M. R. Ejtehadi, S. P. Avall, S. S. Plotkin |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0407019 |
| URL | https://arxiv.org/abs/q-bio/0407019 |
| DOI | 10.1073/pnas.0403486101 |
Abstract
Here we study the effects of many-body interactions on rate and mechanism in protein folding, using the results of molecular dynamics simulations on numerous coarse-grained C-alpha-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Go-like Hamiltonian with native pair-wise interactions only, we have found 1) a significantly increased correlation with experimental phi-values and folding rates, 2) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is ~ 20%, and 3) a considerably larger amount of 3-body energy present in Chymotripsin inhibitor than other proteins studied.
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"date_created": "2026-03-02T18:01:31.872000Z",
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"abstract": "Here we study the effects of many-body interactions on rate and mechanism in\nprotein folding, using the results of molecular dynamics simulations on\nnumerous coarse-grained C-alpha-model single-domain proteins. After adding\nthree-body interactions explicitly as a perturbation to a Go-like Hamiltonian\nwith native pair-wise interactions only, we have found 1) a significantly\nincreased correlation with experimental phi-values and folding rates, 2) a\nstronger correlation of folding rate with contact order, matching the\nexperimental range in rates when the fraction of three-body energy in the\nnative state is ~ 20%, and 3) a considerably larger amount of 3-body energy\npresent in Chymotripsin inhibitor than other proteins studied.",
"arxiv_id": "q-bio/0407019",
"authors": [
"M. R. Ejtehadi",
"S. P. Avall",
"S. S. Plotkin"
],
"categories": [
"q-bio.QM",
"cond-mat.soft",
"physics.bio-ph",
"q-bio.BM"
],
"doi": "10.1073/pnas.0403486101",
"title": "Three-body Interactions Improve the Prediction of Rate and Mechanism in Protein Folding Models",
"url": "https://arxiv.org/abs/q-bio/0407019"
},
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